From 43b14705c70c348f8fe7c949e8f12b50741ded76 Mon Sep 17 00:00:00 2001 From: pestre Date: Wed, 8 Jan 2025 11:11:57 +0100 Subject: [PATCH 01/98] Add doc files from cantera-avbp Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: new file: doc/doxygen/cantera-doxygen.css new file: doc/sphinx/develop/compiling/compilation-reqs.md new file: doc/sphinx/develop/compiling/config-options.rst new file: doc/sphinx/develop/compiling/configure-build.md new file: doc/sphinx/develop/compiling/dependencies.md new file: doc/sphinx/develop/compiling/source-code.md new file: doc/sphinx/develop/compiling/special-cases.md new file: doc/sphinx/develop/index.md new file: doc/sphinx/examples/index.md new file: doc/sphinx/favicon.png new file: doc/sphinx/index.md new file: doc/sphinx/install/conda.md new file: doc/sphinx/install/index.md new file: doc/sphinx/install/pip.md new file: doc/sphinx/python/ck_conversion.rst new file: doc/sphinx/python/constants.rst new file: 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145); + --pst-color-text-muted: rgb(100, 100, 100); +} + +html.dark-mode { + --primary-color: rgb(63, 177, 197); + --pst-color-text-muted: rgb(164, 164, 164); +} + +ul#main-menu li a { + /* Hide Doxygen navigation tabs that are duplicated in the sidebar */ + visibility: hidden; + display: none !important; +} + +div#top { + /* Fix alignment of nav tabs added using header.html */ + justify-content: left; +} + +/* Re-style the nav bar links to approximate pydata-sphinx-theme */ +.sm-dox a { + color: var(--pst-color-text-muted) !important; + font-size: 16px; + padding: 0 8px; +} + +.sm-dox a#selected { + color: var(--primary-color) !important; + font-weight: bold; +} + +.sm-dox a:hover { + background: unset; + color: var(--primary-color) !important; + font-size: 16px; +} diff --git a/doc/sphinx/develop/compiling/compilation-reqs.md b/doc/sphinx/develop/compiling/compilation-reqs.md new file mode 100644 index 00000000000..50e7184ec8d --- /dev/null +++ b/doc/sphinx/develop/compiling/compilation-reqs.md @@ -0,0 +1,565 @@ +(sec-compilation-reqs)= +# Compilation Requirements + +Click the buttons below to see the required software that you must install to +compile Cantera on your operating system. + +`````{grid} auto + +````{grid-item} +```{button-ref} sec-conda +:color: primary +:shadow: +``` +```` + +````{grid-item} +```{button-ref} sec-ubuntu-debian-reqs +:color: primary +:shadow: +``` +```` + +````{grid-item} +```{button-ref} sec-opensuse-reqs +:color: primary +:shadow: + OpenSUSE & SLE +``` +```` + +````{grid-item} +```{button-ref} sec-fedora-reqs +:color: primary +:shadow: + Fedora & RHEL +``` +```` + + +````{grid-item} +```{button-ref} sec-macos +:color: primary +:shadow: +``` +```` + +````{grid-item} +```{button-ref} sec-windows +:color: primary +:shadow: +``` +```` + +````` + +(sec-conda)= +## Conda & Anaconda + +### General Notes + +- These instructions will set you up to build Cantera with the dependencies installed in + a Conda environment +- You will need to install compilers for your system by following the instructions in + the sections below to install the compiler for your operating system. +- By default, Cantera is installed into the active conda environment, where the layout + of the directory structure corresponds to the [configuration option](configure-build) + `layout=conda`. + +(sec-conda-reqs)= +### Conda Requirements + +- Install [Anaconda](https://www.anaconda.com/download/), + [Miniconda](https://conda.io/miniconda.html), or + [Miniforge](https://github.com/conda-forge/miniforge). + +- Launch the command line interface: + + - On macOS and Linux, the installer should add the appropriate activation mechanism + for your normal terminal by default. You can test this by running + + ```bash + conda --version + ``` + + in the terminal. If there is no output or an error appears, locate your Conda + installation and run the following code in the terminal: + + ```bash + /path/to/conda/install/folder/bin/conda init --all + ``` + + Then restart your terminal or shell. + + - On Windows, use the Anaconda PowerShell to run the build process (available from + the Start Menu). When using MSVC compilers, you also need to set environment + variables for x64-native tools (see [Developer command file locations](https://docs.microsoft.com/en-us/cpp/build/building-on-the-command-line?view=msvc-170#developer_command_file_locations)) + by running + + ```bash + . "C:\path\to\MSVC\Auxiliary\Build\vcvars64.bat" + ``` + + (note that the period `'.'` is part of the command). The path can be found as + follows: locate the **x64 Native Tools Command Prompt** in the Start Menu, + right-click, select **More > Open File Location**, right-click on the shortcut, + select **Properties** and copy the **Target** command. + +- Create an environment `ct-build` with the dependencies to build Cantera. Create a + file called `environment.yaml` with the following content + + ```yaml + name: ct-build + channels: + - conda-forge + dependencies: + - python # Cantera supports Python 3.8 and up + - scons # build system + - boost-cpp # C++ dependency + - hdf5 # optional C++ dependency + # - highfive # C++ dependency; uncomment to override Cantera default + # - sundials # uncomment to override Cantera default + # - fmt # uncomment to override Cantera default + # - eigen # uncomment to override Cantera default + # - yaml-cpp # uncomment to override Cantera default + # - libgomp # optional (OpenMP implementation when using GCC) + - cython # needed to build Python package + - numpy # needed to build Python package + - pip # needed to build Python package + - wheel # needed to build Python package + - setuptools # needed to build Python package + - pytest # needed for the Python test suite + # - pytest-cov # optional (needed if running with test coverage enabled) + - ruamel.yaml # needed for converter scripts + # - pandas # optional (needed for pandas interface) + # - scipy # optional (needed for some examples) + # - matplotlib # optional (needed for plots) + # - python-graphviz # optional (needed for reaction path diagrams) + - ipython # optional (needed for nicer interactive command line) + # - jupyter # optional (needed for Jupyter Notebook) + # - sphinx # optional (needed for documentation) + # - pydata-sphinx-theme # optional (needed for documentation) + # - sphinx-argparse # optional (needed for documentation) + # - doxygen # optional (needed for documentation) + # - graphviz # optional (needed for documentation) + # - texlive-core # optional (needed for documentation) + # - perl # optional (needed for documentation) + # - pip: # optional (list of PyPI managed packages) + # - sphinxcontrib-matlabdomain # optional (needed for documentation) + # - sphinxcontrib-doxylink # optional (needed for documentation) + ``` + + The environment is then created and activated using + + ```bash + conda env create -f environment.yaml + conda activate ct-build + ``` + + After creating the environment, it can be updated from within `ct-build` using + + ```bash + conda env update -f environment.yaml --prune + ``` + +- (Optional) If you want to override external libraries packaged with Cantera + (`sundials`, `fmt`, `eigen`, `yaml-cpp`), simply uncomment corresponding lines in the + file `environment.yaml` above. Note that specific versions can be forced by providing + version numbers (example: replace `sundials` by `sundials=5.8` to install version + `5.8`). + +- (Optional) If you want to build the documentation, make sure to uncomment lines for + `pip`, `sphinx`, `doxygen`, and any other lines marked as "needed for documentation" + in the `environment.yaml` sample above. + +- (Cantera \< 2.6 only) On previous Cantera versions, the build process required + configuration options `boost_inc_dir` and `prefix` (see [configuration + options](configure-build)); starting with Cantera 2.6, these settings are detected + automatically. + +:::{note} +As the compiled code is based on the conda environment `ct-build`, it is only +usable from within that environment. This means that in order to use the compiled +Cantera package, you have to activate your `ct-build` environment first. +::: + +```{button-ref} source-code +:color: primary +:shadow: +:align: right +Next: Download the Source Code +``` + +(sec-linux)= +## Linux + +### General Notes + +- To download the source code, installing `git` is highly recommended in addition + to the requirements listed below. +- The following instructions use the system-installed versions of Python, but alternate + installations such as the Anaconda distribution of Python can be used as well. +- Cython is only required to be installed for the version of Python that also has SCons + installed; following the instructions below will install Cython for the version of + Python installed in the system directories. The minimum compatible Cython version is + 0.29.31. If your distribution does not contain a suitable version, you may be able to + install a more recent version using Pip. +- Users of other distributions should install the equivalent packages, which may have + slightly different names. +- In addition to the operating systems below, Cantera should work on any Unix-like + system where the necessary prerequisites are available, but some additional + configuration may be required. + +(sec-ubuntu-debian-reqs)= + +### Ubuntu & Debian + +- Ubuntu 20.04 LTS (Focal Fossa) or newer + +- Debian 11.0 (Bullseye) or newer + +- The following packages must be installed to build any of the Cantera modules using + your choice of package manager: + + ``` + g++ python3 scons libboost-dev libhdf5-dev + ``` + + - The HDF5 headers and libraries are not installed to directories on the compiler's + default search path. When building Cantera, these paths need to be specified as + options to `scons`, for example `extra_inc_dirs=/usr/include/hdf5/serial` and + `extra_lib_dirs=/usr/lib/x86_64-linux-gnu/hdf5/serial`. + +- If you want to use system system packages to provide the following dependencies, + instead of the versions bundled with Cantera, you should also install: + + ``` + libsundials-dev libeigen3-dev libyaml-cpp-dev libfmt-dev + ``` + +- In addition to the general packages, building the Python 3 module also requires: + + ``` + cython3 python3-setuptools python3-wheel python3-numpy python3-ruamel.yaml python3-pytest + ``` + + - Debian 12.0 (Bookworm) and Ubuntu 23.04 (Lunar Lobster) provide compatible Cython + versions. For older releases, install Cython using Pip. + +- In addition to the general packages, building the Fortran module also requires: + + ``` + gfortran + ``` + +- In addition to the general packages, building the MATLAB toolbox also requires: + + - MATLAB version later than 2009a + + - Typically installed to: + + ``` + /opt/MATLAB/R20YYn + ``` + + where `YY` is a two digit year and `n` is either `a` or `b` + +```{button-ref} source-code +:color: primary +:shadow: +:align: right +Next: Download the Source Code +``` + +(sec-fedora-reqs)= +### Fedora & RHEL + +- The following packages must be installed to build any of the Cantera modules using + your choice of package manager: + + ``` + gcc-c++ python3 scons boost-devel hdf5-devel + ``` + +- If you want to use system system packages to provide the following dependencies, + instead of the versions bundled with Cantera, you should also install: + + > sundials-devel eigen3-devel yaml-cpp-devel fmt-devel highfive-devel + +- In addition to the general packages, building the Python 3 module also requires: + + ``` + python3-devel Cython python3-numpy python3-ruamel-yaml python3-pytest + ``` + +- In addition to the general packages, building the Fortran module also requires: + + ``` + gcc-gfortran + ``` + +- In addition to the general packages, building the MATLAB toolbox also requires: + + - MATLAB version later than 2009a + + - Typically installed to: + + ``` + /opt/MATLAB/R20YYn + ``` + + where `YY` is a two digit year and `n` is either `a` or `b` + +```{button-ref} source-code +:color: primary +:shadow: +:align: right +Next: Download the Source Code +``` + +(sec-opensuse-reqs)= +### OpenSUSE & SUSE Linux Enterprise + +- OpenSUSE Leap 15.5 or newer recommended + +- The following packages must be installed to build any of the Cantera modules using + your choice of package manager: + + ``` + gcc11-c++ python311 libboost_headers1_75_0-devel hdf5-devel python311-pip + ``` + + You can specify other version numbers for GCC, Python, and Boost, as long as they meet + Cantera's minimum requirements. + +- You will also need to install `scons` using the Pip version installed above. + +- In addition to the general packages, building the Python module also requires: + + ``` + python3-devel + ``` + + as well as the following packages installed using Pip: + + > numpy wheel cython ruamel.yaml pytest + +- In addition to the general packages, building the Fortran module also requires: + + ``` + gcc11-fortran + ``` + +- In addition to the general packages, building the MATLAB toolbox also requires: + + - MATLAB version later than 2009a + + - Typically installed to: + + ``` + /opt/MATLAB/R20YYn + ``` + + where `YY` is a two digit year and `n` is either `a` or `b` + +```{button-ref} source-code +:color: primary +:shadow: +:align: right +Next: Download the Source Code +``` + +(sec-windows)= +## Windows + +### General Notes + +- The build process will produce a Python module compatible with the version of Python + used for the compilation. To generate different modules for other versions of Python, + you will need to install those versions of Python and recompile. + +- The following instructions use the versions of Python downloaded from + , but alternate installations such as the Anaconda + distribution of Python can be used as well. + +- If you want to build the Matlab toolbox and you have a 64-bit copy of Windows, by + default you will be using a 64-bit copy of Matlab, and therefore you need to compile + Cantera in 64-bit mode. For simplicity, it is highly recommended that you use a 64-bit + version of Python to handle this automatically. + +- It is generally helpful to have SCons and Python in your `PATH` environment variable. + This can be done by checking the appropriate box during the installation of Python or + can be accomplished by adding the top-level Python directory and the `Scripts` + subdirectory (for example, `C:\Python311;C:\Python311\Scripts`) to your `PATH`. The + dialog to change the `PATH` is accessible from: + + ``` + Control Panel > System and Security > System > Advanced System Settings > Environment Variables + ``` + + Make sure that the installation of Python that has SCons comes first on your `PATH`. + +- In order to use SCons to install Cantera to a system folder (for example, + `C:\Program Files\Cantera`) you must run the `scons install` command in a + command prompt that has been launched by selecting the *Run as Administrator* + option. + +(sec-windows-reqs)= +### Windows Requirements + +- Windows 7 or later; either 32-bit or 64-bit + +- To build any of the Cantera modules, you will need to install + + - Python + + - + - Cantera supports Python 3.8 and higher + - Be sure to choose the appropriate architecture for your system - either + 32-bit or 64-bit + - When installing, make sure to choose the option to add to your `PATH` + + - SCons + + - + - Be sure to choose the appropriate architecture for your system - either + 32-bit or 64-bit + + - One of the following supported compilers + + - Microsoft compilers + + - + - Known to work with Visual Studio 2017 (MSVC 14.1), Visual Studio 2019 + (MSVC 14.2), and Visual Studio 2022 (MSVC 14.3). + + - MinGW compilers + + - + - + - Known to work with Mingw-w64 12.2. + + - The Boost headers + + - + - It is not necessary to compile the Boost libraries since Cantera only uses + the headers from Boost + +- In addition to the general software, building the Python module also requires + several Python packages: Cython, NumPy, setuptools, wheel, ruamel.yaml, and pytest. + All of these can be installed using `pip`: + + ```bash + py -m pip install setuptools wheel cython numpy ruamel.yaml pytest + ``` + +- In addition to the general software, building the MATLAB toolbox also requires: + + - MATLAB version later than 2009a + + - Typically installed to: + + ``` + C:\Program Files\MATLAB\R20YYn + ``` + + where `YY` is a two digit year and `n` is either `a` or `b` + +```{button-ref} source-code +:color: primary +:shadow: +:align: right +Next: Download the Source Code +``` + +(sec-macos)= +## macOS + +### General Notes + +- Cantera 2.5.0 and higher do not support Python 2, which may be installed by default + on your computer. You must install Python 3 from another source to be able to build + Cantera. The instructions below use Homebrew. + +(sec-mac-os-reqs)= +### macOS Requirements + +- macOS 10.15 (Catalina) is required; Homebrew requires 11.0 or newer. + +- To build any of the Cantera interfaces, you will need to install + + - Xcode + + - Download and install from the App Store + + - From a Terminal, run: + + ```bash + sudo xcode-select --install + ``` + + and agree to the Xcode license agreement + + - Homebrew + + - + + - From a Terminal, run: + + ```bash + /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" + ``` + + - Once Homebrew is installed, the rest of the dependencies can be installed with: + + ```bash + brew install python scons boost git hdf5 libomp + ``` + + Note that brew installs Python 3 by default, but does not over-write the existing + system Python. When you want to use the brew-installed Python, check to make sure + that `python3` and `pip3` refer to the Homebrew installation by running: + + ```bash + which python3 + which pip3 + ``` + + If these commands do not include the Homebrew path, you can run the correct ones as + `$(brew --prefix)/bin/python3` and `$(brew --prefix)/bin/pip3`. + +- In addition to the general software, building the Python module also requires: + + ```bash + $(brew --prefix)/bin/pip3 install cython numpy wheel setuptools ruamel.yaml pytest + ``` + +- In addition to the general software, building the Fortran module also requires: + + ```bash + brew install gcc + ``` + +- In addition to the general software, building the MATLAB toolbox also requires: + + - MATLAB version later than 2009a + + - Typically installed to: + + ``` + /Applications/MATLAB_R20YYn.app + ``` + + where `YY` is a two digit year and `n` is either `a` or `b` + +- The Homebrew header and library directories will not be on the path for the system + compiler (Xcode), so when compiling Cantera, you will need to provide the command line + options `extra_inc_dirs=$(brew --prefix)/include` and + `extra_lib_dirs=$(brew --prefix)/lib`. + +```{button-ref} source-code +:color: primary +:shadow: +:align: right +Next: Download the Source Code +``` diff --git a/doc/sphinx/develop/compiling/config-options.rst b/doc/sphinx/develop/compiling/config-options.rst new file mode 100644 index 00000000000..bb948cd92df --- /dev/null +++ b/doc/sphinx/develop/compiling/config-options.rst @@ -0,0 +1,38 @@ +.. _scons-config: + +Configuration Options +===================== + +This document lists the options available for compiling Cantera with +SCons. + +The default values are operating-system dependent. To see the defaults for your current +operating system, run the command: + +.. code:: bash + + scons help + +from the command prompt. + +The following options can be passed to SCons to customize the Cantera +build process. They should be given in the form: + +.. code:: bash + + scons build option1=value1 option2=value2 + +Variables set in this way will be stored in the ``cantera.conf`` file and reused +automatically on subsequent invocations of SCons. Alternatively, the +configuration options can be entered directly into ``cantera.conf`` before +running ``scons build``. The format of this file is: + +.. code:: python + + option1 = 'value1' + option2 = 'value2' + +.. + The options list is generated by SCons during the build process + +.. include:: scons-config-options.rst.inc diff --git a/doc/sphinx/develop/compiling/configure-build.md b/doc/sphinx/develop/compiling/configure-build.md new file mode 100644 index 00000000000..21c77c5e94c --- /dev/null +++ b/doc/sphinx/develop/compiling/configure-build.md @@ -0,0 +1,258 @@ +# Configure and Build Cantera + +(sec-determine-config)= +## Determine configuration options + +- Run `scons help --options` to see a list of all of the configuration options for + Cantera, or see all of the options on the [Configuration Options](scons-config) + page. + +- Configuration options are specified as additional arguments to the `scons` + command. For example: + + ```bash + scons command option_name=value + ``` + + where `scons` is the program that manages the build steps, and `command` + is most commonly one of + + - `build` + - `test` + - `clean` + + Other commands are explained in the [Build Commands](sec-build-commands) section. + +- SCons saves configuration options specified on the command line in the file + `cantera.conf` in the root directory of the source tree, so generally it is + not necessary to respecify configuration options when rebuilding Cantera. To + unset a previously set configuration option, either remove the corresponding + line from `cantera.conf` or use the syntax: + + ```bash + scons command option_name= + ``` + +- Sometimes, changes in your environment can cause SCons's configuration tests + (for example, checking for libraries or compiler capabilities) to unexpectedly fail. + To force SCons to re-run these tests rather than trusting the cached results, + run scons with the option `--config=force`. + +- The following lists of options are not complete, they show only some commonly + used options. The entire list of options can be found on the + [Configuration options](scons-config) page. + +### Common Options + +- [`debug`](sconsopt-debug) +- [`optimize`](sconsopt-optimize) +- [`prefix`](sconsopt-prefix) + +### Specifying Paths for Cantera's Dependencies + +- [`blas_lapack_libs`](sconsopt-blas-lapack-libs) + + - On macOS, the Accelerate framework is automatically used to provide optimized + versions of BLAS and LAPACK, so the `blas_lapack_libs` option should generally be + left unspecified. + +- [`blas_lapack_dir`](sconsopt-blas-lapack-dir) + +- [`boost_inc_dir`](sconsopt-boost-inc-dir) + +- [`sundials_include`](sconsopt-sundials-include) + +- [`sundials_libdir`](sconsopt-sundials-libdir) + +- [`hdf_include`](sconsopt-hdf-include) + +- [`hdf_libdir`](sconsopt-hdf-libdir) + +- [`extra_inc_dirs`](sconsopt-extra-inc-dirs) + +- [`extra_lib_dirs`](sconsopt-extra-lib-dirs) + +### Python Module Options + +Compiling the Cantera Python module requires that NumPy and Cython are installed +for the target installation of Python. The following SCons options control how +the Python module is built: + +- [`python_package`](sconsopt-python-package) + +- [`python_cmd`](sconsopt-python-cmd) + + - By default, SCons will try to build the full Python interface for copy of + Python that is running SCons. Use this option if you wish to build Cantera + for a different Python installation. + +- [`python_prefix`](sconsopt-python-prefix) + +### Windows Only Options + +:::{note} +The `cantera.conf` file uses the backslash character `\` as an escape +character. When modifying this file, backslashes in paths need to be escaped +like this: `boost_inc_dir = 'C:\\Program Files (x86)\\boost\\include'` +This does not apply to paths specified on the command line. Alternatively, +you can use forward slashes (`/`) in paths. +::: + +- In Windows there aren't any proper default locations for many of the packages + that Cantera depends on, so you will need to specify these paths explicitly. + +- Remember to put double quotes around any paths with spaces in them, such as + `"C:\Program Files"`. + +- By default, SCons attempts to use the same architecture as the copy of Python + that is running SCons, and the most recent installed version of the Visual + Studio compiler. If you aren't building the Python module, you can override + this with the configuration options `target_arch` and `msvc_toolset_version`. + +- To compile with MinGW, specify the [`toolchain`](sconsopt-toolchain) option: + + ``` + toolchain=mingw + ``` + +- [`msvc_toolset_version`](sconsopt-msvc-toolset-version) + +- [`msvc_version`](sconsopt-msvc-version) + +- [`target_arch`](sconsopt-target-arch) + +- [`toolchain`](sconsopt-toolchain) + +### MATLAB Toolbox Options + +Building the MATLAB toolbox requires an installed copy of MATLAB, and the path +to the directory where MATLAB is installed must be specified using the following +option: + +- [`matlab_toolbox`](sconsopt-matlab-toolbox) +- [`matlab_path`](sconsopt-matlab-path) + +### Fortran Module Options + +Building the Fortran module requires a compatible Fortran compiler. SCons will +attempt to find a compatible compiler by default in the `PATH` environment +variable. The following options control how the Fortran module is built: + +- [`f90_interface`](sconsopt-f90-interface) +- [`FORTRAN`](sconsopt-fortran) + +### Documentation Options + +The following options control if the documentation is built: + +- [`doxygen_docs`](sconsopt-doxygen-docs) +- [`sphinx_docs`](sconsopt-sphinx-docs) + +### Less Common Options + +- [`CC`](sconsopt-cc) +- [`CXX`](sconsopt-cxx) +- [`env_vars`](sconsopt-env-vars) +- [`layout`](sconsopt-layout) +- [`logging`](sconsopt-logging) +- [`gtest_flags`](sconsopt-gtest-flags) + +(sec-build-commands)= +## Build Commands + +The following *commands* are possible as arguments to SCons: + +```bash +scons command +``` + +- `scons help` + : Print a list of available SCons commands. +- `scons help --options` + : Print a description of user-specifiable options. +- `scons build` + : Compile Cantera and the language interfaces using + default options. +- `scons clean` + : Delete files created while building Cantera. +- `scons install` + : Install Cantera. +- `scons uninstall` + : Uninstall Cantera. +- `scons test` + : Run all tests which did not previously pass or for which the + results may have changed. +- `scons test-reset` + : Reset the passing status of all tests. +- `scons test-clean` + : Delete files created while running the tests. +- `scons test-help` + : List available tests. +- `scons test-NAME` + : Run the test named `NAME`. +- `scons dump` + : Dump the state of the SCons environment to the + screen instead of doing ``, for example, + `scons build dump`. For debugging purposes. +- `scons samples` + : Compile the C++ and Fortran samples. +- `scons msi` + : Build a Windows installer (.msi) for Cantera. +- `scons sphinx` + : Build the Sphinx documentation +- `scons doxygen` + : Build the Doxygen documentation + +## Compile Cantera & Test + +- Run SCons with the list of desired configuration options: + + ```bash + scons build ... + ``` + +- If Cantera compiles successfully, you should see a message that looks like: + + ``` + ******************************************************* + Compilation completed successfully. + + - To run the test suite, type 'scons test'. + - To list available tests, type 'scons test-help'. + - To install, type 'scons install'. + ******************************************************* + ``` + +- If you do not see this message, check the output for errors to see what went + wrong. You may also need to examine the contents of `config.log`. + +- Cantera has a series of tests that can be run with the command: + +```bash +scons test +``` + +- When the tests finish, you should see a summary indicating the number of + tests that passed and failed. + +- If you have tests that fail, try looking at the following to determine the + source of the error: + + - Messages printed to the console while running `scons test` + - Output files generated by the tests + +### Building Documentation + +To build the Cantera HTML documentation, run the commands: + +```bash +scons doxygen +scons sphinx +``` + +or append the options `sphinx_docs=y` and `doxygen_docs=y` to the build +command: + +```bash +scons build doxygen_docs=y sphinx_docs=y +``` diff --git a/doc/sphinx/develop/compiling/dependencies.md b/doc/sphinx/develop/compiling/dependencies.md new file mode 100644 index 00000000000..fea05c075fd --- /dev/null +++ b/doc/sphinx/develop/compiling/dependencies.md @@ -0,0 +1,181 @@ +(sec-dependencies)= +# Software used by Cantera + +This section lists the versions of third-party software that are required to build and +use Cantera. + +## Compilers + +You must have one of the following C++ compilers installed on your system. A Fortran +compiler is required only if you plan to build the Fortran module. + +- GNU compilers (C/C++/Fortran) + + - Known to work with versions 9.4 and 11.4. Expected to work with version >= 9.0. + +- Clang/LLVM (C/C++) + + - Known to work with versions 10 and 12. Expected to work with version >= 5.0 + - Works with the versions included in Xcode 13.0 and 14.3.1. + +- Intel compilers (C/C++/Fortran) + + - Known to work with the Intel OneAPI Compilers (version 2022.0.2). + - Some earlier versions of the Intel compiler (including the 2017 version) are + **NOT RECOMMENDED** because of a bug in the C compiler. + +- Microsoft compilers (C/C++) + + - Known to work with Visual Studio 2017 (MSVC 14.1), Visual Studio 2019 (MSVC 14.2) + and Visual Studio 2022 (MSVC 14.3). + +- MinGW (C/C++/Fortran) + + - (64-bit) + - (64-bit) + - Known to work with Mingw-w64 12.2. + +## Other Required Software + +- SCons: + + - + - Works with versions >= 3.0.0 + - On Windows, more recent SCons versions are required to support each new version of + the MSVC compiler. + +- Python: + + - + - Works with versions >= 3.8. + +- Boost + + - + - Known to work with versions 1.71, 1.74, and 1.82; Expected to work with versions >= + 1.70 + - Only the "header-only" portions of Boost are required. Cantera does not currently + depend on any of the compiled Boost libraries. + +- SUNDIALS + + - If SUNDIALS is not installed and you have checked out the Cantera source code using + Git, SUNDIALS will be automatically downloaded and the necessary portions will be + compiled and installed with Cantera. + - + - Known to work with versions >= 3.0. Expected to work with versions \<= 7.0. + - To use SUNDIALS with Cantera on a Linux/Unix system, it must be compiled + with the `-fPIC` flag. You can specify this flag when configuring SUNDIALS as + `cmake -DCMAKE_C_FLAGS=-fPIC ` + +- Eigen + + - If Eigen is not installed and you have checked out the Cantera source code using + Git, Eigen will be automatically downloaded and installed with Cantera. + - + - Known to work with version 3.4.0. + +- fmt + + - If fmt (previously known as cppformat) is not installed and you have checked out the + Cantera source code using Git, fmt will be automatically downloaded and the + necessary portions will be compiled and installed with Cantera. + - + - Known to work with version 9.1.0. + +- yaml-cpp + + - If yaml-cpp is not installed and you have checked out the Cantera source code using + Git, it will be automatically downloaded and the necessary portions will be compiled + and installed with Cantera. + - + - Known to work with version 0.7.0. Version 0.6.0 or newer is required. + +## Optional Dependencies + +- [Numpy](https://www.numpy.org/) + + - Required to build the Cantera Python module, and to run significant portions + of the test suite. + - Expected to work with versions >= 1.12.0. 1.16.0 or newer is recommended. + +- [Cython](https://cython.org/) + + - Required version >=0.29.31 to build the Python module. + +- [Pip](https://pip.pypa.io/en/stable/installing/) (Python) + + - Required to build the Cantera Python module. + - Provides the `pip` command which can be used to install most of + the other Python dependencies. + +- [wheel](https://pypi.org/project/wheel/) (Python) + + - Required to build the Cantera Python module. + +- [setuptools](https://pypi.org/project/setuptools/) (Python) + + - Required to build the Cantera Python module. + +- [Ruamel.yaml](https://pypi.org/project/ruamel.yaml/) (Python) + + - Required to convert input files from Chemkin, CTI, and XML to the YAML + format + - Known to work with versions 0.15.42, 0.15.87, and 0.16.5 + - Expected to work with versions >= 0.15.0 + +- [libhdf5](https://www.hdfgroup.org/solutions/hdf5/) + + - Required to read and write data files in the HDF5 format + - Known to work with versions 1.12 and 1.14. + +- [HighFive](https://github.com/BlueBrain/HighFive) + + - Required to read and write data files in the HDF5 format + - If HighFive is not installed and you have checked out the Cantera source code + using Git, HighFive will be automatically downloaded and the necessary portions will + be compiled as part of the Cantera build process. + - Version 2.5.0 or newer is required. + +- [Google Test](https://github.com/google/googletest) + + - If Google Test is not installed and you have checked out the Cantera source code + using Git, Google Test will be automatically downloaded and the necessary portions + will be compiled as part of the Cantera build process. + - Required to run significant portions of the test suite. + - Known to work with version 1.11.0. + +- [pytest](https://pytest.org) + + - Required to run the Python test suite. + - Known to work with version 7.2.0 + +- Matlab + + - Required to build the Cantera Matlab toolbox. + - Known to work with 2022a. Expected to work with versions >= 2009a. + +- [Windows Installer XML (WiX) toolset](http://wixtoolset.org/) + + - Required to build MSI installers on Windows. + - Known to work with versions 3.5 and 3.8. + +- Packages required for building Sphinx documentation + + - [Sphinx](http://www.sphinx-doc.org/en/stable/) + - [PyData Sphinx theme](https://pydata-sphinx-theme.readthedocs.io/en/stable/) + - [Pygments](http://pygments.org/) + - [pyparsing](https://sourceforge.net/projects/pyparsing/) + - [sphinx-argparse](https://sphinx-argparse.readthedocs.io/en/latest/) + - [doxylink](https://pythonhosted.org/sphinxcontrib-doxylink/) + - [matlabdomain](https://pypi.org/project/sphinxcontrib-matlabdomain) + +- [Doxygen](http://doxygen.nl/) + + - Required for building the C++ API Documentation + - Version 1.8 or newer is recommended. + +- [Graphviz](https://www.graphviz.org/) + + - Required to build the dependency graph images in the C++ API Documentation + - Known to work with version 2.40.1, expected to work with versions >=2.40.1 diff --git a/doc/sphinx/develop/compiling/source-code.md b/doc/sphinx/develop/compiling/source-code.md new file mode 100644 index 00000000000..aa3a9ad6845 --- /dev/null +++ b/doc/sphinx/develop/compiling/source-code.md @@ -0,0 +1,118 @@ +(sec-source-code)= +# Downloading the Cantera source code + +## Stable Release + +- **Option 1**: Check out the code using Git (recommended): + + ```bash + git clone --recursive https://github.com/Cantera/cantera.git + cd cantera + ``` + + Then, check out the tag of the most recent stable version: + + ```bash + git checkout tags/v3.0.0 + git submodule update + ``` + + A list of all the tags can be shown by: + + ```bash + git tag --list + ``` + +- **Option 2**: Download the most recent source `.tar.gz` or `.zip` file from + [GitHub](https://github.com/Cantera/cantera/releases) and extract the contents. In + this case, several dependencies that are linked to the Cantera Git repository will not + be available and will need to be installed elsewhere on your system. + +```{button-ref} configure-build +:color: primary +:shadow: +:align: right +Next: Configure & Build Cantera +``` + +## Beta Release + +- Check out the code using Git: + + ```bash + git clone --recursive https://github.com/Cantera/cantera.git + cd cantera + ``` + + Then pick either **Option 1** or **Option 2** below. + +- **Option 1**: Check out the tag with the most recent beta release: + + ```bash + git checkout tags/v3.0.0b1 + git submodule update + ``` + + Note that the most recent beta version might be older than the most recent stable + release. A list of all the tags, including stable and beta versions can be shown by: + + ```bash + git tag --list + ``` + +- **Option 2**: Check out the branch with all the bug fixes leading to the next minor + release of the stable version: + + ```bash + git checkout 3.0 + git submodule update + ``` + + This branch has all the work on the 3.0.x version of the software. + + If you've already checked out the 3.0 branch, you can get the latest updates from the + main Cantera repository and synchronize your local repository by running: + + ```bash + git checkout 3.0 + git fetch --all + git pull --ff-only + ``` + +```{button-ref} configure-build +:color: primary +:shadow: +:align: right +Next: Configure & Build Cantera +``` + +## Development Version + +Check out the code using Git: + +```bash +git clone --recursive https://github.com/Cantera/cantera.git +cd cantera +``` + +Note that by default, the `main` branch is checked out, containing all of the feature +updates and bug fixes to the code since the previous stable release. The main branch is +usually an alpha release, corresponding to the `a` in the version number, and does not +usually get a tag. + +If you've previously checked out the repository, and haven't made any changes locally, +you can get the latest updates from the main Cantera repository and synchronize your +local repository by running: + +```bash +git checkout main +git fetch --all +git pull --ff-only +``` + +```{button-ref} configure-build +:color: primary +:shadow: +:align: right +Next: Configure & Build Cantera +``` diff --git a/doc/sphinx/develop/compiling/special-cases.md b/doc/sphinx/develop/compiling/special-cases.md new file mode 100644 index 00000000000..0b166184a4f --- /dev/null +++ b/doc/sphinx/develop/compiling/special-cases.md @@ -0,0 +1,60 @@ +(sec-special-compiling-cases)= +# Special Compiling Cases + +This guide explains some of the less common ways to build Cantera. + +(conda-build)= +## Building the Conda Package + +- The recipe for the Cantera Conda package is located at +- See the `README.md` in that repository for instructions. + +(sec-intel-compilers)= +## Intel Compilers + +- The following instructions refer to the [Intel OneAPI Toolkit](https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html). + +- Before compiling Cantera, you may need to set up the appropriate environment + variables for the Intel compiler suite. For example: + + ```bash + source /opt/intel/oneapi/setvars.sh + ``` + +- For the Intel compiler to work with SCons, these environment variables need + to be passed through SCons by using the command line option: + + ```bash + env_vars=all + ``` + +- If you want to use the Intel MKL versions of BLAS and LAPACK, you will need + to provide additional options. The following are typically correct on + 64-bit Linux systems: + + ```bash + blas_lapack_libs=mkl_rt blas_lapack_dir=$(MKLROOT)/lib/intel64 + ``` + + Your final SCons call might then look something like: + + ```bash + scons build env_vars=all CC=icx CXX=icpx FORTRAN=ifx blas_lapack_libs=mkl_rt blas_lapack_dir=$(MKLROOT)/lib/intel64 + ``` + +- When installing Cantera after building with the Intel compiler, the normal + method of using `sudo` to install Cantera to the system default directories + will not work because `sudo` does not pass the environment variables needed + by the Intel compiler. Instead, you will need to do something like: + + ```bash + scons build ... + sudo -s + source /path/to/setvars.sh + scons install + exit + ``` + + Another option is to set the [`prefix`](sconsopt-prefix) option to a directory + for which you have write permissions, and specify the `USER` value to the + [`python_prefix`](sconsopt-python-prefix) option. diff --git a/doc/sphinx/develop/index.md b/doc/sphinx/develop/index.md new file mode 100644 index 00000000000..0216f6a18af --- /dev/null +++ b/doc/sphinx/develop/index.md @@ -0,0 +1,38 @@ +# Develop + +```{caution} +This page is a work in progress. For compilation instructions for Cantera 3.0, please +see this page. +``` + +## Compiling Cantera from Source + +If you're interested in contributing new features to Cantera, or you want to try the +latest and development version, you will need to compile Cantera from source. The first +step is to make sure you have all the [](compiling/compilation-reqs) installed. Then, +you can [download the Cantera source code](compiling/source-code). Finally, you can +determine the appropriate configuration options and [compile +Cantera](compiling/configure-build) on your computer. + +The following additional references may also be useful: + +- [](compiling/dependencies.md) +- [](compiling/config-options) +- [](compiling/special-cases) + +```{toctree} +:caption: Compiling Cantera from Source +:hidden: +:maxdepth: 1 + +compiling/compilation-reqs +compiling/source-code +compiling/configure-build +compiling/dependencies +compiling/config-options +compiling/special-cases +``` + +## How Cantera Works + +## Adding New Models to Cantera diff --git a/doc/sphinx/examples/index.md b/doc/sphinx/examples/index.md new file mode 100644 index 00000000000..e107cc446e0 --- /dev/null +++ b/doc/sphinx/examples/index.md @@ -0,0 +1,107 @@ +# Examples + +Cantera includes examples for a number of applications. To see all examples written in a +particular programming language, select the corresponding category below. Or, to browse +all examples covering a particular topic, regardless of programming language, select +from the {ref}`list of example tags `. + +## Python Examples + +````{grid} 2 2 2 3 +:gutter: 3 + +```{grid-item-card} Thermodynamics +:link: python/thermo/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Kinetics +:link: python/kinetics/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Transport +:link: python/transport/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Reactor networks +:link: python/reactors/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} 1D reacting flows +:link: python/onedim/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Surface chemistry +:link: python/surface_chemistry/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Multiphase +:link: python/multiphase/index +:link-type: doc +:text-align: center +``` + +```` + +## Examples in Other Languages + +````{grid} 2 2 3 3 +:gutter: 3 + +```{grid-item-card} C++ +:link: cxx/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} C +:link: clib/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Matlab (experimental) +:link: matlab_experimental/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Fortran +:link: fortran/index +:link-type: doc +:text-align: center +``` + + +```` + +% The following pages are generated by sphinx-gallery +```{toctree} +:maxdepth: 2 +:hidden: + +python/index +cxx/index +clib/index +matlab_experimental/index +fortran/index +``` + +% The following page is generated by sphinx-tags +```{toctree} +:maxdepth: 1 +:hidden: + +/_tags/tagsindex +``` diff --git a/doc/sphinx/favicon.png b/doc/sphinx/favicon.png new file mode 100644 index 0000000000000000000000000000000000000000..a3af328e23fcd26110dd28ddf4be5797e9a20032 GIT binary patch literal 4879 zcmV+q6Y%VbP)M|H=4r|-S<*vG82yOOMx^|am=wz0rgz&7Mz zlbBaXks?rh2!Xhai=4wwhU#XZ7svrUK&n=PCAEb>1XO?$Fpn||%wd=mtD`_(Ju@sNy{aj_ ziYJ%EYC$AkpVlhi!Q}6FgoA=#fxx$vD+ZAz_o*V{;p&VT9Bhq0eoId+&`@2{A;Y5t z@^2_T3Ltp*6*yu2lF?LX0*`&~~m!(U;ipu)W zwH1n5{g|pjsZ+#2-cWiwln;YHfs_0WBateQ|5;9<_VFZl>xT$wkHj_#BL}e@Ama2& zrb(#SUSawn@TxVsZUSSIN$ij;D>A^dSRJ{kOa<@+owx5{Jc6ke<&0%+OT_$Ui=UU9 z!c<5)c^z1BAqL9w?-)Ljq~4|xfpnQ)k}O|Xc3prH%)V8L0EtQ1<3}ahn~_+qNRppjD7k>5fGTseH>?yd#NOTcIgAQkt z>N37V5TMFVRY77W#Md6Mgt$(sxskWB4zrUOH_0USRGp?{K{I-qjRN&laK|7Bc1Vnc z2(%A$5PDUR5WI-@TG3wznHPvuDMgW#MQU*gS4u#r5DT354L@m>nq)e*tIjp6NFbM! zga}%LqR4<+10I+H44gI0zY+XtP|+i?(cfOYTOo|(MyVA6ELP=`jm)lAsYz%Rta4rT z8nKjtOrrXmM-CA;hCR@f#dsjDmp`&rmZ^i)RDlRsWxEYcA8Q47)<7bINaIzCWd@i? 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z9IC*P3hcKcd#p&hUCdT%7xU9Zz;;z;5#ITU&v4=Jy>y*FN946vV1tof$8@`Rb*YZXdh$(#GjAwogy7g_uBf zb4K-G1r8VCP#F%F;f`2jrxj@`pGa-P`Idz&Dt)R90`K^(C%ACWTS%RIwU$4ny-2o7 z``YqEYLYAdp$yDC>Q@3E!OF~Z$jnsPiYZ!{(jb`5=lb$sF26XmbBuIw@hR0Yij{Jz zI>Bu}&avG;#rE=rvE37sW4k9up4~QajSZzaHdV^>sNUYCy1xtuV%T1CQogeadqU_# zgm}fi)(FUo9NVNyR+VkQZ~WQ^dH$hy;axoKm>Rd=he^iRb32w_*fBC-ZX5q)LVxjq z1qep9cF3X%Qg!#1T|fY{K~FL(&<{-6r6?~?n9lw%{8G)SGt zPyL)!<{X}R4L`U{x%@hDR0^gh$$2m|dWC+C*f>1Fj&KHlKF|K~5hBlL&$ZX-kE;A& z*8#qI|F7`U-SH=;cIj$31j`w{q2g{Y}!;Z zlT=gPF8g@9uw1gNF_TugpsDm2#+)J3HGyH6O4n7on7~%XDa}t4_{HqxI6Yy=_?B%D z1TZy9DvD9#p$3c!K~)LGO%ddMD6lw|^`CyXC5n@6JbvYdMcN9xuKb8x@okREc44{n z8*2v)3{a^}o~4>|CkjPSjK;w8A)}{T^ zSX1^}wp+h`s8Wa(2@udGPggQm5`!9Ud8vllxNoP{Ustk1L22MYU|KESd<`5a3e3ra-f};}bog z8IWFFu%-{UtE!DVRvUzXs2R|z{gAccS6i(nnU3wPA8WUZ@#zV$Oc{|Dv^vCZ{W`IGthis page. +``` + +```{toctree} +:maxdepth: 1 + +install/index +userguide/index +examples/index +reference/index +develop/index +``` diff --git a/doc/sphinx/install/conda.md b/doc/sphinx/install/conda.md new file mode 100644 index 00000000000..110628f22f2 --- /dev/null +++ b/doc/sphinx/install/conda.md @@ -0,0 +1,6 @@ +# Installing with Conda + +```{caution} +This page is a work in progress. For current Conda installation instructions, see +this page. +``` diff --git a/doc/sphinx/install/index.md b/doc/sphinx/install/index.md new file mode 100644 index 00000000000..6d5f7dcf465 --- /dev/null +++ b/doc/sphinx/install/index.md @@ -0,0 +1,18 @@ +# Install + +```{caution} +This page is a work in progress. For installation instructions for Cantera 3.0, please +see this page. +``` + +```{toctree} +:maxdepth: 1 + +conda +pip +``` + +```{seealso} +Check the [FAQ](sec-faq-installation) for solutions to some common installation +problems. +``` diff --git a/doc/sphinx/install/pip.md b/doc/sphinx/install/pip.md new file mode 100644 index 00000000000..4f8d2a2d099 --- /dev/null +++ b/doc/sphinx/install/pip.md @@ -0,0 +1,6 @@ +# Installing with Pip + +```{caution} +This page is a work in progress. For current Pip installation instructions, see +this page. +``` diff --git a/doc/sphinx/python/ck_conversion.rst b/doc/sphinx/python/ck_conversion.rst new file mode 100644 index 00000000000..5e6f7c00cff --- /dev/null +++ b/doc/sphinx/python/ck_conversion.rst @@ -0,0 +1,13 @@ +************************** +Chemkin to YAML conversion +************************** + +.. seealso:: + For documentation of the command line interface, see the :ref:`ck2yaml + ` section. For a tutorial, refer to the `Converting Chemkin-format + files `_ pages. + +Module-level documentation +========================== + +.. automodule:: cantera.ck2yaml diff --git a/doc/sphinx/python/constants.rst b/doc/sphinx/python/constants.rst new file mode 100644 index 00000000000..158b40dfd32 --- /dev/null +++ b/doc/sphinx/python/constants.rst @@ -0,0 +1,54 @@ +.. py:currentmodule:: cantera + +Physical Constants +================== + +These values are the same as those in the Cantera C++ header file ct_defs.h. + +.. data:: avogadro + + Avogadro's Number, kmol\ :sup:`-1` + +.. data:: gas_constant + + The ideal gas constant, J kmol\ :sup:`-1` K\ :sup:`-1` + +.. data:: one_atm + + One atmosphere, Pa + +.. data:: boltzmann + + Boltzmann constant, m\ :sup:`2` kg s\ :sup:`-2` K\ :sup:`-1` + +.. data:: planck + + Planck constant, J s + +.. data:: stefan_boltzmann + + The Stefan-Boltzmann constant, W m\ :sup:`-2` K\ :sup:`-4` + +.. data:: electron_charge + + The charge on an electron, C + +.. data:: electron_mass + + The mass of an electron, kg + +.. data:: faraday + + Faraday constant, C kmol\ :sup:`-1` + +.. data:: light_speed + + Speed of Light, m s\ :sup:`-1` + +.. data:: permeability_0 + + Permeability of free space, m kg s\ :sup:`-2` A\ :sup:`-2` + +.. data:: epsilon_0 + + Permittivity of free space, s\ :sup:`4` A\ :sup:`2` m\ :sup:`-3` kg\ :sup:`-1` diff --git a/doc/sphinx/python/cti_conversion.rst b/doc/sphinx/python/cti_conversion.rst new file mode 100644 index 00000000000..80fff9ce320 --- /dev/null +++ b/doc/sphinx/python/cti_conversion.rst @@ -0,0 +1,13 @@ +*********************** +CTI to YAML conversion +*********************** + +.. seealso:: + For documentation of the command line interface, see the :ref:`cti2yaml + ` section. For a tutorial, refer to the `Converting CTI and XML input + files to YAML `_ pages. + +Module-level documentation +========================== + +.. automodule:: cantera.cti2yaml diff --git a/doc/sphinx/python/ctml_conversion.rst b/doc/sphinx/python/ctml_conversion.rst new file mode 100644 index 00000000000..88f6e9ed171 --- /dev/null +++ b/doc/sphinx/python/ctml_conversion.rst @@ -0,0 +1,60 @@ +*********************** +CTML to YAML conversion +*********************** + +.. seealso:: + For documentation of the command line interface, see the :ref:`ctml2yaml + ` section. For a tutorial, refer to the `Converting CTI and XML input + files to YAML `_ pages. + + +Module-level documentation +========================== + +.. py:module:: cantera.ctml2yaml +.. py:currentmodule:: cantera.ctml2yaml + +The script ``ctml2yaml.py`` will convert files from the legacy CTML format to YAML input +format. The documentation below describes the classes and functions in the script. Each +function/method is annotated with the Python types that the function accepts. + +Most users will access the functionality of this module via the command line with the +``ctml2yaml`` entry-point script. For programmatic access, the `main` and/or `convert` +functions should be used. `main` should be used when command line arguments must be +processed, while `convert` takes an input filename or a string containing the CTML file +to be converted, and optionally the name of the output file. + +Module-level functions +---------------------- + +.. autofunction:: float2string +.. autofunction:: represent_float +.. autofunction:: get_float_or_quantity +.. autofunction:: split_species_value_string +.. autofunction:: clean_node_text +.. autofunction:: create_species_from_data_node +.. autofunction:: create_reactions_from_data_node +.. autofunction:: create_phases_from_data_node +.. autofunction:: convert +.. autofunction:: main + +Conversion classes +------------------ + +.. autoclass:: Phase + :no-undoc-members: +.. autoclass:: Species + :no-undoc-members: +.. autoclass:: SpeciesThermo + :no-undoc-members: +.. autoclass:: SpeciesTransport + :no-undoc-members: +.. autoclass:: Reaction + :no-undoc-members: + +Exceptions +---------- + +.. autoexception:: MissingXMLNode +.. autoexception:: MissingXMLAttribute +.. autoexception:: MissingNodeText diff --git a/doc/sphinx/python/importing.rst b/doc/sphinx/python/importing.rst new file mode 100644 index 00000000000..4f31bf4197c --- /dev/null +++ b/doc/sphinx/python/importing.rst @@ -0,0 +1,46 @@ +.. py:currentmodule:: cantera + +Objects Representing Phases +=========================== + +.. contents:: + :local: + +Composite Phase Objects +----------------------- + +These classes are composite representations of a substance which has +thermodynamic, chemical kinetic, and (optionally) transport properties. + +.. autoclass:: Solution(infile='', name='', *, origin=None, yaml=None, thermo=None, species=(), kinetics=None, reactions=()) + +.. autoclass:: cantera.solutionbase._SolutionBase() + +.. autoclass:: Interface(infile='', name='', adjacent=(), *, origin=None, yaml=None, thermo=None, species=(), kinetics=None, reactions=()) + +.. autoclass:: DustyGas(infile, name='') + +Pure Fluid Phases +----------------- + +The following convenience functions can be used to create `PureFluid` objects +with the indicated equation of state: + +.. autofunction:: CarbonDioxide +.. autofunction:: Heptane +.. autofunction:: Hfc134a +.. autofunction:: Hydrogen +.. autofunction:: Methane +.. autofunction:: Nitrogen +.. autofunction:: Oxygen +.. autofunction:: Water + +Representing Quantities of Phases +--------------------------------- + +.. autoclass:: Quantity + +Representing Multiple States +---------------------------- + +.. autoclass:: SolutionArray diff --git a/doc/sphinx/python/index.rst b/doc/sphinx/python/index.rst new file mode 100644 index 00000000000..557445f69c4 --- /dev/null +++ b/doc/sphinx/python/index.rst @@ -0,0 +1,20 @@ +.. _sec-python-documentation: + +Python Module Documentation +=========================== + +Contents: + +.. toctree:: + :maxdepth: 2 + + importing + thermo + kinetics + transport + zerodim + onedim + constants + units + utilities + scripts diff --git a/doc/sphinx/python/kinetics.rst b/doc/sphinx/python/kinetics.rst new file mode 100644 index 00000000000..0fe83273e81 --- /dev/null +++ b/doc/sphinx/python/kinetics.rst @@ -0,0 +1,156 @@ +.. py:currentmodule:: cantera + +Chemical Kinetics +================= + +.. contents:: + :local: + +Kinetics Managers +----------------- + +Kinetics +^^^^^^^^ +.. autoclass:: Kinetics + +InterfaceKinetics +^^^^^^^^^^^^^^^^^ +.. autoclass:: InterfaceKinetics + +Reactions +--------- + +This class contains the definition of a single reaction, independent of a specific +`Kinetics` object. Reaction rate evaluation is handled by `ReactionRate` objects. + +Reaction +^^^^^^^^ +.. autoclass:: Reaction + :no-undoc-members: + + +Reaction Rates +-------------- + +ReactionRate +^^^^^^^^^^^^ +.. autoclass:: ReactionRate() + +ArrheniusRateBase +^^^^^^^^^^^^^^^^^ +.. autoclass:: ArrheniusRateBase(input_data) + :no-undoc-members: + +ArrheniusRate +^^^^^^^^^^^^^ +.. autoclass:: ArrheniusRate(A, b, Ea) + :no-undoc-members: + +BlowersMaselRate +^^^^^^^^^^^^^^^^ +.. autoclass:: BlowersMaselRate(A, b, Ea, w) + :no-undoc-members: + +TwoTempPlasmaRate +^^^^^^^^^^^^^^^^^ +.. autoclass:: TwoTempPlasmaRate(A, b, Ea_gas, Ea_electron) + :no-undoc-members: + +FalloffRate +^^^^^^^^^^^ +.. autoclass:: FalloffRate() + :no-undoc-members: + +LindemannRate +^^^^^^^^^^^^^ +.. autoclass:: LindemannRate(low, high, falloff_coeffs) + :no-undoc-members: + +TroeRate +^^^^^^^^ +.. autoclass:: TroeRate(low, high, falloff_coeffs) + :no-undoc-members: + +SriRate +^^^^^^^ +.. autoclass:: SriRate(low, high, falloff_coeffs) + :no-undoc-members: + +TsangRate +^^^^^^^^^ +.. autoclass:: TsangRate(low, high, falloff_coeffs) + :no-undoc-members: + +PlogRate +^^^^^^^^ +.. autoclass:: PlogRate(rates) + :no-undoc-members: + +ChebyshevRate +^^^^^^^^^^^^^ +.. autoclass:: ChebyshevRate(temperature_range, pressure_range, data) + :no-undoc-members: + +CustomRate +^^^^^^^^^^ +.. autoclass:: CustomRate(k) + :no-undoc-members: + +ExtensibleRate +^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleRate() + :no-undoc-members: + +InterfaceRateBase +^^^^^^^^^^^^^^^^^ +.. autoclass:: InterfaceRateBase + :no-undoc-members: + +InterfaceArrheniusRate +^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: InterfaceArrheniusRate(A, b, Ea) + :no-undoc-members: + +InterfaceBlowersMaselRate +^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: InterfaceBlowersMaselRate(A, b, Ea0, w) + :no-undoc-members: + +StickRateBase +^^^^^^^^^^^^^ +.. autoclass:: StickRateBase + :no-undoc-members: + +StickingArrheniusRate +^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: StickingArrheniusRate(A, b, Ea) + :no-undoc-members: + +StickingBlowersMaselRate +^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: StickingBlowersMaselRate(A, b, Ea0, w) + :no-undoc-members: + +Auxiliary Reaction Data +----------------------- + +ExtensibleRateData +^^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleRateData + :no-undoc-members: + +ThirdBody +^^^^^^^^^ +.. autoclass:: ThirdBody + :no-undoc-members: + +Arrhenius +^^^^^^^^^ +.. autoclass:: Arrhenius(A, b, E) + +Reaction Path Analysis +---------------------- + +ReactionPathDiagram +^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ReactionPathDiagram(Kinetics kin, str element) diff --git a/doc/sphinx/python/onedim.rst b/doc/sphinx/python/onedim.rst new file mode 100644 index 00000000000..bd14b960822 --- /dev/null +++ b/doc/sphinx/python/onedim.rst @@ -0,0 +1,95 @@ +.. py:currentmodule:: cantera + +.. _sec-python-onedim: + +One-dimensional Reacting Flows +============================== + +.. contents:: + :local: + +Composite Domains +----------------- + +FreeFlame +^^^^^^^^^ +.. autoclass:: FreeFlame + +BurnerFlame +^^^^^^^^^^^ +.. autoclass:: BurnerFlame + +CounterflowDiffusionFlame +^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: CounterflowDiffusionFlame + +CounterflowPremixedFlame +^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: CounterflowPremixedFlame + +CounterflowTwinPremixedFlame +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: CounterflowTwinPremixedFlame + +ImpingingJet +^^^^^^^^^^^^ +.. autoclass:: ImpingingJet + + +Flow Domains +------------ + +FreeFlow +^^^^^^^^ +.. autoclass:: FreeFlow(thermo) + +AxisymmetricFlow +^^^^^^^^^^^^^^^^ +.. autoclass:: AxisymmetricFlow(thermo) + + +Boundaries +---------- + +Inlet1D +^^^^^^^ +.. autoclass:: Inlet1D(phase, *, name=None) + +Outlet1D +^^^^^^^^ +.. autoclass:: Outlet1D(phase, *, name=None) + +OutletReservoir1D +^^^^^^^^^^^^^^^^^ +.. autoclass:: OutletReservoir1D(phase, *, name=None) + +SymmetryPlane1D +^^^^^^^^^^^^^^^ +.. autoclass:: SymmetryPlane1D(phase, *, name=None) + +Surface1D +^^^^^^^^^ +.. autoclass:: Surface1D(phase, * name=None) + +ReactingSurface1D +^^^^^^^^^^^^^^^^^ +.. autoclass:: ReactingSurface1D(phase, *, name=None) + + +Base Classes +------------ +Domain1D +^^^^^^^^ +.. autoclass:: Domain1D(phase, *, name=None) + +Boundary1D +^^^^^^^^^^ +.. autoclass:: Boundary1D(phase, *, name=None) + +Sim1D +^^^^^ +.. autoclass:: Sim1D(domains) + +FlameBase +^^^^^^^^^ +.. autoclass:: FlameBase diff --git a/doc/sphinx/python/scripts.rst b/doc/sphinx/python/scripts.rst new file mode 100644 index 00000000000..b014132afce --- /dev/null +++ b/doc/sphinx/python/scripts.rst @@ -0,0 +1,14 @@ +.. _sec-converter-documentation: + +Mechanism Conversion +==================== + +Contents: + +.. toctree:: + :maxdepth: 1 + + ck_conversion + cti_conversion + ctml_conversion + yaml_conversion diff --git a/doc/sphinx/python/thermo.rst b/doc/sphinx/python/thermo.rst new file mode 100644 index 00000000000..d3d73461243 --- /dev/null +++ b/doc/sphinx/python/thermo.rst @@ -0,0 +1,80 @@ +.. py:currentmodule:: cantera + + +Thermodynamic Properties +======================== + +.. contents:: + :local: + +Phases +------ + +These classes are used to describe the thermodynamic state of a system. + +ThermoPhase +^^^^^^^^^^^ +.. autoclass:: ThermoPhase(infile='', name='', *, origin=None, yaml=None, thermo=None, species=(), **kwargs) + +InterfacePhase +^^^^^^^^^^^^^^ +.. autoclass:: InterfacePhase(infile='', name='', adjacent=(), *, origin=None, yaml=None, thermo=None, species=(), **kwargs) + +PureFluid +^^^^^^^^^ +.. autoclass:: PureFluid(infile='', name='') + +Mixture +------- + +.. autoclass:: Mixture(phases) + +Species +------- + +.. autoclass:: Species + +Species Thermodynamic Properties +-------------------------------- + +These classes are used to describe the reference-state thermodynamic properties +of a pure species. + +SpeciesThermo +^^^^^^^^^^^^^ +.. autoclass:: SpeciesThermo(T_low, T_high, P_ref, coeffs) + +ConstantCp +^^^^^^^^^^ +.. autoclass:: ConstantCp(T_low, T_high, P_ref, coeffs) + :no-undoc-members: + +Mu0Poly +^^^^^^^ +.. autoclass:: Mu0Poly(T_low, T_high, P_ref, coeffs) + :no-undoc-members: + +NasaPoly2 +^^^^^^^^^ +.. autoclass:: NasaPoly2(T_low, T_high, P_ref, coeffs) + :no-undoc-members: + +Nasa9PolyMultiTempRegion +^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: Nasa9PolyMultiTempRegion(T_low, T_high, P_ref, coeffs) + :no-undoc-members: + +ShomatePoly2 +^^^^^^^^^^^^ +.. autoclass:: ShomatePoly2(T_low, T_high, P_ref, coeffs) + :no-undoc-members: + +Element +------- + +.. autoclass:: Element + :no-undoc-members: + + .. autoattribute:: num_elements_defined + .. autoattribute:: element_symbols + .. autoattribute:: element_names diff --git a/doc/sphinx/python/transport.rst b/doc/sphinx/python/transport.rst new file mode 100644 index 00000000000..c38f74a618a --- /dev/null +++ b/doc/sphinx/python/transport.rst @@ -0,0 +1,12 @@ +.. py:currentmodule:: cantera + +Transport Properties +==================== + +.. autoclass:: Transport() +.. autoclass:: DustyGasTransport() + +Species Transport Properties +---------------------------- + +.. autoclass:: GasTransportData(geometry='', diameter=-1, well_depth=-1, dipole=0.0, polarizability=0.0, rotational_relaxation=0.0, acentric_factor=0.0, dispersion_coefficient=0.0, quadrupole_polarizability=0.0) diff --git a/doc/sphinx/python/units.rst b/doc/sphinx/python/units.rst new file mode 100644 index 00000000000..f5036671a15 --- /dev/null +++ b/doc/sphinx/python/units.rst @@ -0,0 +1,49 @@ +.. py:currentmodule:: cantera.with_units + +Python Interface With Units +=========================== + +This interface allows users to specify physical units associated with quantities. +To do so, this interface leverages the `pint `__ +library to provide consistent unit conversion. Several examples of this interface can +be found in the ``samples/python`` folder in the +`root of the repository `__. +Examples that use this interface are suffixed with `_units`. + +The overall goal is to provide a compatible implementation of the `cantera.Solution` and +`cantera.PureFluid` interfaces. Please see those pages for further documentation of the +available properties. + +Solution with Units +------------------- + +.. autoclass:: Solution + :no-members: + +PureFluid Phases With Units +--------------------------- + +The following convenience classes are available to create `PureFluid ` +objects with the indicated equation of state: + +.. autoclass:: CarbonDioxide + :no-members: +.. autoclass:: Heptane + :no-members: +.. autoclass:: Hfc134a + :no-members: +.. autoclass:: Hydrogen + :no-members: +.. autoclass:: Methane + :no-members: +.. autoclass:: Nitrogen + :no-members: +.. autoclass:: Oxygen + :no-members: +.. autoclass:: Water + :no-members: + +The full documentation for the `PureFluid ` class and its properties is here: + +.. autoclass:: PureFluid + :no-members: diff --git a/doc/sphinx/python/utilities.rst b/doc/sphinx/python/utilities.rst new file mode 100644 index 00000000000..55f3f633885 --- /dev/null +++ b/doc/sphinx/python/utilities.rst @@ -0,0 +1,65 @@ +.. py:currentmodule:: cantera + +Utilities +========= + +.. contents:: + :local: + +YAML Input/Output +----------------- + +AnyMap +^^^^^^ + +.. autoclass:: AnyMap + +YamlWriter +^^^^^^^^^^ +.. autoclass:: YamlWriter + +Unit Conversions +---------------- + +UnitSystem +^^^^^^^^^^ +.. autoclass:: UnitSystem + :no-undoc-members: + +Units +^^^^^ +.. autoclass:: Units + :no-undoc-members: + + +Global Functions +---------------- + +.. autofunction:: add_directory +.. autofunction:: get_data_directories +.. autofunction:: import_phases +.. autofunction:: appdelete +.. autofunction:: use_sparse + +.. autofunction:: make_deprecation_warnings_fatal +.. autofunction:: suppress_deprecation_warnings +.. autofunction:: suppress_thermo_warnings +.. autofunction:: use_legacy_rate_constants +.. autofunction:: debug_mode_enabled +.. autofunction:: add_module_directory + +.. autofunction:: extension(name: str) + +Exceptions +---------- + +CanteraError +^^^^^^^^^^^^ +.. autoclass:: CanteraError + :no-undoc-members: + + +ThermoModelMethodError +^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ThermoModelMethodError + :no-undoc-members: diff --git a/doc/sphinx/python/yaml_conversion.rst b/doc/sphinx/python/yaml_conversion.rst new file mode 100644 index 00000000000..76db59e006c --- /dev/null +++ b/doc/sphinx/python/yaml_conversion.rst @@ -0,0 +1,11 @@ +************************** +YAML to Chemkin conversion +************************** + +.. seealso:: + For documentation of the command line interface, see :ref:`sec-yaml2ck`. + +Module-level documentation +========================== + +.. automodule:: cantera.yaml2ck diff --git a/doc/sphinx/python/zerodim.rst b/doc/sphinx/python/zerodim.rst new file mode 100644 index 00000000000..3fae5eabb75 --- /dev/null +++ b/doc/sphinx/python/zerodim.rst @@ -0,0 +1,147 @@ +.. py:currentmodule:: cantera + +.. _sec-python-zerodim: + +Zero-Dimensional Reactor Networks +================================= + +.. contents:: + :local: + +Defining Functions +------------------ + +.. autoclass:: Func1 + +.. autoclass:: Tabulated1 + +Base Classes +------------ + +ReactorBase +^^^^^^^^^^^ +.. autoclass:: ReactorBase + +FlowDevice +^^^^^^^^^^ +.. autoclass:: FlowDevice + +Reactor Networks +---------------- + +.. autoclass:: ReactorNet + +Reactors +-------- + +Reservoir +^^^^^^^^^ +.. autoclass:: Reservoir(contents=None, name=None) + +Reactor +^^^^^^^ +.. autoclass:: Reactor + +MoleReactor +^^^^^^^^^^^ +.. autoclass:: MoleReactor(contents=None, *, name=None, energy='on') + +IdealGasReactor +^^^^^^^^^^^^^^^ +.. autoclass:: IdealGasReactor(contents=None, *, name=None, energy='on') + +IdealGasMoleReactor +^^^^^^^^^^^^^^^^^^^ +.. autoclass:: IdealGasMoleReactor(contents=None, *, name=None, energy='on') + +ConstPressureReactor +^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ConstPressureReactor(contents=None, *, name=None, energy='on') + +ConstPressureMoleReactor +^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ConstPressureMoleReactor(contents=None, *, name=None, energy='on') + +IdealGasConstPressureReactor +^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: IdealGasConstPressureReactor(contents=None, *, name=None, energy='on') + +IdealGasConstPressureMoleReactor +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: IdealGasConstPressureMoleReactor(contents=None, *, name=None, energy='on') + +FlowReactor +^^^^^^^^^^^ +.. autoclass:: FlowReactor(contents=None, *, name=None, energy='on') + +ExtensibleReactor +^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleReactor(contents=None, *, name=None, energy='on') + +ExtensibleIdealGasReactor +^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleIdealGasReactor(contents=None, *, name=None, energy='on') + +ExtensibleConstPressureReactor +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleConstPressureReactor(contents=None, *, name=None, energy='on') + +ExtensibleIdealGasConstPressureReactor +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleIdealGasConstPressureReactor(contents=None, *, name=None, energy='on') + +ExtensibleMoleReactor +^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleMoleReactor(contents=None, *, name=None, energy='on') + +ExtensibleIdealGasMoleReactor +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleIdealGasMoleReactor(contents=None, *, name=None, energy='on') + +ExtensibleConstPressureMoleReactor +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleConstPressureMoleReactor(contents=None, *, name=None, energy='on') + +ExtensibleIdealGasConstPressureMoleReactor +^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: ExtensibleIdealGasConstPressureMoleReactor(contents=None, *, name=None, energy='on') + +Walls +----- + +Wall +^^^^ +.. autoclass:: Wall(left, right, *, name=None, A=None, K=None, U=None, Q=None, velocity=None) + :inherited-members: + +Surfaces +-------- + +ReactorSurface +^^^^^^^^^^^^^^ +.. autoclass:: ReactorSurface(kin=None, r=None, *, A=None) + +Flow Controllers +---------------- + +MassFlowController +^^^^^^^^^^^^^^^^^^ +.. autoclass:: MassFlowController + :inherited-members: + +Valve +^^^^^ +.. autoclass:: Valve + :inherited-members: + +PressureController +^^^^^^^^^^^^^^^^^^ +.. autoclass:: PressureController + :inherited-members: + +Preconditioners +--------------- + +AdaptivePreconditioner +^^^^^^^^^^^^^^^^^^^^^^ +.. autoclass:: AdaptivePreconditioner diff --git a/doc/sphinx/reference/bibliography.md b/doc/sphinx/reference/bibliography.md new file mode 100644 index 00000000000..080507a4b30 --- /dev/null +++ b/doc/sphinx/reference/bibliography.md @@ -0,0 +1,9 @@ +# Bibliography + +```{seealso} +References cited in the C++ Documentation can be found +here. +``` + +```{bibliography} +``` diff --git a/doc/sphinx/reference/glossary.md b/doc/sphinx/reference/glossary.md new file mode 100644 index 00000000000..187507db223 --- /dev/null +++ b/doc/sphinx/reference/glossary.md @@ -0,0 +1,7 @@ +# Glossary + + +```{caution} +This page is a work in progress. Please see +this page for current documentation. +``` diff --git a/doc/sphinx/reference/index.md b/doc/sphinx/reference/index.md new file mode 100644 index 00000000000..2f6faff810b --- /dev/null +++ b/doc/sphinx/reference/index.md @@ -0,0 +1,100 @@ + +# Reference + +This pages provide detailed reference documentation for Cantera. + +```{caution} +This page is a work in progress. For more complete documentation of the current Cantera +release (Cantera 3.0), please see the +documentation index and the +Science & Theory Manual. +``` + +## Programming Reference + +These sections document the classes and functions that define the Cantera interface for +each available programming language, as well as the structure of Cantera's YAML +mechanism files. + +````{grid} 2 +:gutter: 3 + +```{grid-item-card} Python API Reference +:link: /python/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Matlab API Reference +:link: /matlab/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} C++ API Reference +:link: ../cxx/index.html +:text-align: center +``` + +```{grid-item-card} YAML Format Reference +:link: /yaml/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Release Notes +:link: releasenotes/index +:link-type: doc +:text-align: center +``` + +```` + +```{toctree} +:hidden: +:maxdepth: 1 +:caption: API Reference + +/python/index +/matlab/index +/yaml/index +releasenotes/index +``` + +## Science Reference + +These sections document the scientific theories, mathematical models, and numerical +methods implemented by Cantera + +````{grid} 2 +:gutter: 3 + +```{grid-item-card} Reactors +:link: science/reactors/index +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Bibliography +:link: bibliography +:link-type: doc +:text-align: center +``` + +```{grid-item-card} Glossary +:link: glossary +:link-type: doc +:text-align: center +``` + +```` + +```{toctree} +:hidden: +:maxdepth: 1 +:caption: Science Reference + +science/reactors/index +bibliography +glossary +``` diff --git a/doc/sphinx/reference/releasenotes/index.md b/doc/sphinx/reference/releasenotes/index.md new file mode 100644 index 00000000000..2fba9788d36 --- /dev/null +++ b/doc/sphinx/reference/releasenotes/index.md @@ -0,0 +1,6 @@ +# Release Notes + +```{caution} +This page is a work in progress. Please see +this page for current documentation. +``` diff --git a/doc/sphinx/reference/science/reactors/controlreactor.md b/doc/sphinx/reference/science/reactors/controlreactor.md new file mode 100644 index 00000000000..ea0535125fb --- /dev/null +++ b/doc/sphinx/reference/science/reactors/controlreactor.md @@ -0,0 +1,73 @@ +```{py:currentmodule} cantera +``` + +# Control Volume Reactor + +This model represents a homogeneous zero-dimensional reactor, as implemented by the C++ +class {ct}`Reactor`. By default, these reactors are closed (no inlets or outlets), have +fixed volume, and have adiabatic, chemically-inert walls. These properties may all be +changed by adding appropriate components such as {py:class}`Wall`, +{py:class}`ReactorSurface`, {py:class}`MassFlowController`, and +{py:class}`Valve`. + +A control volume reactor is defined by the four state variables: + +- $m$, the mass of the reactor's contents (in kg) +- $V$, the reactor volume (in m$^3$) +- $U$, the total internal energy of the reactors contents (in J) +- $Y_k$, the mass fractions for each species (dimensionless) + +The total mass of the reactor's contents changes as a result of flow through the +reactor's inlets and outlets, and production of homogeneous phase species on the reactor +{py:class}`Wall`. + +$$ +\frac{dm}{dt} = \sum_{in} \dot{m}_{in} - \sum_{out} \dot{m}_{out} + \dot{m}_{wall} +$$ (mass) + +Where the subscripts *in* and *out* refer to the sum of the corresponding property over +all inlets and outlets respectively. A dot above a variable signifies a time derivative. + +The reactor volume changes as a function of time due to the motion of one or more walls: + +$$ +\frac{dV}{dt} = \sum_w f_w A_w v_w(t) +$$ (volume) + +where $f_w = \pm 1$ indicates the facing of the wall (whether moving the wall increases +or decreases the volume of the reactor), $A_w$ is the surface area of the wall, and +$v_w(t)$ is the velocity of the wall as a function of time. + +The equation for the total internal energy is found by writing the first law for an open +system: + +$$ +\frac{dU}{dt} = - p \frac{dV}{dt} + \dot{Q} + + \sum_{in} \dot{m}_{in} h_{in} - h \sum_{out} \dot{m}_{out} +$$ (energy) + +Where $\dot{Q}$ is the net rate of heat addition to the system. + +The rate at which species $k$ is generated through homogeneous phase reactions is +$V \dot{\omega}_k W_k$, and the total rate at which species $k$ is generated is: + +$$ +\dot{m}_{k,gen} = V \dot{\omega}_k W_k + \dot{m}_{k,wall} +$$ + +The rate of change in the mass of each species is: + +$$ +\frac{d(mY_k)}{dt} = \sum_{in} \dot{m}_{in} Y_{k,in} - \sum_{out} \dot{m}_{out} Y_k + + \dot{m}_{k,gen} +$$ + +Expanding the derivative on the left hand side and substituting the equation +for $dm/dt$, the equation for each homogeneous phase species is: + +$$ +m \frac{dY_k}{dt} = \sum_{in} \dot{m}_{in} (Y_{k,in} - Y_k) + + \dot{m}_{k,gen} - Y_k \dot{m}_{wall} +$$ (species) + +Equations 1-4 are the governing equations for a control volume reactor. diff --git a/doc/sphinx/reference/science/reactors/index.md b/doc/sphinx/reference/science/reactors/index.md new file mode 100644 index 00000000000..fe80fddfd33 --- /dev/null +++ b/doc/sphinx/reference/science/reactors/index.md @@ -0,0 +1,67 @@ +# Reactors and Reactor Networks + +```{caution} +This page is a work in progress. For more complete documentation of the current Cantera +release (Cantera 3.0), please see this page. +``` + +## Reactors + +A Cantera *reactor* represents the simplest form of a chemically reacting system. It +corresponds to an extensive thermodynamic control volume $V$, in which all state +variables are homogeneously distributed. The system is generally unsteady -- that is, +all states are functions of time. In particular, transient state changes due to chemical +reactions are possible. However, thermodynamic (but not chemical) equilibrium is assumed +to be present throughout the reactor at all instants of time. + +Reactors can interact with the surrounding environment in multiple ways: + +- Expansion/compression work: By moving the walls of the reactor, its volume can be + changed and expansion or compression work can be done by or on the reactor. + +- Heat transfer: An arbitrary heat transfer rate can be defined to cross the boundaries + of the reactor. + +- Mass transfer: The reactor can have multiple inlets and outlets. For the inlets, + arbitrary states can be defined. Fluid with the current state of the reactor exits the + reactor at the outlets. + +- Surface interaction: One or multiple walls can influence the chemical reactions in the + reactor. This is not just restricted to catalytic reactions, but mass transfer between + the surface and the fluid can also be modeled. + +All of these interactions do not have to be constant, but can vary as a function of time +or state. For example, heat transfer can be described as a function of the temperature +difference between the reactor and the environment, or the wall movement can be modeled +depending on the pressure difference. Interactions of the reactor with the environment +are defined on one or more walls, inlets, and outlets. + +In addition to single reactors, Cantera is also able to interconnect reactors into a +*reactor network*. Each reactor in a network may be connected so that the contents of one +reactor flow into another. Reactors may also be in contact with one another or the +environment via walls that conduct heat or move to do work. + +## Reactor Types and Governing Equations + +All reactor types are modelled using combinations of Cantera's governing equations of +state. The specific governing equations defining Cantera's supported reactor models are +derived and described below. + + +````{grid} 2 +:gutter: 3 + +```{grid-item-card} Control Volume Reactor +:link: controlreactor +:link-type: doc + +A reactor where the volume is prescribed by the motion of the reactor's walls. The state variables are the volume, mass, total internal energy, and species mass fractions. +``` + +```` + +```{toctree} +:hidden: + +controlreactor +``` \ No newline at end of file diff --git a/doc/sphinx/userguide/ck2yaml-tutorial.md b/doc/sphinx/userguide/ck2yaml-tutorial.md new file mode 100644 index 00000000000..b31ff1b54ed --- /dev/null +++ b/doc/sphinx/userguide/ck2yaml-tutorial.md @@ -0,0 +1,289 @@ +# Converting Chemkin Format Files + +Many existing reaction mechanism files are in **CK format**, by which we mean the input +file format developed for use with the Chemkin-II software package (and subsequent +releases) as specified in the report describing the Chemkin software +{cite:p}`kee1989`. Cantera comes with a converter utility program `ck2yaml` (or +`ck2yaml.py`) that converts CK format into Cantera's YAML format. If you want to convert +a Chemkin-format file to YAML format, or you're having errors when you try to do so, +this section will help. + +## Converting gas-phase mechanisms + +:::{seealso} +For documentation of all the command line options that can be used with `ck2yaml`, see +its [documentation in the reference section](sec-ck2yaml). +::: + +To convert a gas phase mechanism where the thermodynamic and transport data are provided +as separate files, run the following command from a terminal (command prompt): + +```bash +ck2yaml --input=chem.inp --thermo=therm.dat --transport=tran.dat +``` + +If the `ck2yaml` script is not on your path but the Cantera Python module is, +`ck2yaml` can also be used by running: + +```bash +python -m cantera.ck2yaml --input=chem.inp --thermo=therm.dat --transport=tran.dat +``` + +:::{tip} +If you're using Cantera from IPython or a Jupyter Notebook, you can run the above shell +command from Python by prefixing it with an exclamation point. For example: + +```ipython +!python -m cantera.ck2yaml --input=chem.inp --thermo=therm.dat --transport=tran.dat +``` +::: + +## Converting surface mechanism files + +For mechanisms involving both surface and gas phase species, an additional input file +is needed to define the surface species and reactions occurring on the surface. This +file is specified with the `--surface` option: + +```bash +python -m cantera.ck2yaml --input=gas.inp --thermo=therm.dat --surface=surf.inp +``` + +## Converting standalone thermo data + +An input file containing only species definitions (which can be referenced from +phase definitions in other input files) can be created by specifying only a +thermo file. For example: + +```bash +ck2yaml --thermo=therm.dat +``` + +## Debugging common errors in CK files + +When `ck2yaml` encounters an error, it attempts to print the surrounding information to +help you to locate the error. Many of the most common errors are due to an inconsistency +of the input files from their standard, as defined in the report for Chemkin referenced +above. Here, we describe some requirements of the CK format that are common sources of +errors. + +:::{tip} +Many existing CK format files cause errors in `ck2yaml` when they are processed. Some of +these errors may be avoided by specifying the `--permissive` option. This option allows +certain recoverable parsing errors (for example, duplicate transport or thermodynamic +data) to be ignored. +::: + +### Input file sections + +Each section of a CK input file must start with a keyword representing that section and +end with the keyword `END`. Keywords that may begin a section include: + + - `ELEMENTS` or `ELEM` + - `SPECIES` or `SPEC` + - `THERMO` or `THERMO ALL` + - `REACTIONS` or `REAC` + - `TRANSPORT` + +### Thermo data + +The thermodynamic data is read in a fixed format. This means that each column of the +input has a particular meaning. The format for each thermodynamic entry should be as +follows: + +``` +CH3OH L 8/88C 1H 4O 1 G 200.000 3500.000 1000.000 1 + 1.78970791E+00 1.40938292E-02-6.36500835E-06 1.38171085E-09-1.17060220E-13 2 +-2.53748747E+04 1.45023623E+01 5.71539582E+00-1.52309129E-02 6.52441155E-05 3 +-7.10806889E-08 2.61352698E-11-2.56427656E+04-1.50409823E+00 4 +``` + +:::{caution} +Many common errors are generated because information is missing or in the wrong column. +Check thoroughly for extraneous or missing spaces. Also make sure that the input file +does not contain tab characters. +::: + +The following table is adapted from the Chemkin manual {cite:p}`kee1989` to describe +the column positioning of each required part of the entry. Empty columns should be +filled with spaces. + +:::{list-table} +:header-rows: 1 + +* - Line No. + - Columns + - Contents +* - 1 + - 1--18 + - Species Name +* - 1 + - 19--24 + - Date (Optional) +* - 1 + - 25--44 + - Atomic Symbols and formula +* - 1 + - 45 + - Phase of species (`S`, `L`, or `G`) +* - 1 + - 46--55 + - Low temperature +* - 1 + - 56--65 + - High temperature +* - 1 + - 66--73 + - Common temperature +* - 1 + - 74--78 + - Additional Atomic Symbols +* - 1 + - 80 + - The integer `1` +* - 2 + - 1--75 + - Coefficients $a_1$ to $a_5$ for the upper temperature interval +* - 2 + - 80 + - The integer `2` +* - 3 + - 1--75 + - Coefficients $a_6,\ a_7$ for the upper temperature interval, and $a_1,\ a_2,\ a_3$ + for the lower temperature interval +* - 3 + - 80 + - The integer `3` +* - 4 + - 1--60 + - Coefficients $a_4$ through $a_7$ for the lower temperature interval +* - 4 + - 80 + - The integer `4` +::: + +#### Line 1 + +The first 18 columns are reserved for the species name. The name assigned to the +species in the thermodynamic data must be the same as the species name defined in the +`SPECIES` section. If the species name is shorter than 18 characters, the rest of the +characters should be filled by spaces. + +The next six columns (columns 19--24) are typically used to write a date; they are not +used further. + +The next 20 columns (25--44) are used to specify the elemental composition of the +species. Five characters are used for each element: the first two specify the element +symbol, while the remaining three specify the number of atoms of that element in the +species. Up to four elements may be specified this way. For species with more than four +elements, the [extended composition format](sec-ck-extended-composition) described below +may be used. + +In column 45, the phase of the species (`S`, `L`, or `G` for solid, liquid, or gas +respectively) should be specified. + +The next 28 columns are reserved for the temperatures that delimit the ranges of the +polynomials specified on the next several lines. The first two temperatures have a width +of 10 columns each (46--55 and 56--65), and represent the lowest temperature and highest +temperature for which the polynomials are valid. The last temperature has a width of 8 +columns (66--73) and is the **common** temperature, where the switch from low to high +occurs. + +The next 5 columns (74--78) are reserved for atomic symbols and are usually left blank +for the default behavior. + +Column 79 is blank; and finally, the row is ended in column 80 with the integer `1`. + +#### Lines 2--4 + +% TODO: Link to NASA polynomials section in Science docs + +The next three lines of the thermodynamic entry have a similar format. They contain the +coefficients of the 7-coefficient polynomial formulation in two temperature regions. + +The second row of the thermo entry (the first after the information row) contains the +first five coefficients that apply to the temperature range between the midpoint and the +upper limit. 15 columns are alloted for each coefficient (for a total of 75 columns), +with no spaces between them. Although the entry above shows spaces between positive +coefficients, it is to be noted that this is done only for formatting consistency with +other lines that contain negative numbers. After the coefficients, four spaces in +columns 76--79 are followed by the integer `2` in column 80. + +On the next line, the last two coefficients for the upper temperature range and the +first three coefficients for the lower temperature range are specified. Once again, this +takes up the first 75 columns, columns 76--79 are blank, and the integer `3` is in +column 80. + +Finally, on the last line of a particular entry, the last four coefficients of the lower +temperature range are specified in columns 1--60, 19 blank spaces are present, and the +integer `4` is in column 80. + +(sec-ck-extended-composition)= +#### Extended composition format + +If the number of atoms of an element in a thermodynamic entry has more than 3 digits, +the standard format for the composition cannot be used. To allow for such species, the +following extended format is allowed. The element symbol should have a `0` in the first +line of the entry. An ampersand (`&`) is added after the index of the first line, and +the element symbols and their amounts should be written on the next line as follows: + +``` +BIN6J PYRENEJ1 C 0H 0 0 0G 300.000 5000.000 1401.000 1& +C 778 H 263 + 3.63345177E+01 3.13968020E-02-1.09044660E-05 1.71125597E-09-1.00056355E-13 2 + 4.05143093E+04-1.77494305E+02-1.20603441E+01 1.59247554E-01-1.41562602E-04 3 + 6.26071650E-08-1.09305161E-11 5.56473533E+04 7.68451211E+01 4 +``` + +or on separate lines with ampersand (`&`) as the last character on the line: + +``` +BIN6 PYRENE C 0H 0 0 0G 300.000 5000.000 1401.000 1& +C 778& +H 264 + 3.65839677E+01 3.36764102E-02-1.16783938E-05 1.83077466E-09-1.06963777E-13 2 + 9.29809483E+03-1.81272070E+02-1.29758980E+01 1.63790064E-01-1.43851166E-04 3 + 6.31057915E-08-1.09568047E-11 2.48866399E+04 7.94950474E+01 4 +``` + +### Transport parameters + +The transport data file also has a specified format, as described in {cite:p}`kee1986`, +although the format is not as strict as for the thermodynamic entries. In particular, +the first 15 columns of a line are reserved for the species name. *One common source of +errors is a species that is present in the transport data file, but not in the +thermodynamic data or in the species list; or a species that is present in the species +list but not the transport data file.* The rest of the columns on a given line have no +particular format, but must be present in the following order: + +:::{list-table} +:header-rows: 1 + +* - Parameter Number + - Parameter Name +* - 1 + - An integer with value 0, 1, or 2 indicating monatomic, linear, or non-linear + molecular geometry. +* - 2 + - The Lennard-Jones potential well depth $\varepsilon/k_B$ in Kelvin +* - 3 + - The Lennard-Jones collision diameter $\sigma$ in Angstrom +* - 4 + - The dipole moment $\mu$ in Debye +* - 5 + - The polarizability $\alpha$ in Angstroms cubed +* - 6 + - The rotational relaxation collision number $Z_{rot}$ at 298 K +::: + +Another common error is if all six of these numbers are not present for every species. + +### Other formatting issues + +It may be the case that scientific formatted numbers are missing the `E`. In this case, +numbers often show up as `1.1+01`, when they should be `1.1E+01`. You can fix this with +a Regular Expression "find and replace": + +``` +Find: (\d+\.\d+)([+-]\d+) +Replace: $1E$2 +``` diff --git a/doc/sphinx/userguide/creating-mechanisms.md b/doc/sphinx/userguide/creating-mechanisms.md new file mode 100644 index 00000000000..d66c199589b --- /dev/null +++ b/doc/sphinx/userguide/creating-mechanisms.md @@ -0,0 +1,691 @@ +# Creating YAML Mechanism Files from Scratch + +Virtually every Cantera simulation involves one or more phases of matter. Depending on +the calculation being performed, it may be necessary to evaluate thermodynamic +properties, transport properties, and/or reaction rates for the phase(s) present. Before +the properties can be evaluated, each phase must be defined, meaning that the models to +use to compute its properties and reaction rates must be specified, along with any +parameters the models require. + +Because the amount of data required can be quite large, this data is imported from a +YAML file that can be read by the application, so that a given phase model can be +re-used for other simulations. This guide describes how to write such files to define +phases and interfaces for use in Cantera simulations. + +```{seealso} +See the [](input-tutorial) for an introduction to the YAML syntax used by Cantera and +a description of how dimensional values are handled. +``` + +## Phases + +For each phase that appears in a problem, a corresponding entry should be present in the +`phases` section of the input file. The phase entry specifies the elements and species +present in that phase, and the models to be used for computing thermodynamic, kinetic, +and transport properties. + +### Naming the Phase + +The `name` entry is a string that identifies the phase. It must be unique within the +file among all phase definitions of any type. Phases are referenced by name when +importing them. The `name` is also used to identify the phase within multiphase mixtures +or at phase boundaries. + +### Setting the Thermodynamic Model + +The thermodynamic model used to represent a phase is specified in the `thermo` field. A +[complete list of supported models](sec-yaml-phase-thermo-models) can be found in the +YAML Input File Reference. Some thermodynamic models use additional fields in the phase +entry, which are described in the linked documentation. + +### Declaring the Elements + +In most cases, it is not necessary to specify the elements present in a phase. If no +`elements` field is present, elements will be added automatically using the definitions +of the standard chemical elements based on the composition of the species present in the +phase. + +If non-standard elements such as isotopes need to be represented, or the ordering of +elements within the phase is important, the elements in the phase may be declared in the +optional `elements` entry. + +If all of the elements to be added are either standard chemical elements or defined in +the [`elements`](sec-yaml-guide-elements) section of the current input file, the +elements can be specified as a list of element symbols. For example: + +``` yaml +phases: +- name: my-mechanism + elements: [H, C, O, Ar] + ... +``` + +To add elements from other top-level sections, from a different file, or from multiple +such sources, a list of single-key mappings can be used where the key of each mapping +specifies the source and the value is a list of element names. The keys can be: + +- The name of a section within the current file. +- The name of an input file and a section in that file, separated by a slash, for + example `myfile.yaml/my_elements`. If a relative path is specified, the directory + containing the current file is searched first, followed by the Cantera data path. +- The name `default` to reference the standard chemical elements. + +Example: + +```yaml + +my-isotopes: +- name: O18 + atomic-weight: 17.9991603 +phases: +- name: my-phase + elements: + - default: [C, H, Ar] + - my-isotopes: [O18] + - myelements.yaml/uranium: [U235, U238] + species: ... + ... +``` + +The order of the elements specified in the input file determines the order of the +elements in the phase when it is imported by Cantera. + +### Declaring the Species + +If the species present in the phase corresponds to those species defined in the +[`species`](sec-yaml-guide-species) section of the input file, the `species` field may +be omitted, and those species will be added to the phase automatically. As a more +explicit alternative, the `species` field may be set to the string `all`. + +To include specific species from the `species` section of the input file, the `species` +entry can be a list of species names from that section. For example: + +```yaml +phases: +- name: my-phase + species: [H2, O2, H2O] + ... +``` + +If species are defined in multiple input file sections, the `species` entry can be a +list of single-key mappings, where the key of each mapping specifies the source and the +value is either the string `all` or a list of species names. Each key can be either the +name of a section within the current input file or the name of a different file and a +section in that file, separated by a slash. If a relative path is specified, the +directory containing the current file is searched first, followed by the Cantera data +path. Example: + +```yaml +phases: +- name: my-phase + species: + - species: [O2, N2] + - more_species: all + - subdir/myfile.yaml/species: [NO2, N2O] + ... +``` + +The order of species specified in the input file determines the order of the species in +the phase when it is imported by Cantera. + +Species containing elements that are not declared within the phase may be skipped by +setting the `skip-undeclared-elements` field to `true`. For example, to add all species +from the `species` section that contain only hydrogen or oxygen, the phase definition +could contain: + +```yaml +phases: +- name: hydrogen-and-oxygen + elements: [H, O] + species: all + skip-undeclared-elements: true + ... +``` + +### Setting the Kinetics Model + +The kinetics model to be used, if any, is specified in the `kinetics` field. Supported +kinetics models are `bulk`, `surface`, and `edge`, depending on the dimensionality of +the phase. If omitted, no kinetics model will be used. For additional details, see the +[list of supported models](sec-yaml-phase-kinetics) in the YAML Input File Reference. + +### Declaring the Reactions + +If a kinetics model has been specified, reactions may be added to the phase. By default, +all reactions from the `reactions` section of the input file will be added. +Equivalently, the `reactions` entry may be specified as the string `all`. + +To disable automatic addition of reactions from the `reactions` section, the `reactions` +entry may be set to `none`. This may be useful if reactions will be added +programmatically after the phase is constructed. The `reactions` field must be set to +`none` if a kinetics model has been specified but there is no `reactions` section in the +input file. + +To include only those reactions from the `reactions` section where all of the species +involved are declared as being in the phase, the `reactions` entry can be set to the +string `declared-species`. + +To include reactions from multiple sections or other files, the `reactions` entry can be +given as a list of section names, for example: + +```yaml +phases: +- name: my-phase + ... + reactions: + - OH_submechanism + - otherfile.yaml/C1-reactions + - otherfile.yaml/C2-reactions + ... +``` + +To include reactions from multiple sections or other files while only including +reactions involving declared species, a list of single-key mappings can be used, where +the key is the section name (or file and section name) and the value is either the +string `all` or the string `declared-species`. For example: + +```yaml +phases: +- name: my-phase + ... + reactions: + - OH_submechanism: all + - otherfile.yaml/C1-reactions: all + - otherfile.yaml/C2-reactions: declared-species + ... +``` + +To permit reactions containing third-body efficiencies for species not present in the +phase, the additional field `skip-undeclared-third-bodies` may be added to the phase +entry with the value `true`. + +### Setting the Transport Model + +To enable transport property calculation, the transport model to be used can be +specified in the `transport` field. A [complete list of supported models](sec-yaml-phase-transport) +can be found in the YAML Input File Reference. For most transport models, additional +parameters need to be specified within each species definition. + +### Declaring Adjacent Phases + +For interface phases (surfaces and edges), the names of phases adjacent to the interface +can be specified, in which case these additional phases can be automatically constructed +when creating the interface phase. This behavior is useful when the interface has +reactions that include species from one of these adjacent phases, since those phases +must be known when adding such reactions to the interface. + +If the definitions of the adjacent phases are contained in the `phases` section of the +same input file as the interface, they can be specified as a list of names: + +```yaml +phases: +- name: my-surface-phase + ... + adjacent: [gas, bulk] + ... +- name: gas + ... +- name: bulk + ... +``` + +Alternatively, if the adjacent phase definitions are in other sections or other input +files, they can be specified as a list of single-key mappings where the key is the +section name (or file and section name) and the value is the phase name: + +```yaml +phases: +- name: my-surface-phase + ... + adjacent: + - {my-other-phases: gas} + # a phase defined in the 'phases' section of a different YAML file + - {path/to/other-file.yaml/phases: bulk} + ... +my-other-phases: +- name: gas + ... +``` + +Since an interface kinetics mechanism is defined for the lowest-dimensional phase +involved in the mechanism, only higher-dimensional adjacent phases should be specified. +For example, when defining a surface, adjacent bulk phases may be specified, but +adjacent edges must not. + +### Setting the Initial State + +The initial state of a phase can be set using two properties to set the thermodynamic +state, plus the composition. This state is specified as a mapping in the `state` field +of `phase` entry. + +The thermodynamic state can be set by specifying two properties, such as temperature +(`T`) and pressure (`P`) or internal energy (`U`) and density (`D`). The full list of +[property names and valid combinations](sec-yaml-setting-state) can be found in the YAML +Input File Reference. In addition the composition can be set by providing a mapping that +gives the mass fractions (`X`), mole fractions (`Y`), `coverages` (for surface phases), +or molalities (`M`, for certain solution models). Where necessary, the values will be +automatically normalized. + +Some examples of setting the state: + +```yaml +phases: +- name: my-phase + ... + state: + T: 300 K + P: 101325 Pa + X: {O2: 1.0, N2: 3.76} +- name: my-other-phase + ... + state: + density: 100 kg/m^3 + T: 298 + Y: + CH4: 0.2 + C3H8: 0.1 + CO2: 0.7 +``` + +For pure fluid phases, the temperature, pressure, and vapor fraction may all be +specified if and only if they define a consistent state. + +### Examples + +The following input file defines two equivalent gas phases including all reactions and +species defined in the input file. The species and reaction data is not shown for +clarity. In the second case, the phase definition is simplified by having the elements +added based on the species definitions, taking the species definitions from the default +`species` section, and reactions from the default `reactions` section. + +```yaml +phases: +- name: gas1 + thermo: ideal-gas + elements: [O, H, N, Ar] + species: [H2, H, O, O2, OH, H2O, HO2, H2O2, N2, AR] + kinetics: gas + reactions: all + transport: mixture-averaged + state: + T: 300.0 + P: 1.01325e+05 +- name: gas2 + thermo: ideal-gas + kinetics: gas + transport: mixture-averaged + state: {T: 300.0, 1 atm} + +species: +- H2: ... +- H: ... +... +- AR: ... + +reactions: +... +``` + +An input file defining an interface and its adjacent bulk phases, with full species data +not shown for clarity: + +```yaml +phases: +- name: graphite + thermo: lattice + species: + - graphite-species: all + state: {T: 300, P: 101325, X: {C6: 1.0, LiC6: 1e-5}} + density: 2.26 g/cm^3 + +- name: electrolyte + thermo: lattice + species: [{electrolyte-species: all}] + density: 1208.2 kg/m^3 + state: + T: 300 + P: 101325 + X: {Li+(e): 0.08, PF6-(e): 0.08, EC(e): 0.28, EMC(e): 0.56} + +- name: anode-surface + thermo: ideal-surface + adjacent: [graphite, electrolyte] + kinetics: surface + reactions: [graphite-anode-reactions] + species: [{anode-species: all}] + site-density: 1.0 mol/cm^2 + state: {T: 300, P: 101325} + +graphite-species: +- name: C6 + ... +- name: LiC6 + ... + +electrolyte-species: +- name: Li+(e) + ... +- name: PF6-(e) + ... +- name: EC(e) + ... +- name: EMC(e) + ... + +anode-species: +- name: (int) + ... + +graphite-anode-reactions: +- equation: LiC6 <=> Li+(e) + C6 + rate-constant: [5.74, 0.0, 0.0] + beta: 0.4 +``` + +(sec-yaml-guide-species)= +## Species + +For each species declared as part of a phase description, a species definition is +required to describe the composition, thermodynamic, and transport parameters of that +species. + +The default location for species entries is in the `species` section of the input file. +Species defined in this section will automatically be considered for addition to phases +defined in the same file. Species can be defined in other sections of the input file or +in other input files, and these species definitions can be used in phase definitions by +explicitly referencing the section name. + +### Species Name + +The name of a species is given in the `name` field of a `species` entry. Names may +include almost all printable characters, with the exception of spaces. The use of some +characters such as `[`, `]`, and `,` may require that species names be enclosed in +quotes when written in YAML. Some valid species names given in a YAML list include: + +```yaml +[CH4, methane, argon_2+, "C[CH2]", CH2(singlet), "H2O,l"] +``` + +### Elemental Composition + +The elemental composition of a species is specified as a mapping in the `composition` +entry. + +For gaseous species, the elemental composition is well-defined, since the species +represent distinct molecules. For species in solid or liquid solutions, or on surfaces, +there may be several possible ways of defining the species. For example, an aqueous +species might be defined with or without including the water molecules in the solvation +cage surrounding it. + +For surface species, it is possible for the `composition` mapping to be empty, in which +case the species is composed of nothing, and represents an empty surface site. This can +also be done to represent vacancies in solids. A charged vacancy can be defined to be +composed solely of electrons. + +The number of atoms of an element must be non-negative, except for the special "element" +`E` that represents an electron. + +Examples: + +```yaml +composition: {C: 1, O: 2} # carbon dioxide +composition: {Ar: 1, E: -2} # Ar++ +composition: {Y: 1, Ba: 2, Cu: 3, O: 6.5} # stoichiometric YBCO +composition: {} # A surface species representing an empty site +``` + +### Thermodynamic Properties + +In addition to the thermodynamic model used at the phase level for computing properties, +parameterizations are usually required for the enthalpy, entropy, and specific heat +capacities of individual species under standard conditions. These parameterizations are +provided in the `thermo` field of each `species` entry, with the type of +parameterization specified by the `model` field. A +[complete list of parameterizations](sec-yaml-species-thermo) and their model-specific +fields can be found in the YAML Input File Reference. + +An example `thermo` field using the 7-coefficient NASA polynomials in two temperature +regions: + +```yaml +thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.14987613, -0.0136709788, 4.91800599e-05, -4.84743026e-08, 1.66693956e-11, + -1.02466476e+04, -4.64130376] + - [0.074851495, 0.0133909467, -5.73285809e-06, 1.22292535e-09, -1.0181523e-13, + -9468.34459, 18.437318] +``` + +### Species Equation of State + +For some phase thermodynamic models, additional equation of state parameterizations are +needed for each species. This information is provided in the `equation-of-state` field +of each `species` entry, with the type of parameterization used specified by the `model` +field of the `equation-of-state` field. A +[complete list of equation of state parameterizations](sec-yaml-species-eos) and their +model-specific fields can be found in the YAML Input File Reference. + +(sec-yaml-guide-species-transport)= +### Species Transport Coefficients + +Transport-related parameters for each species are needed in order to calculate transport +properties of a phase. These parameters are provided in the `transport` field of each +`species` entry, with the type of the parameterization used specified by the `model` +field of the `transport` field. The only model type specifically handled is `gas`. The +parameters used depend on the transport model specified at the phase level. The full set +of possible parameters is described in the {ref}`API documentation +`. + +An example of a `transport` entry for a gas-phase species: + +```yaml +transport: + model: gas + geometry: linear + well-depth: 107.4 + diameter: 3.458 + polarizability: 1.6 + rotational-relaxation: 3.8 +``` + +(sec-yaml-guide-reactions)= +## Reactions + +Cantera supports a number of different types of reactions, including several types of +homogeneous reactions, surface reactions, and electrochemical reactions. The reaction +entries for all reaction types some common features. These general fields of a reaction +entry are described first, followed by fields used for specific reaction types. + + +### The Reaction Equation + +The reaction equation, specified in the `equation` field of the reaction entry, +determines the reactant and product stoichiometry. All tokens (species names, +stoichiometric coefficients, `+`, and `<=>`) in the reaction equation must be separated +with spaces. Some examples of correctly and incorrectly formatted reaction equations are +shown below: + +```yaml +- equation: 2 CH2 <=> CH + CH3 # OK +- equation: 2 CH2<=>CH + CH3 # error - spaces required around '<=>'' +- equation: 2CH2 <=> CH + CH3 # error - space required between '2' and 'CH2' +- equation: CH2 + CH2 <=> CH + CH3 # OK +- equation: 2 CH2 <=> CH+CH3 # error - spaces required around '+' +``` + +Whether the reaction is reversible or not is determined by the form of the equality sign +in the reaction equation. If either `<=>` or `=` is found, then the reaction is regarded +as reversible, and the reverse rate will be computed based on the equilibrium constant. +If, on the other hand, `=>` is found, the reaction will be treated as irreversible. + +### Reaction type + +The type of the rate coefficient parameterization may be specified in the `type` field +of the `reaction` entry. The [fields for specific reaction types](sec-yaml-reactions) +and additional parameters defining the rate constant for each of these reaction types +are described in the YAML Input File Reference. + +The default parameterization is `elementary`. Reactions involving surface species are +automatically identified as [`interface`](sec-yaml-interface-Arrhenius) reactions, +reactions involving surface species with the `type` specified as `Blowers-Masel` are +treated as [`interface-Blowers-Masel`](sec-yaml-interface-Blowers-Masel), and reactions +involving charge transfer are automatically identified as +[`electrochemical`](sec-yaml-electrochemical-reaction) reactions. + +### Arrhenius Expressions + +Most reaction types in Cantera are parameterized by one or more modified Arrhenius +expressions, such as + +$$ A T^b e^{-E_a / RT} $$ + +where $A$ is the pre-exponential factor, $T$ is the temperature, $b$ is the temperature +exponent, $E_a$ is the activation energy, and $R$ is the gas constant. Rates in this +form can be written as YAML mappings. For example: + +```yaml +{A: 1.0e13, b: 0, E: 7.3 kcal/mol} +``` + +The units of $A$ can be specified explicitly if desired. If not specified, they will be +determined based on the `quantity`, `length`, and `time` units specified in the +governing `units` fields. Since the units of $A$ depend on the reaction order, the units +of each reactant concentration (dependent on phase type and dimensionality), and the +units of the rate of progress (different for homogeneous and heterogeneous reactions), +it is usually best not to specify units for $A$, in which case they will be computed +taking all of these factors into account. + +```{note} +If $b \ne 0$, then the term $T^b$ should have units of $\mathrm{K}^b$, which would +change the units of $A$. This is not done, however, so the units associated with $A$ +are really the units for $k_f$. One way to formally express this is to replace $T^b$ +by the non-dimensional quantity $[T/(1\;\mathrm{K})]^b$. +``` + +The key `E` is used to specify $E_a$. + +(sec-yaml-reaction-options)= +### Duplicate Reactions + +When a reaction is imported into a phase, it is checked to see that it is not a +duplicate of another reaction already present in the phase, and normally an error +results if a duplicate is found. But in some cases, it may be appropriate to include +duplicate reactions, for example if a reaction can proceed through two distinctly +different pathways, each with its own rate expression. Another case where duplicate +reactions can be used is if it is desired to implement a reaction rate coefficient of +the form: + +$$ k_f(T) = \sum_{n=1}^{N} A_n T^{b_n} \exp(-E_n/RT) $$ + +While Cantera does not provide such a form for reaction rates, it can be implemented by +defining $N$ duplicate reactions, and assigning one rate coefficient in the sum to each +reaction. By adding the field: + +```yaml +duplicate: true +``` + +to a reaction entry, then the reaction not only *may* have a duplicate, it *must*. Any +reaction that specifies that it is a duplicate, but cannot be paired with another +reaction in the phase that qualifies as its duplicate generates an error. + +### Negative Pre-exponential Factors + +If some of the terms in the above sum have negative $A_n$, this scheme fails, since +Cantera normally does not allow negative pre-exponential factors. But if there are +duplicate reactions such that the total rate is positive, then the fact that negative +$A$ parameters are acceptable can be indicated by adding the field: + +```yaml +negative-A: true +``` + +### Reaction Orders + +Explicit reaction orders different from the stoichiometric coefficients are sometimes +used for non-elementary reactions. For example, consider the global reaction: + +$$ \mathrm{C_8H_{18} + 12.5 O_2 \rightarrow 8 CO_2 + 9 H_2O} $$ + +the forward rate constant might be given as {cite:p}`westbrook1981`: + +$$ +k_f = 4.6 \times 10^{11} [\mathrm{C_8H_{18}}]^{0.25} [\mathrm{O_2}]^{1.5} + \exp\left(\frac{30.0\,\mathrm{kcal/mol}}{RT}\right) +$$ + +This reaction could be defined as: + +```yaml +- equation: C8H18 + 12.5 O2 => 8 CO2 + 9 H2O + rate-constant: {A: 4.6e11, b: 0.0, Ea: 30.0 kcal/mol} + orders: {C8H18: 0.25, O2: 1.5} +``` + +Special care is required in this case since the units of the pre-exponential factor +depend on the sum of the reaction orders, which may not be an integer. + +Note that you can change reaction orders only for irreversible reactions. + +#### Negative Reaction Orders + +Normally, reaction orders are required to be positive. However, in some cases negative +reaction orders provide better fits for experimental data. In these cases, the default +behavior may be overridden by adding the `negative-orders` field to the reaction entry. +For example: + +```yaml +- equation: C8H18 + 12.5 O2 => 8 CO2 + 9 H2O + rate-constant: {A: 4.6e11, b: 0.0, Ea: 30.0 kcal/mol} + orders: {C8H18: -0.25, O2: 1.75} + negative-orders: true +``` + +#### Non-reactant Orders + +Some global reactions could have reactions orders for non-reactant species. In this +case, the `nonreactant-orders` field must be added to the reaction entry: + +```yaml +- equation: C8H18 + 12.5 O2 => 8 CO2 + 9 H2O + rate-constant: {A: 4.6e11, b: 0.0, Ea: 30.0 kcal/mol} + orders: {C8H18: -0.25, CO: 0.15} + negative-orders: true + nonreactant-orders: true +``` + +(sec-yaml-guide-elements)= +## Elements + +Cantera provides built-in definitions for the chemical elements, including values for +their atomic weights taken from IUPAC / CIAAW. These elements can be used by specifying +the corresponding atomic symbols when specifying the composition of species. + +In order to give a name to a particular isotope or a virtual element representing a +surface site, a custom `element` entry can be used. The default location for `element` +entries is the `elements` section of the input file. Elements defined in this section +will automatically be considered for addition to phases defined in the same file. +Elements can be defined in other sections of the input file if those sections are named +explicitly in the `elements` field of the phase definition. + +An element entry has the following fields: + +- `symbol`: The symbol to be used for the element, for example when specifying the + composition of a species. +- `atomic-weight`: The atomic weight of the element, in unified atomic mass units + (dalton) +- `atomic-number`: The atomic number of the element. Optional. +- `entropy298`: The standard molar entropy of the element at 298.15 K. Optional. + +An example `elements` section: + +```yaml +elements: +- symbol: C13 + atomic-weight: 13.003354826 + atomic-number: 6 +- symbol: O-18 + atomic-weight: 17.9991603 +``` diff --git a/doc/sphinx/userguide/faq.md b/doc/sphinx/userguide/faq.md new file mode 100644 index 00000000000..629031f0484 --- /dev/null +++ b/doc/sphinx/userguide/faq.md @@ -0,0 +1,12 @@ +# Frequently Asked Questions + +```{caution} +This page is a work in progress. Sorry. +``` + +(sec-faq-installation)= +## Installation + +## Input Files +* Where can I find chemical mechanisms to use with Cantera? +* How do I fix errors converting Chemkin input files to Cantera's format? diff --git a/doc/sphinx/userguide/index.md b/doc/sphinx/userguide/index.md new file mode 100644 index 00000000000..869c10d35d3 --- /dev/null +++ b/doc/sphinx/userguide/index.md @@ -0,0 +1,47 @@ +# User Guide + +```{caution} +This page is a work in progress. For tutorials covering the current Cantera +release (Cantera 3.0), please see this page. +``` + +## Introductory Tutorials + +For those new to Cantera, we present here a set of short tutorials to familiarize you +with Cantera's basic functionality and capabilities, give some examples of how to work +Cantera within your preferred interface language, and demonstrate some basic +troubleshooting. + +- [Getting Started with Python](python-tutorial) +- [](input-tutorial) + +## Frequently asked questions + +See the [FAQ](faq) for answers to some common issues that arise when using +Cantera. If your question isn't answered here, consider asking us on the +Cantera Users' Group. + +## Task Guides + +The tutorials in this section are designed to help you accomplish a specific task +using Cantera, such as evaluating the ignition delay time for a fuel under different +conditions, or calculating the voltage of a Lithium-ion battery as it is discharged. + +- [](ck2yaml-tutorial) +- [](creating-mechanisms) +- [](thermobuild) +- [](input-errors) +- [](legacy2yaml-tutorial) + +```{toctree} +:hidden: + +python-tutorial +input-tutorial +faq +ck2yaml-tutorial +creating-mechanisms +thermobuild +input-errors +legacy2yaml-tutorial +``` diff --git a/doc/sphinx/userguide/input-errors.md b/doc/sphinx/userguide/input-errors.md new file mode 100644 index 00000000000..25b53097589 --- /dev/null +++ b/doc/sphinx/userguide/input-errors.md @@ -0,0 +1,108 @@ +# Handling Errors in Input Files + +During processing of an input file, errors may be encountered. These could be syntax +errors, or could be ones that are flagged as errors by Cantera due to some apparent +inconsistency in the data---an unphysical value, a species that contains an undeclared +element, a reaction that contains an undeclared species, missing species or element +definitions, multiple definitions of elements, species, or reactions, and so on. This +section is intended to help you understand some causes for these errors and their +solutions. + +## Syntax Errors + +Syntax errors are caught by the YAML parser, and must be corrected before proceeding +further. If a syntax error is encountered, Cantera will raise an exception which +includes the location of the error. Additional information such as a traceback showing +where in the code the input file was being read may be printed as well. + +For example, consider the following input file, which is intended to create a gas with +the species and reactions of GRI-Mech 3.0, but is missing the colon which is needed +after the `thermo` key: + +```yaml +phases: +- name: gas + thermo ideal-gas + kinetics: gas + elements: [H, O] + species: [{gri30.yaml/species: all}] + reactions: [gri30.yaml/reactions] +``` + +When this definition is imported into an application, an error message like the +following would be printed to the screen, and execution of the program or script would +terminate: + +```pytb +Traceback (most recent call last): + File "", line 1, in + File "/some/path/cantera/base.pyx", line 25, in cantera._cantera._SolutionBase.__cinit__ + self._init_yaml(infile, phaseid, phases, yaml) + File "/some/path/cantera/base.pyx", line 49, in cantera._cantera._SolutionBase._init_yaml + root = AnyMapFromYamlFile(stringify(infile)) +cantera._cantera.CanteraError: +*********************************************************************** +InputFileError thrown by AnyMap::fromYamlFile: +Error on line 4 of ./gas.yaml: +illegal map value +| Line | +| 1 | phases: +| 2 | - name: gas +| 3 | thermo ideal-gas +> 4 > kinetics: gas + ^ +| 5 | elements: [H, O] +| 6 | species: [{gri30.yaml/species: all}] +| 7 | reactions: [gri30.yaml/reactions] +*********************************************************************** +``` + +The top part of the error message shows the chain of functions that were called before +the error was encountered. For the most part, these are internal Cantera functions not +of direct concern here. The relevant part of this error message is the part between the +lines of asterisks. This message says that the YAML parser ran into a problem on line 4 +of `gas.yaml`. In many cases, including this one, the parser will fail somewhere *after* +the actual problem with the input file, since it must continue parsing until it finds +something that cannot possibly be valid YAML syntax. In this case, the problem from the +parser's perspective is that the key which started on line 3 continues across a new line +before it finds a colon that can be considered as the separator. Since a key can't be +broken across lines like this, the parser indicates the error at the point where it +found the colon. By looking back from the indicated point of the error, we can see that +the problem is the missing colon in the previous line. + +## Cantera Errors + +Now let's consider the other class of errors, ones that Cantera itself detects. +Continuing the example above, suppose that the missing colon is corrected, and the input +file processed again. Again an error message results, but this time it is from Cantera: + +```pytb +Traceback (most recent call last): + File "", line 1, in + File "/some/path/cantera/base.pyx", line 25, in cantera._cantera._SolutionBase.__cinit__ + self._init_yaml(infile, phaseid, phases, yaml) + File "/some/path/cantera/base.pyx", line 49, in cantera._cantera._SolutionBase._init_yaml + root = AnyMapFromYamlFile(stringify(infile)) +cantera._cantera.CanteraError: +*********************************************************************** +CanteraError thrown by Phase::addSpecies: +Species 'C' contains an undefined element 'C'. +*********************************************************************** +``` + +The problem is that the phase definition specifies that all species are to be imported +from the `gri30` mechanism, but only the elements H and O are declared. The `gri30` +mechanism contains species composed of the elements H, O, C, N, and Ar. If the +definition is modified to declare these additional elements: + +```yaml +phases: +- name: gas + thermo: ideal-gas + kinetics: gas + elements: [H, O, C, N, Ar] + species: [{gri30.yaml/species: all}] + reactions: [gri30.yaml/reactions] +``` + +it may be imported successfully. diff --git a/doc/sphinx/userguide/input-tutorial.md b/doc/sphinx/userguide/input-tutorial.md new file mode 100644 index 00000000000..f1295e8f419 --- /dev/null +++ b/doc/sphinx/userguide/input-tutorial.md @@ -0,0 +1,250 @@ +# Introduction to YAML Input Files + +All calculations in Cantera require an input file to describe the properties of the +relevant phase(s) of matter. These input files can be provided via one of several +methods: + +- *Use an existing input file*. The input files included with Cantera should suffice for + tutorials and introductory work with thermodynamic phases and reaction kinetics. A + number of additional input files are available from various sources on the web. + +- *Convert a mechanism from Chemkin (CK) format to YAML format*. Many reaction + mechanisms are published in Chemkin (CK) format, and can be converted to Cantera's + YAML format using the `ck2yaml` conversion tool. see [](ck2yaml-tutorial) for more + information. + +- *Create your own YAML file from scratch or by editing an existing file*. Advanced + users may need to edit an existing input file in order to define additional species, + reactions, or entirely new phases. See [](creating-mechanisms) for more information. + +```{tip} +Whenever you edit a Cantera input file, it is *highly advised* that you begin by copying +the existing file and saving it under a new name, before editing the new file. Editing a +file under its original name can easily lead to errors, if one forgets that this file +does not represent the original mechanism. +``` + +## Understanding Cantera's Input File Syntax + +With any input file, it can be helpful to understand the syntax requirements. Clearly, +anyone writing directly in the YAML formats must conform to these standards. However, +even when importing an externally-provided file or converting from CK format, +understanding the input file syntax can help diagnose and correct any errors (although +many/most of the CK conversion errors will be related to errors in the CK syntax +formatting). + +Cantera YAML files use a subset of the [YAML 1.2](https://yaml.org/spec/1.2/spec.html) +specification. Cantera YAML files consist of individual values, which may be strings, +numbers or booleans, that are then composed as elements of nested mappings and +sequences. + +### Strings + +Strings may be generally written without quotes, but may be enclosed in single +quotes or double quotes if needed in order to avoid certain parsing ambiguities. + +```yaml +A string +Another 'string' +"A string: that requires quotes" +``` + +### Numbers + +Numbers can be written as integers, decimal values, or using E-notation + +```yaml +3 +3.14 +6.022e23 +``` + +### Booleans + +Boolean values in YAML are written as the words `true` or `false`. + +### Sequences + +A sequence of multiple items is specified by separating the items by commas and +enclosing them in square brackets. The individual items can have any type -- strings, +integers, floating-point numbers, mappings, or sequences. + +```yaml +elements: [O, H, C, N, Ar] +temperature-ranges: [200.0, 1000.0, 3500.0] +``` + +The syntax above, using square brackets to define a list, is called **flow style** in +YAML. Sequences can also be written in **block style**, using one line for each item in +the sequence, with each line starting with a dash: + +```yaml +elements: +- O +- H +- C +- N +- Ar +``` + +Sequences can also be nested. The following examples are all equivalent: + +```yaml +data: [[1, 2], [3, 4]] + +data: +- + - 1 + - 2 +- + - 3 + - 4 + +data: +- - 1 + - 2 +- - 3 + - 4 +``` + +### Mappings + +A mapping is a container consisting of key--value pairs. The keys in a mapping must be +unique. Like sequences, there are two ways to write a mapping. In the **flow style**, +the mapping is enclosed in curly brackets, colons (followed by spaces) are used to +separate keys and values, and key--value pairs are separated by commas: + +```yaml +composition: {H: 2, C: 1, O: 1} +``` + +In the **block style**, each key is written on a new line, followed by a colon. The +value can be placed either on the same line, or on the following line, indented one +level: + +```yaml +composition: + H: 2 + C: + 1 + O: 1 +``` + +All keys in Cantera YAML files are treated as strings. A Cantera YAML file is itself a +mapping, usually in the **block style**. We refer to the keys in this top-level mapping +as the **sections** of the input file. + +### Sequences of Mappings + +A common structure in Cantera input files is a nested sequence of mappings. This can be +written in the **block style** as: + +```yaml +- equation: O2 + CO <=> O + CO2 + rate-constant: {A: 2.5e+12, b: 0, Ea: 47800} +- equation: O2 + CH2O <=> HO2 + HCO + rate-constant: {A: 1.0e+14, b: 0, Ea: 40000} +- equation: H + O2 + M <=> HO2 + M + type: three-body + rate-constant: {A: 2.8e+18, b: -0.86, Ea: 0} + efficiencies: {AR: 0, C2H6: 1.5, CO: 0.75, CO2: 1.5, H2O: 0, N2: 0, O2: 0} +``` + +The keys in each mapping need not be the same. In this example, each of the three +mappings in the sequence has `equation` and `rate-constant` keys, while only the third +entry has `type` and `efficiencies` keys. + +### Comments + +The character `#` is the comment character. Everything to the right of this character on +a line is ignored: + +```yaml +# set the default units +units: + length: cm # use centimeters for length + quantity: mol # use moles for quantity +``` + +### Dimensional Values + +Many fields have numerical values that represent dimensional quantities---a pressure, or +a density, for example. If these are entered without specifying the units, the default +units (set by the `units` directive) will be used. However, it is also possible to +specify the units for each individual dimensional quantity, unless stated otherwise. All +that is required is to write the units after the value, separated by a space: + +```yaml +pressure: 1.0e5 # default is Pascals +pressure: 1.0 bar # this is equivalent +density: 4.0 g/cm^3 +density: 4000.0 # kg/m^3 +``` + +Compound unit strings may be used, as long as a few rules are followed: + +1. Units in the denominator follow `/`. +2. Units in the numerator follow `*`, except for the first one. +3. Numerical exponents follow the unit string with a `^` character. + +Examples of compound units: + +```yaml +A: 1.0e20 cm^6/mol^2/s # OK +h: 6.626e-34 J*s # OK +density: 3.0 g*cm^-3 # OK +A: 1.0e20 cm6/mol/s # error (missing '^') +A: 1.0e20 cm^6/mol^2-s # error ('s' should be in denominator) +density: 3.0g/cm^3 # error (missing space between value and units) +``` + +See the [Units API](sec-yaml-units) documentation for additional details, including the +full set of supported units. + +### Default units + +Default units that apply to a whole input file or some portion thereof can be set using +`units` mapping. A `units` mapping placed at the top level of an input file applies to +the entire file. A `units` mapping placed as a member of another mapping applies to that +mapping and any nested mappings or sequences, and overrides higher-level `units` +mappings: + +```yaml +units: {length: cm, mass: kg} +section1: + units: {length: m} + density: 4000 # interpreted as 4000 kg/m^3 +section2: + density: 0.1 # interpreted as 0.1 kg/cm^3 +section3: +- units: {mass: mg} # must be the first item in the list +- name: species1 + density: 5e4 # interpreted as 5e4 mg/cm^3 +``` + +Default units may be set for `mass`, `length`, `time`, `quantity`, `pressure`, `energy`, +and `activation-energy`. + +## Input Files Distributed with Cantera + +Several reaction mechanism files are included in the Cantera distribution, including +ones that model natural gas combustion (`gri30.yaml`), high-temperature air +(`air.yaml`), a hydrogen/oxygen reaction mechanism (`h2o2.yaml`), some pure fluids in +the liquid-vapor region (`liquidvapor.yaml`), and a few surface reaction mechanisms +(such as `ptcombust.yaml`, `diamond.yaml`, etc.), among others. + +```{caution} +The input files included with Cantera are provided for convenience, and may not be +suited for research purposes. +``` + +Under Windows, these files may be located in `C:\Program Files\Cantera\data` depending +on how you installed Cantera and the options you specified. On a Unix/Linux/macOS +machine, they are usually kept in the `data` subdirectory within the Cantera +installation directory. You can also browse the [list of data +files](https://github.com/Cantera/cantera/tree/main/data) in the Cantera source +repository. + +% TODO: add link to the Matlab tutorial +Please see the tutorials for [Python](python-tutorial) and Matlab for +instructions on how to import from these pre-existing files. diff --git a/doc/sphinx/userguide/legacy2yaml-tutorial.md b/doc/sphinx/userguide/legacy2yaml-tutorial.md new file mode 100644 index 00000000000..6b94d91214e --- /dev/null +++ b/doc/sphinx/userguide/legacy2yaml-tutorial.md @@ -0,0 +1,82 @@ +# Converting Legacy CTI and XML Input Files to YAML + +If you want to convert an existing, legacy CTI or XML input file to the YAML format, +this section will help. + +## cti2yaml + +Cantera comes with a converter utility `cti2yaml` (or `cti2yaml.py`) that converts +legacy CTI format mechanisms into the new YAML format introduced in Cantera 2.5. This +program can be run from the command line to convert files to the YAML format. + +**Usage:** + +```bash +cti2yaml [-h] input [output] +``` + +The `input` argument is required, and specifies the name of the input file to be +converted. The optional `output` argument specifies the name of the new output file. If +`output` is not specified, then the output file will have the same name as the input +file, with the extension replaced with `.yaml`. The full command line interface for +`cti2yaml` is documented [here](/yaml/cti2yaml). + +**Example:** + +```bash +cti2yaml mymech.cti +``` + +will generate the output file `mymech.yaml`. + +If the `cti2yaml` script is not on your path, but the Cantera Python module is, +`cti2yaml` can be used by running: + +```bash +python -m cantera.cti2yaml mymech.cti +``` + +It is not necessary to use `cti2yaml` to convert any of the CTI input files previously +included with Cantera. YAML versions of these files are already included with Cantera. + +```{tip} +For input files where you have both the CTI and XML versions, `cti2yaml` is recommended +over `ctml2yaml`. In cases where the mechanism was originally converted from a CK-format +mechanism, it is recommended to use `ck2yaml` if the original input files are available. +``` + +## ctml2yaml + +Cantera comes with a converter utility `ctml2yaml` (or `ctml2yaml.py`) that converts +legacy XML (CTML) format mechanisms into the new YAML format introduced in Cantera 2.5. +This program can be run from the command line to convert files to the YAML format. + +**Usage:** + +```bash +ctml2yaml [-h] input [output] +``` + +The `input` argument is required, and specifies the name of the input file to be +converted. The optional `output` argument specifies the name of the new output file. If +`output` is not specified, then the output file will have the same name as the input +file, with the extension replaced with `.yaml`. The full command line interface for +`ctml2yaml` is documented [here](/yaml/ctml2yaml). + +**Example:** + +```bash +ctml2yaml mymech.xml +``` + +will generate the output file `mymech.yaml`. + +If the `ctml2yaml` script is not on your path, but the Cantera Python module is, +`ctml2yaml` can be used by running: + +```bash +python -m cantera.cti2yaml mymech.xml +``` + +It is not necessary to use `ctml2yaml` to convert any of the XML input files included +with Cantera. YAML versions of these files are already included with Cantera. diff --git a/doc/sphinx/userguide/python-tutorial.md b/doc/sphinx/userguide/python-tutorial.md new file mode 100644 index 00000000000..2d733370d02 --- /dev/null +++ b/doc/sphinx/userguide/python-tutorial.md @@ -0,0 +1,451 @@ +--- +file_format: mystnb +kernelspec: + name: python3 +--- + +```{py:currentmodule} cantera +``` + +# Python Tutorial + +## Getting Started + +```{seealso} +If you haven't already installed Cantera, we have instructions for +many platforms in our [Installation section](/install/index). +``` + +Start by opening an interactive Python session, for example by running +[IPython](http://ipython.org/). Import the Cantera Python module and NumPy by running: + +```{code-cell} python +import cantera as ct +import numpy as np +``` + +When using Cantera, the first thing you usually need is an object representing: some +phase of matter. Here, we'll create a gas mixture + +```{code-cell} python +gas1 = ct.Solution('gri30.yaml') +``` + +To view the state of the mixture, *call* the `gas1` object as if it were +a function: + +```{code-cell} +gas1() +``` + +What you have just done is to create an object, `gas1` that implements GRI-Mech 3.0, the +53-species, 325-reaction natural gas combustion mechanism developed by +{cite:t}`smith1999`. + +The `gas1` object has properties you would expect for a gas mixture - it has a +temperature, a pressure, species mole and mass fractions, etc. As we'll soon see, it has +many more properties. + +The summary of the state of `gas1` printed above shows that new objects created from the +`gri30.yaml` input file start out with a temperature of 300 K, a pressure of 1 atm, and +have a composition that consists of only one species, in this case hydrogen. There is +nothing special about H2 - it just happens to be the first species listed in the input +file defining GRI-Mech 3.0. In general, whichever species is listed first will initially +have a mole fraction of 1.0, and all of the others will be zero. + +## Setting the State + +The state of the object can easily be changed. For example: + +```{code-cell} +gas1.TP = 1200, 101325 +``` + +sets the temperature to 1200 K and the pressure to 101325 Pa (Cantera always uses SI +units). After this statement, calling `gas1()` results in: + +```{code-cell} +gas1() +``` + +Thermodynamics generally requires that *two* properties in addition to composition +information be specified to fix the intensive state of a substance (or mixture). The +state of the mixture can be set using several combinations of two properties. The +following are all equivalent: + +```{code-cell} pythonconsole +gas1.TP = 1200, 101325 # temperature, pressure +gas1.TD = 1200, 0.020473 # temperature, density +gas1.HP = 1.3295e7, 101325 # specific enthalpy, pressure +gas1.UV = 8.3457e6, 1/0.020473 # specific internal energy, specific volume +gas1.SP = 85222, 101325 # specific entropy, pressure +gas1.SV = 85222, 1/0.020473 # specific entropy, specific volume +``` + +In each case, the values of the extensive properties must be entered *per unit mass*. + +Properties may be read independently or together: + +```{code-cell} +gas1.T +``` + +```{code-cell} +gas1.h +``` + +```{code-cell} +gas1.UV +``` + +The composition can be set in terms of either mole fractions (`X`) or mass fractions +(`Y`): + +```{code-cell} +gas1.X = 'CH4:1, O2:2, N2:7.52' +``` + +Mass and mole fractions can also be set using `dict` objects, which is convenient in +cases where the composition is stored in a variable or being computed: + +```{code-cell} python +phi = 0.8 +gas1.X = {'CH4':1, 'O2':2/phi, 'N2':2*3.76/phi} +``` + +When the composition alone is changed, the temperature and density are held constant. +This means that the pressure and other intensive properties will change. The composition +can also be set in conjunction with the intensive properties of the mixture: + +```{code-cell} python +gas1.TPX = 1200, 101325, 'CH4:1, O2:2, N2:7.52' +gas1() +``` + +The composition above was specified using a string. The format is a comma-separated list +of `:` pairs. The mole numbers will be normalized +to produce the mole fractions, and therefore they are "relative" mole numbers. Mass +fractions can be set in this way too by changing `X` to `Y` in the above statements. + +The composition can also be set using an array, which must have the same size as the +number of species. For example, to set all 53 mole fractions to the same value, do this: + +```{code-cell} python +gas1.X = np.ones(53) # NumPy array of 53 ones +``` + +Or, to set all the mass fractions to equal values: + +```{code-cell} +gas1.Y = np.ones(53) +``` + +When setting the state, you can control what properties are held constant by passing the +special value `None` to the property setter. For example, to change the specific volume +to 2.1 m$^3$/kg while holding entropy constant: + +```{code-cell} +gas1.SV = None, 2.1 +``` + +Or to set the mass fractions while holding temperature and pressure constant: + +```{code-cell} +gas1.TPX = None, None, 'CH4:1.0, O2:0.5' +``` + +## Working with a Subset of Species + +Many properties of a {py:class}`Solution` provide values for each species +present in the phase. If you want to get values only for a subset of these species, you +can use Python's "slicing" syntax to select data for just the species of interest. To +get the mole fractions of just the major species in `gas1`, in the order specified, you +can write: + +```{code-cell} python +Xmajor = gas1['CH4','O2','CO2','H2O','N2'].X +``` + +If you want to use the same set of species repeatedly, you can keep a reference to the +sliced phase object: + +```{code-cell} python +major = gas1['CH4','O2','CO2','H2O','N2'] +cp_major = major.partial_molar_cp +wdot_major = major.net_production_rates +``` + +The slice object and the original object share the same internal state, so modifications +to one will affect the other. + +## Working With Mechanism Files + +In previous example, we created an object that models an ideal gas mixture with the +species and reactions of GRI-Mech 3.0, using the `gri30.yaml` input file included with +Cantera. Several other reaction mechanism files are included with Cantera, including +ones that model high- temperature air, a hydrogen/oxygen reaction mechanism, and a few +surface reaction mechanisms. These files are usually located in the `data` subdirectory +of the Cantera installation directory, for example `C:\Program Files\Cantera\data` on +Windows or `/usr/local/cantera/data/` on Unix/Linux/Mac OS X machines, depending on how +you installed Cantera and the options you specified. + +If for some reason Cantera has difficulty finding where these files are on your system, +set environment variable `CANTERA_DATA` to the directory or directories (separated using +`;` on Windows or `:` on other operating systems) where they are located. Alternatively, +you can call function {py:func}`add_directory` to add a directory to the +Cantera search path: + +```{code-cell} python +ct.add_directory('~/cantera/my_data_files') +``` + +% TODO: Add link to input file guide +Cantera input files are plain text files, and can be created with any text editor. See +the document `Working With Input Files` for more information. + +A Cantera input file may contain more than one phase specification, or may contain +specifications of interfaces (surfaces). Here we import definitions of two bulk phases +and the interface between them from file `diamond.yaml`: + +% TODO: Demonstrate the syntax that starts with creating the Interface +```{code-cell} python +gas2 = ct.Solution('diamond.yaml', 'gas') +diamond = ct.Solution('diamond.yaml', 'diamond') +diamond_surf = ct.Interface('diamond.yaml' , 'diamond_100', + [gas2, diamond]) +``` + +Note that the bulk (3D) phases that participate in the surface reactions must also be +passed as arguments to {py:class}`Interface`. + +## Converting CK-format files + +% TODO: Add link to the ck2yaml guide +`Converting CK-format Files` documentation for information on how to convert from +CK-format to Cantera's YAML format. + +## Getting Help + +In addition to the Sphinx-generated [Python documentation](/python/index), documentation +of the Python classes and their methods can be accessed from within the Python +interpreter as well. + +Suppose you have created a Cantera object and want to know what methods are available +for it, and get help on using the methods: + +```{code-cell} +g = ct.Solution('gri30.yaml') +``` + +To get help on the Python class that this object is an instance of: + +```{code-cell} +:tags: [hide-output] +help(g) +``` + +For a simple list of the properties and methods of this object: + +```{code-cell} +:tags: [hide-output] +dir(g) +``` + +To get help on a specific method, such as the `species_index` method: + +```{code-cell} +help(g.species_index) +``` + +For properties, getting the documentation is slightly trickier, as the usual method will +give you the help for the *result*. For example: + +```{code-cell} +:tags: [hide-output] +help(g.T) +``` + +will provide help on Python's `float` class. To get the help for the temperature +property, ask for the attribute of the class object itself: + +```{code-cell} +help(g.__class__.T) +``` + +If you are using the IPython shell, help can also be obtained using the `?` syntax: + +```{code-cell} +In[1]: g.species_index? +``` + +## Chemical Equilibrium + +To set a gas mixture to a state of chemical equilibrium, use the +{py:meth}`ThermoPhase.equilibrate` method: + +```{code-cell} python +import cantera as ct +g = ct.Solution('gri30.yaml') +g.TPX = 300.0, ct.one_atm, 'CH4:0.95,O2:2,N2:7.52' +g.equilibrate('TP') +``` + +The above statement sets the state of object `g` to the state of chemical equilibrium +holding temperature and pressure fixed. Alternatively, the specific enthalpy and +pressure can be held fixed: + +```{code-cell} python +g.TPX = 300.0, ct.one_atm, 'CH4:0.95,O2:2,N2:7.52' +g.equilibrate('HP') +``` + +Other options are: + +- `UV`: fixed specific internal energy and specific volume +- `SV`: fixed specific entropy and specific volume +- `SP`: fixed specific entropy and pressure + +How can you tell if `equilibrate` has correctly found the chemical equilibrium state? +One way is verify that the net rates of progress of all reversible reactions are zero. +Here is the code to do this: + +```{code-cell} python +:tags: [hide-output] +g.TPX = 300.0, ct.one_atm, 'CH4:0.95,O2:2,N2:7.52' +g.equilibrate('HP') + +rf = g.forward_rates_of_progress +rr = g.reverse_rates_of_progress +for i in range(g.n_reactions): + if g.reaction(i).reversible and rf[i] != 0.0: + print(' %4i %10.4g ' % (i, (rf[i] - rr[i])/rf[i])) +``` + +If the magnitudes of the numbers in this list are all very small, then each reversible +reaction is very nearly equilibrated, which only occurs if the gas is in chemical +equilibrium. + +You might be wondering how `equilibrate` works. (Then again, you might not). Method +`equilibrate` invokes Cantera's chemical equilibrium solver, which uses an element +potential method. The element potential method is one of a class of equivalent +*nonstoichiometric* methods that all have the characteristic that the problem reduces to +solving a set of $M$ nonlinear algebraic equations, where $M$ is the number of elements +(not species). The so-called *stoichiometric* methods, on the other hand, (including +Gibbs minimization), require solving $K$ nonlinear equations, where $K$ is the number of +species (usually $K >> M$). See {cite:t}`smith1982` for more information on the various +algorithms and their characteristics. + +Cantera uses a damped Newton method to solve these equations, and does a few other +things to generate a good starting guess and to produce a reasonably robust algorithm. +If you want to know more about the details, look at the C++ class {ct}`ChemEquil`. + +## Chemical Kinetics + +{py:class}`Solution` objects are also {py:class}`Kinetics` objects, and provide all of +the methods necessary to compute the thermodynamic quantities associated with each +reaction, reaction rates, and species creation and destruction rates. They also provide +methods to inspect the quantities that define each reaction such as the rate constants +and the stoichiometric coefficients. The rate calculation functions are used extensively +within Cantera's [reactor network model](../python/zerodim) and [1D flame +model](../python/onedim). + +Information about individual reactions that is independent of the thermodynamic state +can be obtained by accessing {py:class}`Reaction` objects with the +{py:meth}`Kinetics.reaction` method: + +```{code-cell} python +g = ct.Solution('gri30.yaml') +r = g.reaction(2) # get a Reaction object +r +``` + +```{code-cell} +r.reactants +``` + +```{code-cell} +r.products +``` + +Information about specific reaction rate parameterizations should be queried using the +`input_data` property, which returns a YAML-compatible dictionary that represents input +data needed to create the corresponding rate object: + +```{code-cell} +r.rate +``` + +```{code-cell} +r.rate.input_data +``` + +If we are interested in only certain types of reactions, we can use this information to +filter the full list of reactions to find the just the ones of interest. For example, +here we find the indices of just those reactions which convert `CO` into `CO2`: + +```{code-cell} python +II = [i for i,r in enumerate(g.reactions()) + if 'CO' in r.reactants and 'CO2' in r.products] +for i in II: + print(g.reaction(i).equation) +``` + +(Actually, we should also include reactions where the reaction is written such that +`CO2` is a reactant and `CO` is a product, but for this example, we'll just stick to +this smaller set of reactions.) Now, let's set the composition to an interesting +equilibrium state: + +```{code-cell} +g.TPX = 300, 101325, {'CH4':0.6, 'O2':1.0, 'N2':3.76} +g.equilibrate('HP') +``` + +We can verify that this is an equilibrium state by seeing that the net reaction rates +are essentially zero: + +```{code-cell} +g.net_rates_of_progress[II] +``` + +Now, let's see what happens if we decrease the temperature of the mixture: + +```{code-cell} python +g.TP = g.T-100, None +g.net_rates_of_progress[II] +``` + +All of the reaction rates are positive, favoring the formation of `CO2` from `CO`, with +the third reaction, `CO + OH <=> CO2 + H` proceeding the fastest. If we look at the +enthalpy change associated with each of these reactions: + +```{code-cell} +g.delta_enthalpy[II] +``` + +we see that the change is negative in each case, indicating a net release of thermal +energy. The total heat release rate can be computed either from the reaction rates: + +```{code-cell} +np.dot(g.net_rates_of_progress, g.delta_enthalpy) +``` + +or from the species production rates: + +```{code-cell} +np.dot(g.net_production_rates, g.partial_molar_enthalpies) +``` + +The contribution from just the selected reactions is: + +```{code-cell} +np.dot(g.net_rates_of_progress[II], g.delta_enthalpy[II]) +``` + +Or about 16% of the total heat release rate. + +## Next Steps + +Congratulations! You have finished the Cantera Python tutorial. You should now be ready +to begin using Cantera on your own. Please see additional sections of the [Cantera User +Guide](/userguide/index) for assistance with intermediate and advanced Cantera +functionality. Good luck! diff --git a/doc/sphinx/userguide/thermobuild.md b/doc/sphinx/userguide/thermobuild.md new file mode 100644 index 00000000000..ce52f712562 --- /dev/null +++ b/doc/sphinx/userguide/thermobuild.md @@ -0,0 +1,114 @@ +(sec-thermobuild)= +# Converting Data from NASA ThermoBuild + +% TODO: Link to NASA9 Science docs + +Thermodynamic data for a range of species can be obtained from the +[NASA ThermoBuild](https://cearun.grc.nasa.gov/ThermoBuild/index_ds.html) tool. +This thermodynamic data is described using the 9-coefficient NASA polynomial parameterization, which is implemented by Cantera. + +To generate an input file containing thermodynamic data, use the ThermoBuild web +interface to select the elements you want to include, and click *process*. Then, select +the species you want to include in your mechanism and click *continue*. Select the +content on the resulting page starting with the line that says `thermo`, and ending with +the line that says `END REACTANTS` and save it to a file. + +Next, we need to make a few modifications to this file so it contains all of the +information needed to be processed by Cantera's CK file parser. For this example, let's +suppose you have selected just the species `CO` and `CO2` from ThermoBuild. + +- Modify the first line of the file so that it reads `thermo nasa9`. This is done to + distinguish this input format from the one used for the 7-coefficient NASA + polynomials. +- Replace the last two lines (`END PRODUCTS` and `END REACTANTS`) with a single line + that reads `END`. + +## Creating species definitions only + +If you only want to generate a species database that can be referenced from other +Cantera input files, the above modifications are sufficient. The last step is simply to +convert the input file to the Cantera YAML format using `ck2yaml`. If you named the file +`mythermo.txt`, then the command to convert it would be: + +```bash +ck2yaml --thermo=mythermo.txt +``` + +This will generate the file `mythermo.yaml`. You can then reference the species +definitions from this file in phase definitions in other Cantera input files, for +example: + +```yaml +phases: +- name: gas + thermo: ideal-gas + species: + - {mythermo.yaml/species: all} +``` + +## Creating a complete phase definition + +To create a complete phase definition, you also need to add two sections to the top of +the ThermoBuild input file. First, a section declaring all of the elements: + +``` +elements +C O +end +``` + +And second, a section declaring all of the species: + +``` +species +CO CO2 +end +``` + +The resulting input file should look like the following: + +``` +elements +C O +end + +species +CO CO2 +end + +thermo nasa9 + 200.000 1000.000 6000.000 20000.000 9/09/04 +CO Gurvich,1979 pt1 p25 pt2 p29. + 3 tpis79 C 1.00O 1.00 0.00 0.00 0.00 0 28.0101000 -110535.196 + 200.000 1000.0007 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 0.0 8671.104 + 1.489045326D+04-2.922285939D+02 5.724527170D+00-8.176235030D-03 1.456903469D-05 +-1.087746302D-08 3.027941827D-12 -1.303131878D+04-7.859241350D+00 + 1000.000 6000.0007 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 0.0 8671.104 + 4.619197250D+05-1.944704863D+03 5.916714180D+00-5.664282830D-04 1.398814540D-07 +-1.787680361D-11 9.620935570D-16 -2.466261084D+03-1.387413108D+01 + 6000.000 20000.0007 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 0.0 8671.104 + 8.868662960D+08-7.500377840D+05 2.495474979D+02-3.956351100D-02 3.297772080D-06 +-1.318409933D-10 1.998937948D-15 5.701421130D+06-2.060704786D+03 +CO2 Gurvich,1991 pt1 p27 pt2 p24. + 3 g 9/99 C 1.00O 2.00 0.00 0.00 0.00 0 44.0095000 -393510.000 + 200.000 1000.0007 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 0.0 9365.469 + 4.943650540D+04-6.264116010D+02 5.301725240D+00 2.503813816D-03-2.127308728D-07 +-7.689988780D-10 2.849677801D-13 -4.528198460D+04-7.048279440D+00 + 1000.000 6000.0007 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 0.0 9365.469 + 1.176962419D+05-1.788791477D+03 8.291523190D+00-9.223156780D-05 4.863676880D-09 +-1.891053312D-12 6.330036590D-16 -3.908350590D+04-2.652669281D+01 + 6000.000 20000.0007 -2.0 -1.0 0.0 1.0 2.0 3.0 4.0 0.0 9365.469 +-1.544423287D+09 1.016847056D+06-2.561405230D+02 3.369401080D-02-2.181184337D-06 + 6.991420840D-11-8.842351500D-16 -8.043214510D+06 2.254177493D+03 +END +``` + +This file (saved for example as `myphase.txt`) can then be converted to the Cantera YAML +format using the [`ck2yaml`](/yaml/ck2yaml) utility from a shell: + +```bash +ck2yaml --input=myphase.txt +``` + +This will generate a an input file named `myphase.yaml` with a phase named `gas` that +can be directly imported in Cantera. From dbacaadf6f71332581864682511593127398ba3e Mon Sep 17 00:00:00 2001 From: pestre Date: Mon, 13 Jan 2025 19:21:29 +0100 Subject: [PATCH 02/98] Add missing files in include directory from cantera-avbp and merge differences Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: new file: doc/sphinx/_static/images/favicon.png new file: include/cantera/base/Parser.h modified: include/cantera/base/ct_defs.h new file: include/cantera/kinetics/CustomKinetics.h modified: include/cantera/kinetics/Kinetics.h modified: include/cantera/oneD/Boundary1D.h modified: include/cantera/oneD/Domain1D.h modified: include/cantera/oneD/DomainFactory.h new file: include/cantera/oneD/Flamelet.h modified: include/cantera/oneD/OneDim.h modified: include/cantera/oneD/Sim1D.h modified: include/cantera/oneD/StFlow.h modified: include/cantera/oneD/refine.h new file: include/cantera/transport/AVBPTransport.h --- doc/sphinx/_static/images/favicon.png | Bin 0 -> 4879 bytes include/cantera/base/Parser.h | 66 ++ include/cantera/base/ct_defs.h | 38 ++ include/cantera/kinetics/CustomKinetics.h | 49 ++ include/cantera/kinetics/Kinetics.h | 2 + include/cantera/oneD/Boundary1D.h | 13 + include/cantera/oneD/Domain1D.h | 3 +- include/cantera/oneD/DomainFactory.h | 6 +- include/cantera/oneD/Flamelet.h | 180 ++++++ include/cantera/oneD/OneDim.h | 2 +- include/cantera/oneD/Sim1D.h | 5 + include/cantera/oneD/StFlow.h | 723 +++++++++++++++++++++- include/cantera/oneD/refine.h | 32 + include/cantera/transport/AVBPTransport.h | 120 ++++ 14 files changed, 1214 insertions(+), 25 deletions(-) create mode 100644 doc/sphinx/_static/images/favicon.png create mode 100644 include/cantera/base/Parser.h create mode 100644 include/cantera/kinetics/CustomKinetics.h create mode 100644 include/cantera/oneD/Flamelet.h create mode 100644 include/cantera/transport/AVBPTransport.h diff --git a/doc/sphinx/_static/images/favicon.png b/doc/sphinx/_static/images/favicon.png new file mode 100644 index 0000000000000000000000000000000000000000..a3af328e23fcd26110dd28ddf4be5797e9a20032 GIT binary patch literal 4879 zcmV+q6Y%VbP)M|H=4r|-S<*vG82yOOMx^|am=wz0rgz&7Mz zlbBaXks?rh2!Xhai=4wwhU#XZ7svrUK&n=PCAEb>1XO?$Fpn||%wd=mtD`_(Ju@sNy{aj_ ziYJ%EYC$AkpVlhi!Q}6FgoA=#fxx$vD+ZAz_o*V{;p&VT9Bhq0eoId+&`@2{A;Y5t z@^2_T3Ltp*6*yu2lF?LX0*`&~~m!(U;ipu)W zwH1n5{g|pjsZ+#2-cWiwln;YHfs_0WBateQ|5;9<_VFZl>xT$wkHj_#BL}e@Ama2& zrb(#SUSawn@TxVsZUSSIN$ij;D>A^dSRJ{kOa<@+owx5{Jc6ke<&0%+OT_$Ui=UU9 z!c<5)c^z1BAqL9w?-)Ljq~4|xfpnQ)k}O|Xc3prH%)V8L0EtQ1<3}ahn~_+qNRppjD7k>5fGTseH>?yd#NOTcIgAQkt z>N37V5TMFVRY77W#Md6Mgt$(sxskWB4zrUOH_0USRGp?{K{I-qjRN&laK|7Bc1Vnc z2(%A$5PDUR5WI-@TG3wznHPvuDMgW#MQU*gS4u#r5DT354L@m>nq)e*tIjp6NFbM! zga}%LqR4<+10I+H44gI0zY+XtP|+i?(cfOYTOo|(MyVA6ELP=`jm)lAsYz%Rta4rT z8nKjtOrrXmM-CA;hCR@f#dsjDmp`&rmZ^i)RDlRsWxEYcA8Q47)<7bINaIzCWd@i? 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z9IC*P3hcKcd#p&hUCdT%7xU9Zz;;z;5#ITU&v4=Jy>y*FN946vV1tof$8@`Rb*YZXdh$(#GjAwogy7g_uBf zb4K-G1r8VCP#F%F;f`2jrxj@`pGa-P`Idz&Dt)R90`K^(C%ACWTS%RIwU$4ny-2o7 z``YqEYLYAdp$yDC>Q@3E!OF~Z$jnsPiYZ!{(jb`5=lb$sF26XmbBuIw@hR0Yij{Jz zI>Bu}&avG;#rE=rvE37sW4k9up4~QajSZzaHdV^>sNUYCy1xtuV%T1CQogeadqU_# zgm}fi)(FUo9NVNyR+VkQZ~WQ^dH$hy;axoKm>Rd=he^iRb32w_*fBC-ZX5q)LVxjq z1qep9cF3X%Qg!#1T|fY{K~FL(&<{-6r6?~?n9lw%{8G)SGt zPyL)!<{X}R4L`U{x%@hDR0^gh$$2m|dWC+C*f>1Fj&KHlKF|K~5hBlL&$ZX-kE;A& z*8#qI|F7`U-SH=;cIj$31j`w{q2g{Y}!;Z zlT=gPF8g@9uw1gNF_TugpsDm2#+)J3HGyH6O4n7on7~%XDa}t4_{HqxI6Yy=_?B%D z1TZy9DvD9#p$3c!K~)LGO%ddMD6lw|^`CyXC5n@6JbvYdMcN9xuKb8x@okREc44{n z8*2v)3{a^}o~4>|CkjPSjK;w8A)}{T^ zSX1^}wp+h`s8Wa(2@udGPggQm5`!9Ud8vllxNoP{Ustk1L22MYU|KESd<`5a3e3ra-f};}bog z8IWFFu%-{UtE!DVRvUzXs2R|z{gAccS6i(nnU3wPA8WUZ@#zV$Oc{|Dv^vCZ{W`IG +#include +#include +using std::cout; +using std::endl; +using std::string; +#include +using std::ifstream; +#include + +class Param { +private: + size_t m_count; + string m_name; + std::vector m_args; +public: + Param() { + m_count = 0; + } + Param(const string& name) { + m_count = 0; + setName(name); + } + void setName(const string& name) { + m_name = name; + } + string Name() { + return m_name; + } + void print(); + void addArgs(const string& arg) { + m_args.push_back(arg); + } + size_t nbArgs() { + return(m_args.size()); + } + void incrCount() { + ++m_count; + } + double readDouble(const int i); + int readInteger(const int i); + bool readBool(const int i); + string readString(const int i); +}; + +class Parser { +private: + std::list m_params; + //std::list i_count; + size_t m_count; +public: + Parser() { + m_count = 0; + } + void parseFile(const string& file); + bool addParamFromLine(Param& param,const string& line); + Param * getParam(const string& name); + Param * getParam(const string& name, const size_t n); + Param * getParam(const string& name, const size_t n, const size_t m); + Param * getParam(const string& name, const size_t n, const size_t m, const size_t l); + size_t getParamNumber(const string& name, const size_t n); + bool checkParam(const string& name); + bool checkParam(const string& name, const size_t n, const size_t m); + size_t nbParamOccurence(const string& name); +}; diff --git a/include/cantera/base/ct_defs.h b/include/cantera/base/ct_defs.h index 4980529b096..fc889ab9302 100644 --- a/include/cantera/base/ct_defs.h +++ b/include/cantera/base/ct_defs.h @@ -194,6 +194,44 @@ typedef vector vector_int [[deprecated("replaceable by vector")]]; //! index returned by functions to indicate "no position" const size_t npos = static_cast(-1); +//! Soot +// Thermal accomodation factor +const double alphaT = 0.9; +// Active sites : Blanquart and Pitsch (2017) [kmol4/kg4] +const double Cn_cst = 7.5e-12; +// Soot particle density [kg/m3] +const double rho_soot = 1.86e3; +//C2 molecule volume : 2*Wc/rho_soot/Avogadro [m3] +const double V_C2 = 2. * 12. / rho_soot / Avogadro; +// C2 molecule surface area [m2] +const double S_C2 = Pi * pow(6.0 * V_C2 / Pi, 2.0/3.0); +// Soot particle fractal dimension +const double Df = 1.80; +// Amplification factors +const double eps_nucl = 2.5; +const double eps_cond = 1.3; +const double eps_coag = 2.2; +// Biggest soot [m-3] +const double bigSoot = 1.0e-15; +//Condensation +const double alphaV = 1.0 - 2.0 / Df; +const double alphaS = 3.0 / Df - 1.0; +const double vlim1 = 3.98 * 1.0e-25; // [m3] +//Coagulation +const double d_gaz = 2.0e-10; // [m] +const double Csut1 = 1.4558e-6; // [Pa/s] +const double Csut2 = 110.4; +//Surface +const double alpha_surf = 1.0; // Proportion of active sites at soot surface +// Radiative +const double aRadSoot = 1.57; +const double bRadSoot = 0.56; +const double CRad0 = 36 * Pi * aRadSoot * bRadSoot / (pow(pow(aRadSoot,2.0) - pow(bRadSoot,2.0) + + 2, 2.0) + pow(2 * aRadSoot * bRadSoot, 2.0)); +const double CRad2 = Planck * lightSpeed / Boltzmann; +// Soot soret +const double C_soot_soret = 0.554; + } // namespace #endif diff --git a/include/cantera/kinetics/CustomKinetics.h b/include/cantera/kinetics/CustomKinetics.h new file mode 100644 index 00000000000..4c720b33800 --- /dev/null +++ b/include/cantera/kinetics/CustomKinetics.h @@ -0,0 +1,49 @@ +/** + * @file CustomKinetics.h + * + * @ingroup chemkinetics + */ + +// Author: Q. Cazeres, A. Felden, P. Pepiot + +#include "GasKinetics.h" + +namespace Cantera +{ + /** + * Kinetics manager implementing reaction mechanism GRI-Mech 3.0 + * @deprecated + */ + class CustomKinetics : public GasKinetics + { + public: + /// Default constructor. + CustomKinetics(); + + // virtual int type() const { + // return cCustomKinetics; + // } + + void getNetProductionRates(double* net) { + get_wdot_reduced(net); + } + + string kineticsType() const override { + return "custom"; + } + + void closeDynamicLib() { + close_dl(); + } + + void* handle; + +private: + typedef void (*ck_t)(double*,double*,const double*, double*); + // New yarc2 format + //typedef void (*ck_t)(const double*,const double*,const double*,const double*,double*); + ck_t ck; + void get_wdot_reduced(double* wdot); + void close_dl(); + }; +} diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h index 6c62c464098..22fc23d32ca 100644 --- a/include/cantera/kinetics/Kinetics.h +++ b/include/cantera/kinetics/Kinetics.h @@ -133,6 +133,8 @@ class Kinetics virtual ~Kinetics() = default; + virtual void closeDynamicLib(); + //! Kinetics objects are not copyable or assignable Kinetics(const Kinetics&) = delete; Kinetics& operator=(const Kinetics&)= delete; diff --git a/include/cantera/oneD/Boundary1D.h b/include/cantera/oneD/Boundary1D.h index d79aa96b9b5..1f69c402e2e 100644 --- a/include/cantera/oneD/Boundary1D.h +++ b/include/cantera/oneD/Boundary1D.h @@ -77,6 +77,16 @@ class Boundary1D : public Domain1D throw NotImplementedError("Boundary1D::setMoleFractions"); } + //! Set the mass fractions by specifying a string. + virtual void setMassFractions(const std::string& xin) { + throw NotImplementedError("Boundary1D::setMassFractions"); + } + + //! Set the mass fractions by specifying an array. + virtual void setMassFractions(const double* xin) { + throw NotImplementedError("Boundary1D::setMassFractions"); + } + //! Mass fraction of species k. virtual double massFraction(size_t k) { throw NotImplementedError("Boundary1D::massFraction"); @@ -160,6 +170,9 @@ class Inlet1D : public Boundary1D void setMoleFractions(const string& xin) override; void setMoleFractions(const double* xin) override; + void setMassFractions(const std::string& xin) override; + void setMassFractions(const double* xin) override; + double massFraction(size_t k) override { return m_yin[k]; } diff --git a/include/cantera/oneD/Domain1D.h b/include/cantera/oneD/Domain1D.h index 95e6c17a896..633b05304ef 100644 --- a/include/cantera/oneD/Domain1D.h +++ b/include/cantera/oneD/Domain1D.h @@ -15,6 +15,7 @@ namespace Cantera const int cFlowType = 50; const int cFreeFlow = 51; const int cAxisymmetricStagnationFlow = 52; +const int cFlameletFlow = 53; const int cConnectorType = 100; const int cSurfType = 102; const int cInletType = 104; @@ -46,7 +47,7 @@ class Domain1D * @param points Number of grid points. * @param time (unused) */ - Domain1D(size_t nv=1, size_t points=1, double time=0.0); + Domain1D(size_t nv=1, size_t points=1, double time=0.0, size_t nsoot=0, size_t neq=0); virtual ~Domain1D(); Domain1D(const Domain1D&) = delete; diff --git a/include/cantera/oneD/DomainFactory.h b/include/cantera/oneD/DomainFactory.h index 747c2f7a713..0b5211979cf 100644 --- a/include/cantera/oneD/DomainFactory.h +++ b/include/cantera/oneD/DomainFactory.h @@ -19,7 +19,7 @@ namespace Cantera //! ```cpp //! shared_ptr d1 = newDomain("Inlet", sol, "reactants"); //! ``` -class DomainFactory : public Factory, const string&> +class DomainFactory : public Factory, const string&, const size_t&> { public: /** @@ -51,7 +51,7 @@ class DomainFactory : public Factory, const strin //! @ingroup onedGroup template shared_ptr newDomain( - const string& domainType, shared_ptr solution, const string& id="") + const string& domainType, shared_ptr solution, const string& id="", const size_t& sections=0) { string id_ = id; if (id_ == "") { @@ -59,7 +59,7 @@ shared_ptr newDomain( } auto ret = std::dynamic_pointer_cast( shared_ptr( - DomainFactory::factory()->create(domainType, solution, id_))); + DomainFactory::factory()->create(domainType, solution, id_, sections))); if (!ret) { throw CanteraError("newDomain", "Invalid cast: unable to access 'Domain1D' as '{}'.", demangle(typeid(T))); diff --git a/include/cantera/oneD/Flamelet.h b/include/cantera/oneD/Flamelet.h new file mode 100644 index 00000000000..a76dfc09edd --- /dev/null +++ b/include/cantera/oneD/Flamelet.h @@ -0,0 +1,180 @@ +#ifndef CT_FLAMELET_H +#define CT_FLAMELET_H + +// #include "Domain1D.h" +#include "cantera/base/Array.h" +#include "cantera/oneD/StFlow.h" +#include "cantera/kinetics/Kinetics.h" +#include "cantera/thermo/IdealGasPhase.h" +#include "cantera/thermo/ThermoPhase.h" + + + +#include +/** + * A class for counter-flow diffusion flames in mixture fraction space + * @ingroup onedim + * L. Esclapez - 01/2018 + */ + +namespace Cantera +{ + +class Flamelet : public StFlow +{ +public: + Flamelet(IdealGasPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); + + //! Delegating constructor + Flamelet(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); + + //! Create a new flow domain. + //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and + //! transport properties + //! @param id name of flow domain + //! @param points initial number of grid points + Flamelet(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points=1); + + virtual ~Flamelet(); + + virtual void eval(size_t j, double* x, double* r, integer* mask, double rdt) override; + + virtual string type() const override{ + return "flamelet-flow"; + } + + virtual string flowType() const override{ + return "Flamelet"; + } + + virtual void resize(size_t components, size_t points) override; + + virtual string componentName(size_t n) const override; + + virtual size_t componentIndex(const string& name) const override; + + vector dCpdT(const Array2D sol); + + vector d2CpdT2(const Array2D sol); + + virtual void setGas(const double* x, size_t j) override; + + virtual void setGasAtMidpoint(const double* x, size_t j) override; + + virtual void resetBadValues(double* xg) override; + + virtual void setChiSt(double chiSt) { + m_chiSt = chiSt; + m_updateChi = true; + } + + virtual void setzSt(double zSt) { + m_zSt = zSt; + m_updateChi = true; + } + + virtual double chiSt() const { + return m_chiSt; + } + + virtual double zSt() const { + return m_zSt; + } + + void setChi(); + + void setUnityLewisNumber(bool doLewisNumber) { + m_do_unityLewisNumber = doLewisNumber; + } + + virtual void updateTransport(double* x, size_t j0, size_t j1) override; + + virtual void _getInitialSoln(double* x) override{ + for (size_t j = 0; j < m_points; j++) { + T(x,j) = m_thermo->temperature(); + m_thermo->getMassFractions(&Y(x, 0, j)); + } + } + + void showChiProfile() { + std::cout << "Chi profile " << std::endl; + for (size_t i = 0; i < m_points; i++) { + std::cout << z(i) << " " << m_chi[i] << std::endl; + } + } + + double chi(size_t j) const { + return m_chi[j]; + } + + size_t indexSt() const + { + auto low = std::lower_bound(m_z.begin(), m_z.end(), m_zSt); + return (low - m_z.begin()); + } + + virtual double T(const double* x, size_t j) const override { + return x[index(c_offset_Tflamelet, j)]; + } + virtual double& T(double* x, size_t j) override { + return x[index(c_offset_Tflamelet, j)]; + } + virtual double T_prev(size_t j) const override { + return prevSoln(c_offset_Tflamelet, j); + } + + virtual double Y(const double* x, size_t k, size_t j) const override { + return x[index(c_offset_Yflamelet + k, j)]; + } + + virtual double& Y(double* x, size_t k, size_t j) override { + return x[index(c_offset_Yflamelet + k, j)]; + } + + virtual double Y_prev(size_t k, size_t j) const override { + return prevSoln(c_offset_Yflamelet + k, j); + } + + double d2Ydz2(const double* x, size_t k, size_t j) const { + double c1 = (Y(x,k,j) - Y(x,k,j-1)); + double c2 = (Y(x,k,j+1) - Y(x,k,j)); + return 2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + + double d2Tdz2(const double* x, size_t j) const { + double c1 = (T(x,j) - T(x,j-1)); + double c2 = (T(x,j+1) - T(x,j)); + return 2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + + double Lek(size_t k, size_t j) { + return m_Lek[j*m_nsp+k]; + } + + double exactChi(double zz); + + double erfinv(double p1, double q1); + + // Lewis number stuff + bool m_do_unityLewisNumber = true; + vector m_Lek; + + // Thermo stuff + vector h_RT; + vector cp_R; + + + // Scalar dissipation rate stuff + vector m_chi; + vector m_exactchi; + double m_chiSt = 0.0; + double m_zSt = 0.0; + bool m_updateChi = true; + +// private: + // vector m_ybar; +}; + +} + +#endif \ No newline at end of file diff --git a/include/cantera/oneD/OneDim.h b/include/cantera/oneD/OneDim.h index 0c06da3eef8..989b8e2b0f4 100644 --- a/include/cantera/oneD/OneDim.h +++ b/include/cantera/oneD/OneDim.h @@ -377,7 +377,7 @@ class OneDim int m_nsteps = 0; //! Maximum number of timesteps allowed per call to solve() - int m_nsteps_max = 500; + int m_nsteps_max = 5000; private: // statistics diff --git a/include/cantera/oneD/Sim1D.h b/include/cantera/oneD/Sim1D.h index 25a5651259b..54c98ef72e2 100644 --- a/include/cantera/oneD/Sim1D.h +++ b/include/cantera/oneD/Sim1D.h @@ -241,6 +241,11 @@ class Sim1D : public OneDim //! Refine the grid in all domains. int refine(int loglevel=0); + /// Remesh the grid in all domains. + double remesh(int loglevel, const double dist_min=1e9, const double domain_size=50.0); //from MUTAGEN + void addPoint(size_t ndomain, double zpoint, vector xpoint, int loglevel, bool newjac=true); //from MUTAGEN + void getRatio(); //from MUTAGEN + //! Add node for fixed temperature point of freely propagating flame int setFixedTemperature(double t); diff --git a/include/cantera/oneD/StFlow.h b/include/cantera/oneD/StFlow.h index c01dd407d9e..dc4b3b36fd6 100644 --- a/include/cantera/oneD/StFlow.h +++ b/include/cantera/oneD/StFlow.h @@ -30,6 +30,14 @@ enum offset , c_offset_Y //! mass fractions }; +//! Offsets of solution components in the 1D solution array for mixture fraction space +enum offset_z +{ + c_offset_Tflamelet, //! Temperature + c_offset_Yflamelet, //! Species mass fractions + // c_offset_Chi not used +}; + class Transport; //! @defgroup flowGroup Flow Domains @@ -53,28 +61,32 @@ class StFlow : public Domain1D //! to evaluate all thermodynamic, kinetic, and transport properties. //! @param nsp Number of species. //! @param points Initial number of grid points - StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t points = 1); + //! @param n_eq Number of non-species equations (default = 4 for spatial resolution) + + //StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t points = 1); + StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); //! Delegating constructor - StFlow(shared_ptr th, size_t nsp = 1, size_t points = 1); + StFlow(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); //! Create a new flow domain. //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and //! transport properties //! @param id name of flow domain //! @param points initial number of grid points - StFlow(shared_ptr sol, const string& id="", size_t points=1); + StFlow(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Y, size_t points=1); - ~StFlow(); + virtual ~StFlow(); // virtual kw required for derived class destructors (flamelet) - string type() const override; + virtual string type() const override; //! @name Problem Specification //! @{ void setupGrid(size_t n, const double* z) override; + void setupGrid(size_t n); - void resetBadValues(double* xg) override; + virtual void resetBadValues(double* xg) override; ThermoPhase& phase() { return *m_thermo; @@ -134,6 +146,16 @@ class StFlow : public Domain1D return m_press; } + //! Set the number of non-species equations + void setNequation(size_t neq){ + m_neq = neq; + } + + //! The current number of non-species equations + size_t nEq(){ + return m_neq; + } + //! Write the initial solution estimate into array x. void _getInitialSoln(double* x) override; @@ -161,6 +183,18 @@ class StFlow : public Domain1D return m_fixedtemp[j]; } + /// Returns the mixture fraction at point j + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + double getMixFrac(size_t j) { + return m_zmixfrac[j]; + } + + /// Updates the mixture fraction at point j + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + void calcMixFrac(const double* x,size_t j); + //! @} string componentName(size_t n) const override; @@ -203,12 +237,23 @@ class StFlow : public Domain1D m_usesLambda = false; } + void setFlameletFlow() { + m_type = cFlameletFlow; + m_dovisc = true; + m_isFree = false; + m_usesLambda = true; + } + //! Return the type of flow domain being represented, either "Free Flame" or //! "Axisymmetric Stagnation". //! @see setFreeFlow setAxisymmetricFlow //! @deprecated To be removed after %Cantera 3.0; replaced by type(). virtual string flowType() const; + virtual void setFuelSpecies(const std::string fuel) { + m_fuel = fuel; + } + void solveEnergyEqn(size_t j=npos); //! Get the solving stage (used by IonFlow specialization) @@ -266,6 +311,342 @@ class StFlow : public Domain1D */ void setBoundaryEmissivities(double e_left, double e_right); + // Turn soot formation on / off. + // setSections + const size_t getSections() const{ + return m_nsoot; + } + + void setSections(size_t nSec) { + m_nsoot = nSec; + } + + void setPrecursors(std::vector id_precursors); + + void setSootLoglevel(size_t loglevel){ + soot_loglevel = loglevel; + } + + size_t getSootLoglevel(){ + return soot_loglevel; + } + + void enableCondensation(bool doCondensation) { + m_do_condensation = doCondensation; + } + bool condensationEnabled(){ + return m_do_condensation; + } + + void enableCoagulation(bool doCoagulation) { + m_do_coagulation = doCoagulation; + } + bool coagulationEnabled(){ + return m_do_coagulation; + } + + void setCollisionModel(std::string collisionModel){ + m_collision_model = collisionModel; + } + + std::string getCollisionModel(){ + return m_collision_model; + } + + void setSootMorphology(std::string morphologyModel){ + m_soot_morphology = morphologyModel; + } + + std::string getSootMorphology(){ + return m_soot_morphology; + } + + void enableRetroaction(bool doRetroaction){ + m_do_retroaction = doRetroaction; + } + bool retroactionEnabled(){ + return m_do_retroaction; + } + + void enableSootRadiation(bool do_soot_radiation){ + m_do_soot_radiation = do_soot_radiation; + } + + bool sootRadiationEnabled(){ + return m_do_soot_radiation; + } + + void enableSootSoret(bool do_soot_soret){ + m_do_soot_soret = do_soot_soret; + } + + bool sootSoretEnabled(){ + return m_do_soot_soret; + } + + void enableSurfaceGrowth(bool do_sg){ + m_do_sg = do_sg; + } + bool surfaceGrowthEnabled(){ + return m_do_sg; + } + + void enableOxidation(bool do_oxidation){ + m_do_oxidation = do_oxidation; + } + bool oxidationEnabled(){ + return m_do_oxidation; + } + + void enableTrashSection(double trash_section){ + if (trash_section > 0){ + m_trash_section = true; + dTrashLowLim = trash_section; + }else{ + m_trash_section = false; + dTrashLowLim = 0.0; + } + } + + bool trashSectionEnabled(){ + return m_trash_section; + } + + void setHaca(size_t haca_model){ + m_haca_model = haca_model; + } + + size_t getHaca(){ + return m_haca_model; + } + + double getKazakovTad(){ + return kazakovTad; + } + void setKazakovTad(double kazakov_tad){ + kazakovTad = kazakov_tad; + } + + void loadHaca(size_t m_haca_model){ + if (m_haca_model == 1){ //Mauss + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.0 / S_C2; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Mauss HACA-RC model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; + ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; + // S-H + OH <-> S* + H2O + ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; + ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; + // S* + H <-> S-H + ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; + ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; + // S* + C2H2 <-> S-H + ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; + ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; + // S* <-> S-H + H + ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; + ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; + // S* + O2 -> S-H + 2CO + ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 8.4000e03; + // S* + O2 -> S-H + 2HCO + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + }else if (m_haca_model == 11){ //Mauss tuned (Guo 2016) + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.0 / S_C2; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Mauss HACA-RC model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; + ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; + // S-H + OH <-> S* + H2O + ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; + ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; + // S* + H <-> S-H + ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; + ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; + // S* + C2H2 <-> S-H + ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; + ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; + // S* <-> S-H + H + ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; + ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; + // S* + O2 -> S-H + 2CO + ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 190.000e03; + // S* + O2 -> S-H + 2HCO + // S-H + OH -> S-H + CO + gamma_oh = 0.10; + }else if (m_haca_model == 2){ //Blanquart + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.7e19; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Blanquart HACA model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.0e8 * 1e-3; nk01f = 1.8; ek01f = 68420.0; + ak01b = 8.68e4 * 1e-3; nk01b = 2.36; ek01b = 25460.0; + // S-H + OH <-> S* + H2O + ak02f = 6.72e1 * 1e-3; nk02f = 3.33; ek02f = 6090.0; + ak02b = 6.44e-1 * 1e-3; nk02b = 3.79; ek02b = 27960.0; + // S-H <-> S* + H + ak03f = 1.13e16; nk03f = -0.06; ek03f = 476050.0; + ak03b = 4.17e13 * 1e-3; nk03b = 0.15; ek03b = 0.0; + // S* + C2H2 -> S-H + ak04f = 2.52e9 * 1e-3; nk04f = 1.77; ek04f = 13540.0; + // S* + O2 -> S + 2CO + ak05f = 2.2e12 * 1e-3; nk05f = 0.0; ek05f = 31380.0; + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + }else if (m_haca_model == 3){ + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [m-2] + double lambda = 2.3e19; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Kazakov HACA model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/mol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 2.5e14 * 1e-3; nk01f = 0.0; ek01f = 66900.0; + ak01b = 3.9e12 * 1e-3; nk01b = 0.0; ek01b = 39000.0; + // S* + H -> S-H + ak02f = 1.0e14 * 1e-3; nk02f = 0.0; ek02f = 0.0; + // S* + C2H2 -> S-H + H + ak03f = 8.4e11 * 1e-3; nk03f = 0.4; ek03f = 35100.0; + // S* + O2 -> S + 2CO + ak04f = 2.2e12 * 1e-3; nk04f = 0.0; ek04f = 31300.0; + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + } + } + + void finalizeSoot(); + void loadSurface(); + //Initialize soot + void initSoot(); + void showSootInfo(); + // Sections generation and display + void sootCreationVol(); + void showSootSections(); + void sootCollisionModel(); + void getDistributionOrdre0(const double* x, size_t j); + // Soot source terms + void sootSource(const double* x, size_t j); + void sootDimerization(const double* x, size_t j); + void sootNucleation(const double* x, size_t j); + void sootCondensation(const double* x, size_t j); + void sootCoagulation(const double* x, size_t j); + void sootSurface(const double* x, size_t j); + void sootSurfaceInitialization(const double* x, size_t j); + void sootCollisionInverse(); + // Returns section name + std::string sectionName(size_t n) const { + return m_section_name[n]; + } + + const vector& vMin() const { + return vSectMin; + } + + const vector& vMax() const { + return vSectMax; + } + + const vector& vMean() const { + return vSectMean; + } + + const vector& dMean() const { + return dSectMean; + } + + const vector& dCol() const { + return dSectCol; + } + + const vector& aCol() const { + return aSectCol; + } + + const vector& sMean() const { + return sSectMean; + } + + const vector& thetaSoot() const { + return theta_surf; + } + + const vector& fractalPrefactor() const { + return kfractal; + } + + const vector& fractalDimension() const { + return Dfractal; + } + + const double rhoSoot() const { + return rho_soot; + } + + const double getSootInception(size_t j) const { + return m_qdotNucleation[j] * m_rho[j]; + } + + const double getSootCondensation(size_t k, size_t j) const { + return m_qdotCondensation(k,j) * m_rho[j]; + } + + const double getSootCoagulation(size_t k, size_t j) const { + return m_qdotCoagulation(k,j) * m_rho[j]; + } + + const double getSootSg(size_t k, size_t j) const { + return m_qdotSg(k,j) * m_rho[j]; + } + + const double getSootOxidation(size_t k, size_t j) const { + return m_qdotOxidation(k,j) * m_rho[j]; + } + + const double fv(const double* x, size_t j){ + double val = 0.0; + for (size_t k=0; k < m_nsoot; k++){ + val += Ys(x,k,j); + } + val *= m_rho[j] / rho_soot; + return val; + } + + const double sootPrimaryDiam(size_t k) const { + return 2.0 * rNucMean[k]; + } + + const double sootPrimaryPart(size_t k) const { + return nNucMean[k]; + } + + void setThick(double thickness){ + m_thick = thickness; + AVBPReadInputChem(); + } + + double getThick() const { + return m_thick; + } + //! Return emissivity at left boundary double leftEmissivity() const { return m_epsilon_left; } @@ -282,16 +663,33 @@ class StFlow : public Domain1D void resize(size_t components, size_t points) override; //! Set the gas object state to be consistent with the solution at point j. - void setGas(const double* x, size_t j); + virtual void setGas(const double* x, size_t j); //! Set the gas state to be consistent with the solution at the midpoint //! between j and j + 1. - void setGasAtMidpoint(const double* x, size_t j); + virtual void setGasAtMidpoint(const double* x, size_t j); double density(size_t j) const { return m_rho[j]; } + //! seems unused + double cpBar(size_t j) const { + return m_cpm[j]; + } + + double enthalpy(size_t j) const { + return m_h[j]; + } + + double thCond(size_t j) const { + return m_tcon[j]; + } + + double HR(size_t j) const { + return m_hr[j]; + } + //! @deprecated To be removed after %Cantera 3.0. Superseded by isFree() virtual bool fixed_mdot(); @@ -320,6 +718,20 @@ class StFlow : public Domain1D m_dovisc = dovisc; } + + // P. Wolf + void AVBPReadInputPea(); + + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + // B. Franzelli modifications to perform thickening + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + void AVBPReadInputChem(); + void AVBPcompute_local_thick(double* x,size_t j); + + double AVBPthick(size_t j) const { + return avbp_thick[j]; + } + /** * Evaluate the residual function for axisymmetric stagnation flow. If * j == npos, the residual function is evaluated at all grid points. @@ -355,9 +767,120 @@ class StFlow : public Domain1D } //! Write the net production rates at point `j` into array `m_wdot` - void getWdot(double* x, size_t j) { - setGas(x,j); - m_kin->getNetProductionRates(&m_wdot(0,j)); + // void getWdot(double* x, size_t j) { + // setGas(x,j); + // m_kin->getNetProductionRates(&m_wdot(0,j)); + // } +/// write the net production rates at point j into array m_wdot +/// Modified by P. Wolf March 2010 - Thanks to Alireza N. +/// when PEA activated: production rates depends on mixture fraction at point j +/// WARNING: the following is valid only for fuel/AIR right now + void getWdot(double *x, size_t j) + { + double zloc; + double phi; + setGas(x, j); // We'll need to set the gas before retrieving + // std::cout << "after setGas" << std::endl; + zloc = getMixFrac(j); // the Mixture Fraction and calculating wdot + phi = zloc / (1. - zloc) * phi_cst; + + switch (avbp_ipea) + { + case 0: + m_kin->getNetProductionRates(&m_wdot(0, j)); + break; + // ipea = 1, apply the PEA on fuel oxydation reaction only + case 1: + double pea_f; // pea correction function + // Now set the PEA correction function + pea_f = 0.5 * (1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) + + avbp_pea_coeffs[2] / 4. * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) + * (1. + tanh((avbp_pea_coeffs[5] - phi) / avbp_pea_coeffs[6])); + + // Multiply reaction rate of reaction 1 by the pea coeff + m_kin->setMultiplier(1, pea_f); + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + // Restore the original reaction rates (not necessary) + m_kin->setMultiplier(1, 1.0 / pea_f); + break; + // ipea = 2, apply PEA on both reactions + case 2: + // TEST 081014: differencie bien les cas + double pea2_f[2]; // pea correction function + // Now set the PEA correction function + pea2_f[0] = 2. / ((1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) + + avbp_pea_coeffs[2] * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) + + avbp_pea_coeffs[5] * (1. + tanh((phi - avbp_pea_coeffs[6]) / avbp_pea_coeffs[7]))); + + pea2_f[1] = 0.5 * ((1. + tanh((avbp_pea_coeffs[8] - phi) / avbp_pea_coeffs[9])) + + avbp_pea_coeffs[10] * (1. + tanh((phi - avbp_pea_coeffs[11]) / avbp_pea_coeffs[12])) + + avbp_pea_coeffs[13] * (1. + tanh((phi - avbp_pea_coeffs[14]) / avbp_pea_coeffs[15])) + * (1. + tanh((avbp_pea_coeffs[16] - phi) / avbp_pea_coeffs[17]))); + // Multiply reaction rates by the pea coeff + if (m_kin->nReactions() == 2) + { + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, pea2_f[n]); + } + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + // Restore the original reaction rates (not necessary) + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, 1.0 / pea2_f[n]); + } + } + else + { + throw CanteraError("getWdot", "ipea = 2 but there ain't 2 reactions"); + } + break; + // ipea = 3, apply PEA on both reactions (for CM2 only) + case 3: + double pea3_f[2]; // pea correction function + + // Now set the PEA correction function + if (phi > 1.0) + { + // pea3_f[0] = max(avbp_pea_coeffs[0]*phi*phi + avbp_pea_coeffs[1]*phi + avbp_pea_coeffs[2],0.0); + pea3_f[0] = avbp_pea_coeffs[0] * phi * phi + avbp_pea_coeffs[1] * phi + avbp_pea_coeffs[2]; + } + else + { + pea3_f[0] = 1; + } + pea3_f[1] = pea3_f[0]; + + // Multiply reaction rates by the pea coeff + if (m_kin->nReactions() == 2) + { + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, pea2_f[n]); + } + + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + + // Restore the original reaction rates (not necessary) + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, 1.0 / pea2_f[n]); + } + } + else + { + throw CanteraError("getWdot", "ipea = 3 but there ain't 2 reactions"); + } + + break; + + default: + throw CanteraError("getWdot", "ipea is set to a weird value"); + break; + } } //! Update the properties (thermo, transport, and diffusion flux). @@ -374,7 +897,7 @@ class StFlow : public Domain1D * Update the thermodynamic properties from point j0 to point j1 * (inclusive), based on solution x. */ - void updateThermo(const double* x, size_t j0, size_t j1) { + virtual void updateThermo(const double* x, size_t j0, size_t j1) { for (size_t j = j0; j <= j1; j++) { setGas(x,j); m_rho[j] = m_thermo->density(); @@ -384,16 +907,32 @@ class StFlow : public Domain1D } } + //-------------------------------- + // central-differenced derivatives + //-------------------------------- + double cdif1(const double*x, size_t n, size_t j) const { + double c1 = (x[index(n,j+1)] - x[index(n,j-1)]); + return c1/(z(j+1) - z(j-1)); + } + + //! seems unused + double cdif2(const double* x, size_t n, size_t j, + const double* f) const { + double c1 = (f[j] + f[j-1])*(x[index(n,j)] - x[index(n,j-1)]); + double c2 = (f[j+1] + f[j])*(x[index(n,j+1)] - x[index(n,j)]); + return (c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + //! @name Solution components //! @{ - double T(const double* x, size_t j) const { + virtual double T(const double* x, size_t j) const { return x[index(c_offset_T, j)]; } - double& T(double* x, size_t j) { + virtual double& T(double* x, size_t j) { return x[index(c_offset_T, j)]; } - double T_prev(size_t j) const { + virtual double T_prev(size_t j) const { return prevSoln(c_offset_T, j); } @@ -416,18 +955,32 @@ class StFlow : public Domain1D return x[index(c_offset_L, j)]; } - double Y(const double* x, size_t k, size_t j) const { + virtual double Y(const double* x, size_t k, size_t j) const { return x[index(c_offset_Y + k, j)]; } - double& Y(double* x, size_t k, size_t j) { + virtual double& Y(double* x, size_t k, size_t j) { return x[index(c_offset_Y + k, j)]; } - double Y_prev(size_t k, size_t j) const { + virtual double Y_prev(size_t k, size_t j) const { return prevSoln(c_offset_Y + k, j); } + //Soot + double Ys(const double* x, size_t k, size_t j) const { + return x[index(c_offset_S+k, j)]; + } + + double& Ys(double* x, size_t k, size_t j) { + return x[index(c_offset_S+k, j)]; + } + + double Ys_prev(size_t k, size_t j) const { + return prevSoln(c_offset_S + k, j); + } + //---- + double X(const double* x, size_t k, size_t j) const { return m_wtm[j]*Y(x,k,j)/m_wt[k]; } @@ -451,6 +1004,12 @@ class StFlow : public Domain1D return (Y(x,k,jloc) - Y(x,k,jloc-1))/m_dz[jloc-1]; } + // Soot + double dYsdz(const double* x, size_t k, size_t j) const { + size_t jloc = (u(x,j) > 0.0 ? j : j + 1); + return (Ys(x,k,jloc) - Ys(x,k,jloc-1))/m_dz[jloc-1]; + } + double dTdz(const double* x, size_t j) const { size_t jloc = (u(x,j) > 0.0 ? j : j + 1); return (T(x,jloc) - T(x,jloc-1))/m_dz[jloc-1]; @@ -469,12 +1028,19 @@ class StFlow : public Domain1D return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); } + double AVBPdivHeatFlux(const double* x, size_t j) const { + double c1 = avbp_thick[j-1]*m_tcon[j-1]*(T(x,j) - T(x,j-1)); + double c2 = avbp_thick[j]*m_tcon[j]*(T(x,j+1) - T(x,j)); + return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + size_t mindex(size_t k, size_t j, size_t m) { return m*m_nsp*m_nsp + m_nsp*j + k; } //! Update the diffusive mass fluxes. virtual void updateDiffFluxes(const double* x, size_t j0, size_t j1); + virtual void updateSootDiffFluxes(const double* x, size_t j0, size_t j1); //! Get the gradient of species specific molar enthalpies virtual void grad_hk(const double* x, size_t j); @@ -492,11 +1058,18 @@ class StFlow : public Domain1D vector m_rho; vector m_wtm; + // P. Wolf + vector m_zmixfrac; + + vector m_cpm; + vector m_h; + // species thermo properties vector m_wt; vector m_cp; // transport properties + vector m_ybar; vector m_visc; vector m_tcon; vector m_diff; @@ -511,14 +1084,20 @@ class StFlow : public Domain1D Array2D m_dhk_dz; // production rates + vector m_hr; Array2D m_wdot; size_t m_nsp; //!< Number of species in the mechanism + size_t m_neq; //!< Number of non-species equations + size_t m_nsoot; + std::string m_fuel; ThermoPhase* m_thermo = nullptr; Kinetics* m_kin = nullptr; Transport* m_trans = nullptr; + MultiJac* m_jac = nullptr; + // boundary emissivities for the radiation calculations double m_epsilon_left = 0.0; double m_epsilon_right = 0.0; @@ -527,6 +1106,20 @@ class StFlow : public Domain1D //! for CO2, second is for H2O. vector m_kRadiating; + // Pierre WOLF: added parameters for input_pea.dat + size_t avbp_ipea = 0; + std::string avbp_fuel; + vector avbp_pea_coeffs; + double phi_cst; + + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + // B. Franzelli modifications to perform thickening + // input_chem parameters + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + double avbp_fthick; + vector avbp_thick; + double m_thick = 1.0; + // flags vector m_do_energy; bool m_do_soret = false; @@ -539,6 +1132,96 @@ class StFlow : public Domain1D //! radiative heat loss vector vector m_qdotRadiation; + // ---------------------- + // SOOT RELATED VARIABLES + // ---------------------- + bool m_do_soot_soret = true; + bool m_do_condensation = false; + bool m_do_soot_radiation = false; + bool m_do_coagulation = false; + std::string m_soot_morphology; + bool m_do_retroaction = false; + bool m_do_sg = false; + bool m_do_oxidation = false; + bool m_trash_section = false; + std::string m_collision_model = "rodrigues"; + size_t soot_loglevel=1; + size_t c_offset_S = 6; + size_t n_PAH = 0; + size_t m_haca_model; + double Y_PAH; + double C_PAH; + double dTrashLowLim; + vector W_PAH; + double W_C; + vector n_C; + double N_dimer; + double beta_dimer; + double r_dimer; + double V_dimer; + double beta_fm; + double n_sites; + double kazakovTad; + double ksg; + double kox; + vector sootConsumption; + vector vSectMin; + vector vSectMax; + vector dSectMean; + vector dSectCol; + vector rSectCol; + vector aSectCol; + vector vSectMean; + vector sSectMean; + vector Dfractal; + vector kfractal; + vector nNucMean; + vector rNucMean; + vector rSmolMean; + vector PAMean; + vector m_qdotNucleation; + Array2D m_qdotCondensation; + Array2D m_qdotCoagulation; + Array2D m_qdotSg; + Array2D m_qdotOxidation; + vector q; + vector theta_surf; + vector jpower; + vector kpower; + vector mpower; + vector vc2power; + vector vc2powerm; + vector vmax_kpower; + vector vmin_kpower; + vector vmax_jpower; + vector vmin_jpower; + vector vmax_mpower; + vector vmin_mpower; + vector vmaxmc2_kpower; + vector vminpc2_kpower; + vector vmaxmc2_jpower; + vector vminpc2_jpower; + vector vmaxmc2_mpower; + vector vminpc2_mpower; + vector vc2powervect; + vector vc2powermvect; + vector m_section_name; + vector m_precursors; + Array2D m_soot_diff ; + Array2D m_soot_soret ; + Array2D collision_mat; + //Surface reactions + double ak00f, nk00f, ek00f, ak01f, nk01f, ek01f, ak02f, nk02f, ek02f, + ak03f, nk03f, ek03f, ak04f, nk04f, ek04f, ak05f, nk05f, ek05f, + ak06f, nk06f, ek06f, ak07f, nk07f, ek07f; + double ak00b, nk00b, ek00b, ak01b, nk01b, ek01b, ak02b, nk02b, ek02b, + ak03b, nk03b, ek03b, ak04b, nk04b, ek04b, ak05b, nk05b, ek05b, + ak06b, nk06b, ek06b, ak07b, nk07b, ek07b; + double gamma_oh; + // ----------------------------- + // END OF SOOT RELATED VARIABLES + // ----------------------------- + // fixed T and Y values vector m_fixedtemp; vector m_zfix; @@ -565,8 +1248,8 @@ class StFlow : public Domain1D //! Temperature at the point used to fix the flame location double m_tfixed = -1.0; -private: - vector m_ybar; +// private: +// vector m_ybar; }; } diff --git a/include/cantera/oneD/refine.h b/include/cantera/oneD/refine.h index 59261f10041..19fb85807ff 100644 --- a/include/cantera/oneD/refine.h +++ b/include/cantera/oneD/refine.h @@ -71,6 +71,13 @@ class Domain1D; int analyze(size_t n, const double* z, const double* x); int getNewGrid(int n, const double* z, int nn, double* znew); + + double remeshFromSolution(int np, const double* z, const double* x, const double dist_min=1e9, const double domain_size=50.0); //from MUTAGEN + + int indxtp(int np,double val,const double* array); //from MUTAGEN + + void getRatio(int np, const double* z, double* x); //from MUTAGEN + int nNewPoints() { return static_cast(m_loc.size()); } @@ -81,6 +88,29 @@ class Domain1D; bool keepPoint(size_t j) { return (m_keep[j] != -1); } + + + double z_new(const int m) //from MUTAGEN + { + return m_z_new[m]; + } + + int z_new_size() //from MUTAGEN + { + return m_z_new.size(); + } + + double grad_max() //from MUTAGEN + { + return m_grad_max; + } + + double curve_max() //from MUTAGEN + { + return m_curve_max; + } + + double value(const double* x, size_t i, size_t j); double maxRatio() { @@ -111,6 +141,8 @@ class Domain1D; Domain1D* m_domain; size_t m_nv; size_t m_npmax = 1000; + vector m_z_new; //from MUTAGEN + double m_grad_max, m_curve_max; //from MUTAGEN double m_thresh = std::sqrt(std::numeric_limits::epsilon()); double m_gridmin = 1e-10; //!< minimum grid spacing [m] }; diff --git a/include/cantera/transport/AVBPTransport.h b/include/cantera/transport/AVBPTransport.h new file mode 100644 index 00000000000..f6680b4b2ed --- /dev/null +++ b/include/cantera/transport/AVBPTransport.h @@ -0,0 +1,120 @@ +/** + * + * @file AVBPTransport.h + * Header file defining class AVBPTransport which implements + * the simplified transport model used in the solver AVBP + */ + +/* $Author: B. Franzelli (v. 1.7) $ + * $Revision: A. Felden (v 2.1-2.3) $ + * $Date: 01/2018 $ + */ + + +#ifndef CT_AVBPTRAN_H +#define CT_AVBPTRAN_H + +#include "GasTransport.h" +#include "cantera/numerics/DenseMatrix.h" + +// STL includes +#include +#include +#include +#include +#include + +namespace Cantera +{ + +// class GasTransportParams; + +/** + * Class AVBPTransport + * Constant Sch for each species, Pr, and simplified viscosity + */ +class AVBPTransport : public GasTransport +{ + +public: + //! Default constructor. + AVBPTransport() = default; + + //! Return the model id for transport + /*! + * @return cAVBPAverage + */ + // virtual int model() const { + // warn_deprecated("AVBPTransport::model", + // "To be removed after Cantera 2.3."); + // return cAVBPTransport; + // } + string transportModel() const override { + return (m_mode == CK_Mode) ? "AVBP-CK" : "AVBP"; + } + // virtual std::string transportType() const { + // return "AVBP"; + // } + + //! Return the thermal diffusion coefficients + //virtual void getThermalDiffCoeffs(double* const dt); + + //! Returns the mixture thermal conductivity + double thermalConductivity() override; + + //! Get the Electrical mobilities (m^2/V/s). + //virtual void getMobilities(double* const mobil); + + //! Update the internal parameters whenever the temperature has changed + void update_T() override; + + //! Update the internal parameters whenever the concentrations have changed + void update_C() override; + + //virtual void getSpeciesFluxes(size_t ndim, + // const double* const grad_T, + // size_t ldx, + // const double* const grad_X, + // size_t ldf, double* const fluxes); + + //! Initialize the transport object + //virtual bool initGas(GasTransportParams& tr); + void init(ThermoPhase* thermo, int mode=0, int log_level=0) override; + + //! Viscosity of the mixture + virtual double viscosity(); + + virtual void getSpeciesViscosities(double* const visc) { + update_T(); + updateViscosity_T(); + std::copy(m_visc.begin(), m_visc.end(), visc); + } + + //! Mixture diffusion coefficients [m^2/s]. + virtual void getMixDiffCoeffs(double* const d); + + virtual void read_mixture(std::string s); + + size_t avbp_ipea; + vector avbp_pea_coeffs; + +protected: + + //! Calculate the pressure from the ideal gas law + double pressure_ig(); + + double m_lambda; + //bool m_debug; + + // AVBP variables + vector avbp_Sch; + vector avbp_Le; + double avbp_Prandtl; + double avbp_mu0; + double avbp_T0; + double avbp_beta; + std::string avbp_fuel; + +}; +} +#endif From 08696f03bdae8d7366dc6de52ca47230b573c915 Mon Sep 17 00:00:00 2001 From: pestre Date: Fri, 17 Jan 2025 12:43:31 +0100 Subject: [PATCH 03/98] Change refine_grid param type to string Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: modified: include/cantera/clib/ctonedim.h modified: include/cantera/oneD/Sim1D.h --- include/cantera/clib/ctonedim.h | 2 +- include/cantera/oneD/Sim1D.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/include/cantera/clib/ctonedim.h b/include/cantera/clib/ctonedim.h index 33f14c17f1a..9b92765e17f 100644 --- a/include/cantera/clib/ctonedim.h +++ b/include/cantera/clib/ctonedim.h @@ -78,7 +78,7 @@ extern "C" { CANTERA_CAPI int sim1D_showSolution(int i, const char* fname); CANTERA_CAPI int sim1D_setTimeStep(int i, double stepsize, size_t ns, const int* nsteps); CANTERA_CAPI int sim1D_getInitialSoln(int i); - CANTERA_CAPI int sim1D_solve(int i, int loglevel, int refine_grid); + CANTERA_CAPI int sim1D_solve(int i, int loglevel, const char* refine_grid); CANTERA_CAPI int sim1D_refine(int i, int loglevel); CANTERA_CAPI int sim1D_setRefineCriteria(int i, int dom, double ratio, double slope, double curve, double prune); diff --git a/include/cantera/oneD/Sim1D.h b/include/cantera/oneD/Sim1D.h index 54c98ef72e2..3a900e8d9ab 100644 --- a/include/cantera/oneD/Sim1D.h +++ b/include/cantera/oneD/Sim1D.h @@ -227,7 +227,7 @@ class Sim1D : public OneDim void setTimeStep(double stepsize, size_t n, const int* tsteps); - void solve(int loglevel = 0, bool refine_grid = true); + void solve(int loglevel = 0, const string& refine_grid = "refine"); void eval(double rdt=-1.0, int count = 1) { OneDim::eval(npos, m_state->data(), m_xnew.data(), rdt, count); From 20ede9dafe69bad69e206f976ad85344b457395a Mon Sep 17 00:00:00 2001 From: pestre Date: Fri, 17 Jan 2025 13:35:01 +0100 Subject: [PATCH 04/98] Merge differences in interfaces directory Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: modified: interfaces/cython/cantera/_onedim.pxd modified: interfaces/cython/cantera/_onedim.pyx modified: interfaces/cython/cantera/composite.py modified: interfaces/cython/cantera/cti2yaml.py modified: interfaces/cython/cantera/kinetics.pxd modified: interfaces/cython/cantera/kinetics.pyx modified: interfaces/cython/cantera/onedim.py modified: interfaces/cython/setup.cfg.in modified: interfaces/python_minimal/setup.cfg.in modified: interfaces/python_sdist/SConscript modified: interfaces/python_sdist/pyproject.toml modified: interfaces/python_sdist/setup.cfg.in modified: interfaces/python_sdist/setup.py modified: interfaces/sourcegen/sourcegen/_orchestrate.py --- interfaces/cython/cantera/_onedim.pxd | 75 +- interfaces/cython/cantera/_onedim.pyx | 626 +++++++++++++++- interfaces/cython/cantera/composite.py | 5 + interfaces/cython/cantera/cti2yaml.py | 7 +- interfaces/cython/cantera/kinetics.pxd | 2 + interfaces/cython/cantera/kinetics.pyx | 7 + interfaces/cython/cantera/onedim.py | 957 ++++++++++++++++++++++++- 7 files changed, 1636 insertions(+), 43 deletions(-) diff --git a/interfaces/cython/cantera/_onedim.pxd b/interfaces/cython/cantera/_onedim.pxd index a2af11c7a4b..68d12423349 100644 --- a/interfaces/cython/cantera/_onedim.pxd +++ b/interfaces/cython/cantera/_onedim.pxd @@ -13,7 +13,7 @@ from .thermo cimport * cdef extern from "cantera/oneD/DomainFactory.h" namespace "Cantera": cdef shared_ptr[CxxDomain1D] CxxNewDomain1D "newDomain" ( - string, shared_ptr[CxxSolution], string) except +translate_exception + string, shared_ptr[CxxSolution], string, size_t) except +translate_exception cdef extern from "cantera/oneD/Domain1D.h": @@ -38,6 +38,7 @@ cdef extern from "cantera/oneD/Domain1D.h": double transient_atol(size_t) double grid(size_t) void setupGrid(size_t, double*) except +translate_exception + void setupGrid(size_t) except +translate_exception void setID(string) string& id() string domainType "type"() @@ -85,16 +86,76 @@ cdef extern from "cantera/oneD/StFlow.h": void setBoundaryEmissivities(double, double) double leftEmissivity() double rightEmissivity() + void setThick(double) + double getThick() void solveEnergyEqn() void fixTemperature() cbool doEnergy(size_t) void enableSoret(cbool) except +translate_exception cbool withSoret() + # void setzSt(double) + # void setChiSt(double) + void setSections(size_t) + # double chiSt() + # double zSt() + size_t getSections() + void setFreeFlow() void setAxisymmetricFlow() + void setFlameletFlow() string flowType() + void setPrecursors(vector[size_t]&) + void showSootSections() + void setSootSoret(cbool) + void enableCondensation(cbool) + cbool condensationEnabled() + void enableCoagulation(cbool) + cbool coagulationEnabled() + void setCollisionModel(string) + string getCollisionModel() + void enableRetroaction(cbool) + cbool retroactionEnabled() + void setSootMorphology(string) + cbool getSootMorphology() + void enableSurfaceGrowth(cbool) + cbool surfaceGrowthEnabled() + void enableOxidation(cbool) + cbool oxidationEnabled() + void enableSootRadiation(cbool) + cbool sootRadiationEnabled() + void enableSootSoret(cbool) + cbool sootSoretEnabled() + void enableTrashSection(double) + cbool trashSectionEnabled() + void finalizeSoot() + size_t getHaca() + void setHaca(size_t) + double getKazakovTad() + void setKazakovTad(double) + size_t getSootLoglevel() + void setSootLoglevel(size_t) + + vector[double]& vMin() + vector[double]& vMax() + vector[double]& vMean() + vector[double]& dMean() + vector[double]& sMean() + vector[double]& dCol() + vector[double]& aCol() + vector[double]& thetaSoot() + vector[double]& fractalPrefactor() + vector[double]& fractalDimension() + double sootPrimaryPart(size_t) + double sootPrimaryDiam(size_t) + double rhoSoot() + double getSootInception(size_t) + double getSootCondensation(size_t, size_t) + double getSootCoagulation(size_t, size_t) + double getSootSg(size_t, size_t) + double getSootOxidation(size_t, size_t) + cdef extern from "cantera/oneD/Sim1D.h": cdef cppclass CxxSim1D "Cantera::Sim1D": CxxSim1D(vector[shared_ptr[CxxDomain1D]]&) except +translate_exception @@ -108,7 +169,7 @@ cdef extern from "cantera/oneD/Sim1D.h": void setMaxTimeStepCount(int) int maxTimeStepCount() void getInitialSoln() except +translate_exception - void solve(int, cbool) except +translate_exception + void solve(int, string&) except +translate_exception void refine(int) except +translate_exception void setRefineCriteria(size_t, double, double, double, double) except +translate_exception vector[double] getRefineCriteria(int) except +translate_exception @@ -149,6 +210,13 @@ cdef extern from "cantera/oneD/Sim1D.h": cdef extern from "cantera/thermo/IdealGasPhase.h": cdef cppclass CxxIdealGasPhase "Cantera::IdealGasPhase" +cdef extern from "cantera/oneD/Flamelet.h": + cdef cppclass CxxFlamelet "Cantera::Flamelet" (CxxStFlow): + CxxFlamelet(CxxStFlow*) + double chiSt() #except +translate_exception + double zSt() #except +translate_exception + void setChiSt(double) #except +translate_exception + void setzSt(double) #except +translate_exception cdef class Domain1D: cdef shared_ptr[CxxDomain1D] _domain @@ -168,6 +236,9 @@ cdef class ReactingSurface1D(Boundary1D): cdef class _FlowBase(Domain1D): cdef CxxStFlow* flow +cdef class FlameletFlow(_FlowBase): + cdef CxxFlamelet* flamelet + cdef class Sim1D: cdef CxxSim1D* sim cdef readonly object domains diff --git a/interfaces/cython/cantera/_onedim.pyx b/interfaces/cython/cantera/_onedim.pyx index e1337732e8b..019b1b4cf49 100644 --- a/interfaces/cython/cantera/_onedim.pyx +++ b/interfaces/cython/cantera/_onedim.pyx @@ -313,11 +313,14 @@ cdef class Boundary1D(Domain1D): self.boundary = NULL else: self._domain = CxxNewDomain1D( - stringify(self._domain_type), phase._base, stringify(name)) + stringify(self._domain_type), phase._base, stringify(name), + #add kwargs if kwargs provided + kwargs['sections'] if 'sections' in kwargs else 0, + ) self.domain = self._domain.get() self.boundary = self.domain - def __init__(self, phase, name=None): + def __init__(self, phase, name=None, **kwargs): if self.boundary is NULL: raise TypeError("Can't instantiate abstract class Boundary1D.") Domain1D.__init__(self, phase, name=name) @@ -430,7 +433,10 @@ cdef class ReactingSurface1D(Boundary1D): self.surf = new CxxReactingSurf1D() self.domain = (self.surf) else: - self._domain = CxxNewDomain1D(stringify(self._domain_type), phase._base, stringify(name)) + self._domain = CxxNewDomain1D(stringify(self._domain_type), phase._base, stringify(name), + #add kwargs if kwargs provided + kwargs['sections'] if 'sections' in kwargs else 0, + ) self.domain = self._domain.get() self.surf = self.domain self.boundary = (self.surf) @@ -499,7 +505,10 @@ cdef class _FlowBase(Domain1D): """ Base class for 1D flow domains """ def __cinit__(self, _SolutionBase phase, *args, name="", **kwargs): self._domain = CxxNewDomain1D( - stringify(self._domain_type), phase._base, stringify(name)) + stringify(self._domain_type), phase._base, stringify(name), + #add kwargs if kwargs provided + kwargs['sections'] if 'sections' in kwargs else 0, + ) self.domain = self._domain.get() self.flow = self.domain @@ -710,6 +719,543 @@ cdef class _FlowBase(Domain1D): data[j] = self.flow.radiativeHeatLoss(j) return data + # BEGIN of soot API + + property soot_loglevel: + """ + Outputs soot sections informations. + + :param None + + :return None + """ + def __set__(self, loglevel): + self.flow.setSootLoglevel(loglevel) + def __get__(self): + return self.flow.getSootLoglevel() + + property soot_sections: + """ + Returns number of soot sections. + + :param None + + :return int : + Number of sections + """ + def __set__(self, nSec): + #self.flow.setSections(nSec) + raise KeyError ('/!\ SOOT ERROR : You cannot set sections number this way !') + def __get__(self): + return self.flow.getSections() + + property soot_precursors: + """ + Sets soot precursors. + + : param precrursors = list[str] : + precursors names (in mechanism nomenclature) + + : return None + """ + def __set__(self, precursors): + cdef vector[size_t] id_precursors + if isinstance(precursors, str): + precursors = [precursors] + av_precursors = [precursor for precursor in precursors if precursor in self.gas.species_names] + id_precursors = [self.component_index(precursor) for precursor in av_precursors] + if len(id_precursors) == 0: + raise KeyError('/!\ SOOT ERROR : No acceptable precursors !') + else: + self.flow.setPrecursors(id_precursors) + def __get__(self): + raise NotImplementedError('Getter not implemented yet.') + + property soot_trash_section: + """ + Gets / sets trash section size (<0 if disabled). + + : param trash_section = float : + trash section size [m] + + : return bool : + trash section enabled + """ + def __set__(self, trash_section): + self.flow.enableTrashSection(trash_section) + def __get__(self): + return self.flow.trashSectionEnabled() + + property soot_do_retroaction: + """ + Gets / sets whether retroaction on gas phase is activated or not. + + : param do_retroaction = bool : + reatroaction enabled + + : return bool : + retroaction enabled + """ + def __set__(self, do_retroaction): + self.flow.enableRetroaction(do_retroaction) + def __get__(self): + return self.flow.retroactionEnabled() + + property soot_do_condensation: + """ + Gets / sets whether dimer condensation on soot particles is activated or not. + + : param do_condensation = bool : + condensation enabled + + : return bool : + condensation enabled + """ + def __set__(self, do_condensation): + self.flow.enableCondensation(do_condensation) + def __get__(self): + return self.flow.condensationEnabled() + + property soot_do_coagulation: + """ + Gets / sets whether coagulation between soot particles is activated or not. + + : param do_coagulation = bool : + coagulation enabled + + : return bool : + coagulation enabled + """ + def __set__(self, do_coagulation): + self.flow.enableCoagulation(do_coagulation) + def __get__(self): + return self.flow.coagulationEnabled() + + property soot_morphology: + """ + """ + def __set__(self, morphology_model): + self.flow.setSootMorphology(stringify(morphology_model)) + def __get__(self): + self.flow.getSootMorphology() + + property soot_collision_model: + """ + Gets / sets whether coagulation between soot particles is activated or not. + + : return str : + coagulation enabled + """ + def __set__(self, collision_model): + self.flow.setCollisionModel(stringify(collision_model)) + def __get__(self): + return self.flow.getCollisionModel() + + property soot_haca: + """ + Gets / sets haca model. + : param haca_model = str or int : + "mauss" : 1 + "blanquart" : 2 + "kazakov" : 3 + "mauss tuned" : 11 + : return int : + haca model + """ + def __set__(self, haca_model): + haca = 0 + if haca_model in [1, 'mauss']: + haca = 1 + if haca_model in [11, 'mauss tuned']: + haca = 11 + elif haca_model in [2, 'blanquart']: + haca = 2 + elif haca_model in [3, 'kazakov']: + haca = 3 + if haca not in [1,11,2,3]: + raise KeyError ('/!\ SOOT ERROR : haca_model must be mauss(1), mauss tuned(11), blanquart(2), or kazakov(3)') + self.flow.setHaca(haca) + def __get__(self): + return self.flow.getHaca() + + property soot_do_surface_growth: + """ + Gets / sets whether acetylene condensation on soot particles is activated or not. + + : param do_surface_growth = bool : + surface growth enabled + + : return bool : + surface growth enabled + """ + def __set__(self, do_surface_growth): + self.flow.enableSurfaceGrowth(do_surface_growth) + def __get__(self): + return self.flow.surfaceGrowthEnabled() + + property soot_do_oxidation: + """ + Gets / sets whether soot particles oxidation is activated or not. + + : param do_oxidation = bool : + oxidation enabled + + : return bool : + oxidation enabled + """ + def __set__(self, do_oxidation): + self.flow.enableOxidation(do_oxidation) + def __get__(self): + return self.flow.oxidationEnabled() + + property kazakov_flame_temperature : + """ + Gets / sets flame temperature used as reference for Kazakov's surface reactions model + + : param adiabatic_temperature = double : + adiabatic temperature (K) + + : return double : + adiabatic temperature (K) + """ + def __set__(self, tad): + self.flow.setKazakovTad(tad) + def __get__(self): + return self.flow.getKazakovTad() + + property soot_do_radiation: + """ + Gets / sets whether soot particles radiative heat losses are considered or not. + + : param do_soot_radiation = bool : + soot radiation enabled + + : return bool : + soot radiation enabled + """ + def __set__(self,do_soot_radiation): + if not self.energy_enabled and do_soot_radiation: + if self.soot_loglevel >= 1: + print(' ') + print('SOOT INFO : Energy equation is disabled') + print(" ==> RHL won't be computed") + self.radiation_enabled = False + if not self.radiation_enabled and do_soot_radiation: + if self.soot_loglevel >= 1: + print(' ') + print('SOOT INFO : RHL were disabled') + print(" ==> RHL now enabled") + self.radiation_enabled = True + self.flow.enableSootRadiation(do_soot_radiation) + def __get__(self): + return self.flow.sootRadiationEnabled() + + property soot_do_soret: + """ + Gets / sets whether soret effect is computed on soot particles. + + : param do_soot_soret = bool : + soot soret enabled + + : return bool : + soot soret enabled + """ + def __set__(self,do_soot_soret): + self.flow.enableSootSoret(do_soot_soret) + def __get__(self): + return self.flow.sootSoretEnabled() + + property soot_finalize: + """ + Generates sections, collision matrix and loads surface reactions constants if needed. + To be used after modifications on : collision model, precursors, oxidation or surface growth. + + : param None + + : return None + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return self.flow.finalizeSoot() + + + property sections_min_v: + """" + Gets soot sections minimal volumes. + + : param None + + : return (sections) numpy array : + minimal volume of each section [m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.vMin()) + + property sections_max_v: + """" + Gets soot sections maximal volumes. + + : param None + + : return (sections) numpy array : + maximal volume of each section [m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.vMax()) + + property sections_mean_v: + """" + Gets soot sections mean volumes. + + : param None + + : return (sections) numpy array : + mean volume of each section [m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.vMean()) + + property sections_mean_d: + """" + Gets soot sections mean diameters. + + : param None + + : return (sections) numpy array : + mean diameter of each section [m] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.dMean()) + + property sections_col_d: + """" + Gets soot sections colision diameters. + + : param None + + : return (sections) numpy array : + colision diameter of each section [m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.dCol()) + + property sections_col_a: + """" + Gets soot sections collisional cross-section + + : param None + + : return (sections) numpy array : + mean section of each section [m-2] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.aCol()) + + property sections_mean_s: + """" + Gets soot sections surface area + + : param None + + : return (sections) numpy array : + mean section of each section [m-2] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.sMean()) + + property sections_fractal_prefactor: + """ + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.fractalPrefactor()) + + property sections_fractal_dimension: + """ + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.fractalDimension()) + + property sections_theta: + """ + Gets soot sections theta value (fractality). + + : param None + + : return (sections) numpy array : + theta factor of each section + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.thetaSoot()) + + property soot_density: + """" + Gets soot density. + + : param None + + : return float : + soot density [kg.m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return self.flow.rhoSoot() + + # property soot_dump_inception: + # """ + # Gets soot nucleation source terms. + + # : param None + + # : return (sections x points) numpy array : + # inception source terms [s-1] + # """ + # def __set__(self, dummy): + # raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + # def __get__(self): + # data = np.zeros((self.soot_sections, self.n_points)) + # for j in range(self.n_points): + # data[0,j] = self.flow.getSootInception(j) + # return data + + property soot_dump_condensation: + """ + Gets soot condensation source terms. + + : param None + + : return (sections x points) numpy array : + condensation source terms [s-1] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty((self.soot_sections, self.n_points)) + for k in range(self.soot_sections): + for j in range(self.n_points): + data[k,j] = self.flow.getSootCondensation(k,j) + return data + + property soot_dump_coagulation: + """ + Gets soot coagulation source terms. + + : param None + + : return (sections x points) numpy array : + coagulation source terms [s-1] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty((self.soot_sections, self.n_points)) + for k in range(self.soot_sections): + for j in range(self.n_points): + data[k,j] = self.flow.getSootCoagulation(k,j) + return data + + property soot_dump_surface_growth: + """ + Gets soot surface growth source terms. + + : param None + + : return (sections x points) numpy array : + surface growth source terms [s-1] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty((self.soot_sections, self.n_points)) + for k in range(self.soot_sections): + for j in range(self.n_points): + data[k,j] = self.flow.getSootSg(k,j) + return data + + property soot_dump_oxidation: + """ + Gets soot oxidation source terms. + + : param None + + : return (sections x points) numpy array : + oxidation source terms [s-1] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty((self.soot_sections, self.n_points)) + for k in range(self.soot_sections): + for j in range(self.n_points): + data[k,j] = self.flow.getSootOxidation(k,j) + return data + + property sections_np: + """ + Gets number of primary particles per aggregate. + + : param None + + : return (sections) numpy array : + number of primary particles per aggregate + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty(self.soot_sections) + for k in range(self.soot_sections): + data[k] = self.flow.sootPrimaryPart(k) + return data + + property sections_dp: + """ + Gets primary particles diameter. + + : param None + + : return (sections) numpy array : + primary particles diameter [m] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty(self.soot_sections) + for k in range(self.soot_sections): + data[k] = self.flow.sootPrimaryDiam(k) + return data + + # END of soot API + + property thick: + """ + Thickening that will be applied [JW] + """ + def __set__(self, thickness): + self.flow.setThick(thickness) + def __get__(self): + return self.flow.getThick() + def set_free_flow(self): """ Set flow configuration for freely-propagating flames, using an internal @@ -725,6 +1271,13 @@ cdef class _FlowBase(Domain1D): """ self.flow.setAxisymmetricFlow() + def set_flamelet_flow(self): + """ + Set flow configuration for flamelet solutions, using specified inlet + mass fluxes. + """ + self.flow.setFlameletFlow() + property flow_type: """ Return the type of flow domain being represented, either "Free Flame" or @@ -795,6 +1348,37 @@ cdef class FreeFlow(_FlowBase): _domain_type = "free-flow" +cdef class FlameletFlow(_FlowBase): + """A flamelet flow domain. The equations solved are standard equations for + adiabatic one-dimensional flow in Z-space. The solution variables are: + + *T* + temperature + + *Y_k* + species mass fractions + + """ + _domain_type = "flamelet-flow" + + def __cinit__(self, _SolutionBase phase, *args, name="", **kwargs): + self.flamelet = self.flow + + property ChiSt: + """ ChiSt """ + def __get__(self): + return self.flamelet.chiSt() + def __set__(self, val): + self.flamelet.setChiSt(val) + + property ZSt: + """ ZSt """ + def __get__(self): + return self.flamelet.zSt() + def __set__(self, val): + self.flamelet.setzSt(val) + + cdef class UnstrainedFlow(_FlowBase): r"""An unstrained flow domain. The equations solved are standard equations for adiabatic one-dimensional flow. The solution variables are: @@ -1226,8 +1810,8 @@ cdef class Sim1D: def show(self): """ print the current solution. """ - if not self._initialized: - self.set_initial_guess() + # if not self._initialized: + # self.set_initial_guess() self.sim.show() def show_solution(self): @@ -1289,7 +1873,7 @@ cdef class Sim1D: """ return False - def solve(self, loglevel=1, refine_grid=True, auto=False): + def solve(self, loglevel=1, refine_grid='refine', auto=False): """ Solve the problem. @@ -1297,7 +1881,8 @@ cdef class Sim1D: integer flag controlling the amount of diagnostic output. Zero suppresses all output, and 5 produces very verbose output. :param refine_grid: - if True, enable grid refinement. + if "refine", enable grid refinement, + if "remesh", remeshing of the grid. :param auto: if True, sequentially execute the different solution stages and attempt to automatically recover from errors. Attempts to first solve on the initial grid with energy enabled. If that does not @@ -1308,10 +1893,19 @@ cdef class Sim1D: will be calculated. """ + if type(refine_grid) == bool: + print("WARNING : Keyword status has been changed to string to enable the remesh feature") + print("True --> 'refine' or 'remesh'") + print("False --> 'disabled'") + if refine_grid: + refine_grid = 'refine' + else: + refine_grid = 'disabled' + if not auto: if not self._initialized: self.set_initial_guess() - self.sim.solve(loglevel, refine_grid) + self.sim.solve(loglevel, stringify(refine_grid)) return def set_transport(multi): @@ -1385,7 +1979,7 @@ cdef class Sim1D: log('Solving on {} point grid with energy equation enabled', N) self.energy_enabled = True try: - self.sim.solve(loglevel, False) + self.sim.solve(loglevel, stringify('disabled')) solved = True except CanteraError as e: log(str(e)) @@ -1407,7 +2001,7 @@ cdef class Sim1D: log('Initial solve failed; Retrying with energy equation disabled') self.energy_enabled = False try: - self.sim.solve(loglevel, False) + self.sim.solve(loglevel, stringify('disabled')) solved = True except CanteraError as e: log(str(e)) @@ -1423,7 +2017,7 @@ cdef class Sim1D: log('Solving on {} point grid with energy equation re-enabled', N) self.energy_enabled = True try: - self.sim.solve(loglevel, False) + self.sim.solve(loglevel, stringify('disabled')) solved = True except CanteraError as e: log(str(e)) @@ -1435,11 +2029,11 @@ cdef class Sim1D: restore_tolerances() raise e - if solved and not self.extinct() and refine_grid: + if solved and not self.extinct() and refine_grid != 'disabled': # Found a non-extinct solution on the fixed grid log('Solving with grid refinement enabled') try: - self.sim.solve(loglevel, True) + self.sim.solve(loglevel, stringify('refine')) solved = True except CanteraError as e: log(str(e)) @@ -1458,7 +2052,7 @@ cdef class Sim1D: if self.extinct(): log('Flame is extinct on {} point grid', N) - if not refine_grid: + if refine_grid == 'disabled': break if not solved: @@ -1478,7 +2072,7 @@ cdef class Sim1D: # Final call with expensive options enabled if have_user_tolerances or solve_multi or soret_doms: - self.sim.solve(loglevel, refine_grid) + self.sim.solve(loglevel, stringify('refine')) def refine(self, loglevel=1): """ diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py index 19ec4926670..fa879ece2fe 100644 --- a/interfaces/cython/cantera/composite.py +++ b/interfaces/cython/cantera/composite.py @@ -7,6 +7,11 @@ import csv as _csv import importlib.metadata import warnings +import shutil +import filecmp +import subprocess +import time +import os _h5py = None def _import_h5py(): diff --git a/interfaces/cython/cantera/cti2yaml.py b/interfaces/cython/cantera/cti2yaml.py index d8d5a282e6a..1f70b5d6fe2 100644 --- a/interfaces/cython/cantera/cti2yaml.py +++ b/interfaces/cython/cantera/cti2yaml.py @@ -110,12 +110,17 @@ def applyUnits(value): 'GasKinetics': 'gas', 'Interface': 'surface', 'Edge': 'edge', + 'AVBP': 'AVBP', 'Mix': 'mixture-averaged', + 'mixture-averaged': 'mixture-averaged', 'Multi': 'multicomponent', + 'multicomponent': 'multicomponent', 'Ion': 'ionized-gas', 'molar_volume': 'species-molar-volume', 'solvent_volume': 'solvent-molar-volume', - 'unity': 'unity' + 'unity': 'unity', + 'UnityLewis': 'unity', + 'custom': 'custom', } # constants that can be used in .cti files diff --git a/interfaces/cython/cantera/kinetics.pxd b/interfaces/cython/cantera/kinetics.pxd index 48b2cfb23aa..cd22019b5b8 100644 --- a/interfaces/cython/cantera/kinetics.pxd +++ b/interfaces/cython/cantera/kinetics.pxd @@ -41,6 +41,8 @@ cdef extern from "cantera/kinetics/Kinetics.h" namespace "Cantera": void invalidateCache() except +translate_exception void resizeReactions() + void closeDynamicLib() except +translate_exception + shared_ptr[CxxReaction] reaction(size_t) except +translate_exception double reactantStoichCoeff(int, int) except +translate_exception double productStoichCoeff(int, int) except +translate_exception diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx index a445fa57306..fe8039c7da8 100644 --- a/interfaces/cython/cantera/kinetics.pyx +++ b/interfaces/cython/cantera/kinetics.pyx @@ -134,6 +134,13 @@ cdef class Kinetics(_SolutionBase): if not 0 <= n < self.n_total_species: raise ValueError("Kinetics Species index ({0}) out of range".format(n)) + def reset_custom(self): + """ + Function calling the dlclose in CustomKinetics + in order to close the dynamic library (handle) + """ + self.kinetics.closeDynamicLib() + def kinetics_species_index(self, species, int phase=0): """ The index of species ``species`` of phase ``phase`` within arrays returned diff --git a/interfaces/cython/cantera/onedim.py b/interfaces/cython/cantera/onedim.py index c5fda35099a..0f9679db0be 100644 --- a/interfaces/cython/cantera/onedim.py +++ b/interfaces/cython/cantera/onedim.py @@ -5,6 +5,8 @@ from pathlib import Path import warnings import numpy as np +import csv as _csv +import os from ._cantera import * from .composite import Solution, SolutionArray @@ -27,6 +29,7 @@ def __init__(self, domains, gas, grid=None): if grid is None: grid = np.linspace(0.0, 0.1, 6) self.flame.grid = grid + # self.flame.soot_sections = sections super().__init__(domains) #: The `Solution` object representing the species and reactions in the flame @@ -63,7 +66,7 @@ def other_components(self, domain=None): if isinstance(dom, Inlet1D): return tuple([e for e in self._other if e not in {'grid', 'lambda', 'eField'}]) - elif isinstance(dom, (FreeFlow, AxisymmetricFlow, IdealGasFlow)): + elif isinstance(dom, (FreeFlow, AxisymmetricFlow, IdealGasFlow, FlameletFlow)): return self._other else: return () @@ -273,6 +276,476 @@ def boundary_emissivities(self, epsilon): if len(epsilon) != 2: raise ValueError("Boundary emissivities must both be set at the same time.") self.flame.boundary_emissivities = epsilon[0], epsilon[1] + + # BEGIN of soot API + + def soot_setup(self, precursors=["A2"], condensation=True, coagulation=True, morphology='rodrigues', collision_model='rodrigues', + retroaction=True, haca_model = 'mauss', kazakov_temperature = 0, + surface_growth=True, oxidation=True, radiation=True, trash_section=-1.0, + loglevel = 2): + """ + Sets soot computation up. + + : param precursors = list[str] : + list of precursors in mechanism nomenclature (default : ['A2']) + : param condensation = bool : + condensation enabled (default : True) + : param coagulation = bool : + coagulation enabled (default : True) + : param retroaction = bool : + retroaction on gas phase enabled (default : True) + : param collision_model = str : + Collision model :sphere, rodrigues or thajudeen (default : rodrigues) + : param haca_model = string or int : + haca_model to use (default : Mauss) + 1 : Mauss + 11 : Mauss (tuned as Guo 2016) + 2 : Blanquart + 3 : Kazakov + : param suface_growth = bool : + surface growth enabled (default : True) + : param oxidation = bool : + oxidation enabled (default : True) + : param kazakov = double : + adiabatic flame temperature, only for Kazakov's haca model (default : 0 (automatically computed)) + : param radiation = bool : + soot radiative heat losses enabled (default : True) + : param trash_section = float : + trash section size, <=0 if no trash section (default : -1.0) + : param show_sections = bool : + show sections informations (default : False) + + : return None + """ + if self.flame.soot_sections == 0: + raise CanteraError('/!\ SOOT ERROR : cannot set sections properties (no sections)') + self.flame.soot_loglevel = loglevel + # Impacts geomery, need to use "flame.soot_finalize" + self.flame.soot_precursors = precursors + self.flame.soot_trash_section = trash_section + self.flame.soot_morphology = morphology + self.flame.soot_collision_model = collision_model + # Processes, need to use "flame.soot_finalize" + self.flame.soot_haca = haca_model + if self.flame.soot_haca == 3 : + if kazakov_temperature > 0: + self.flame.kazakov_flame_temperature = kazakov_temperature + else: + self.flame.kazakov_flame_temperature = self.adiabatic_flame_temperature + self.flame.soot_do_surface_growth = surface_growth + self.flame.soot_do_oxidation = oxidation + # Processes, do not impact geometry + self.flame.soot_do_retroaction = retroaction + self.flame.soot_do_condensation = condensation + self.flame.soot_do_coagulation = coagulation + self.flame.soot_do_radiation = radiation + self.flame.soot_finalize + + @property + def soot_Y(self): + """ + Gets soot mass fraction. + + : param None + + : return (sections x points) numpy array : + soot mass fraction for each section at each point + """ + data = np.empty((self.flame.soot_sections, self.flame.n_points)) + ns = self.flame.soot_sections + for k in range(ns): + data[k,:] = self.profile(self.flame, 'Ys'+str(k)) + return data + + @property + def soot_Q(self): + """ + + """ + Ys = self.soot_Y + density = self.density + soot_density = self.flame.soot_density + + data = np.empty(np.shape(Ys)) + for section in range(self.flame.soot_sections): + data[section,:] = density / soot_density * Ys[section,:] + + return data + + @property + def soot_q(self): + """" + Gets the volume distribution of the soot volume fraction + + : param None + + : return (sections x points) numpy array : + volume distribution of the soot volume fraction for each section at each point [m-3] + """ + Q = self.soot_Q + vMin = self.flame.sections_min_v + vMax = self.flame.sections_max_v + + data = np.empty(np.shape(Q)) + for section in range(self.flame.soot_sections): + data[section, :] = Q[section,:] / (vMax[section] - vMin[section]) + + return data + + @property + def soot_N(self): + """" + Gets the particles number density relative to each section + + : param None + + : return (sections x points) numpy array : + particles number density for each section at each point [m-3] + """ + q = self.soot_q + vMin = self.flame.sections_min_v + vMax = self.flame.sections_max_v + + data = np.empty(np.shape(q)) + for section in range(self.flame.soot_sections): + data[section, :] = q[section, :] * np.log(vMax[section]/vMin[section]) + + return data + + def soot_fv(self, **kwargs): + """ + Gets the soot volume fraction. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + soot volume fraction at each point + """ + first, last = self.getSectionBounds(**kwargs) + + data = np.sum(self.soot_Q[first:last, :], axis=0) + + return data + + def soot_Np(self, **kwargs): + """ + Gets the soot particles number density. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + soot particles number density at each point [m-3] + """ + first, last = self.getSectionBounds(**kwargs) + + data = np.sum(self.soot_N[first:last,:], axis=0) + + return data + + def soot_psdf(self, HAB, out='dNp/dlogd'): + """ + Gets the particles size distribution function at specified HAB. + + : param HAB = float : + Height Above the Burner surface at which PSDF shall be taken [m] + : param out = str : + Output to be computed : 'Np', 'Q' or 'dNp/dlogd' (default) + + : return (sections) numpy array : + particle size distribution for each section at specified HAB [m-3] + """ + if out in ['Q', 'dNp/dlogd', 'dV/dlogd']: + vals = self.soot_q + elif (out == 'Np'): + vals = self.soot_N + else: + raise KeyError("PSDF type should be 'Np', 'Q' or 'dNp/dlogd', not " + out) + if out == 'dV/dlogd': + vals = np.multiply(vals, np.pi * self.soot_mean_d ** 3 / 6) + z = self.flame.grid + data = np.asarray([np.interp(HAB,z,vals[k,:]) for k in range(self.flame.soot_sections)]) + if out=='dNp/dlogd': + data *= 3/(3-self.flame.sections_theta) + + return data + + def soot_mean_d(self, **kwargs): + """" + Gets soot particles mean diameter. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + mean diameter of soot particles at each point [m] + """ + first, last = self.getSectionBounds(**kwargs) + Ys = self.soot_Y[first:last,:] + dMean = self.flame.sections_mean_d[first:last] + data = [sum(Ys[:,i]*dMean)/sum(Ys[:,i]) for i in range(self.flame.n_points)] + return np.asarray(data) + + def soot_mean_s(self, **kwargs): + """" + Gets soot particles mean sections. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + mean section of soot particles at each point [m] + """ + first, last = self.getSectionBounds(**kwargs) + Ys = self.soot_Y[first:last,:] + sMean = self.flame.sections_mean_s[first:last] + data = [sum(Ys[:,i]*sMean)/sum(Ys[:,i]) for i in range(self.flame.n_points)] + return np.asarray(data) + + def soot_mean_v(self, **kwargs): + """" + Gets soot particles mean volumes. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + mean volume of soot particles at each point [m^3] + """ + first, last = self.getSectionBounds(**kwargs) + Ys = self.soot_Y[first:last,:] + vMean = self.flame.sections_mean_v[first:last] + data = [sum(Ys[:,i]*vMean)/sum(Ys[:,i]) for i in range(self.flame.n_points)] + return np.asarray(data) + + def soot_np(self, **kwargs): + """ + Gets number of primary particles per aggregate. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + number of primary particles per aggregate + """ + first, last = self.getSectionBounds(**kwargs) + Ys = self.soot_Y[first:last,:] + npart = self.flame.sections_np[first:last] + data = [max(1, sum(Ys[:,i]*npart)/sum(Ys[:,i])) if sum(Ys[:,i])>0 else None for i in range(self.flame.n_points)] + + return np.asarray(data) + + def soot_dp(self, **kwargs): + """ + Gets primary particles diameter. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + mean primary particles diameter [m] + """ + first, last = self.getSectionBounds(**kwargs) + + dpart = self.flame.sections_dp[first:last] * 1e7 + Ys = self.soot_Y[first:last,:] + data = [max(dpart[0], sum(Ys[:,i]*dpart)/sum(Ys[:,i])) if sum(Ys[:,i])>0 else None for i in range(self.flame.n_points)] + + return np.asarray(data) + + @property + def soot_source(self): + """ + Gets soot source terms. + + : param None + + : return dictionnary of (sections x points) numpy arrays : + soot source terms [s-1] + keys : + ['inception', 'condensation', 'coagulation', 'surface_growth', 'oxidation'] + """ + soot_source = {} + soot_source['inception'] = self.flame.soot_dump_inception + soot_source['condensation'] = self.flame.soot_dump_condensation + soot_source['coagulation'] = self.flame.soot_dump_coagulation + soot_source['surface_growth'] = self.flame.soot_dump_surface_growth + soot_source['oxidation'] = self.flame.soot_dump_oxidation + + return soot_source + + def soot_mcac_input(self, output='CANTERA2MCAC.dat', d_min=5e-9, fv_min=1e-10, x_max=0, t_max=0): + """ + Generates inputs for flame coupling with MCAC + + : param output : Output file to write the MCAC input file on + : param min_diam : Diameter of the smallest particle considered in MCAC + : param min_fv : Minimal volume fraction to consider (remove flame foot) + : param max_x : Maximal HAB to consider (remove flame end) (starting from the end if max_x < 0) + : param max_t : Maximal residence time to consider (remove flame end) (starting from the end if max_t < 0) + + : return : Dict containing MCAC inputs + """ + + ########################## + # RECOVER LOWER BOUNDARY # + ########################## + # Soot particles with diameter < min_diam are not considered in MCAC + first_section = self.getSectionBounds(d_min=d_min)[0] + if first_section == None: + first_section = 0 + + ########################## + # RECOVER RESIDENCE TIME # + ########################## + velocity = np.where(self.u == 0, 1e-10, self.u) # To avoid integration errors + time = [np.trapz(1/velocity[:idx+1], self.grid[:idx+1]) for idx in range(self.flame.n_points)] + + ####################### + # RECOVER SOURCE TERM # + ####################### + # Get source term for each section at each point + soot_source = self.soot_source + source_terms = soot_source['inception'][first_section:,:] + soot_source['surface_growth'][first_section:,:] + soot_source['oxidation'][first_section:,:] + soot_source['condensation'][first_section:,:] + soot_source['coagulation'][first_section:,:] + source_term = np.sum(source_terms, axis=0) + + # Nucleation is the mass entering the first section + nucleation = np.clip(source_terms[0,:], 0., None) + # Surface reactions are the rest + surface_reactions = source_term - nucleation + + # Recover the expected overall sourceterm dfv/dt to correct (don't ) + fv = self.soot_fv(first=first_section) + target_source_term = np.gradient(fv, time) + correction_factor = np.divide(target_source_term, source_term, out=np.zeros(source_term.shape, dtype=float), where=source_term!=0.) + nucleation *= correction_factor * self.flame.soot_density + surface_reactions *= correction_factor * self.flame.soot_density + + #################### + # RECOVER THE REST # + #################### + temperature = self.T + mean_diameter = self.soot_mean_d(first=first_section) + + ############# + # CLIP DATA # + ############# + # Clip flame beggining (no soot) + first_point = next(idx for idx,val in enumerate(fv) if val >= fv_min) + # Clip flame end (long residence times possible) + if x_max <= 0: + x_max = self.grid[-1] + x_max + last_point_x = next(idx for idx,val in enumerate(self.grid) if val >= x_max) + if t_max <= 0: + t_max = time[-1] + t_max + last_point_t = next(idx for idx,val in enumerate(time) if val >= t_max) + last_point = min(last_point_x, last_point_t) + + #################### + # WRITE INPUT FILE # + #################### + if output is not None: + with open(output, 'w') as f: + for index in range(first_point, last_point+1): + f.write('%.4e %.4e %.4e %.4e 0. %.4e %.4e\n' % (time[index], temperature[index], fv[index], mean_diameter[index], surface_reactions[index], nucleation[index])) + + return {'time':time, 'temperature':temperature, 'fv':fv, 'mean_diameter':mean_diameter, 'surface_reactions':surface_reactions, 'nucleation':nucleation} + + + def getSectionBounds(self, **kwargs): + """ + Gets index of sections given their mean diameter + :param first: Index of the first section to consider + :param d_min: Mean diameter of the first section to consider [m] + :param v_min: Mean volume of the first section to consider [m^3] + :param last: Index of the first section to consider + :param d_max: Mean diameter of the last section to consider [m] + :param v_max: Mean volume of the last section to consider [m^3] + """ + first = None + last = None + + if 'first' in kwargs and 'min' in kwargs : + raise KeyError('Cannot specify both section indice and diameter') + elif 'first' in kwargs : + first = kwargs['first'] + elif 'd_min' in kwargs: + dMean = self.flame.sections_mean_d + if kwargs['d_min'] > dMean[0] and kwargs['d_min'] < dMean[-1]: + first = next(idx for idx,val in enumerate(dMean) if val >= kwargs['d_min']) + elif 'v_min' in kwargs: + vMean = self.flame.sections_mean_v + if kwargs['v_min'] > vMean[0] and kwargs['v_min'] < vMean[-1]: + first = next(idx for idx,val in enumerate(vMean) if val >= kwargs['v_min']) + + if 'last' in kwargs and 'max' in kwargs: + raise KeyError('Cannot specify both section indice and diameter') + elif 'last' in kwargs: + last = kwargs['last'] + if last > 0 : + last += 1 + elif 'd_max' in kwargs: + dMean = self.flame.sections_mean_d + if kwargs['d_max'] > dMean[0] and kwargs['d_max'] < dMean[-1]: + last = next(idx for idx,val in enumerate(dMean) if val > kwargs['d_max']) + elif 'v_max' in kwargs: + vMean = self.flame.sections_mean_v + if kwargs['v_max'] > vMean[0] and kwargs['v_max'] < vMean[-1]: + last = next(idx for idx,val in enumerate(vMean) if val > kwargs['v_max']) + + return first, last + + # END of soot API @property def grid(self): @@ -432,6 +905,87 @@ def write_csv(self, filename, species='X', quiet=True, normalize=True): if not quiet: print("Solution saved to '{0}'.".format(filename)) + def write_AVBP(self, filename, quiet=True): + """ + Instanciate a solution for can2av + to a CSV file. + + :param filename: + Output file name + """ + II = self.gas.n_reactions + KK = self.gas.n_species + JJ = self.flame.n_points + z = self.grid + T = self.T + u = self.velocity + Lreac = list(self.gas.forward_rates_of_progress) + for index, object in enumerate(Lreac): + Lreac[index] = "FwRate_" +str(index+1) + Lreac_r = list(self.gas.reverse_rates_of_progress) + for index, object in enumerate(Lreac_r): + Lreac_r[index] = "RvRate_" +str(index+1) + Wspec = list(self.gas.species_names) + for index, object in enumerate(Wspec): + Wspec[index] = "w_" +object + Lreac_n = list(self.gas.net_rates_of_progress) + for index, object in enumerate(Lreac_n): + Lreac_n[index] = "NetRate_" +str(index+1) + fcsv = open(filename,'w') + writer = _csv.writer(fcsv) + writer.writerow(['Grid Points: ', str(JJ),' Sl= ',u[0]]) + writer.writerow(['x_axis','u','Temperature','rho','Pressure'] + + self.gas.species_names + + Wspec + + Lreac + + Lreac_r + + Lreac_n + + ['Heat_release']) + for n in range(self.flame.n_points): + self.set_gas_state(n) + HR = 0.0 + for m in range(KK): + HR = HR - self.gas.standard_enthalpies_RT[m]*self.gas.net_production_rates[m] + HR = HR * 8313.608 * T[n] + writer.writerow([z[n], u[n], T[n], self.gas.density, self.flame.P] + + list(self.gas.Y/np.sum(self.gas.Y)) + + list(self.gas.molecular_weights) + + list(1000*self.gas.forward_rates_of_progress) + + list(1000*self.gas.reverse_rates_of_progress) + + list(1000*self.gas.net_rates_of_progress) + + list([HR])) + + fcsv.close() + if not quiet: + print("Solution saved to '{0}'.".format(filename)) + + def write_AVBP_energy(self, filename='AVBP_energy.csv', quiet = False): + """ + Dumps energy profile to be imposed in AVBP as : + Line 1 : number of grid points + Next lines : grid | Temperature | density | Cv mass + + : param filename: + Output file name + + : returns : + File with inputs + """ + f = open(filename,'w') + grid = self.grid + T = self.T + points = len(grid) + f.write("%d\n"%(points)) + for i in range(points): + self.set_gas_state(i) + density = self.gas.density + cv_mass = self.gas.cv_mass + f.write("%1.5e %1.5e %1.5e %1.5e \n"%(grid[i], T[i], density, cv_mass)) + f.close() + if not quiet: + print("\nAVBP energy inputs saved to '{0}'.".format(filename)) + + def to_array(self, domain=None, normalize=False): """ Retrieve domain data as a `SolutionArray` object. @@ -844,7 +1398,7 @@ class FreeFlame(FlameBase): __slots__ = ('inlet', 'flame', 'outlet') _other = ('grid', 'velocity') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ A domain of type `FreeFlow` named 'flame' will be created to represent the flame. The three domains comprising the stack are stored as ``self.inlet``, @@ -860,15 +1414,15 @@ def __init__(self, gas, grid=None, width=None): """ #: `Inlet1D` at the left of the domain representing premixed reactants - self.inlet = Inlet1D(name='reactants', phase=gas) + self.inlet = Inlet1D(name='reactants', phase=gas, sections=sections) #: `Outlet1D` at the right of the domain representing the burned products - self.outlet = Outlet1D(name='products', phase=gas) + self.outlet = Outlet1D(name='products', phase=gas, sections=sections) if not hasattr(self, 'flame'): # Create flame domain if not already instantiated by a child class #: `FreeFlow` domain representing the flame - self.flame = FreeFlow(gas, name='flame') + self.flame = FreeFlow(gas, name='flame', sections=sections) if width is not None: grid = np.array([0.0, 0.2, 0.3, 0.4, 0.5, 0.6, 0.8, 1.0]) * width @@ -1055,7 +1609,7 @@ class BurnerFlame(FlameBase): __slots__ = ('burner', 'flame', 'outlet') _other = ('grid', 'velocity') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1074,15 +1628,15 @@ def __init__(self, gas, grid=None, width=None): """ #: `Inlet1D` at the left of the domain representing the burner surface through #: which reactants flow - self.burner = Inlet1D(name='burner', phase=gas) + self.burner = Inlet1D(name='burner', phase=gas, sections=sections) #: `Outlet1D` at the right of the domain representing the burned gas - self.outlet = Outlet1D(name='outlet', phase=gas) + self.outlet = Outlet1D(name='outlet', phase=gas, sections=sections) if not hasattr(self, 'flame'): # Create flame domain if not already instantiated by a child class #: `UnstrainedFlow` domain representing the flame - self.flame = UnstrainedFlow(gas, name='flame') + self.flame = UnstrainedFlow(gas, name='flame', sections=sections) if width is not None: grid = np.array([0.0, 0.1, 0.2, 0.3, 0.5, 0.7, 1.0]) * width @@ -1209,7 +1763,7 @@ class CounterflowDiffusionFlame(FlameBase): __slots__ = ('fuel_inlet', 'flame', 'oxidizer_inlet') _other = ('grid', 'velocity', 'spread_rate', 'lambda') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1228,15 +1782,15 @@ def __init__(self, gas, grid=None, width=None): """ #: `Inlet1D` at the left of the domain representing the fuel mixture - self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas) + self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas, sections=sections) self.fuel_inlet.T = gas.T #: `Inlet1D` at the right of the domain representing the oxidizer mixture - self.oxidizer_inlet = Inlet1D(name='oxidizer_inlet', phase=gas) + self.oxidizer_inlet = Inlet1D(name='oxidizer_inlet', phase=gas, sections=sections) self.oxidizer_inlet.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame') + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) if width is not None: grid = np.array([0.0, 0.2, 0.4, 0.6, 0.8, 1.0]) * width @@ -1538,7 +2092,7 @@ class ImpingingJet(FlameBase): __slots__ = ('inlet', 'flame', 'surface') _other = ('grid', 'velocity', 'spread_rate', 'lambda') - def __init__(self, gas, grid=None, width=None, surface=None): + def __init__(self, gas, grid=None, width=None, surface=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1559,10 +2113,10 @@ def __init__(self, gas, grid=None, width=None, surface=None): """ #: `Inlet1D` at the left of the domain representing the incoming reactants - self.inlet = Inlet1D(name='inlet', phase=gas) + self.inlet = Inlet1D(name='inlet', phase=gas, sections=sections) #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame') + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) self.flame.set_axisymmetric_flow() if width is not None: @@ -1627,7 +2181,7 @@ class CounterflowPremixedFlame(FlameBase): __slots__ = ('reactants', 'flame', 'products') _other = ('grid', 'velocity', 'spread_rate', 'lambda') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1645,15 +2199,15 @@ def __init__(self, gas, grid=None, width=None): """ #: `Inlet1D` at the left of the domain representing premixed reactants - self.reactants = Inlet1D(name='reactants', phase=gas) + self.reactants = Inlet1D(name='reactants', phase=gas, sections=sections) self.reactants.T = gas.T #: `Inlet1D` at the right of the domain representing burned products - self.products = Inlet1D(name='products', phase=gas) + self.products = Inlet1D(name='products', phase=gas, sections=sections) self.products.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame') + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) if width is not None: # Create grid points aligned with initial guess profile @@ -1729,7 +2283,7 @@ class CounterflowTwinPremixedFlame(FlameBase): __slots__ = ('reactants', 'flame', 'products') _other = ('grid', 'velocity', 'spread_rate', 'lambda') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1745,14 +2299,14 @@ def __init__(self, gas, grid=None, width=None): represent the flame. The three domains comprising the stack are stored as ``self.reactants``, ``self.flame``, and ``self.products``. """ - self.reactants = Inlet1D(name='reactants', phase=gas) + self.reactants = Inlet1D(name='reactants', phase=gas, sections=sections) self.reactants.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame') + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) #The right boundary is a symmetry plane - self.products = SymmetryPlane1D(name='products', phase=gas) + self.products = SymmetryPlane1D(name='products', phase=gas, sections=sections) if width is not None: # Create grid points aligned with initial guess profile @@ -1799,3 +2353,358 @@ def set_initial_guess(self, data=None, group=None): self.set_profile('velocity', [0.0, 1.0], [uu, 0]) self.set_profile('spread_rate', [0.0, 1.0], [0.0, a]) self.set_profile("lambda", [0.0, 1.0], [L, L]) + + +class Flamelet(FlameBase): + """ A diffusion flamelet (Z-space) """ + __slots__ = ('oxidizer_inlet', 'flame', 'fuel_inlet') + _other = ('grid') + + def __init__(self, gas, grid=None,): + """ + :param gas: + `Solution` (using the IdealGas thermodynamic model) used to + evaluate all gas properties and reaction rates. + :param grid: + A list of points to be used as the initial grid. Not recommended + unless solving only on a fixed grid; Use the `width` parameter + instead. + + A domain of class `FlameletFlow` named ``flame`` will be created to + represent the flame. The three domains comprising the stack are stored as + ``self.oxidizer_inlet``, ``self.flame``, and ``self.fuel_inlet``. + """ + + #: `Inlet1D` at the left of the domain representing the fuel mixture + self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas) + self.fuel_inlet.T = gas.T + + #: `Inlet1D` at the right of the domain representing the oxidizer mixture + self.oxidizer_inlet = Inlet1D(name='oxidizer_inlet', phase=gas) + self.oxidizer_inlet.T = gas.T + + #: `FlameletFlow` domain representing the flame + self.flame = FlameletFlow(gas, name='flame') + + if grid is None: + grid = np.array([0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]) + # Note: flamelet initialisation is very sensitive to the number of grid points. + # Do not hesitate to try some: experience shows that between 10 and 20 is often a good guess + + grid = grid / max(grid) # Width of the grid must anyway be 1 because in Z-space + + super().__init__((self.oxidizer_inlet, self.flame, self.fuel_inlet), gas, grid) + + @property + def ChiSt(self): + return self.flame.ChiSt + + @ChiSt.setter + def ChiSt(self, val): + self.flame.ChiSt = val + + @property + def ZSt(self): + return self.flame.ZSt + + @ZSt.setter + def ZSt(self, val): + self.flame.ZSt = val + + def set_initial_guess(self, data=None, group=None): + """ + Set the initial guess for the solution. By default, the initial guess + is generated by assuming infinitely-fast chemistry. Alternatively, a + previously calculated result can be supplied as an initial guess via + 'data' and 'key' inputs (see `FlameBase.set_initial_guess`). + """ + super().set_initial_guess(data=data, group=group) + if data: + return + + moles = lambda el: (self.gas.elemental_mass_fraction(el) / + self.gas.atomic_weight(el)) + + # Compute stoichiometric mixture composition + Yin_f = self.fuel_inlet.Y + self.gas.TPY = self.fuel_inlet.T, self.P, Yin_f + + T0f = self.fuel_inlet.T + + sFuel = moles('O') + if 'C' in self.gas.element_names: + sFuel -= 2 * moles('C') + if 'H' in self.gas.element_names: + sFuel -= 0.5 * moles('H') + + Yin_o = self.oxidizer_inlet.Y + self.gas.TPY = self.oxidizer_inlet.T, self.P, Yin_o + + T0o = self.oxidizer_inlet.T + + sOx = moles('O') + if 'C' in self.gas.element_names: + sOx -= 2 * moles('C') + if 'H' in self.gas.element_names: + sOx -= 0.5 * moles('H') + + zst = 1.0 / (1 - sFuel / sOx) + Yst = zst * Yin_f + (1.0 - zst) * Yin_o + + self.flame.ZSt = zst + + # get adiabatic flame temperature and composition + Tbar = 0.5 * (T0f + T0o) + self.gas.TPY = Tbar, self.P, Yst + self.gas.equilibrate('HP') + Teq = self.gas.T + Yeq = self.gas.Y + + # estimate strain rate + zz = self.flame.grid + nz = len(zz) + + Y = np.zeros((nz, self.gas.n_species)) + T = np.zeros(nz) + for j, zmix in enumerate(zz): + if zmix > zst: + Y[j] = Yeq + (Yin_f - Yeq) * (zmix - zst) / (1.0 - zst) + T[j] = Teq + (T0f - Teq) * (zmix - zst) / (1.0 - zst) + else: + Y[j] = Yin_o + zmix * (Yeq - Yin_o) / zst + T[j] = T0o + (Teq - T0o) * zmix / zst + + T[0] = T0f + T[-1] = T0o + + self.set_profile('T', zz, T) + for k,spec in enumerate(self.gas.species_names): + self.set_profile(spec, zz, Y[:,k]) + + def extinct(self): + return max(self.T) - max(self.fuel_inlet.T, self.oxidizer_inlet.T) < 10 + + def solve(self, loglevel=1, refine_grid='refine', auto=False, stage=1): + """ + Solve the problem. + + :param loglevel: + integer flag controlling the amount of diagnostic output. Zero + suppresses all output, and 5 produces very verbose output. + :param refine_grid: + if True, enable grid refinement. + :param auto: if True, sequentially execute the different solution stages + and attempt to automatically recover from errors. Attempts to first + solve on the initial grid with energy enabled. If that does not + succeed, a fixed-temperature solution will be tried followed by + enabling the energy equation, and then with grid refinement enabled. + If non-default tolerances have been specified or multicomponent + transport is enabled, an additional solution using these options + will be calculated. + :param stage: solution stage; only used when transport model is ``ionized-gas``. + """ + if self.flame.transport_model == 'ionized-gas': + warnings.warn( + "The 'ionized-gas' transport model is untested for " + "'Flamelet' objects.", UserWarning) + self.flame.solving_stage = stage + + super().solve(loglevel, refine_grid, auto) + # Do some checks if loglevel is set + if loglevel > 0: + if self.extinct(): + print('WARNING: Flame is extinct.') + # else: + # # Check if the flame is very thick + # # crude width estimate based on temperature + # z_flame = self.grid[self.T > np.max(self.T) / 2] + # flame_width = z_flame[-1] - z_flame[0] + # domain_width = self.grid[-1] - self.grid[0] + # if flame_width / domain_width > 0.4: + # print('WARNING: The flame is thick compared to the domain ' + # 'size. The flame might be affected by the plug-flow ' + # 'boundary conditions. Consider increasing the inlet mass ' + # 'fluxes or using a larger domain.') + + # # Check if the temperature peak is close to a boundary + # z_center = (self.grid[np.argmax(self.T)] - self.grid[0]) / domain_width + # if z_center < 0.25: + # print('WARNING: The flame temperature peak is close to the ' + # 'fuel inlet. Consider increasing the ratio of the ' + # 'fuel inlet mass flux to the oxidizer inlet mass flux.') + # if z_center > 0.75: + # print('WARNING: The flame temperature peak is close to the ' + # 'oxidizer inlet. Consider increasing the ratio of the ' + # 'oxidizer inlet mass flux to the fuel inlet mass flux.') + + def write_csv(self, filename, species='X', quiet=True): + """ + Write the velocity, temperature, density, and species profiles + to a CSV file. + + :param filename: + Output file name + :param species: + Attribute to use obtaining species profiles, e.g. ``X`` for + mole fractions or ``Y`` for mass fractions. + """ + + z = self.grid + T = self.T + + csvfile = open(filename, 'w') + writer = _csv.writer(csvfile) + writer.writerow(['z (m)', + 'T (K)', 'rho (kg/m3)'] + self.gas.species_names) + for n in range(self.flame.n_points): + self.set_gas_state(n) + writer.writerow([z[n], T[n], self.gas.density] + + list(getattr(self.gas, species))) + csvfile.close() + if not quiet: + print("Solution saved to '{0}'.".format(filename)) + # def strain_rate(self, definition, fuel=None, oxidizer='O2', stoich=None): + # r""" + # Return the axial strain rate of the counterflow diffusion flame in 1/s. + + # :param definition: + # The definition of the strain rate to be calculated. Options are: + # ``mean``, ``max``, ``stoichiometric``, ``potential_flow_fuel``, and + # ``potential_flow_oxidizer``. + # :param fuel: The fuel species. Used only if ``definition`` is + # ``stoichiometric``. + # :param oxidizer: The oxidizer species, default ``O2``. Used only if + # ``definition`` is ``stoichiometric``. + # :param stoich: The molar stoichiometric oxidizer-to-fuel ratio. + # Can be omitted if the oxidizer is ``O2``. Used only if ``definition`` + # is ``stoichiometric``. + + # The parameter ``definition`` sets the method to compute the strain rate. + # Possible options are: + + # ``mean``: + # The mean axial velocity gradient in the entire domain + + # .. math:: a_{mean} = \left| \frac{\Delta u}{\Delta z} \right| + + # ``max``: + # The maximum axial velocity gradient + + # .. math:: a_{max} = \max \left( \left| \frac{du}{dz} \right| \right) + + # ``stoichiometric``: + # The axial velocity gradient at the stoichiometric surface. + + # .. math:: + + # a_{stoichiometric} = \left| \left. \frac{du}{dz} + # \right|_{\phi=1} \right| + + # This method uses the additional keyword arguments ``fuel``, + # ``oxidizer``, and ``stoich``. + + # >>> f.strain_rate('stoichiometric', fuel='H2', oxidizer='O2', + # stoich=0.5) + + # ``potential_flow_fuel``: + # The corresponding axial strain rate for a potential flow boundary + # condition at the fuel inlet. + + # .. math:: a_{f} = \sqrt{-\frac{\Lambda}{\rho_{f}}} + + # ``potential_flow_oxidizer``: + # The corresponding axial strain rate for a potential flow boundary + # condition at the oxidizer inlet. + + # .. math:: a_{o} = \sqrt{-\frac{\Lambda}{\rho_{o}}} + # """ + # if definition == 'mean': + # return - (self.velocity[-1] - self.velocity[0]) / self.grid[-1] + + # elif definition == 'max': + # return np.max(np.abs(np.gradient(self.velocity) / np.gradient(self.grid))) + + # elif definition == 'stoichiometric': + # if fuel is None: + # raise KeyError('Required argument "fuel" not defined') + # if oxidizer != 'O2' and stoich is None: + # raise KeyError('Required argument "stoich" not defined') + + # if stoich is None: + # # oxidizer is O2 + # stoich = - 0.5 * self.gas.n_atoms(fuel, 'O') + # if 'H' in self.gas.element_names: + # stoich += 0.25 * self.gas.n_atoms(fuel, 'H') + # if 'C' in self.gas.element_names: + # stoich += self.gas.n_atoms(fuel, 'C') + + # d_u_d_z = np.gradient(self.velocity) / np.gradient(self.grid) + # phi = (self.X[self.gas.species_index(fuel)] * stoich / + # np.maximum(self.X[self.gas.species_index(oxidizer)], 1e-20)) + # z_stoich = np.interp(-1., -phi, self.grid) + # return np.abs(np.interp(z_stoich, self.grid, d_u_d_z)) + + # elif definition == 'potential_flow_fuel': + # return np.sqrt(- self.L[0] / self.density[0]) + + # elif definition == 'potential_flow_oxidizer': + # return np.sqrt(- self.L[0] / self.density[-1]) + + # else: + # raise ValueError('Definition "' + definition + '" is not available') + + # def mixture_fraction(self, m): + # r""" + # Compute the mixture fraction based on element ``m`` or from the + # Bilger mixture fraction by setting ``m="Bilger"`` + + # The mixture fraction is computed from the elemental mass fraction of + # element ``m``, normalized by its values on the fuel and oxidizer + # inlets: + + # .. math:: Z = \frac{Z_{\mathrm{mass},m}(z) - + # Z_{\mathrm{mass},m}(z_\mathrm{oxidizer})} + # {Z_{\mathrm{mass},m}(z_\mathrm{fuel}) - + # Z_{\mathrm{mass},m}(z_\mathrm{oxidizer})} + + # or from the Bilger mixture fraction: + + # .. math:: Z = \frac{\beta-\beta_{\mathrm{oxidizer}}} + # {\beta_{\mathrm{fuel}}-\beta_{\mathrm{oxidizer}}} + + # with + + # .. math:: \beta = 2\frac{Z_C}{M_C}+2\frac{Z_S}{M_S} + # +\frac{1}{2}\frac{Z_H}{M_H}-\frac{Z_O}{M_O} + + # :param m: + # The element based on which the mixture fraction is computed, + # may be specified by name or by index, or "Bilger" for the + # Bilger mixture fraction, which considers the elements C, + # H, S, and O + + # >>> f.mixture_fraction('H') + # >>> f.mixture_fraction('Bilger') + # """ + + # Yf = [self.value(self.flame, k, 0) for k in self.gas.species_names] + # Yo = [self.value(self.flame, k, self.flame.n_points - 1) + # for k in self.gas.species_names] + + # vals = np.empty(self.flame.n_points) + # for i in range(self.flame.n_points): + # self.set_gas_state(i) + # vals[i] = self.gas.mixture_fraction(Yf, Yo, 'mass', m) + # return vals + + # @property + # def equivalence_ratio(self): + # Yf = [self.value(self.flame, k, 0) for k in self.gas.species_names] + # Yo = [self.value(self.flame, k, self.flame.n_points - 1) + # for k in self.gas.species_names] + + # vals = np.empty(self.flame.n_points) + # for i in range(self.flame.n_points): + # self.set_gas_state(i) + # vals[i] = self.gas.equivalence_ratio(Yf, Yo, "mass") + # return vals \ No newline at end of file From 925ed423abaf17c0a6380e5aefe962b2a63141ba Mon Sep 17 00:00:00 2001 From: pestre Date: Fri, 24 Jan 2025 10:46:23 +0100 Subject: [PATCH 05/98] Merge differences in samples directory Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: new file: samples/clib/README.rst new file: samples/cxx/README.rst modified: samples/cxx/bvp/BoundaryValueProblem.h modified: samples/cxx/flamespeed/flamespeed.cpp new file: samples/f77/f77_demo.f new file: samples/f90/README.rst new file: samples/matlab_experimental/README.rst new file: samples/python/AVBP/1-runBurner.py new file: samples/python/AVBP/2-restoreBurner.py new file: samples/python/AVBP/3-plotBurner.py new file: samples/python/AVBP/ARC.py new file: samples/python/AVBP/FLAMELET.py new file: samples/python/AVBP/PEA.py new file: samples/python/AVBP/RESULTS/BISETTI.xml new file: samples/python/AVBP/RESULTS/BISETTI.yaml new file: samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml new file: samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.yaml new file: samples/python/AVBP/THICKENING.py new file: samples/python/AVBP/inputs/BFER_methane.cti new file: samples/python/AVBP/inputs/BFER_methane.yaml new file: samples/python/AVBP/inputs/BISETTI.cti new file: samples/python/AVBP/inputs/BISETTI.yaml new file: samples/python/AVBP/inputs/Lu.cti new file: samples/python/AVBP/inputs/Lu.yaml new file: samples/python/AVBP/inputs/Lu_ARC.cti new file: samples/python/AVBP/inputs/Lu_ARC.f90 new file: samples/python/AVBP/inputs/Lu_ARC.yaml new file: samples/python/AVBP/inputs/T_vs_x.dat new file: samples/python/AVBP/mech_lib/Makefile new file: samples/python/AVBP/mech_lib/customkinetics.f90 new file: samples/python/AVBP/mixture_database.dat new file: samples/python/AVBP/postproc.py new file: samples/python/AVBP/write_csv.py new file: samples/python/README.rst new file: samples/python/kinetics/README.rst new file: samples/python/multiphase/README.rst new file: samples/python/onedim/README.rst new file: samples/python/onedim/adiabatic_flame.csv new file: samples/python/onedim/adiabatic_flame.yaml new file: samples/python/reactors/README.rst new file: samples/python/surface_chemistry/README.rst new file: samples/python/thermo/README.rst new file: samples/python/transport/README.rst --- samples/clib/README.rst | 6 + samples/cxx/README.rst | 2 + samples/cxx/bvp/BoundaryValueProblem.h | 2 +- samples/cxx/flamespeed/flamespeed.cpp | 6 +- samples/f77/f77_demo.f | 101 + samples/f90/README.rst | 4 + samples/matlab_experimental/README.rst | 5 + samples/python/AVBP/1-runBurner.py | 62 + samples/python/AVBP/2-restoreBurner.py | 54 + samples/python/AVBP/3-plotBurner.py | 53 + samples/python/AVBP/ARC.py | 45 + samples/python/AVBP/FLAMELET.py | 111 + samples/python/AVBP/PEA.py | 50 + samples/python/AVBP/RESULTS/BISETTI.xml | 7624 +++++++++++++++++ samples/python/AVBP/RESULTS/BISETTI.yaml | 6778 +++++++++++++++ .../RESULTS/CH4-O2-converged-flamelet-Lu.xml | 1844 ++++ .../RESULTS/CH4-O2-converged-flamelet-Lu.yaml | 1565 ++++ samples/python/AVBP/THICKENING.py | 67 + samples/python/AVBP/inputs/BFER_methane.cti | 149 + samples/python/AVBP/inputs/BFER_methane.yaml | 151 + samples/python/AVBP/inputs/BISETTI.cti | 1537 ++++ samples/python/AVBP/inputs/BISETTI.yaml | 1367 +++ samples/python/AVBP/inputs/Lu.cti | 1351 +++ samples/python/AVBP/inputs/Lu.yaml | 997 +++ samples/python/AVBP/inputs/Lu_ARC.cti | 1338 +++ samples/python/AVBP/inputs/Lu_ARC.f90 | 2317 +++++ samples/python/AVBP/inputs/Lu_ARC.yaml | 2230 +++++ samples/python/AVBP/inputs/T_vs_x.dat | 203 + samples/python/AVBP/mech_lib/Makefile | 4 + .../python/AVBP/mech_lib/customkinetics.f90 | 2317 +++++ samples/python/AVBP/mixture_database.dat | 102 + samples/python/AVBP/postproc.py | 79 + samples/python/AVBP/write_csv.py | 37 + samples/python/README.rst | 7 + samples/python/kinetics/README.rst | 2 + samples/python/multiphase/README.rst | 2 + samples/python/onedim/README.rst | 2 + samples/python/onedim/adiabatic_flame.csv | 141 + samples/python/onedim/adiabatic_flame.yaml | 1338 +++ samples/python/reactors/README.rst | 2 + samples/python/surface_chemistry/README.rst | 2 + samples/python/thermo/README.rst | 2 + samples/python/transport/README.rst | 2 + 43 files changed, 34054 insertions(+), 4 deletions(-) create mode 100644 samples/clib/README.rst create mode 100644 samples/cxx/README.rst create mode 100644 samples/f77/f77_demo.f create mode 100644 samples/f90/README.rst create mode 100644 samples/matlab_experimental/README.rst create mode 100644 samples/python/AVBP/1-runBurner.py create mode 100644 samples/python/AVBP/2-restoreBurner.py create mode 100644 samples/python/AVBP/3-plotBurner.py create mode 100644 samples/python/AVBP/ARC.py create mode 100644 samples/python/AVBP/FLAMELET.py create mode 100644 samples/python/AVBP/PEA.py create mode 100644 samples/python/AVBP/RESULTS/BISETTI.xml create mode 100644 samples/python/AVBP/RESULTS/BISETTI.yaml create mode 100644 samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml create mode 100644 samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.yaml create mode 100644 samples/python/AVBP/THICKENING.py create mode 100755 samples/python/AVBP/inputs/BFER_methane.cti create mode 100644 samples/python/AVBP/inputs/BFER_methane.yaml create mode 100644 samples/python/AVBP/inputs/BISETTI.cti create mode 100644 samples/python/AVBP/inputs/BISETTI.yaml create mode 100755 samples/python/AVBP/inputs/Lu.cti create mode 100644 samples/python/AVBP/inputs/Lu.yaml create mode 100755 samples/python/AVBP/inputs/Lu_ARC.cti create mode 100755 samples/python/AVBP/inputs/Lu_ARC.f90 create mode 100644 samples/python/AVBP/inputs/Lu_ARC.yaml create mode 100644 samples/python/AVBP/inputs/T_vs_x.dat create mode 100644 samples/python/AVBP/mech_lib/Makefile create mode 100755 samples/python/AVBP/mech_lib/customkinetics.f90 create mode 100755 samples/python/AVBP/mixture_database.dat create mode 100644 samples/python/AVBP/postproc.py create mode 100644 samples/python/AVBP/write_csv.py create mode 100644 samples/python/README.rst create mode 100644 samples/python/kinetics/README.rst create mode 100644 samples/python/multiphase/README.rst create mode 100644 samples/python/onedim/README.rst create mode 100644 samples/python/onedim/adiabatic_flame.csv create mode 100644 samples/python/onedim/adiabatic_flame.yaml create mode 100644 samples/python/reactors/README.rst create mode 100644 samples/python/surface_chemistry/README.rst create mode 100644 samples/python/thermo/README.rst create mode 100644 samples/python/transport/README.rst diff --git a/samples/clib/README.rst b/samples/clib/README.rst new file mode 100644 index 00000000000..3b6b460fa1d --- /dev/null +++ b/samples/clib/README.rst @@ -0,0 +1,6 @@ +C Examples +========== + +These examples demonstrate the usage of Cantera's C interface library, ``clib``, +which can also be used to call Cantera from other languages that are able to +call C functions. diff --git a/samples/cxx/README.rst b/samples/cxx/README.rst new file mode 100644 index 00000000000..3bf4d017c6a --- /dev/null +++ b/samples/cxx/README.rst @@ -0,0 +1,2 @@ +C++ Examples +============ diff --git a/samples/cxx/bvp/BoundaryValueProblem.h b/samples/cxx/bvp/BoundaryValueProblem.h index df9a0990fed..5b037163456 100644 --- a/samples/cxx/bvp/BoundaryValueProblem.h +++ b/samples/cxx/bvp/BoundaryValueProblem.h @@ -146,7 +146,7 @@ class BoundaryValueProblem : public Cantera::Domain1D if (m_sim == 0) { start(); } - bool refine = true; + std::string refine = "refine"; m_sim->solve(loglevel, refine); } diff --git a/samples/cxx/flamespeed/flamespeed.cpp b/samples/cxx/flamespeed/flamespeed.cpp index caf48db3cae..cd6e91da645 100644 --- a/samples/cxx/flamespeed/flamespeed.cpp +++ b/samples/cxx/flamespeed/flamespeed.cpp @@ -22,7 +22,7 @@ using namespace Cantera; using fmt::print; -int flamespeed(double phi, bool refine_grid, int loglevel) +int flamespeed(double phi, std::string refine_grid, int loglevel) { try { auto sol = newSolution("gri30.yaml", "gri30", "mixture-averaged"); @@ -197,7 +197,7 @@ int main(int argc, char** argv) { double phi; int loglevel = 1; - bool refine_grid = true; + std::string refine_grid = "refine"; if (argc >= 2) { phi = fpValue(argv[1]); } else { @@ -205,7 +205,7 @@ int main(int argc, char** argv) std::cin >> phi; } if (argc >= 3) { - refine_grid = bool(std::stoi(argv[2])); + refine_grid = std::string(argv[2]); } if (argc >= 4) { loglevel = std::stoi(argv[3]); diff --git a/samples/f77/f77_demo.f b/samples/f77/f77_demo.f new file mode 100644 index 00000000000..facac04c2c2 --- /dev/null +++ b/samples/f77/f77_demo.f @@ -0,0 +1,101 @@ +c Fortran 77 demo +c =============== +c +c This program uses functions defined in :doc:`demo_ftnlib.cpp +c ` to create an ideal gas mixture and print some of +c its properties. +c +c For a C++ version of this program, see :doc:`demo.cpp +c <../cxx/demo>`. +c +c Replace this sample main program with your program +c +c .. tags:: Fortran 77, tutorial, thermodynamics, kinetics, +c transport + +c This file is part of Cantera. See License.txt in the top-level directory or +c at https://cantera.org/license.txt for license and copyright information. + + program demo + implicit double precision (a-h,o-z) + parameter (MAXSP = 20, MAXRXNS = 100) + double precision q(MAXRXNS), qf(MAXRXNS), qr(MAXRXNS) + double precision diff(MAXSP) + character*80 eq + character*20 name +c + write(*,*) + write(*,*) '******** Fortran 77 Test Program ********' + + call newIdealGasMix('h2o2.yaml','ohmech','mixture-averaged') + t = 1200.0 + p = 101325.0 + call setState_TPX_String(t, p, + $ 'H2:2, O2:1, OH:0.01, H:0.01, O:0.01') + +c + write(*,*) 'Initial state properties:' + write(*,10) temperature(), pressure(), density(), + $ enthalpy_mole(), entropy_mole(), cp_mole() + +c %% +c Compute the equilibrium state +c ----------------------------- +c +c Hold the specific enthalpy and pressure constant. + call equilibrate('HP') + + write(*,*) 'Equilibrium state properties:' + write(*,10) temperature(), pressure(), density(), + $ enthalpy_mole(), entropy_mole(), cp_mole() + + 10 format(//'Temperature: ',g14.5,' K'/ + $ 'Pressure: ',g14.5,' Pa'/ + $ 'Density: ',g14.5,' kg/m3'/ + $ 'Molar Enthalpy:',g14.5,' J/kmol'/ + $ 'Molar Entropy: ',g14.5,' J/kmol-K'/ + $ 'Molar cp: ',g14.5,' J/kmol-K'//) + + +c %% +c Reaction information +c -------------------- +c + irxns = nReactions() + +c forward and reverse rates of progress should be equal +c in equilibrium states + call getFwdRatesOfProgress(qf) + call getRevRatesOfProgress(qr) + +c net rates of progress should be zero in equilibrium states + call getNetRatesOfProgress(q) + +c for each reaction, print the equation and the rates of progress + do i = 1,irxns + call getReactionEqn(i,eq) + write(*,20) eq,qf(i),qr(i),q(i) + 20 format(a27,3e14.5,' kmol/m3/s') + end do + +c %% +c Transport properties +c -------------------- + dnu = viscosity() + dlam = thermalConductivity() + call getMixDiffCoeffs(diff) + + write(*,30) dnu, dlam + 30 format(//'Viscosity: ',g14.5,' Pa-s'/ + $ 'Thermal conductivity: ',g14.5,' W/m/K'/) + write(*,*) 'Species ', + $ ' Diffusion Coefficient' + nsp = nSpecies() + do k = 1, nsp + call getSpeciesName(k, name) + write(*,40) name, diff(k) + 40 format(' ',a20,e14.5,' m2/s') + end do + + stop + end diff --git a/samples/f90/README.rst b/samples/f90/README.rst new file mode 100644 index 00000000000..90db496632b --- /dev/null +++ b/samples/f90/README.rst @@ -0,0 +1,4 @@ +Fortran Examples +================ + +Examples for both Fortran 77 and Fortran 90. diff --git a/samples/matlab_experimental/README.rst b/samples/matlab_experimental/README.rst new file mode 100644 index 00000000000..dbeb918df88 --- /dev/null +++ b/samples/matlab_experimental/README.rst @@ -0,0 +1,5 @@ +Matlab (experimental) Examples +============================== + +These examples are written for use with the "experimental" version of the Cantera Matlab +toolbox that was introduced with Cantera 3.0. diff --git a/samples/python/AVBP/1-runBurner.py b/samples/python/AVBP/1-runBurner.py new file mode 100644 index 00000000000..25902d7b859 --- /dev/null +++ b/samples/python/AVBP/1-runBurner.py @@ -0,0 +1,62 @@ +# Importing necessary libraries +import cantera as ct +import numpy as np +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Setting the mechanism name +mech = 'BISETTI' + +#Setting pressure +pressure = ct.one_atm + +# Setting temperature +temperature = 298.00 + +# Setting inlet velocity +velocity = 6.73e-2 + +# Setting flame initial composition +composition = 'C2H4:14.08, O2:18.05, N2:67.87' + +# Creating gas object +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/%s.yaml' % mech) +else: + gas = ct.Solution('./inputs/%s.cti' % mech) + +# Settng gas properties +gas.TPX = temperature, pressure, composition + +# Loading experimental data (temperature vs. height) +z, T = np.genfromtxt('./inputs/T_vs_x.dat').T + +# Creating flame object of the same size as the experimental flame +f = ct.BurnerFlame(gas=gas, width=z[-1]) + +# Setting the flame's mass flow rate +f.burner.mdot = velocity * gas.density + +# Disabling energy equation +f.energy_enabled = False + +#Imposing proposed temperature profile +f.flame.set_fixed_temp_profile(z/max(z), T) + +# Setting the transport model to mixture-averaged +f.transport_model = 'Mix' + +# Setting mesh refinement criteria +f.set_refine_criteria(ratio=2.0, slope=0.1, curve=0.1) + +# Solving the problem +f.solve(1, 'refine') + +# Showing the result +f.show_solution() + +# Saving the result +if ct.__version__ >= '2.5.0': + f.save('./RESULTS/%s.yaml' % mech, 'non-sooting',overwrite=True) +else: + f.save('./RESULTS/%s.xml' % mech, 'non-sooting') diff --git a/samples/python/AVBP/2-restoreBurner.py b/samples/python/AVBP/2-restoreBurner.py new file mode 100644 index 00000000000..3dd46de3365 --- /dev/null +++ b/samples/python/AVBP/2-restoreBurner.py @@ -0,0 +1,54 @@ +# Importing necessary libraries +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Setting the mechanism name +mech = 'BISETTI' + +# Creating gas object +#if cantera version is 2.5.0 or higher, use the following line instead +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/%s.yaml' % mech) +else: + gas = ct.Solution('./inputs/%s.cti' % mech) + +# Loading experimental data (temperature vs. height) +z, T = np.genfromtxt('./inputs/T_vs_x.dat').T + +# Creating flame object of the same size as the experimental flame with 25 soot sections +f = ct.BurnerFlame(gas=gas, width=z[-1], sections = 25) + +# Setting transport model +f.transport_model = 'Mix' + +# Setting up soot calculation +f.soot_setup(precursors =['A2'], + retroaction =True, + condensation =True, + coagulation =True, + surface_growth =True, + oxidation =True, + #fractal_aggregates=True, + radiation =True, + trash_section =-1, + #show_sections = True + ) + +# Restoring the non-sooting flame +if ct.__version__ >= '2.5.0': + f.restore('./RESULTS/%s.yaml' % mech, 'non-sooting') +else: + f.restore('./RESULTS/%s.xml' % mech, 'non-sooting') +f.radiation_enabled = True + +# Solving the sooting flame +f.solve(1,refine_grid='disabled') + +# # Saving the result +if ct.__version__ >= '2.5.0': + f.save('./RESULTS/%s.yaml' % mech,'sooting',overwrite=True) +else: + f.save('./RESULTS/%s.xml' % mech,'sooting') \ No newline at end of file diff --git a/samples/python/AVBP/3-plotBurner.py b/samples/python/AVBP/3-plotBurner.py new file mode 100644 index 00000000000..60388f4e7a8 --- /dev/null +++ b/samples/python/AVBP/3-plotBurner.py @@ -0,0 +1,53 @@ +# Importing necessary libraries +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Setting the mechanism name +mech = 'BISETTI' + +# Creating gas object +#if cantera version is 2.5.0 or higher, use the following line instead +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/%s.yaml' % mech) +else: + gas = ct.Solution('./inputs/%s.cti' % mech) + +# Loading experimental data (temperature vs. height) +z, T = np.genfromtxt('./inputs/T_vs_x.dat').T + +# Creating flame object of the same size as the experimental flame with 25 soot sections +f = ct.BurnerFlame(gas=gas, width=z[-1], sections=25) + +# Setting up soot computation +f.soot_setup(precursors =['A2'], + #fractal_aggregates=True, + trash_section =-1 + ) + +# Restoring the sooting flame +if ct.__version__ >= '2.5.0': + f.restore('./RESULTS/%s.yaml' % mech, 'sooting') +else: + f.restore('./RESULTS/%s.xml' % mech, 'sooting') + +# Plot volume fraction +# Particles under 2nm and in last section are excluded +plt.figure(0) +plt.plot(f.grid * 100, f.soot_fv(min=2e-7, last=-1)) +plt.yscale('log') +plt.ylabel('Volume fraction') +plt.xlabel('HAB ($cm$)') + +# Plot particles number density +# Particles under 2nm and in last section are excluded +plt.figure(1) +plt.plot(f.grid * 100, f.soot_Np(min=2e-7, last=-1)) +plt.yscale('log') +plt.ylabel('Soot particles number density ($cm^{-3}$)') +plt.xlabel('HAB ($cm$)') + +# Displaying graphs +plt.show() diff --git a/samples/python/AVBP/ARC.py b/samples/python/AVBP/ARC.py new file mode 100644 index 00000000000..edc2a530c53 --- /dev/null +++ b/samples/python/AVBP/ARC.py @@ -0,0 +1,45 @@ +import cantera as ct +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +p = 1e5 +tin = 400.0 +phi = 1.0 +fuel = {'CH4':1} +oxidizer = {'O2': 1, 'N2': 3.76} + +ct.compile_fortran('./inputs/Lu_ARC.f90') + +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/Lu_ARC.yaml') +else: + gas = ct.Solution('./inputs/Lu_ARC.cti') + +gas.TP = tin, p +gas.set_equivalence_ratio(phi, fuel, oxidizer) +# gas.transport_model = 'UnityLewis' + +loglevel = 1 +refine_grid = 'refine' + +f = ct.FreeFlame(gas, width=0.02) +f.inlet.X = gas.X +f.inlet.T = gas.T + +f.energy_enabled = True +f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05, prune=0.01) +f.set_max_jac_age(10, 10) +f.set_time_step(1e-8, [10, 20, 40, 80, 100, 100, 150,]) +f.max_time_step_count = 500 + +f.solve(loglevel, refine_grid) + +if ct.__version__ >= '2.5.0': + plt.plot(f.flame.grid, f.velocity) +else: + plt.plot(f.flame.grid, f.u) + +plt.xlabel('Flame grid [m]') +plt.ylabel('Velocity [m/s]') +plt.show() \ No newline at end of file diff --git a/samples/python/AVBP/FLAMELET.py b/samples/python/AVBP/FLAMELET.py new file mode 100644 index 00000000000..f7a367acad6 --- /dev/null +++ b/samples/python/AVBP/FLAMELET.py @@ -0,0 +1,111 @@ +import cantera as ct +import time +import numpy as np +from scipy.special import erfinv, erfcinv, erf +from scipy import integrate +import matplotlib.pyplot as plt + +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +#gas init + +T = 300.0 # temperature +P = 101325.0 # pressure + +rho_o = P / (8.314 / 0.032 * T) # oxidizer density +tin_o = 300.0 # oxidizer inlet temperature +mdot_o = 0.8 # kg/m^2/s +comp_o = 'O2:1' # oxidizer composition +u_o = mdot_o / rho_o # oxidizer speed + +rho_f = P / (8.314 / 0.016 * T) # fuel density +tin_f = 300.0 # fuel inlet temperature +mdot_f = 0.2 # kg/m^2/s +comp_f = 'CH4:1' # fuel composition +u_f = mdot_f / rho_f # fuel speed + +width = 1.0 # width +SR = (u_o + u_f) / (width) # strain rate + +if ct.__version__ >= '2.5.0': + ct.compile_fortran('./inputs/Lu_ARC.f90') + gas_1 = ct.Solution('./inputs/Lu_ARC.yaml') +else: + gas_1 = ct.Solution('./inputs/Lu.cti') + +gas_1.TP = T, P + +#flamelet creation +plt.rcParams['figure.figsize'] = (14, 10) + +initial_grid = np.linspace(0,width,11) # initial grid for the calculation + +f_1 = ct.Flamelet(gas_1) # Flamelet object creation + +f_1.fuel_inlet.mdot = mdot_f # Fuel inlet conditions +f_1.fuel_inlet.Y = comp_f +f_1.fuel_inlet.T = tin_f + # Oxidizer inlet conditions +f_1.oxidizer_inlet.mdot = mdot_o +f_1.oxidizer_inlet.Y = comp_o +f_1.oxidizer_inlet.T = tin_o +chist = SR/np.pi*(np.exp(-2*((erfinv(1-2*0.2))**2))) +f_1.ChiSt = chist # Stochiometric scalar dissipation rate + +f_1.set_initial_guess() + +# plt.plot(f_1.flame.grid, f_1.T) + +# Calculation properties + +loglevel = 1 +f_1.set_max_jac_age(1, 1) +f_1.set_time_step(1.e-9, [50, 100, 150]) +f_1.energy_enabled = True +f_1.set_refine_criteria(ratio=4, slope=0.1, curve=0.1) + +# Solver +t1_A = time.time() +f_1.solve(loglevel, refine_grid = 'refine') +t1_B = time.time() + +if ct.__version__ >= '2.5.0': + f_1.save('./RESULTS/CH4-O2-converged-flamelet-Lu.yaml', 'Lu.yaml-zspace',overwrite=True) +else: + f_1.save('./RESULTS/CH4-O2-converged-flamelet-Lu.xml') + +# Calculation of the heat release +hr_1 = -np.sum(f_1.standard_enthalpies_RT * f_1.net_production_rates, 0) * ct.gas_constant * f_1.T +# print('Heat release rate = ', hr_1) + +plt.rcParams['figure.figsize'] = (14, 10) + +# Get interesting indices for computation of species +fuel_species = 'CH4' +ifuel = gas_1.species_index(fuel_species) +io2 = gas_1.species_index('O2') +ico = gas_1.species_index('CO') + +# Initiate interesting vectors +ch4_1 = np.zeros(f_1.flame.n_points,'d') +o2_1 = np.zeros(f_1.flame.n_points,'d') +co_1 = np.zeros(f_1.flame.n_points,'d') + +# Computes interesting quantities for analyzing a counter-flow flame +for n in range(f_1.flame.n_points): + f_1.set_gas_state(n) + ch4_1[n]= gas_1.Y[ifuel] + o2_1[n]= gas_1.Y[io2] + co_1[n]= gas_1.Y[ico] + +T_1 = f_1.T + +plt.plot(f_1.flame.grid,T_1/np.max(T_1),f_1.flame.grid,ch4_1/np.max(ch4_1), + f_1.flame.grid,o2_1/np.max(o2_1),f_1.flame.grid,co_1/np.max(co_1), f_1.flame.grid,hr_1/np.max(hr_1)) +plt.title(r'$T_{adiabatic}, Y_{CH_4}, Y_{O_2}, Y_{CO}$, HR vs. Mixture fraction',fontsize=25) +plt.xlabel(r'Mixture fraction', fontsize=15) +plt.ylabel('Normalized values of different quantities',fontsize=15) +plt.legend(['Temperature','$Y_{CH_4}$', '$Y_{O_2}$', '$Y_{CO}$', 'HR'],fontsize=15) + +plt.show() \ No newline at end of file diff --git a/samples/python/AVBP/PEA.py b/samples/python/AVBP/PEA.py new file mode 100644 index 00000000000..98b248dcafd --- /dev/null +++ b/samples/python/AVBP/PEA.py @@ -0,0 +1,50 @@ +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Parameters of the solver +loglevel = 1 +refine_grid = 'refine' + +if ct.__version__ >= '2.5.0': + mechanism_list = ['gri30.yaml', './inputs/BFER_methane.yaml', './inputs/BFER_methane.yaml'] +else: + mechanism_list = ['gri30.cti', './inputs/BFER_methane.cti', './inputs/BFER_methane.cti'] +gas_list = ['', 'BFER_nopea', 'BFER_pea'] + +for mechanism_name, gas_name in zip(mechanism_list, gas_list): + # Setting up the gas object (operating conditions) + gas = ct.Solution(mechanism_name, gas_name) + p = 1e5 + tin = 473.0 + phi = 1.4 + fuel = {'CH4': 1} + oxidizer = {'O2': 1, 'N2': 3.76} + gas.TP = tin, p + gas.set_equivalence_ratio(phi, fuel, oxidizer) + + # Setting up the flame object + f = ct.FreeFlame(gas, width=0.2) # Careful about the domain size if you want to retrieve the same profile ! + f.inlet.X = gas.X + f.inlet.T = gas.T + + f.energy_enabled = True + f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05, prune=0.01) + f.set_max_jac_age(10, 10) + f.set_time_step(1e-8, [10, 20, 40, 80, 100, 100, 150]) + f.max_time_step_count = 5000 + + f.solve(loglevel, refine_grid) + + # Checking the results + if ct.__version__ >= '2.5.0': + plt.plot(f.flame.grid, f.velocity, label=mechanism_name + ' - ' + gas_name) + else: + plt.plot(f.grid, f.u, label=mechanism_name + ' - ' + gas_name) + +plt.xlabel('Flame grid [m]') +plt.ylabel('Veloctity [m/s]') +plt.legend() +plt.show() diff --git a/samples/python/AVBP/RESULTS/BISETTI.xml b/samples/python/AVBP/RESULTS/BISETTI.xml new file mode 100644 index 00000000000..239852c413e --- /dev/null +++ b/samples/python/AVBP/RESULTS/BISETTI.xml @@ -0,0 +1,7624 @@ + + + Thu Dec 28 11:45:10 2023 + none + + + + + + 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b/samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.yaml @@ -0,0 +1,1565 @@ +Lu.yaml-zspace: + generator: Cantera SolutionArray + cantera-version: 3.0.0 + git-commit: "'21efa45'" + date: Thu Dec 28 11:33:17 2023 + oxidizer_inlet: + size: 1 + type: inlet + points: 1 + mass-flux: 0.8 + temperature: 300.0 + pressure: 1.01325e+05 + mass-fractions: + O2: 1.0 + flame: + T: [300.0, 465.1904977036727, 620.4304130308964, 766.7641155145853, + 837.1831799934906, 906.0891373118185, 973.6181617938894, + 1039.874136216077, 1168.945333665799, 1293.721873666220, + 1414.432289112165, 1531.177474977598, 1643.874262033837, + 1752.211757862348, 1855.670760021945, 1953.587053580184, + 2045.258460204648, 2130.093250683040, 2207.750479699913, + 2278.211584911320, 2341.760858897393, 2398.901539766076, + 2450.253919797286, 2496.469874814826, 2538.179323539410, + 2610.274465703083, 2670.316382322947, 2721.084262048567, + 2764.597651519653, 2802.326986405840, 2835.356037898136, + 2864.495662924666, 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2.097239934018185e-23, + 2.029223671651144e-23, 1.039150043002606e-22, 8.572315829734414e-25, + 9.969350204483684e-26, 2.206213741426378e-26, 8.491437863994048e-27, + 4.716602785763271e-27, 3.074147504932471e-27, 2.066824137239012e-27, + 1.340188612079251e-27, 7.845386992529860e-28, 3.490018573822431e-28, 0.0] + type: flamelet-flow + size: 144 + points: 145 + tolerances: + steady-reltol: 1.0e-04 + steady-abstol: 1.0e-09 + transient-reltol: 1.0e-04 + transient-abstol: 1.0e-11 + transport-model: mixture-averaged + phase: + name: gas + source: ././inputs/Lu.yaml + radiation-enabled: false + energy-enabled: true + Soret-enabled: false + species-enabled: true + refine-criteria: + ratio: 4.0 + slope: 0.1 + curve: 0.1 + prune: 0.0 + grid-min: 1.0e-10 + max-points: 1000 + basis: mass + components: [grid, T, D, H2, H, O, O2, OH, H2O, HO2, H2O2, CH3, CH4, CO, CO2, CH2O, + CH3OH, C2H2, C2H4, C2H6, CH2CO, N2] + fuel_inlet: + size: 1 + type: inlet + points: 1 + mass-flux: 0.2 + temperature: 300.0 + pressure: 1.01325e+05 + mass-fractions: + CH4: 1.0 diff --git a/samples/python/AVBP/THICKENING.py b/samples/python/AVBP/THICKENING.py new file mode 100644 index 00000000000..94ee0d1860a --- /dev/null +++ b/samples/python/AVBP/THICKENING.py @@ -0,0 +1,67 @@ +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +p = 101325 # pressure +tin = 300.0 # unburned gas temperature +phi = 0.8 # equivalence ratio + +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/BFER_methane.yaml') +else: + gas = ct.Solution('./inputs/BFER_methane.cti') + +m = gas.n_species +x = np.zeros(m,'d') +fuel_species = 'CH4' +ifuel = gas.species_index(fuel_species) +io2 = gas.species_index('O2') + +refine_grid = "disabled" +tol_ss = [1.0e-5, 1.0e-8] # [rtol atol] for steady-state problem +tol_ts = [1.0e-5, 1.0e-8] # [rtol atol] for time stepping +loglevel = 1 # amount of diagnostic output (0 to 5) + +n_points = 1000 +F = [1.0, 2.0, 5.0, 10.0, 15.0, 20.0] +temperature = [] +position = [] + +for ind_thick, thick in enumerate(F): + gas.set_equivalence_ratio(phi, 'CH4:1', 'O2:1.0, N2:3.76') + gas.TP = tin, p + initial_grid = np.linspace(0, 0.02, int(1000/thick)) + f = ct.FreeFlame(gas, grid=initial_grid) + + # This is where thickening is applied + f.flame.thick = thick + + f.energy_enabled = True + f.flame.set_steady_tolerances(default=tol_ss) + f.flame.set_transient_tolerances(default=tol_ts) + f.inlet.X = gas.X + f.inlet.T = tin + #f.set_refine_criteria(ratio = 7.0, slope = 1, curve = 1) + f.set_max_jac_age(50, 50) + f.set_time_step(5.e-06, [10, 20, 80]) #s + #f.set_refine_criteria(ratio = 2.0, slope = 0.02, curve = 0.02, prune = 0.01) + f.solve(loglevel, refine_grid) + + temperature.append(f.T) + position.append(f.flame.grid) + +fig = plt.figure(figsize=(18,16)) +a=fig.add_subplot(111) +for ind_thick, thick in enumerate(F): + a.plot(position[ind_thick],temperature[ind_thick], label="F = "+str(thick)) +plt.title(r'$T_{adiabatic}$ vs. Position', fontsize=25) +plt.xlabel(r'Position [m]', fontsize=20) +plt.ylabel("Adiabatic Flame Temperature [K]", fontsize=20) +plt.xticks(fontsize=15) +plt.yticks(fontsize=15) +#a.xaxis.set_major_locator(MaxNLocator(10)) # this controls the number of tick marks on the axis +plt.legend(fontsize=15) + +plt.show() \ No newline at end of file diff --git a/samples/python/AVBP/inputs/BFER_methane.cti b/samples/python/AVBP/inputs/BFER_methane.cti new file mode 100755 index 00000000000..d8fde74b17b --- /dev/null +++ b/samples/python/AVBP/inputs/BFER_methane.cti @@ -0,0 +1,149 @@ +# CH4_BFER mechanisme: CH4 + 1.5 O2 => CO +2H2O +# CO + 0.5 O2 <=> CO2 +# +# Transport data from file ../transport/gri30_tran.dat. + +units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol") + +ideal_gas(name = "BFER_nopea", + elements = " O H C N Ar", + species = """ CH4 CO2 CO O2 H2O N2 """, + reactions = "all", + transport = "AVBP", + initial_state = state(temperature = 300.0, + pressure = OneAtm) ) + +ideal_gas(name = "BFER_pea", + elements = " O H C N Ar", + species = """ CH4 CO2 CO O2 H2O N2 """, + reactions = "all", + transport = "AVBP", + initial_state = state(temperature = 300.0, + pressure = OneAtm) ) + +#------------------------------------------------------------------------------- +# Species data +#------------------------------------------------------------------------------- + +species(name = "O2", + atoms = " O:2 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 3.782456360E+00, -2.996734160E-03, + 9.847302010E-06, -9.681295090E-09, 3.243728370E-12, + -1.063943560E+03, 3.657675730E+00] ), + NASA( [ 1000.00, 3500.00], [ 3.282537840E+00, 1.483087540E-03, + -7.579666690E-07, 2.094705550E-10, -2.167177940E-14, + -1.088457720E+03, 5.453231290E+00] ) + ), + transport = gas_transport( + geom = "linear", + diam = 3.46, + well_depth = 107.40, + polar = 1.60, + rot_relax = 3.80), + note = "TPIS89" + ) + +species(name = "H2O", + atoms = " H:2 O:1 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 4.198640560E+00, -2.036434100E-03, + 6.520402110E-06, -5.487970620E-09, 1.771978170E-12, + -3.029372670E+04, -8.490322080E-01] ), + NASA( [ 1000.00, 3500.00], [ 3.033992490E+00, 2.176918040E-03, + -1.640725180E-07, -9.704198700E-11, 1.682009920E-14, + -3.000429710E+04, 4.966770100E+00] ) + ), + transport = gas_transport( + geom = "nonlinear", + diam = 2.60, + well_depth = 572.40, + dipole = 1.84, + rot_relax = 4.00), + note = "L 8/89" + ) + +species(name = "CH4", + atoms = " C:1 H:4 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 5.149876130E+00, -1.367097880E-02, + 4.918005990E-05, -4.847430260E-08, 1.666939560E-11, + -1.024664760E+04, -4.641303760E+00] ), + NASA( [ 1000.00, 3500.00], [ 7.485149500E-02, 1.339094670E-02, + -5.732858090E-06, 1.222925350E-09, -1.018152300E-13, + -9.468344590E+03, 1.843731800E+01] ) + ), + transport = gas_transport( + geom = "nonlinear", + diam = 3.75, + well_depth = 141.40, + polar = 2.60, + rot_relax = 13.00), + note = "L 8/88" + ) + +species(name = "CO", + atoms = " C:1 O:1 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 3.579533470E+00, -6.103536800E-04, + 1.016814330E-06, 9.070058840E-10, -9.044244990E-13, + -1.434408600E+04, 3.508409280E+00] ), + NASA( [ 1000.00, 3500.00], [ 2.715185610E+00, 2.062527430E-03, + -9.988257710E-07, 2.300530080E-10, -2.036477160E-14, + -1.415187240E+04, 7.818687720E+00] ) + ), + transport = gas_transport( + geom = "linear", + diam = 3.65, + well_depth = 98.10, + polar = 1.95, + rot_relax = 1.80), + note = "TPIS79" + ) + +species(name = "CO2", + atoms = " C:1 O:2 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 2.356773520E+00, 8.984596770E-03, + -7.123562690E-06, 2.459190220E-09, -1.436995480E-13, + -4.837196970E+04, 9.901052220E+00] ), + NASA( [ 1000.00, 3500.00], [ 3.857460290E+00, 4.414370260E-03, + -2.214814040E-06, 5.234901880E-10, -4.720841640E-14, + -4.875916600E+04, 2.271638060E+00] ) + ), + transport = gas_transport( + geom = "linear", + diam = 3.76, + well_depth = 244.00, + polar = 2.65, + rot_relax = 2.10), + note = "L 7/88" + ) + +species(name = "N2", + atoms = " N:2 ", + thermo = ( + NASA( [ 300.00, 1000.00], [ 3.298677000E+00, 1.408240400E-03, + -3.963222000E-06, 5.641515000E-09, -2.444854000E-12, + -1.020899900E+03, 3.950372000E+00] ), + NASA( [ 1000.00, 5000.00], [ 2.926640000E+00, 1.487976800E-03, + -5.684760000E-07, 1.009703800E-10, -6.753351000E-15, + -9.227977000E+02, 5.980528000E+00] ) + ), + transport = gas_transport( + geom = "linear", + diam = 3.62, + well_depth = 97.53, + polar = 1.76, + rot_relax = 4.00), + note = "121286" + ) + +#------------------------------------------------------------------------------- +# Reaction data +#------------------------------------------------------------------------------- +# Reaction +reaction( " CH4 + 1.5 O2 => CO + 2 H2O ", [4.9E+09, 0.0, 35500], order="CH4:0.5 O2:0.65 ") + +# Reaction 2 +reaction( " CO + 0.5 O2 <=> CO2", [2.00E+08, 0.7, 12000]) \ No newline at end of file diff --git a/samples/python/AVBP/inputs/BFER_methane.yaml b/samples/python/AVBP/inputs/BFER_methane.yaml new file mode 100644 index 00000000000..e063132325b --- /dev/null +++ b/samples/python/AVBP/inputs/BFER_methane.yaml @@ -0,0 +1,151 @@ +description: |- + CH4_BFER mechanisme: CH4 + 1.5 O2 => CO +2H2O + CO + 0.5 O2 <=> CO2 + + Transport data from file ../transport/gri30_tran.dat. + +generator: cti2yaml +cantera-version: 3.0.0 +date: Tue, 19 Dec 2023 15:25:36 +0100 +input-files: [BFER_methane.cti] + +units: {length: cm, quantity: mol, activation-energy: cal/mol} + +phases: +- name: BFER_nopea + thermo: ideal-gas + elements: [O, H, C, N, Ar] + species: [CH4, CO2, CO, O2, H2O, N2] + kinetics: gas + reactions: all + transport: AVBP + state: + T: 300.0 + P: 1.01325e+05 +- name: BFER_pea + thermo: ideal-gas + elements: [O, H, C, N, Ar] + species: [CH4, CO2, CO, O2, H2O, N2] + kinetics: gas + reactions: all + transport: AVBP + state: + T: 300.0 + P: 1.01325e+05 + +species: +- name: O2 + composition: {O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.78245636, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09, 3.24372837e-12, + -1063.94356, 3.65767573] + - [3.28253784, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10, -2.16717794e-14, + -1088.45772, 5.45323129] + transport: + model: gas + geometry: linear + diameter: 3.46 + well-depth: 107.4 + polarizability: 1.6 + rotational-relaxation: 3.8 + note: TPIS89 +- name: H2O + composition: {H: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19864056, -2.0364341e-03, 6.52040211e-06, -5.48797062e-09, 1.77197817e-12, + -3.02937267e+04, -0.849032208] + - [3.03399249, 2.17691804e-03, -1.64072518e-07, -9.7041987e-11, 1.68200992e-14, + -3.00042971e+04, 4.9667701] + transport: + model: gas + geometry: nonlinear + diameter: 2.6 + well-depth: 572.4 + dipole: 1.84 + rotational-relaxation: 4.0 + note: L 8/89 +- name: CH4 + composition: {C: 1, H: 4} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.14987613, -0.0136709788, 4.91800599e-05, -4.84743026e-08, 1.66693956e-11, + -1.02466476e+04, -4.64130376] + - [0.074851495, 0.0133909467, -5.73285809e-06, 1.22292535e-09, -1.0181523e-13, + -9468.34459, 18.437318] + transport: + model: gas + geometry: nonlinear + diameter: 3.75 + well-depth: 141.4 + polarizability: 2.6 + rotational-relaxation: 13.0 + note: L 8/88 +- name: CO + composition: {C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.57953347, -6.1035368e-04, 1.01681433e-06, 9.07005884e-10, -9.04424499e-13, + -1.4344086e+04, 3.50840928] + - [2.71518561, 2.06252743e-03, -9.98825771e-07, 2.30053008e-10, -2.03647716e-14, + -1.41518724e+04, 7.81868772] + transport: + model: gas + geometry: linear + diameter: 3.65 + well-depth: 98.1 + polarizability: 1.95 + rotational-relaxation: 1.8 + note: TPIS79 +- name: CO2 + composition: {C: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.35677352, 8.98459677e-03, -7.12356269e-06, 2.45919022e-09, -1.43699548e-13, + -4.83719697e+04, 9.90105222] + - [3.85746029, 4.41437026e-03, -2.21481404e-06, 5.23490188e-10, -4.72084164e-14, + -4.8759166e+04, 2.27163806] + transport: + model: gas + geometry: linear + diameter: 3.76 + well-depth: 244.0 + polarizability: 2.65 + rotational-relaxation: 2.1 + note: L 7/88 +- name: N2 + composition: {N: 2} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12, + -1020.8999, 3.950372] + - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15, + -922.7977, 5.980528] + transport: + model: gas + geometry: linear + diameter: 3.62 + well-depth: 97.53 + polarizability: 1.76 + rotational-relaxation: 4.0 + note: '121286' + +reactions: +- equation: ' CH4 + 1.5 O2 => CO + 2 H2O ' # Reaction 1 + rate-constant: {A: 4.9e+09, b: 0.0, Ea: 35500} + orders: {CH4: 0.5, O2: 0.65} +- equation: ' CO + 0.5 O2 <=> CO2' # Reaction 2 + rate-constant: {A: 2.0e+08, b: 0.7, Ea: 12000} diff --git a/samples/python/AVBP/inputs/BISETTI.cti b/samples/python/AVBP/inputs/BISETTI.cti new file mode 100644 index 00000000000..5d440837551 --- /dev/null +++ b/samples/python/AVBP/inputs/BISETTI.cti @@ -0,0 +1,1537 @@ +units(length='cm', time='s', quantity='mol', act_energy='cal/mol') + +ideal_gas(name='gas', + elements="N C H O Ar", + species="""AR N2 S-CH2 T-CH2 O H2 H + OH H2O O2 HO2 CH CO + HCO CH2O CH3 CO2 CH4 C2H3 + C2H4 C2H5 C2H HCCO C2H2 C3H3 + A-C3H5 N-C3H7 C2H6 P-C3H4 A-C3H4 A1 + A1- C5H5 C3H6 C4H8 C5H6 A2 + C5H10 C5H11 A1C2H2 A1CH2 A1CHO A1CH3 + C7H15 N-C7H16 A1C2H* A2- A1C2H""", + reactions='all', + transport='Mix', + initial_state=state(temperature=300.0, pressure=OneAtm)) + +#------------------------------------------------------------------------------- +# Species data +#------------------------------------------------------------------------------- + +species(name='AR', + atoms='Ar:1', + thermo=(NASA([200.00, 1000.00], + [ 2.50000000E+00, 0.00000000E+00, 0.00000000E+00, + 0.00000000E+00, 0.00000000E+00, -7.45375000E+02, + 4.37967491E+00]), + NASA([1000.00, 6000.00], + [ 2.50000000E+00, 0.00000000E+00, 0.00000000E+00, + 0.00000000E+00, 0.00000000E+00, -7.45375000E+02, + 4.37967491E+00])), + transport=gas_transport(geom='atom', + diam=3.33, + well_depth=136.5), + note='REFELEMENTG5/97') + +species(name=u'N2', + atoms='N:2', + thermo=(NASA([300.00, 1000.00], + [ 3.29867700E+00, 1.40824040E-03, -3.96322200E-06, + 5.64151500E-09, -2.44485400E-12, -1.02089990E+03, + 3.95037200E+00]), + NASA([1000.00, 5000.00], + [ 2.92664000E+00, 1.48797680E-03, -5.68476000E-07, + 1.00970380E-10, -6.75335100E-15, -9.22797700E+02, + 5.98052800E+00])), + transport=gas_transport(geom='linear', + diam=3.621, + well_depth=97.53, + polar=1.76, + rot_relax=4.0), + note=u'121286') + +species(name=u'S-CH2', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19860411E+00, -2.36661419E-03, 8.23296220E-06, + -6.68815981E-09, 1.94314737E-12, 5.04968163E+04, + -7.69118967E-01]), + NASA([1000.00, 3500.00], + [ 2.29203842E+00, 4.65588637E-03, -2.01191947E-06, + 4.17906000E-10, -3.39716365E-14, 5.09259997E+04, + 8.62650169E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'LS/93') + +species(name=u'T-CH2', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.76267867E+00, 9.68872143E-04, 2.79489841E-06, + -3.85091153E-09, 1.68741719E-12, 4.60040401E+04, + 1.56253185E+00]), + NASA([1000.00, 3500.00], + [ 2.87410113E+00, 3.65639292E-03, -1.40894597E-06, + 2.60179549E-10, -1.87727567E-14, 4.62636040E+04, + 6.17119324E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'LS/93') + +species(name=u'O', + atoms='O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.16826710E+00, -3.27931884E-03, 6.64306396E-06, + -6.12806624E-09, 2.11265971E-12, 2.91222592E+04, + 2.05193346E+00]), + NASA([1000.00, 3500.00], + [ 2.56942078E+00, -8.59741137E-05, 4.19484589E-08, + -1.00177799E-11, 1.22833691E-15, 2.92175791E+04, + 4.78433864E+00])), + transport=gas_transport(geom='atom', + diam=2.75, + well_depth=80.0), + note=u'L1/90') + +species(name=u'H2', + atoms='H:2', + thermo=(NASA([200.00, 1000.00], + [ 2.34433112E+00, 7.98052075E-03, -1.94781510E-05, + 2.01572094E-08, -7.37611761E-12, -9.17935173E+02, + 6.83010238E-01]), + NASA([1000.00, 3500.00], + [ 3.33727920E+00, -4.94024731E-05, 4.99456778E-07, + -1.79566394E-10, 2.00255376E-14, -9.50158922E+02, + -3.20502331E+00])), + transport=gas_transport(geom='linear', + diam=2.92, + well_depth=38.0, + polar=0.79, + rot_relax=280.0), + note=u'TPIS78') + +species(name=u'H', + atoms='H:1', + thermo=(NASA([200.00, 1000.00], + [ 2.50000000E+00, 7.05332819E-13, -1.99591964E-15, + 2.30081632E-18, -9.27732332E-22, 2.54736599E+04, + -4.46682853E-01]), + NASA([1000.00, 3500.00], + [ 2.50000001E+00, -2.30842973E-11, 1.61561948E-14, + -4.73515235E-18, 4.98197357E-22, 2.54736599E+04, + -4.46682914E-01])), + transport=gas_transport(geom='atom', + diam=2.05, + well_depth=145.0), + note=u'L7/88') + +species(name=u'OH', + atoms='H:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.12530561E+00, -3.22544939E-03, 6.52764691E-06, + -5.79853643E-09, 2.06237379E-12, 3.38153812E+03, + -6.90432960E-01]), + NASA([1000.00, 6000.00], + [ 2.86472886E+00, 1.05650448E-03, -2.59082758E-07, + 3.05218674E-11, -1.33195876E-15, 3.71885774E+03, + 5.70164073E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note=u'S9/01') + +species(name=u'H2O', + atoms='H:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19864056E+00, -2.03643410E-03, 6.52040211E-06, + -5.48797062E-09, 1.77197817E-12, -3.02937267E+04, + -8.49032208E-01]), + NASA([1000.00, 3500.00], + [ 3.03399249E+00, 2.17691804E-03, -1.64072518E-07, + -9.70419870E-11, 1.68200992E-14, -3.00042971E+04, + 4.96677010E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.605, + well_depth=572.4, + dipole=1.844, + rot_relax=4.0), + note=u'L8/89') + +species(name=u'O2', + atoms='O:2', + thermo=(NASA([200.00, 1000.00], + [ 3.78245636E+00, -2.99673416E-03, 9.84730201E-06, + -9.68129509E-09, 3.24372837E-12, -1.06394356E+03, + 3.65767573E+00]), + NASA([1000.00, 3500.00], + [ 3.28253784E+00, 1.48308754E-03, -7.57966669E-07, + 2.09470555E-10, -2.16717794E-14, -1.08845772E+03, + 5.45323129E+00])), + transport=gas_transport(geom='linear', + diam=3.458, + well_depth=107.4, + polar=1.6, + rot_relax=3.8), + note=u'TPIS89') + +species(name=u'HO2', + atoms='H:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30179801E+00, -4.74912051E-03, 2.11582891E-05, + -2.42763894E-08, 9.29225124E-12, 2.94808040E+02, + 3.71666245E+00]), + NASA([1000.00, 3500.00], + [ 4.01721090E+00, 2.23982013E-03, -6.33658150E-07, + 1.14246370E-10, -1.07908535E-14, 1.11856713E+02, + 3.78510215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=1.0), + note=u'L5/89') + +species(name=u'CH', + atoms='H:1 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.48981665E+00, 3.23835541E-04, -1.68899065E-06, + 3.16217327E-09, -1.40609067E-12, 7.07972934E+04, + 2.08401108E+00]), + NASA([1000.00, 3500.00], + [ 2.87846473E+00, 9.70913681E-04, 1.44445655E-07, + -1.30687849E-10, 1.76079383E-14, 7.10124364E+04, + 5.48497999E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note=u'TPIS79') + +species(name=u'CO', + atoms='C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.57953347E+00, -6.10353680E-04, 1.01681433E-06, + 9.07005884E-10, -9.04424499E-13, -1.43440860E+04, + 3.50840928E+00]), + NASA([1000.00, 3500.00], + [ 2.71518561E+00, 2.06252743E-03, -9.98825771E-07, + 2.30053008E-10, -2.03647716E-14, -1.41518724E+04, + 7.81868772E+00])), + transport=gas_transport(geom='linear', + diam=3.65, + well_depth=98.1, + polar=1.95, + rot_relax=1.8), + note=u'TPIS79') + +species(name=u'HCO', + atoms='H:1 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.22118584E+00, -3.24392532E-03, 1.37799446E-05, + -1.33144093E-08, 4.33768865E-12, 3.83956496E+03, + 3.39437243E+00]), + NASA([1000.00, 3500.00], + [ 2.77217438E+00, 4.95695526E-03, -2.48445613E-06, + 5.89161778E-10, -5.33508711E-14, 4.01191815E+03, + 9.79834492E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0), + note=u'L12/89') + +species(name=u'CH2O', + atoms='H:2 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.79372315E+00, -9.90833369E-03, 3.73220008E-05, + -3.79285261E-08, 1.31772652E-11, -1.43089567E+04, + 6.02812900E-01]), + NASA([1000.00, 3500.00], + [ 1.76069008E+00, 9.20000082E-03, -4.42258813E-06, + 1.00641212E-09, -8.83855640E-14, -1.39958323E+04, + 1.36563230E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0, + rot_relax=2.0), + note=u'L8/88') + 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-2.18859615E-12, 4.83995303E+03, + 3.25574963E+01]), + NASA([1000.00, 5000.00], + [ 4.88920629E+00, 4.22834537E-02, -1.85843100E-05, + 3.04124763E-09, 0.00000000E+00, 3.43475468E+03, + 3.43704878E+00])), + transport=gas_transport(geom='nonlinear', + diam=5.041, + well_depth=440.735), + note=u'000000') + +species(name=u'A1C2H2', + atoms='H:7 C:8', + thermo=(NASA([300.00, 1000.00], + [-6.31199276E+00, 9.51097942E-02, -9.56352102E-05, + 4.97780207E-08, -1.02323717E-11, 4.57330975E+04, + 5.35475222E+01]), + NASA([1000.00, 3000.00], + [ 5.85935080E+00, 4.72571459E-02, -2.69864733E-05, + 7.35311775E-09, -7.74900830E-13, 4.33198974E+04, + -5.22359403E+00])), + transport=gas_transport(geom='nonlinear', + diam=6.0, + well_depth=546.2, + dipole=0.13, + polar=15.0, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1CH2', + atoms='H:7 C:7', + thermo=(NASA([300.00, 1000.00], + [-6.07053038E+00, 8.35201507E-02, -7.41700083E-05, + 3.13153847E-08, -4.23670868E-12, 2.35894712E+04, + 5.07932172E+01]), + NASA([1000.00, 3000.00], + [ 3.30049696E+00, 4.80055340E-02, -2.78443022E-05, + 7.72371356E-09, -8.27154136E-13, 2.17498572E+04, + 5.42371919E+00])), + transport=gas_transport(geom='nonlinear', + diam=5.68, + well_depth=495.3, + dipole=0.43, + polar=12.3, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1CHO', + atoms='H:6 C:7 O:1', + thermo=(NASA([300.00, 1000.00], + [-3.47171048E+00, 6.92891889E-02, -4.32603509E-05, + 3.43871096E-09, 4.81010261E-12, -6.14558774E+03, + 4.14094024E+01]), + NASA([1000.00, 3000.00], + [ 1.87355756E+00, 5.26231551E-02, -3.17644962E-05, + 9.06403069E-09, -9.90306123E-13, -7.23603865E+03, + 1.49787009E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.68, + well_depth=495.3, + dipole=0.43, + polar=12.3, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1CH3', + atoms='H:8 C:7', + thermo=(NASA([300.00, 1000.00], + [-4.54072038E+00, 6.85427145E-02, -3.57113024E-05, + -4.19397642E-09, 7.41779795E-12, 4.64121087E+03, + 4.57564849E+01]), + NASA([1000.00, 3000.00], + [-1.01117220E+00, 5.85301912E-02, -3.47595069E-05, + 9.82180993E-09, -1.06680870E-12, 3.99363395E+03, + 2.83610783E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.68, + well_depth=495.3, + dipole=0.43, + polar=12.3, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'C7H15', + atoms='H:15 C:7', + thermo=(NASA([300.00, 1000.00], + [-3.79155767E-02, 7.56726570E-02, -4.07473634E-05, + 9.32678943E-09, -4.92360745E-13, -2.35605303E+03, + 3.37321506E+01]), + NASA([1000.00, 5000.00], + [ 3.74721159E+00, 6.49345162E-02, -3.01341025E-05, + 5.17418142E-09, 0.00000000E+00, -3.37018357E+03, + 1.42780413E+01])), + transport=gas_transport(geom='nonlinear', + diam=6.253, + well_depth=459.6, + rot_relax=1.0), + note=u'000000') + +species(name=u'N-C7H16', + atoms='H:16 C:7', + thermo=(NASA([300.00, 1000.00], + [-1.26836187E+00, 8.54355820E-02, -5.25346786E-05, + 1.62945721E-08, -2.02394925E-12, -2.56586565E+04, + 3.53732912E+01]), + NASA([1000.00, 5000.00], + [ 5.14079241E+00, 6.53078671E-02, -2.94827624E-05, + 4.93726726E-09, 0.00000000E+00, -2.72533890E+04, + 2.98195967E+00])), + transport=gas_transport(geom='nonlinear', + diam=6.253, + well_depth=459.6, + rot_relax=1.0), + note=u'000000') + +species(name=u'A1C2H*', + atoms='H:5 C:8', + thermo=(NASA([300.00, 1000.00], + [-4.42757639E+00, 8.36668645E-02, -8.70106362E-05, + 4.70285661E-08, -1.01816985E-11, 6.73302359E+04, + 4.48118287E+01]), + NASA([1000.00, 3000.00], + [ 7.23812069E+00, 3.83812109E-02, -2.18850731E-05, + 5.97161247E-09, -6.30351467E-13, 6.49528135E+04, + -1.17512654E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.72, + well_depth=535.6, + dipole=0.77, + polar=12.0, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A2-', + atoms='H:7 C:10', + thermo=(NASA([300.00, 1000.00], + [-8.02718034E+00, 1.02924518E-01, -8.34272010E-05, + 2.72135383E-08, -7.24559554E-13, 5.01363344E+04, + 6.08902264E+01]), + NASA([1000.00, 3000.00], + [ 3.22892303E+00, 6.31264486E-02, -3.80582381E-05, + 1.08454069E-08, -1.18342512E-12, 4.78400840E+04, + 5.82016697E+00])), + transport=gas_transport(geom='nonlinear', + diam=6.18, + well_depth=630.4, + polar=16.5, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1C2H', + atoms='H:6 C:8', + thermo=(NASA([300.00, 1000.00], + [-5.21036925E+00, 8.65551944E-02, -8.45007483E-05, + 4.21920706E-08, -8.16766167E-12, 3.52488620E+04, + 4.69445057E+01]), + NASA([1000.00, 3000.00], + [ 5.81520488E+00, 4.40872933E-02, -2.52053858E-05, + 6.90275228E-09, -7.31378908E-13, 3.30271906E+04, + -6.49320690E+00])), + transport=gas_transport(geom='nonlinear', + diam=5.72, + well_depth=535.6, + dipole=0.77, + polar=12.0, + rot_relax=1.0), + note=u'G3B3') + +#------------------------------------------------------------------------------- +# Reaction data +#------------------------------------------------------------------------------- + +# Reaction 1 +reaction('S-CH2 + N2 <=> T-CH2 + N2', [1.500000e+13, 0.0, 599.9]) + +# Reaction 2 +reaction('O + H2 <=> H + OH', [4.590000e+04, 2.7, 6259.56]) + +# Reaction 3 +three_body_reaction('H + O + M => OH + M', [9.430000e+18, -1.0, 0.0], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0') + +# Reaction 4 +three_body_reaction('H + OH + M => H2O + M', [4.400000e+22, -2.0, 0.0], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:6.3 CH4:2.0 C2H6:3.0') + +# Reaction 5 +reaction('OH + H2 <=> H + H2O', [1.730000e+08, 1.51, 3429.73]) + +# Reaction 6 +reaction('2 OH <=> O + H2O', [3.970000e+04, 2.4, -2110.42]) + +# Reaction 7 +falloff_reaction('H + O2 (+ M) => HO2 (+ M)', + kf=[5.120000e+12, 0.44, 0.0], + kf0=[6.330000e+19, -1.4, 0.0], + efficiencies='H2:0.75 H2O:11.89 CO2:2.18 CO:1.09 O2:0.85', + falloff=Troe(A=0.5, T3=0.0, T1=10000000000.0, T2=10000000000.0)) + +# Reaction 8 +reaction('H + O2 <=> O + OH', [2.640000e+16, -0.67, 17041.11]) + +# Reaction 9 +reaction('HO2 + H => O2 + H2', [3.649000e+06, 2.07, -1092.26]) + +# Reaction 10 +reaction('HO2 + H => O + H2O', [3.970000e+12, 0.0, 671.61]) + +# Reaction 11 +reaction('HO2 + H => 2 OH', [7.490000e+13, 0.0, 635.76]) + +# Reaction 12 +reaction('HO2 + O => OH + O2', [4.000000e+13, 0.0, 0.0]) + +# Reaction 13 +reaction('HO2 + OH => H2O + O2', [2.380000e+13, 0.0, -499.52], + options='duplicate') + +# Reaction 14 +reaction('HO2 + OH => H2O + O2', [1.000000e+16, 0.0, 17330.31], + options='duplicate') + +# Reaction 15 +reaction('CH + O => CO + H', [5.700000e+13, 0.0, 0.0]) + +# Reaction 16 +reaction('CH + OH => HCO + H', [3.000000e+13, 0.0, 0.0]) + +# Reaction 17 +reaction('CH + H2 <=> T-CH2 + H', [1.080000e+14, 0.0, 3109.46]) + +# Reaction 18 +reaction('CH + H2O => CH2O + H', [5.710000e+12, 0.0, -755.26]) + +# Reaction 19 +reaction('CH + O2 => HCO + O', [6.710000e+13, 0.0, 0.0]) + +# Reaction 20 +reaction('T-CH2 + O => HCO + H', [8.000000e+13, 0.0, 0.0]) + +# Reaction 21 +reaction('T-CH2 + OH => CH2O + H', [2.000000e+13, 0.0, 0.0]) + +# Reaction 22 +reaction('T-CH2 + OH <=> CH + H2O', [1.130000e+07, 2.0, 2999.52]) + +# Reaction 23 +reaction('T-CH2 + H2 <=> H + CH3', [5.000000e+05, 2.0, 7229.92]) + +# Reaction 24 +reaction('T-CH2 + O2 => CO2 + 2 H', [5.800000e+12, 0.0, 1500.96]) + +# Reaction 25 +reaction('T-CH2 + O2 => CH2O + O', [2.400000e+12, 0.0, 1500.96]) + +# Reaction 26 +reaction('T-CH2 + O2 => OH + H + CO', [5.000000e+12, 0.0, 1500.96]) + +# Reaction 27 +reaction('S-CH2 + H2 <=> CH3 + H', [7.000000e+13, 0.0, 0.0]) + +# Reaction 28 +reaction('S-CH2 + O2 => H + OH + CO', [2.800000e+13, 0.0, 0.0]) + +# Reaction 29 +reaction('S-CH2 + O2 => CO + H2O', [1.200000e+13, 0.0, 0.0]) + +# Reaction 30 +falloff_reaction('S-CH2 + H2O (+ M) => CH2O + H2 (+ M)', + kf=[4.820000e+17, -1.16, 1144.84], + kf0=[1.880000e+38, -6.36, 5040.63], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.6027, T3=208.0, T1=3922.0, T2=10180.0)) + +# Reaction 31 +reaction('S-CH2 + H2O <=> T-CH2 + H2O', [3.000000e+13, 0.0, 0.0]) + +# Reaction 32 +reaction('S-CH2 + H2O => H2 + CH2O', [6.820000e+10, 0.25, -934.51]) + +# Reaction 33 +falloff_reaction('CH3 + H (+ M) <=> CH4 (+ M)', + kf=[6.920000e+13, 0.18, 0.0], + kf0=[3.470000e+38, -6.3, 5074.09], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:3.0 C2H6:3.0') + +# Reaction 34 +reaction('CH3 + O => CH2O + H', [5.060000e+13, 0.0, 0.0]) + +# Reaction 35 +reaction('CH3 + O => H + H2 + CO', [3.370000e+13, 0.0, 0.0]) + +# Reaction 36 +falloff_reaction('CH3 + OH (+ M) => CH2O + H2 (+ M)', + kf=[2.790000e+18, -1.43, 1331.26], + kf0=[4.000000e+36, -5.92, 3140.54], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.412, T3=195.0, T1=5900.0, T2=6394.0)) + +# Reaction 37 +reaction('CH3 + OH <=> T-CH2 + H2O', [5.600000e+07, 1.6, 5420.65]) + +# Reaction 38 +reaction('CH3 + OH <=> S-CH2 + H2O', [6.440000e+17, -1.34, 1417.3]) + +# Reaction 39 +reaction('CH3 + O2 => CH2O + O + H', [1.380000e+13, 0.0, 30480.4]) + +# Reaction 40 +reaction('CH3 + O2 => CH2O + OH', [5.870000e+11, 0.0, 13840.82]) + +# Reaction 41 +reaction('CH3 + HO2 => CH2O + OH + H', [1.000000e+13, 0.0, 0.0]) + +# Reaction 42 +reaction('CH3 + HO2 => CH4 + O2', [3.610000e+12, 0.0, 0.0]) + +# Reaction 43 +reaction('CH3 + CH => C2H3 + H', [3.000000e+13, 0.0, 0.0]) + +# Reaction 44 +reaction('CH3 + T-CH2 => C2H4 + H', [1.000000e+14, 0.0, 0.0]) + +# Reaction 45 +reaction('2 CH3 <=> C2H5 + H', [6.840000e+12, 0.1, 10599.9]) + +# Reaction 46 +reaction('2 CH3 => S-CH2 + CH4', [2.632000e+12, -0.06, 13661.57]) + +# Reaction 47 +reaction('CH4 + H <=> CH3 + H2', [6.600000e+08, 1.62, 10841.3]) + +# Reaction 48 +reaction('CH4 + O <=> CH3 + OH', [1.020000e+09, 1.5, 8599.43]) + +# Reaction 49 +reaction('CH4 + OH <=> CH3 + H2O', [1.000000e+08, 1.6, 3119.02]) + +# Reaction 50 +reaction('CH4 + CH => C2H4 + H', [6.000000e+13, 0.0, 0.0]) + +# Reaction 51 +reaction('CH4 + T-CH2 <=> 2 CH3', [2.460000e+06, 2.0, 8269.6]) + +# Reaction 52 +falloff_reaction('CO + O (+ M) => CO2 (+ M)', + kf=[1.360000e+10, 0.0, 2385.28], + kf0=[1.170000e+24, -2.79, 4192.16], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=1.0, T3=1.0, T1=10000000.0, T2=10000000.0)) + +# Reaction 53 +reaction('CO + OH <=> CO2 + H', [8.000000e+11, 0.14, 7351.82], + options='duplicate') + +# Reaction 54 +reaction('CO + OH <=> CO2 + H', [8.780000e+10, 0.03, -16.73], + options='duplicate') + +# Reaction 55 +reaction('CO + HO2 => CO2 + OH', [3.010000e+13, 0.0, 22999.52]) + +# Reaction 56 +reaction('CO + S-CH2 <=> CO + T-CH2', [9.000000e+12, 0.0, 0.0]) + +# Reaction 57 +reaction('HCO + H => CO + H2', [1.200000e+14, 0.0, 0.0]) + +# Reaction 58 +reaction('HCO + O => CO + OH', [3.000000e+13, 0.0, 0.0]) + +# Reaction 59 +reaction('HCO + O => CO2 + H', [3.000000e+13, 0.0, 0.0]) + +# Reaction 60 +reaction('HCO + OH => CO + H2O', [3.020000e+13, 0.0, 0.0]) + +# Reaction 61 +three_body_reaction('HCO + M <=> CO + H + M', [1.870000e+17, -1.0, 17000.48], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:0.0 CH4:2.0 C2H6:3.0') + +# Reaction 62 +reaction('HCO + H2O <=> CO + H + H2O', [2.240000e+18, -1.0, 17000.48]) + +# Reaction 63 +reaction('HCO + O2 => CO + HO2', [1.200000e+10, 0.81, -726.58]) + +# Reaction 64 +reaction('CH3 + HCO => CH4 + CO', [2.650000e+13, 0.0, 0.0]) + +# Reaction 65 +reaction('CH2O + H <=> HCO + H2', [5.740000e+07, 1.9, 2741.4]) + +# Reaction 66 +reaction('CH2O + O => HCO + OH', [3.900000e+13, 0.0, 3539.67]) + +# Reaction 67 +reaction('CH2O + OH => HCO + H2O', [3.430000e+09, 1.18, -446.94]) + +# Reaction 68 +reaction('CH3 + CH2O => CH4 + HCO', [3.320000e+03, 2.81, 5860.42]) + +# Reaction 69 +reaction('CO2 + CH => HCO + CO', [1.900000e+14, 0.0, 15791.11]) + +# Reaction 70 +reaction('CO2 + S-CH2 <=> CO2 + T-CH2', [7.000000e+12, 0.0, 0.0]) + +# Reaction 71 +reaction('CO2 + S-CH2 => CH2O + CO', [1.400000e+13, 0.0, 0.0]) + +# Reaction 72 +reaction('C2H + O => CH + CO', [5.000000e+13, 0.0, 0.0]) + +# Reaction 73 +reaction('C2H + OH => HCCO + H', [2.000000e+13, 0.0, 0.0]) + +# Reaction 74 +reaction('C2H + O2 => HCO + CO', [1.000000e+13, 0.0, -755.26]) + +# Reaction 75 +reaction('C2H + H2 <=> C2H2 + H', [3.310000e+06, 2.26, 901.05]) + +# Reaction 76 +falloff_reaction('C2H2 + H (+ M) <=> C2H3 (+ M)', + kf=[1.710000e+10, 1.27, 2707.93], + kf0=[6.340000e+31, -4.66, 3781.07], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.2122, T3=1.0, T1=-10210.0)) + +# Reaction 77 +reaction('C2H2 + O => HCCO + H', [8.100000e+06, 2.0, 1900.1]) + +# Reaction 78 +reaction('C2H2 + O => T-CH2 + CO', [1.250000e+07, 2.0, 1900.1]) + +# Reaction 79 +reaction('C2H2 + O => C2H + OH', [3.324000e+16, -0.44, 30697.9]) + +# Reaction 80 +reaction('C2H2 + OH => C2H + H2O', [2.630000e+06, 2.14, 17060.23]) + +# Reaction 81 +reaction('C2H2 + OH => CH3 + CO', [7.530000e+06, 1.55, 2105.64], + options='duplicate') + +# Reaction 82 +reaction('C2H2 + OH => CH3 + CO', [1.280000e+09, 0.73, 2578.87], + options='duplicate') + +# Reaction 83 +reaction('C2H2 + S-CH2 <=> C3H3 + H', [1.900000e+14, 0.0, 0.0]) + +# Reaction 84 +falloff_reaction('C2H3 + H (+ M) => C2H4 (+ M)', + kf=[6.080000e+12, 0.27, 279.64], + kf0=[1.400000e+30, -3.86, 3319.79], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.782, T3=207.5, T1=2663.0, T2=6095.0)) + +# Reaction 85 +reaction('C2H3 + H => C2H2 + H2', [3.000000e+13, 0.0, 0.0]) + +# Reaction 86 +reaction('C2H3 + O => CH3 + CO', [1.030000e+13, 0.21, -427.82]) + +# Reaction 87 +reaction('C2H3 + OH => C2H2 + H2O', [5.000000e+12, 0.0, 0.0]) + +# Reaction 88 +reaction('C2H3 + O2 => C2H2 + HO2', [1.340000e+06, 1.61, -384.8]) + +# Reaction 89 +reaction('C2H3 + O2 => CH3 + CO + O', [3.030000e+11, 0.29, 11.95]) + +# Reaction 90 +reaction('C2H3 + O2 => HCO + CH2O', [4.580000e+16, -1.39, 1015.77]) + +# Reaction 91 +reaction('C2H3 + HCO => C2H4 + CO', [9.000000e+13, 0.0, 0.0]) + +# Reaction 92 +reaction('C2H3 + CH3 => C2H2 + CH4', [9.030000e+12, 0.0, -764.82]) + +# Reaction 93 +reaction('C2H3 + CH3 <=> A-C3H5 + H', [1.930000e+18, -1.25, 7669.69]) + +# Reaction 94 +falloff_reaction('C2H4 + H (+ M) <=> C2H5 (+ M)', + kf=[1.370000e+09, 1.46, 1355.16], + kf0=[2.030000e+39, -6.64, 5769.6], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=-0.569, T3=299.0, T1=-9147.0, T2=152.4)) + +# Reaction 95 +reaction('C2H4 + H => C2H3 + H2', [1.330000e+06, 2.53, 12239.48]) + +# Reaction 96 +reaction('C2H4 + O => CH3 + CO + H', [7.660000e+09, 0.88, 1140.06]) + +# Reaction 97 +reaction('C2H4 + O => T-CH2 + CH2O', [7.150000e+04, 2.47, 929.73]) + +# Reaction 98 +reaction('C2H4 + O => CH3 + HCO', [3.890000e+08, 1.36, 886.71]) + +# Reaction 99 +reaction('C2H4 + OH => C2H3 + H2O', [1.310000e-01, 4.2, -860.42]) + +# Reaction 100 +reaction('C2H4 + OH => CH3 + CH2O', [3.750000e+36, -7.8, 7060.23]) + +# Reaction 101 +reaction('C2H4 + CH3 => C2H3 + CH4', [2.270000e+05, 2.0, 9199.33]) + +# Reaction 102 +falloff_reaction('C2H4 + CH3 (+ M) <=> N-C3H7 (+ M)', + kf=[2.550000e+06, 1.6, 5700.29], + kf0=[3.000000e+63, -14.6, 18169.22], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.1894, T3=277.0, T1=8748.0, T2=7891.0)) + +# Reaction 103 +falloff_reaction('C2H5 + H (+ M) <=> C2H6 (+ M)', + kf=[5.210000e+17, -0.99, 1579.83], + kf0=[1.990000e+41, -7.08, 6684.99], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.8422, T3=125.0, T1=2219.0, T2=6882.0)) + +# Reaction 104 +reaction('C2H5 + O => CH3 + CH2O', [3.170000e+13, 0.03, -394.36]) + +# Reaction 105 +reaction('C2H5 + O2 => C2H4 + HO2', [1.920000e+07, 1.02, -2033.94]) + +# Reaction 106 +reaction('C2H5 + HCO => C2H6 + CO', [1.200000e+14, 0.0, 0.0]) + +# Reaction 107 +reaction('C2H5 + HO2 => C2H6 + O2', [3.000000e+11, 0.0, 0.0]) + +# Reaction 108 +reaction('C2H5 + HO2 => CH3 + CH2O + OH', [3.100000e+13, 0.0, 0.0]) + +# Reaction 109 +falloff_reaction('C2H6 (+ M) <=> 2 CH3 (+ M)', + kf=[1.880000e+50, -9.72, 107342.26], + kf0=[3.720000e+65, -13.14, 101579.83], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.39, T3=100.0, T1=1900.0, T2=6000.0)) + +# Reaction 110 +reaction('C2H6 + H => C2H5 + H2', [1.700000e+05, 2.7, 5740.92]) + +# Reaction 111 +reaction('C2H6 + O => C2H5 + OH', [8.980000e+07, 1.92, 5690.73]) + +# Reaction 112 +reaction('C2H6 + OH => C2H5 + H2O', [1.610000e+06, 2.22, 740.92]) + +# Reaction 113 +reaction('C2H6 + CH3 => C2H5 + CH4', [8.430000e+14, 0.0, 22256.21]) + +# Reaction 114 +falloff_reaction('HCCO (+ M) => CO + CH (+ M)', + kf=[2.255000e+20, -1.44, 74732.31], + kf0=[1.213000e+35, -5.18, 76668.26], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.5757, T3=237.0, T1=1652.0, T2=5069.0)) + +# Reaction 115 +reaction('HCCO + H => S-CH2 + CO', [1.000000e+14, 0.0, 0.0]) + +# Reaction 116 +reaction('HCCO + O => H + 2 CO', [1.000000e+14, 0.0, 0.0]) + +# Reaction 117 +reaction('HCCO + O2 => OH + 2 CO', [4.200000e+10, 0.0, 853.25]) + +# Reaction 118 +reaction('2 HCCO => C2H2 + 2 CO', [1.000000e+13, 0.0, 0.0]) + +# Reaction 119 +reaction('HCCO + C2H2 => C3H3 + CO', [1.000000e+11, 0.0, 2999.52]) + +# Reaction 120 +reaction('HCCO + CH3 => C2H4 + CO', [5.000000e+13, 0.0, 0.0]) + +# Reaction 121 +reaction('HCCO + OH => 2 HCO', [1.000000e+13, 0.0, 0.0]) + +# Reaction 122 +reaction('C3H3 + H <=> P-C3H4', [7.940000e+29, -5.06, 4861.38]) + +# Reaction 123 +reaction('C3H3 + H <=> A-C3H4', [3.160000e+29, -5.0, 4710.8]) + +# Reaction 124 +reaction('C3H3 + OH => C2H4 + CO', [1.280000e+09, 0.73, 2578.87]) + +# Reaction 125 +reaction('C3H3 + O => C2H2 + CO + H', [6.950000e+13, 0.0, 0.0]) + +# Reaction 126 +reaction('C3H3 + O2 => CH3 + 2 CO', [1.700000e+05, 1.7, 1500.96]) + +# Reaction 127 +reaction('C3H3 + HO2 => OH + CO + C2H3', [8.000000e+11, 0.0, 0.0]) + +# Reaction 128 +reaction('2 C3H3 <=> A1', [1.870000e+46, -9.84, 16804.49]) + +# Reaction 129 +reaction('2 C3H3 <=> A1- + H', [5.770000e+37, -7.0, 31505.74]) + +# Reaction 130 +reaction('C3H3 + C2H2 <=> C5H5', [2.350000e+11, 0.0, 9995.22]) + +# Reaction 131 +reaction('P-C3H4 + H <=> C2H2 + CH3', [3.460000e+12, 0.44, 5463.67]) + +# Reaction 132 +reaction('P-C3H4 + H <=> C3H3 + H2', [8.500000e+04, 2.7, 5740.92]) + +# Reaction 133 +reaction('P-C3H4 + OH => C3H3 + H2O', [8.050000e+05, 2.22, 740.92]) + +# Reaction 134 +reaction('P-C3H4 + CH3 => C3H3 + CH4', [4.220000e+14, 0.0, 22256.21]) + +# Reaction 135 +reaction('P-C3H4 + O => HCCO + CH3', [4.050000e+06, 2.0, 1900.1]) + +# Reaction 136 +reaction('P-C3H4 + O => C2H4 + CO', [6.250000e+06, 2.0, 1900.1]) + +# Reaction 137 +reaction('P-C3H4 + OH => C2H5 + CO', [1.280000e+09, 0.73, 2578.87]) + +# Reaction 138 +reaction('A-C3H4 + H <=> C2H2 + CH3', [8.950000e+13, -0.02, 11250.0]) + +# Reaction 139 +reaction('A-C3H4 <=> P-C3H4', [7.760000e+39, -7.8, 78446.46]) + +# Reaction 140 +reaction('A-C3H4 + H <=> P-C3H4 + H', [2.470000e+15, -0.33, 6436.42]) + +# Reaction 141 +reaction('A-C3H4 + H => C3H3 + H2', [1.330000e+06, 2.53, 12239.48]) + +# Reaction 142 +reaction('A-C3H4 + OH => C3H3 + H2O', [1.310000e-01, 4.2, -860.42]) + +# Reaction 143 +reaction('A-C3H4 + CH3 => C3H3 + CH4', [2.270000e+05, 2.0, 9199.33]) + +# Reaction 144 +reaction('A-C3H4 + H <=> A-C3H5', [2.010000e+49, -10.77, 19622.37]) + +# Reaction 145 +reaction('A-C3H5 + H => A-C3H4 + H2', [9.560000e+03, 2.8, 3291.11]) + +# Reaction 146 +reaction('A-C3H5 + OH => A-C3H4 + H2O', [6.030000e+12, 0.0, 0.0]) + +# Reaction 147 +reaction('A-C3H5 + CH3 => A-C3H4 + CH4', [4.860000e+11, -0.32, -131.45]) + +# Reaction 148 +reaction('A-C3H5 + O2 => C2H2 + CH2O + OH', [9.710000e+20, -2.7, 24980.88]) + +# Reaction 149 +reaction('A-C3H5 + C3H3 => A1 + 2 H', [2.160000e+39, -7.74, 23852.77]) + +# Reaction 150 +falloff_reaction('C3H6 + H (+ M) <=> N-C3H7 (+ M)', + kf=[3.060000e+14, -0.37, 4032.03], + kf0=[6.260000e+38, -6.66, 7000.48], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=1.0, T3=1000.0, T1=1310.0, T2=48100.0)) + +# Reaction 151 +reaction('C3H6 <=> C2H3 + CH3', [4.040000e+42, -7.67, 111830.78]) + +# Reaction 152 +reaction('A-C3H5 + H <=> C3H6', [5.930000e+54, -11.76, 23549.24]) + +# Reaction 153 +reaction('C3H6 + H <=> C2H4 + CH3', [8.000000e+21, -2.39, 11180.69]) + +# Reaction 154 +reaction('C3H6 + O => 2 CH3 + CO', [1.200000e+08, 1.6, 327.44]) + +# Reaction 155 +reaction('C3H6 + O => C2H5 + HCO', [3.500000e+07, 1.6, -972.75]) + +# Reaction 156 +reaction('C3H6 + H => A-C3H5 + H2', [6.600000e+05, 2.54, 6756.69]) + +# Reaction 157 +reaction('C3H6 + O => A-C3H5 + OH', [9.650000e+04, 2.68, 3716.54]) + +# Reaction 158 +reaction('C3H6 + OH => A-C3H5 + H2O', [2.000000e+08, 1.46, 537.76]) + +# Reaction 159 +reaction('C3H6 + CH3 => A-C3H5 + CH4', [4.520000e-01, 3.65, 7153.44]) + +# Reaction 160 +reaction('C4H8 + H => C2H5 + C2H4', [7.680000e+12, 0.11, 1479.45]) + +# Reaction 161 +reaction('C4H8 => A-C3H5 + CH3', [5.000000e+15, 0.0, 70999.04]) + +# Reaction 162 +reaction('C5H5 + HO2 => O2 + C5H6', [2.561000e+12, 0.06, 3116.63]) + +# Reaction 163 +reaction('2 C5H5 => A2 + 2 H', [6.390000e+29, -4.03, 35205.54]) + +# Reaction 164 +reaction('C5H5 + O => C2H3 + C2H2 + CO', [7.000000e+13, 0.0, 0.0]) + +# Reaction 165 +reaction('C5H5 + HO2 => C2H3 + C2H2 + CO + OH', [6.776000e+29, -4.7, 11658.7]) + +# Reaction 166 +reaction('C5H5 + HO2 => 2 C2H2 + CO + H2O', [1.190000e+33, -6.52, 13401.05]) + +# Reaction 167 +reaction('C5H5 + OH => C2H3 + C2H2 + CO + H', [3.020000e+13, 0.0, 0.0]) + +# Reaction 168 +reaction('C5H6 <=> C5H5 + H', [1.730000e+68, -15.16, 116371.89]) + +# Reaction 169 +reaction('C5H6 + H => C5H5 + H2', [2.800000e+13, 0.0, 2258.6]) + +# Reaction 170 +reaction('C5H6 + H => A-C3H5 + C2H2', [6.600000e+14, 0.0, 12344.65]) + +# Reaction 171 +reaction('C5H6 + O => C5H5 + OH', [4.770000e+04, 2.71, 1106.6]) + +# Reaction 172 +reaction('C5H6 + OH => C5H5 + H2O', [3.080000e+06, 2.0, 0.0]) + +# Reaction 173 +reaction('C5H6 + CH3 => C5H5 + CH4', [1.800000e-01, 4.0, 0.0]) + +# Reaction 174 +reaction('C5H10 + H => C5H11', [7.100000e+12, 0.12, 1460.33]) + +# Reaction 175 +reaction('C5H10 => C2H5 + A-C3H5', [9.170000e+20, -1.63, 73989.01]) + +# Reaction 176 +reaction('C5H11 => C2H4 + N-C3H7', [7.460000e+21, -2.61, 32026.77]) + +# Reaction 177 +reaction('C5H11 => H + C5H10', [8.460000e+14, -0.47, 37617.11]) + +# Reaction 178 +reaction('C5H11 => C3H6 + C2H5', [3.150000e-19, 8.84, 7105.64]) + +# Reaction 179 +reaction('A1- + O2 => C5H5 + CO + O', [2.600000e+13, 0.0, 6120.94]) + +# Reaction 180 +reaction('A1- + O2 => 2 CO + 2 C2H2 + H', [3.000000e+13, 0.0, 8979.45]) + +# Reaction 181 +reaction('A1- + O => C5H5 + CO', [1.000000e+14, 0.0, 0.0]) + +# Reaction 182 +reaction('A1- + OH => C5H6 + CO', [3.000000e+13, 0.0, 0.0]) + +# Reaction 183 +reaction('A1- + HO2 => C5H5 + CO + OH', [3.000000e+13, 0.0, 0.0]) + +# Reaction 184 +reaction('A1- + C2H2 <=> A1C2H2', [3.290000e+06, 2.05, 3162.05]) + +# Reaction 185 +reaction('A1 <=> A1- + H', [1.290000e+61, -12.48, 148085.56]) + +# Reaction 186 +reaction('A1 + H => A1- + H2', [6.020000e+08, 1.8, 16352.77]) + +# Reaction 187 +reaction('A1 + OH => A1- + H2O', [4.030000e+02, 3.33, 1455.54]) + +# Reaction 188 +reaction('A1 + CH3 => A1- + CH4', [2.752000e-02, 4.46, 13637.67]) + +# Reaction 189 +reaction('A1 + O => C5H5 + CO + H', [2.220000e+13, 0.0, 4531.55]) + +# Reaction 190 +reaction('A1 + OH => C5H6 + CO + H', [1.320000e+02, 3.25, 5590.34]) + +# Reaction 191 +reaction('A1CH2 <=> C5H5 + C2H2', [8.200000e+14, 0.0, 80676.39]) + +# Reaction 192 +reaction('A1CH2 + H <=> A1- + CH3', [5.830000e+67, -14.15, 68329.35]) + +# Reaction 193 +reaction('A1CH2 + O => A1CHO + H', [3.310000e+14, 0.0, 0.0]) + +# Reaction 194 +reaction('A1CH2 + HO2 => A1CHO + OH + H', [1.060000e+16, -0.94, 2523.9]) + +# Reaction 195 +reaction('A1CH2 + C3H3 => A2 + 2 H', [4.320000e+39, -7.74, 23852.77]) + +# Reaction 196 +reaction('A1CH3 + H <=> A1 + CH3', [2.310000e+06, 2.17, 4163.48]) + +# Reaction 197 +reaction('A1CH3 <=> A1CH2 + H', [1.250000e+18, -0.6, 94787.28]) + +# Reaction 198 +reaction('A1CH3 <=> A1- + CH3', [2.160000e+29, -3.58, 110164.91]) + +# Reaction 199 +reaction('A1CH3 + H => A1CH2 + H2', [6.470000e+00, 3.98, 3384.32]) + +# Reaction 200 +reaction('A1CH3 + OH => A1CH2 + H2O', [1.620000e+13, 0.0, 2770.08]) + +# Reaction 201 +reaction('A1CH3 + CH3 => A1CH2 + CH4', [4.220000e+14, 0.0, 22256.21]) + +# Reaction 202 +reaction('C7H15 => C5H11 + C2H4', [1.890000e+12, 0.02, 27784.42]) + +# Reaction 203 +reaction('C7H15 => C2H5 + C2H4 + C3H6', [7.730000e+18, -1.75, 31974.19]) + +# Reaction 204 +reaction('C7H15 => C4H8 + N-C3H7', [2.530000e+18, -1.65, 31682.6]) + +# Reaction 205 +reaction('C7H15 => C2H5 + C5H10', [2.490000e+16, -1.18, 29517.21]) + +# Reaction 206 +reaction('N-C7H16 => C5H11 + C2H5', [8.100000e+77, -17.62, 120399.14]) + +# Reaction 207 +reaction('N-C7H16 => C2H5 + C2H4 + N-C3H7', [1.420000e+78, -17.71, 120700.29]) + +# Reaction 208 +reaction('N-C7H16 + H => C7H15 + H2', [1.750000e+06, 2.6, 4361.85]) + +# Reaction 209 +reaction('N-C7H16 + O => C7H15 + OH', [1.720000e+05, 2.81, 2260.99]) + +# Reaction 210 +reaction('N-C7H16 + OH => C7H15 + H2O', [7.400000e+08, 1.5, 258.13]) + +# Reaction 211 +reaction('N-C7H16 + CH3 => C7H15 + CH4', [1.460000e+04, 2.57, 6933.56]) + +# Reaction 212 +reaction('A1CHO => A1- + HCO', [2.610000e+15, 0.15, 80549.71]) + +# Reaction 213 +reaction('A1CHO + H => A1- + CO + H2', [2.050000e+09, 1.16, 2404.4]) + +# Reaction 214 +reaction('A1CHO + CH3 => A1- + CO + CH4', [2.720000e+06, 1.77, 5920.17]) + +# Reaction 215 +reaction('A1C2H* + C2H2 <=> A2-', [1.340000e+04, 2.5, 1283.46]) + +# Reaction 216 +reaction('A1C2H* + C2H4 <=> A2 + H', [3.620000e+28, -4.24, 23864.72]) + +# Reaction 217 +reaction('A1C2H <=> A1C2H* + H', [2.100000e+60, -12.4, 148076.0]) + +# Reaction 218 +reaction('A1C2H + H <=> A1C2H* + H2', [1.320000e+08, 1.88, 16821.22]) + +# Reaction 219 +reaction('A1C2H + OH <=> A1C2H* + H2O', [1.340000e+02, 3.33, 1455.54]) + +# Reaction 220 +reaction('A1C2H2 <=> A1C2H + H', [1.340000e+17, -0.86, 41238.05]) + +# Reaction 221 +reaction('A1C2H2 + C2H2 <=> A2 + H', [7.091000e+13, -0.26, 7002.87]) + +# Reaction 222 +reaction('A2 <=> A2- + H', [8.600000e+60, -12.48, 148076.0]) + +# Reaction 223 +reaction('A2 + H <=> A2- + H2', [2.650000e+08, 1.87, 17096.08]) + +# Reaction 224 +reaction('A2 + OH <=> A2- + H2O', [9.630000e+02, 3.02, 4373.8]) diff --git a/samples/python/AVBP/inputs/BISETTI.yaml b/samples/python/AVBP/inputs/BISETTI.yaml new file mode 100644 index 00000000000..fe0e0b7e836 --- /dev/null +++ b/samples/python/AVBP/inputs/BISETTI.yaml @@ -0,0 +1,1367 @@ +description: |- + nits(length='cm', time='s', quantity='mol', act_energy='cal/mol') + +generator: cti2yaml +cantera-version: 3.0.0 +date: Wed, 20 Dec 2023 16:58:00 +0100 +input-files: [BISETTI.cti] + +units: {length: cm, quantity: mol, activation-energy: cal/mol} + +phases: +- name: gas + thermo: ideal-gas + elements: [N, C, H, O, Ar] + species: [AR, N2, S-CH2, T-CH2, O, H2, H, OH, H2O, O2, HO2, CH, CO, HCO, + CH2O, CH3, CO2, CH4, C2H3, C2H4, C2H5, C2H, HCCO, C2H2, C3H3, A-C3H5, + N-C3H7, C2H6, P-C3H4, A-C3H4, A1, A1-, C5H5, C3H6, C4H8, C5H6, A2, C5H10, + C5H11, A1C2H2, A1CH2, A1CHO, A1CH3, C7H15, N-C7H16, A1C2H*, A2-, A1C2H] + kinetics: gas + reactions: all + transport: mixture-averaged + state: + T: 300.0 + P: 1.01325e+05 + +species: +- name: AR + composition: {Ar: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 6000.0] + data: + - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.37967491] + - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.37967491] + transport: + model: gas + geometry: atom + diameter: 3.33 + well-depth: 136.5 + note: REFELEMENTG5/97 +- name: N2 + composition: {N: 2} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12, + -1020.8999, 3.950372] + - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15, + -922.7977, 5.980528] + transport: + model: gas + geometry: linear + diameter: 3.621 + well-depth: 97.53 + polarizability: 1.76 + rotational-relaxation: 4.0 + note: '121286' +- name: S-CH2 + composition: {H: 2, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19860411, -2.36661419e-03, 8.2329622e-06, -6.68815981e-09, 1.94314737e-12, + 5.04968163e+04, -0.769118967] + - [2.29203842, 4.65588637e-03, -2.01191947e-06, 4.17906e-10, -3.39716365e-14, + 5.09259997e+04, 8.62650169] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 +- name: T-CH2 + composition: {H: 2, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.76267867, 9.68872143e-04, 2.79489841e-06, -3.85091153e-09, 1.68741719e-12, + 4.60040401e+04, 1.56253185] + - [2.87410113, 3.65639292e-03, -1.40894597e-06, 2.60179549e-10, -1.87727567e-14, + 4.6263604e+04, 6.17119324] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 +- name: O + composition: {O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.1682671, -3.27931884e-03, 6.64306396e-06, -6.12806624e-09, 2.11265971e-12, + 2.91222592e+04, 2.05193346] + - [2.56942078, -8.59741137e-05, 4.19484589e-08, -1.00177799e-11, 1.22833691e-15, + 2.92175791e+04, 4.78433864] + transport: + model: gas + geometry: atom + diameter: 2.75 + well-depth: 80.0 + note: L1/90 +- name: H2 + composition: {H: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.34433112, 7.98052075e-03, -1.9478151e-05, 2.01572094e-08, -7.37611761e-12, + -917.935173, 0.683010238] + - [3.3372792, -4.94024731e-05, 4.99456778e-07, -1.79566394e-10, 2.00255376e-14, + -950.158922, -3.20502331] + transport: + model: gas + geometry: linear + diameter: 2.92 + well-depth: 38.0 + polarizability: 0.79 + rotational-relaxation: 280.0 + note: TPIS78 +- name: H + composition: {H: 1} + thermo: + model: NASA7 + 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geometry: nonlinear + diameter: 5.2 + well-depth: 400.0 + note: G3B3 +- name: A2 + composition: {H: 8, C: 10} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-8.72434585, 0.105376008, -8.0171069e-05, 2.18545974e-08, 1.42066606e-12, + 1.48059774e+04, 61.982754] + - [1.76826275, 0.0689143506, -4.14322176e-05, 1.17914309e-08, -1.28597061e-12, + 1.26883657e+04, 10.6256608] + transport: + model: gas + geometry: nonlinear + diameter: 6.18 + well-depth: 630.4 + polarizability: 16.5 + rotational-relaxation: 1.0 + note: G3B3 +- name: C5H10 + composition: {H: 10, C: 5} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-1.06223481, 0.0574218294, -3.7448689e-05, 1.27364989e-08, -1.79609789e-12, + -4465.46666, 32.273979] + - [3.98580522, 0.0412429986, -1.84390497e-05, 3.06155241e-09, 0.0, -5701.12071, + 6.85332264] + transport: + model: gas + geometry: nonlinear + diameter: 5.489 + well-depth: 386.2 + dipole: 0.4 + rotational-relaxation: 1.0 + note: '000000' +- name: C5H11 + composition: {H: 11, C: 5} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-0.905255912, 0.0610632852, -4.09491825e-05, 1.4609347e-08, -2.18859615e-12, + 4839.95303, 32.5574963] + - [4.88920629, 0.0422834537, -1.858431e-05, 3.04124763e-09, 0.0, 3434.75468, + 3.43704878] + transport: + model: gas + geometry: nonlinear + diameter: 5.041 + well-depth: 440.735 + note: '000000' +- name: A1C2H2 + composition: {H: 7, C: 8} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-6.31199276, 0.0951097942, -9.56352102e-05, 4.97780207e-08, -1.02323717e-11, + 4.57330975e+04, 53.5475222] + - [5.8593508, 0.0472571459, -2.69864733e-05, 7.35311775e-09, -7.7490083e-13, + 4.33198974e+04, -5.22359403] + transport: + model: gas + geometry: nonlinear + diameter: 6.0 + well-depth: 546.2 + dipole: 0.13 + polarizability: 15.0 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1CH2 + composition: {H: 7, C: 7} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-6.07053038, 0.0835201507, -7.41700083e-05, 3.13153847e-08, -4.23670868e-12, + 2.35894712e+04, 50.7932172] + - [3.30049696, 0.048005534, -2.78443022e-05, 7.72371356e-09, -8.27154136e-13, + 2.17498572e+04, 5.42371919] + transport: + model: gas + geometry: nonlinear + diameter: 5.68 + well-depth: 495.3 + dipole: 0.43 + polarizability: 12.3 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1CHO + composition: {H: 6, C: 7, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-3.47171048, 0.0692891889, -4.32603509e-05, 3.43871096e-09, 4.81010261e-12, + -6145.58774, 41.4094024] + - [1.87355756, 0.0526231551, -3.17644962e-05, 9.06403069e-09, -9.90306123e-13, + -7236.03865, 14.9787009] + transport: + model: gas + geometry: nonlinear + diameter: 5.68 + well-depth: 495.3 + dipole: 0.43 + polarizability: 12.3 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1CH3 + composition: {H: 8, C: 7} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-4.54072038, 0.0685427145, -3.57113024e-05, -4.19397642e-09, 7.41779795e-12, + 4641.21087, 45.7564849] + - [-1.0111722, 0.0585301912, -3.47595069e-05, 9.82180993e-09, -1.0668087e-12, + 3993.63395, 28.3610783] + transport: + model: gas + geometry: nonlinear + diameter: 5.68 + well-depth: 495.3 + dipole: 0.43 + polarizability: 12.3 + rotational-relaxation: 1.0 + note: G3B3 +- name: C7H15 + composition: {H: 15, C: 7} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-0.0379155767, 0.075672657, -4.07473634e-05, 9.32678943e-09, -4.92360745e-13, + -2356.05303, 33.7321506] + - [3.74721159, 0.0649345162, -3.01341025e-05, 5.17418142e-09, 0.0, -3370.18357, + 14.2780413] + transport: + model: gas + geometry: nonlinear + diameter: 6.253 + well-depth: 459.6 + rotational-relaxation: 1.0 + note: '000000' +- name: N-C7H16 + composition: {H: 16, C: 7} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-1.26836187, 0.085435582, -5.25346786e-05, 1.62945721e-08, -2.02394925e-12, + -2.56586565e+04, 35.3732912] + - [5.14079241, 0.0653078671, -2.94827624e-05, 4.93726726e-09, 0.0, -2.7253389e+04, + 2.98195967] + transport: + model: gas + geometry: nonlinear + diameter: 6.253 + well-depth: 459.6 + rotational-relaxation: 1.0 + note: '000000' +- name: A1C2H* + composition: {H: 5, C: 8} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-4.42757639, 0.0836668645, -8.70106362e-05, 4.70285661e-08, -1.01816985e-11, + 6.73302359e+04, 44.8118287] + - [7.23812069, 0.0383812109, -2.18850731e-05, 5.97161247e-09, -6.30351467e-13, + 6.49528135e+04, -11.7512654] + transport: + model: gas + geometry: nonlinear + diameter: 5.72 + well-depth: 535.6 + dipole: 0.77 + polarizability: 12.0 + rotational-relaxation: 1.0 + note: G3B3 +- name: A2- + composition: {H: 7, C: 10} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-8.02718034, 0.102924518, -8.3427201e-05, 2.72135383e-08, -7.24559554e-13, + 5.01363344e+04, 60.8902264] + - [3.22892303, 0.0631264486, -3.80582381e-05, 1.08454069e-08, -1.18342512e-12, + 4.7840084e+04, 5.82016697] + transport: + model: gas + geometry: nonlinear + diameter: 6.18 + well-depth: 630.4 + polarizability: 16.5 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1C2H + composition: {H: 6, C: 8} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-5.21036925, 0.0865551944, -8.45007483e-05, 4.21920706e-08, -8.16766167e-12, + 3.5248862e+04, 46.9445057] + - [5.81520488, 0.0440872933, -2.52053858e-05, 6.90275228e-09, -7.31378908e-13, + 3.30271906e+04, -6.4932069] + transport: + model: gas + geometry: nonlinear + diameter: 5.72 + well-depth: 535.6 + dipole: 0.77 + polarizability: 12.0 + rotational-relaxation: 1.0 + note: G3B3 + +reactions: +- equation: S-CH2 + N2 <=> T-CH2 + N2 # Reaction 1 + rate-constant: {A: 1.5e+13, b: 0.0, Ea: 599.9} +- equation: O + H2 <=> H + OH # Reaction 2 + rate-constant: {A: 4.59e+04, b: 2.7, Ea: 6259.56} +- equation: H + O + M => OH + M # Reaction 3 + type: three-body + rate-constant: {A: 9.43e+18, b: -1.0, Ea: 0.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: H + OH + M => H2O + M # Reaction 4 + type: three-body + rate-constant: {A: 4.4e+22, b: -2.0, Ea: 0.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 6.3, CH4: 2.0, C2H6: 3.0} +- equation: OH + H2 <=> H + H2O # Reaction 5 + rate-constant: {A: 1.73e+08, b: 1.51, Ea: 3429.73} +- equation: 2 OH <=> O + H2O # Reaction 6 + rate-constant: {A: 3.97e+04, b: 2.4, Ea: -2110.42} +- equation: H + O2 (+ M) => HO2 (+ M) # Reaction 7 + type: falloff + low-P-rate-constant: {A: 6.33e+19, b: -1.4, Ea: 0.0} + high-P-rate-constant: {A: 5.12e+12, b: 0.44, Ea: 0.0} + Troe: {A: 0.5, T3: 0.0, T1: 1.0e+10, T2: 1.0e+10} + efficiencies: {H2: 0.75, H2O: 11.89, CO2: 2.18, CO: 1.09, O2: 0.85} +- equation: H + O2 <=> O + OH # Reaction 8 + rate-constant: {A: 2.64e+16, b: -0.67, Ea: 1.704111e+04} +- equation: HO2 + H => O2 + H2 # Reaction 9 + rate-constant: {A: 3.649e+06, b: 2.07, Ea: -1092.26} +- equation: HO2 + H => O + H2O # Reaction 10 + rate-constant: {A: 3.97e+12, b: 0.0, Ea: 671.61} +- equation: HO2 + H => 2 OH # Reaction 11 + rate-constant: {A: 7.49e+13, b: 0.0, Ea: 635.76} +- equation: HO2 + O => OH + O2 # Reaction 12 + rate-constant: {A: 4.0e+13, b: 0.0, Ea: 0.0} +- equation: HO2 + OH => H2O + O2 # Reaction 13 + rate-constant: {A: 2.38e+13, b: 0.0, Ea: -499.52} + duplicate: true +- equation: HO2 + OH => H2O + O2 # Reaction 14 + rate-constant: {A: 1.0e+16, b: 0.0, Ea: 1.733031e+04} + duplicate: true +- equation: CH + O => CO + H # Reaction 15 + rate-constant: {A: 5.7e+13, b: 0.0, Ea: 0.0} +- equation: CH + OH => HCO + H # Reaction 16 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: CH + H2 <=> T-CH2 + H # Reaction 17 + rate-constant: {A: 1.08e+14, b: 0.0, Ea: 3109.46} +- equation: CH + H2O => CH2O + H # Reaction 18 + rate-constant: {A: 5.71e+12, b: 0.0, Ea: -755.26} +- equation: CH + O2 => HCO + O # Reaction 19 + rate-constant: {A: 6.71e+13, b: 0.0, Ea: 0.0} +- equation: T-CH2 + O => HCO + H # Reaction 20 + rate-constant: {A: 8.0e+13, b: 0.0, Ea: 0.0} +- equation: T-CH2 + OH => CH2O + H # Reaction 21 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: T-CH2 + OH <=> CH + H2O # Reaction 22 + rate-constant: {A: 1.13e+07, b: 2.0, Ea: 2999.52} +- equation: T-CH2 + H2 <=> H + CH3 # Reaction 23 + rate-constant: {A: 5.0e+05, b: 2.0, Ea: 7229.92} +- equation: T-CH2 + O2 => CO2 + 2 H # Reaction 24 + rate-constant: {A: 5.8e+12, b: 0.0, Ea: 1500.96} +- equation: T-CH2 + O2 => CH2O + O # Reaction 25 + rate-constant: {A: 2.4e+12, b: 0.0, Ea: 1500.96} +- equation: T-CH2 + O2 => OH + H + CO # Reaction 26 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 1500.96} +- equation: S-CH2 + H2 <=> CH3 + H # Reaction 27 + rate-constant: {A: 7.0e+13, b: 0.0, Ea: 0.0} +- equation: S-CH2 + O2 => H + OH + CO # Reaction 28 + rate-constant: {A: 2.8e+13, b: 0.0, Ea: 0.0} +- equation: S-CH2 + O2 => CO + H2O # Reaction 29 + rate-constant: {A: 1.2e+13, b: 0.0, Ea: 0.0} +- equation: S-CH2 + H2O (+ M) => CH2O + H2 (+ M) # Reaction 30 + type: falloff + low-P-rate-constant: {A: 1.88e+38, b: -6.36, Ea: 5040.63} + high-P-rate-constant: {A: 4.82e+17, b: -1.16, Ea: 1144.84} + Troe: {A: 0.6027, T3: 208.0, T1: 3922.0, T2: 1.018e+04} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: S-CH2 + H2O <=> T-CH2 + H2O # Reaction 31 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: S-CH2 + H2O => H2 + CH2O # Reaction 32 + rate-constant: {A: 6.82e+10, b: 0.25, Ea: -934.51} +- equation: CH3 + H (+ M) <=> CH4 (+ M) # Reaction 33 + type: falloff + low-P-rate-constant: {A: 3.47e+38, b: -6.3, Ea: 5074.09} + high-P-rate-constant: {A: 6.92e+13, b: 0.18, Ea: 0.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 3.0, C2H6: 3.0} +- equation: CH3 + O => CH2O + H # Reaction 34 + rate-constant: {A: 5.06e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + O => H + H2 + CO # Reaction 35 + rate-constant: {A: 3.37e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + OH (+ M) => CH2O + H2 (+ M) # Reaction 36 + type: falloff + low-P-rate-constant: {A: 4.0e+36, b: -5.92, Ea: 3140.54} + high-P-rate-constant: {A: 2.79e+18, b: -1.43, Ea: 1331.26} + Troe: {A: 0.412, T3: 195.0, T1: 5900.0, T2: 6394.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: CH3 + OH <=> T-CH2 + H2O # Reaction 37 + rate-constant: {A: 5.6e+07, b: 1.6, Ea: 5420.65} +- equation: CH3 + OH <=> S-CH2 + H2O # Reaction 38 + rate-constant: {A: 6.44e+17, b: -1.34, Ea: 1417.3} +- equation: CH3 + O2 => CH2O + O + H # Reaction 39 + rate-constant: {A: 1.38e+13, b: 0.0, Ea: 3.04804e+04} +- equation: CH3 + O2 => CH2O + OH # Reaction 40 + rate-constant: {A: 5.87e+11, b: 0.0, Ea: 1.384082e+04} +- equation: CH3 + HO2 => CH2O + OH + H # Reaction 41 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + HO2 => CH4 + O2 # Reaction 42 + rate-constant: {A: 3.61e+12, b: 0.0, Ea: 0.0} +- equation: CH3 + CH => C2H3 + H # Reaction 43 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + T-CH2 => C2H4 + H # Reaction 44 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: 2 CH3 <=> C2H5 + H # Reaction 45 + rate-constant: {A: 6.84e+12, b: 0.1, Ea: 1.05999e+04} +- equation: 2 CH3 => S-CH2 + CH4 # Reaction 46 + rate-constant: {A: 2.632e+12, b: -0.06, Ea: 1.366157e+04} +- equation: CH4 + H <=> CH3 + H2 # Reaction 47 + rate-constant: {A: 6.6e+08, b: 1.62, Ea: 1.08413e+04} +- equation: CH4 + O <=> CH3 + OH # Reaction 48 + rate-constant: {A: 1.02e+09, b: 1.5, Ea: 8599.43} +- equation: CH4 + OH <=> CH3 + H2O # Reaction 49 + rate-constant: {A: 1.0e+08, b: 1.6, Ea: 3119.02} +- equation: CH4 + CH => C2H4 + H # Reaction 50 + rate-constant: {A: 6.0e+13, b: 0.0, Ea: 0.0} +- equation: CH4 + T-CH2 <=> 2 CH3 # Reaction 51 + rate-constant: {A: 2.46e+06, b: 2.0, Ea: 8269.6} +- equation: CO + O (+ M) => CO2 (+ M) # Reaction 52 + type: falloff + low-P-rate-constant: {A: 1.17e+24, b: -2.79, Ea: 4192.16} + high-P-rate-constant: {A: 1.36e+10, b: 0.0, Ea: 2385.28} + Troe: {A: 1.0, T3: 1.0, T1: 1.0e+07, T2: 1.0e+07} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: CO + OH <=> CO2 + H # Reaction 53 + rate-constant: {A: 8.0e+11, b: 0.14, Ea: 7351.82} + duplicate: true +- equation: CO + OH <=> CO2 + H # Reaction 54 + rate-constant: {A: 8.78e+10, b: 0.03, Ea: -16.73} + duplicate: true +- equation: CO + HO2 => CO2 + OH # Reaction 55 + rate-constant: {A: 3.01e+13, b: 0.0, Ea: 2.299952e+04} +- equation: CO + S-CH2 <=> CO + T-CH2 # Reaction 56 + rate-constant: {A: 9.0e+12, b: 0.0, Ea: 0.0} +- equation: HCO + H => CO + H2 # Reaction 57 + rate-constant: {A: 1.2e+14, b: 0.0, Ea: 0.0} +- equation: HCO + O => CO + OH # Reaction 58 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: HCO + O => CO2 + H # Reaction 59 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: HCO + OH => CO + H2O # Reaction 60 + rate-constant: {A: 3.02e+13, b: 0.0, Ea: 0.0} +- equation: HCO + M <=> CO + H + M # Reaction 61 + type: three-body + rate-constant: {A: 1.87e+17, b: -1.0, Ea: 1.700048e+04} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 0.0, CH4: 2.0, C2H6: 3.0} +- equation: HCO + H2O <=> CO + H + H2O # Reaction 62 + rate-constant: {A: 2.24e+18, b: -1.0, Ea: 1.700048e+04} +- equation: HCO + O2 => CO + HO2 # Reaction 63 + rate-constant: {A: 1.2e+10, b: 0.81, Ea: -726.58} +- equation: CH3 + HCO => CH4 + CO # Reaction 64 + rate-constant: {A: 2.65e+13, b: 0.0, Ea: 0.0} +- equation: CH2O + H <=> HCO + H2 # Reaction 65 + rate-constant: {A: 5.74e+07, b: 1.9, Ea: 2741.4} +- equation: CH2O + O => HCO + OH # Reaction 66 + rate-constant: {A: 3.9e+13, b: 0.0, Ea: 3539.67} +- equation: CH2O + OH => HCO + H2O # Reaction 67 + rate-constant: {A: 3.43e+09, b: 1.18, Ea: -446.94} +- equation: CH3 + CH2O => CH4 + HCO # Reaction 68 + rate-constant: {A: 3320.0, b: 2.81, Ea: 5860.42} +- equation: CO2 + CH => HCO + CO # Reaction 69 + rate-constant: {A: 1.9e+14, b: 0.0, Ea: 1.579111e+04} +- equation: CO2 + S-CH2 <=> CO2 + T-CH2 # Reaction 70 + rate-constant: {A: 7.0e+12, b: 0.0, Ea: 0.0} +- equation: CO2 + S-CH2 => CH2O + CO # Reaction 71 + rate-constant: {A: 1.4e+13, b: 0.0, Ea: 0.0} +- equation: C2H + O => CH + CO # Reaction 72 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: C2H + OH => HCCO + H # Reaction 73 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: C2H + O2 => HCO + CO # Reaction 74 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: -755.26} +- equation: C2H + H2 <=> C2H2 + H # Reaction 75 + rate-constant: {A: 3.31e+06, b: 2.26, Ea: 901.05} +- equation: C2H2 + H (+ M) <=> C2H3 (+ M) # Reaction 76 + type: falloff + low-P-rate-constant: {A: 6.34e+31, b: -4.66, Ea: 3781.07} + high-P-rate-constant: {A: 1.71e+10, b: 1.27, Ea: 2707.93} + Troe: {A: 0.2122, T3: 1.0, T1: -1.021e+04} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H2 + O => HCCO + H # Reaction 77 + rate-constant: {A: 8.1e+06, b: 2.0, Ea: 1900.1} +- equation: C2H2 + O => T-CH2 + CO # Reaction 78 + rate-constant: {A: 1.25e+07, b: 2.0, Ea: 1900.1} +- equation: C2H2 + O => C2H + OH # Reaction 79 + rate-constant: {A: 3.324e+16, b: -0.44, Ea: 3.06979e+04} +- equation: C2H2 + OH => C2H + H2O # Reaction 80 + rate-constant: {A: 2.63e+06, b: 2.14, Ea: 1.706023e+04} +- equation: C2H2 + OH => CH3 + CO # Reaction 81 + rate-constant: {A: 7.53e+06, b: 1.55, Ea: 2105.64} + duplicate: true +- equation: C2H2 + OH => CH3 + CO # Reaction 82 + rate-constant: {A: 1.28e+09, b: 0.73, Ea: 2578.87} + duplicate: true +- equation: C2H2 + S-CH2 <=> C3H3 + H # Reaction 83 + rate-constant: {A: 1.9e+14, b: 0.0, Ea: 0.0} +- equation: C2H3 + H (+ M) => C2H4 (+ M) # Reaction 84 + type: falloff + low-P-rate-constant: {A: 1.4e+30, b: -3.86, Ea: 3319.79} + high-P-rate-constant: {A: 6.08e+12, b: 0.27, Ea: 279.64} + Troe: {A: 0.782, T3: 207.5, T1: 2663.0, T2: 6095.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H3 + H => C2H2 + H2 # Reaction 85 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: C2H3 + O => CH3 + CO # Reaction 86 + rate-constant: {A: 1.03e+13, b: 0.21, Ea: -427.82} +- equation: C2H3 + OH => C2H2 + H2O # Reaction 87 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0} +- equation: C2H3 + O2 => C2H2 + HO2 # Reaction 88 + rate-constant: {A: 1.34e+06, b: 1.61, Ea: -384.8} +- equation: C2H3 + O2 => CH3 + CO + O # Reaction 89 + rate-constant: {A: 3.03e+11, b: 0.29, Ea: 11.95} +- equation: C2H3 + O2 => HCO + CH2O # Reaction 90 + rate-constant: {A: 4.58e+16, b: -1.39, Ea: 1015.77} +- equation: C2H3 + HCO => C2H4 + CO # Reaction 91 + rate-constant: {A: 9.0e+13, b: 0.0, Ea: 0.0} +- equation: C2H3 + CH3 => C2H2 + CH4 # Reaction 92 + rate-constant: {A: 9.03e+12, b: 0.0, Ea: -764.82} +- equation: C2H3 + CH3 <=> A-C3H5 + H # Reaction 93 + rate-constant: {A: 1.93e+18, b: -1.25, Ea: 7669.69} +- equation: C2H4 + H (+ M) <=> C2H5 (+ M) # Reaction 94 + type: falloff + low-P-rate-constant: {A: 2.03e+39, b: -6.64, Ea: 5769.6} + high-P-rate-constant: {A: 1.37e+09, b: 1.46, Ea: 1355.16} + Troe: {A: -0.569, T3: 299.0, T1: -9147.0, T2: 152.4} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H4 + H => C2H3 + H2 # Reaction 95 + rate-constant: {A: 1.33e+06, b: 2.53, Ea: 1.223948e+04} +- equation: C2H4 + O => CH3 + CO + H # Reaction 96 + rate-constant: {A: 7.66e+09, b: 0.88, Ea: 1140.06} +- equation: C2H4 + O => T-CH2 + CH2O # Reaction 97 + rate-constant: {A: 7.15e+04, b: 2.47, Ea: 929.73} +- equation: C2H4 + O => CH3 + HCO # Reaction 98 + rate-constant: {A: 3.89e+08, b: 1.36, Ea: 886.71} +- equation: C2H4 + OH => C2H3 + H2O # Reaction 99 + rate-constant: {A: 0.131, b: 4.2, Ea: -860.42} +- equation: C2H4 + OH => CH3 + CH2O # Reaction 100 + rate-constant: {A: 3.75e+36, b: -7.8, Ea: 7060.23} +- equation: C2H4 + CH3 => C2H3 + CH4 # Reaction 101 + rate-constant: {A: 2.27e+05, b: 2.0, Ea: 9199.33} +- equation: C2H4 + CH3 (+ M) <=> N-C3H7 (+ M) # Reaction 102 + type: falloff + low-P-rate-constant: {A: 3.0e+63, b: -14.6, Ea: 1.816922e+04} + high-P-rate-constant: {A: 2.55e+06, b: 1.6, Ea: 5700.29} + Troe: {A: 0.1894, T3: 277.0, T1: 8748.0, T2: 7891.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H5 + H (+ M) <=> C2H6 (+ M) # Reaction 103 + type: falloff + low-P-rate-constant: {A: 1.99e+41, b: -7.08, Ea: 6684.99} + high-P-rate-constant: {A: 5.21e+17, b: -0.99, Ea: 1579.83} + Troe: {A: 0.8422, T3: 125.0, T1: 2219.0, T2: 6882.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H5 + O => CH3 + CH2O # Reaction 104 + rate-constant: {A: 3.17e+13, b: 0.03, Ea: -394.36} +- equation: C2H5 + O2 => C2H4 + HO2 # Reaction 105 + rate-constant: {A: 1.92e+07, b: 1.02, Ea: -2033.94} +- equation: C2H5 + HCO => C2H6 + CO # Reaction 106 + rate-constant: {A: 1.2e+14, b: 0.0, Ea: 0.0} +- equation: C2H5 + HO2 => C2H6 + O2 # Reaction 107 + rate-constant: {A: 3.0e+11, b: 0.0, Ea: 0.0} +- equation: C2H5 + HO2 => CH3 + CH2O + OH # Reaction 108 + rate-constant: {A: 3.1e+13, b: 0.0, Ea: 0.0} +- equation: C2H6 (+ M) <=> 2 CH3 (+ M) # Reaction 109 + type: falloff + low-P-rate-constant: {A: 3.72e+65, b: -13.14, Ea: 1.0157983e+05} + high-P-rate-constant: {A: 1.88e+50, b: -9.72, Ea: 1.0734226e+05} + Troe: {A: 0.39, T3: 100.0, T1: 1900.0, T2: 6000.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H6 + H => C2H5 + H2 # Reaction 110 + rate-constant: {A: 1.7e+05, b: 2.7, Ea: 5740.92} +- equation: C2H6 + O => C2H5 + OH # Reaction 111 + rate-constant: {A: 8.98e+07, b: 1.92, Ea: 5690.73} +- equation: C2H6 + OH => C2H5 + H2O # Reaction 112 + rate-constant: {A: 1.61e+06, b: 2.22, Ea: 740.92} +- equation: C2H6 + CH3 => C2H5 + CH4 # Reaction 113 + rate-constant: {A: 8.43e+14, b: 0.0, Ea: 2.225621e+04} +- equation: HCCO (+ M) => CO + CH (+ M) # Reaction 114 + type: falloff + low-P-rate-constant: {A: 1.213e+35, b: -5.18, Ea: 7.666826e+04} + high-P-rate-constant: {A: 2.255e+20, b: -1.44, Ea: 7.473231e+04} + Troe: {A: 0.5757, T3: 237.0, T1: 1652.0, T2: 5069.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: HCCO + H => S-CH2 + CO # Reaction 115 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: HCCO + O => H + 2 CO # Reaction 116 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: HCCO + O2 => OH + 2 CO # Reaction 117 + rate-constant: {A: 4.2e+10, b: 0.0, Ea: 853.25} +- equation: 2 HCCO => C2H2 + 2 CO # Reaction 118 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: HCCO + C2H2 => C3H3 + CO # Reaction 119 + rate-constant: {A: 1.0e+11, b: 0.0, Ea: 2999.52} +- equation: HCCO + CH3 => C2H4 + CO # Reaction 120 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: HCCO + OH => 2 HCO # Reaction 121 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: C3H3 + H <=> P-C3H4 # Reaction 122 + rate-constant: {A: 7.94e+29, b: -5.06, Ea: 4861.38} +- equation: C3H3 + H <=> A-C3H4 # Reaction 123 + rate-constant: {A: 3.16e+29, b: -5.0, Ea: 4710.8} +- equation: C3H3 + OH => C2H4 + CO # Reaction 124 + rate-constant: {A: 1.28e+09, b: 0.73, Ea: 2578.87} +- equation: C3H3 + O => C2H2 + CO + H # Reaction 125 + rate-constant: {A: 6.95e+13, b: 0.0, Ea: 0.0} +- equation: C3H3 + O2 => CH3 + 2 CO # Reaction 126 + rate-constant: {A: 1.7e+05, b: 1.7, Ea: 1500.96} +- equation: C3H3 + HO2 => OH + CO + C2H3 # Reaction 127 + rate-constant: {A: 8.0e+11, b: 0.0, Ea: 0.0} +- equation: 2 C3H3 <=> A1 # Reaction 128 + rate-constant: {A: 1.87e+46, b: -9.84, Ea: 1.680449e+04} +- equation: 2 C3H3 <=> A1- + H # Reaction 129 + rate-constant: {A: 5.77e+37, b: -7.0, Ea: 3.150574e+04} +- equation: C3H3 + C2H2 <=> C5H5 # Reaction 130 + rate-constant: {A: 2.35e+11, b: 0.0, Ea: 9995.22} +- equation: P-C3H4 + H <=> C2H2 + CH3 # Reaction 131 + rate-constant: {A: 3.46e+12, b: 0.44, Ea: 5463.67} +- equation: P-C3H4 + H <=> C3H3 + H2 # Reaction 132 + rate-constant: {A: 8.5e+04, b: 2.7, Ea: 5740.92} +- equation: P-C3H4 + OH => C3H3 + H2O # Reaction 133 + rate-constant: {A: 8.05e+05, b: 2.22, Ea: 740.92} +- equation: P-C3H4 + CH3 => C3H3 + CH4 # Reaction 134 + rate-constant: {A: 4.22e+14, b: 0.0, Ea: 2.225621e+04} +- equation: P-C3H4 + O => HCCO + CH3 # Reaction 135 + rate-constant: {A: 4.05e+06, b: 2.0, Ea: 1900.1} +- equation: P-C3H4 + O => C2H4 + CO # Reaction 136 + rate-constant: {A: 6.25e+06, b: 2.0, Ea: 1900.1} +- equation: P-C3H4 + OH => C2H5 + CO # Reaction 137 + rate-constant: {A: 1.28e+09, b: 0.73, Ea: 2578.87} +- equation: A-C3H4 + H <=> C2H2 + CH3 # Reaction 138 + rate-constant: {A: 8.95e+13, b: -0.02, Ea: 1.125e+04} +- equation: A-C3H4 <=> P-C3H4 # Reaction 139 + rate-constant: {A: 7.76e+39, b: -7.8, Ea: 7.844646e+04} +- equation: A-C3H4 + H <=> P-C3H4 + H # Reaction 140 + rate-constant: {A: 2.47e+15, b: -0.33, Ea: 6436.42} +- equation: A-C3H4 + H => C3H3 + H2 # Reaction 141 + rate-constant: {A: 1.33e+06, b: 2.53, Ea: 1.223948e+04} +- equation: A-C3H4 + OH => C3H3 + H2O # Reaction 142 + rate-constant: {A: 0.131, b: 4.2, Ea: -860.42} +- equation: A-C3H4 + CH3 => C3H3 + CH4 # Reaction 143 + rate-constant: {A: 2.27e+05, b: 2.0, Ea: 9199.33} +- equation: A-C3H4 + H <=> A-C3H5 # Reaction 144 + rate-constant: {A: 2.01e+49, b: -10.77, Ea: 1.962237e+04} +- equation: A-C3H5 + H => A-C3H4 + H2 # Reaction 145 + rate-constant: {A: 9560.0, b: 2.8, Ea: 3291.11} +- equation: A-C3H5 + OH => A-C3H4 + H2O # Reaction 146 + rate-constant: {A: 6.03e+12, b: 0.0, Ea: 0.0} +- equation: A-C3H5 + CH3 => A-C3H4 + CH4 # Reaction 147 + rate-constant: {A: 4.86e+11, b: -0.32, Ea: -131.45} +- equation: A-C3H5 + O2 => C2H2 + CH2O + OH # Reaction 148 + rate-constant: {A: 9.71e+20, b: -2.7, Ea: 2.498088e+04} +- equation: A-C3H5 + C3H3 => A1 + 2 H # Reaction 149 + rate-constant: {A: 2.16e+39, b: -7.74, Ea: 2.385277e+04} +- equation: C3H6 + H (+ M) <=> N-C3H7 (+ M) # Reaction 150 + type: falloff + low-P-rate-constant: {A: 6.26e+38, b: -6.66, Ea: 7000.48} + high-P-rate-constant: {A: 3.06e+14, b: -0.37, Ea: 4032.03} + Troe: {A: 1.0, T3: 1000.0, T1: 1310.0, T2: 4.81e+04} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C3H6 <=> C2H3 + CH3 # Reaction 151 + rate-constant: {A: 4.04e+42, b: -7.67, Ea: 1.1183078e+05} +- equation: A-C3H5 + H <=> C3H6 # Reaction 152 + rate-constant: {A: 5.93e+54, b: -11.76, Ea: 2.354924e+04} +- equation: C3H6 + H <=> C2H4 + CH3 # Reaction 153 + rate-constant: {A: 8.0e+21, b: -2.39, Ea: 1.118069e+04} +- equation: C3H6 + O => 2 CH3 + CO # Reaction 154 + rate-constant: {A: 1.2e+08, b: 1.6, Ea: 327.44} +- equation: C3H6 + O => C2H5 + HCO # Reaction 155 + rate-constant: {A: 3.5e+07, b: 1.6, Ea: -972.75} +- equation: C3H6 + H => A-C3H5 + H2 # Reaction 156 + rate-constant: {A: 6.6e+05, b: 2.54, Ea: 6756.69} +- equation: C3H6 + O => A-C3H5 + OH # Reaction 157 + rate-constant: {A: 9.65e+04, b: 2.68, Ea: 3716.54} +- equation: C3H6 + OH => A-C3H5 + H2O # Reaction 158 + rate-constant: {A: 2.0e+08, b: 1.46, Ea: 537.76} +- equation: C3H6 + CH3 => A-C3H5 + CH4 # Reaction 159 + rate-constant: {A: 0.452, b: 3.65, Ea: 7153.44} +- equation: C4H8 + H => C2H5 + C2H4 # Reaction 160 + rate-constant: {A: 7.68e+12, b: 0.11, Ea: 1479.45} +- equation: C4H8 => A-C3H5 + CH3 # Reaction 161 + rate-constant: {A: 5.0e+15, b: 0.0, Ea: 7.099904e+04} +- equation: C5H5 + HO2 => O2 + C5H6 # Reaction 162 + rate-constant: {A: 2.561e+12, b: 0.06, Ea: 3116.63} +- equation: 2 C5H5 => A2 + 2 H # Reaction 163 + rate-constant: {A: 6.39e+29, b: -4.03, Ea: 3.520554e+04} +- equation: C5H5 + O => C2H3 + C2H2 + CO # Reaction 164 + rate-constant: {A: 7.0e+13, b: 0.0, Ea: 0.0} +- equation: C5H5 + HO2 => C2H3 + C2H2 + CO + OH # Reaction 165 + rate-constant: {A: 6.776e+29, b: -4.7, Ea: 1.16587e+04} +- equation: C5H5 + HO2 => 2 C2H2 + CO + H2O # Reaction 166 + rate-constant: {A: 1.19e+33, b: -6.52, Ea: 1.340105e+04} +- equation: C5H5 + OH => C2H3 + C2H2 + CO + H # Reaction 167 + rate-constant: {A: 3.02e+13, b: 0.0, Ea: 0.0} +- equation: C5H6 <=> C5H5 + H # Reaction 168 + rate-constant: {A: 1.73e+68, b: -15.16, Ea: 1.1637189e+05} +- equation: C5H6 + H => C5H5 + H2 # Reaction 169 + rate-constant: {A: 2.8e+13, b: 0.0, Ea: 2258.6} +- equation: C5H6 + H => A-C3H5 + C2H2 # Reaction 170 + rate-constant: {A: 6.6e+14, b: 0.0, Ea: 1.234465e+04} +- equation: C5H6 + O => C5H5 + OH # Reaction 171 + rate-constant: {A: 4.77e+04, b: 2.71, Ea: 1106.6} +- equation: C5H6 + OH => C5H5 + H2O # Reaction 172 + rate-constant: {A: 3.08e+06, b: 2.0, Ea: 0.0} +- equation: C5H6 + CH3 => C5H5 + CH4 # Reaction 173 + rate-constant: {A: 0.18, b: 4.0, Ea: 0.0} +- equation: C5H10 + H => C5H11 # Reaction 174 + rate-constant: {A: 7.1e+12, b: 0.12, Ea: 1460.33} +- equation: C5H10 => C2H5 + A-C3H5 # Reaction 175 + rate-constant: {A: 9.17e+20, b: -1.63, Ea: 7.398901e+04} +- equation: C5H11 => C2H4 + N-C3H7 # Reaction 176 + rate-constant: {A: 7.46e+21, b: -2.61, Ea: 3.202677e+04} +- equation: C5H11 => H + C5H10 # Reaction 177 + rate-constant: {A: 8.46e+14, b: -0.47, Ea: 3.761711e+04} +- equation: C5H11 => C3H6 + C2H5 # Reaction 178 + rate-constant: {A: 3.15e-19, b: 8.84, Ea: 7105.64} +- equation: A1- + O2 => C5H5 + CO + O # Reaction 179 + rate-constant: {A: 2.6e+13, b: 0.0, Ea: 6120.94} +- equation: A1- + O2 => 2 CO + 2 C2H2 + H # Reaction 180 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 8979.45} +- equation: A1- + O => C5H5 + CO # Reaction 181 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: A1- + OH => C5H6 + CO # Reaction 182 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: A1- + HO2 => C5H5 + CO + OH # Reaction 183 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: A1- + C2H2 <=> A1C2H2 # Reaction 184 + rate-constant: {A: 3.29e+06, b: 2.05, Ea: 3162.05} +- equation: A1 <=> A1- + H # Reaction 185 + rate-constant: {A: 1.29e+61, b: -12.48, Ea: 1.4808556e+05} +- equation: A1 + H => A1- + H2 # Reaction 186 + rate-constant: {A: 6.02e+08, b: 1.8, Ea: 1.635277e+04} +- equation: A1 + OH => A1- + H2O # Reaction 187 + rate-constant: {A: 403.0, b: 3.33, Ea: 1455.54} +- equation: A1 + CH3 => A1- + CH4 # Reaction 188 + rate-constant: {A: 0.02752, b: 4.46, Ea: 1.363767e+04} +- equation: A1 + O => C5H5 + CO + H # Reaction 189 + rate-constant: {A: 2.22e+13, b: 0.0, Ea: 4531.55} +- equation: A1 + OH => C5H6 + CO + H # Reaction 190 + rate-constant: {A: 132.0, b: 3.25, Ea: 5590.34} +- equation: A1CH2 <=> C5H5 + C2H2 # Reaction 191 + rate-constant: {A: 8.2e+14, b: 0.0, Ea: 8.067639e+04} +- equation: A1CH2 + H <=> A1- + CH3 # Reaction 192 + rate-constant: {A: 5.83e+67, b: -14.15, Ea: 6.832935e+04} +- equation: A1CH2 + O => A1CHO + H # Reaction 193 + rate-constant: {A: 3.31e+14, b: 0.0, Ea: 0.0} +- equation: A1CH2 + HO2 => A1CHO + OH + H # Reaction 194 + rate-constant: {A: 1.06e+16, b: -0.94, Ea: 2523.9} +- equation: A1CH2 + C3H3 => A2 + 2 H # Reaction 195 + rate-constant: {A: 4.32e+39, b: -7.74, Ea: 2.385277e+04} +- equation: A1CH3 + H <=> A1 + CH3 # Reaction 196 + rate-constant: {A: 2.31e+06, b: 2.17, Ea: 4163.48} +- equation: A1CH3 <=> A1CH2 + H # Reaction 197 + rate-constant: {A: 1.25e+18, b: -0.6, Ea: 9.478728e+04} +- equation: A1CH3 <=> A1- + CH3 # Reaction 198 + rate-constant: {A: 2.16e+29, b: -3.58, Ea: 1.1016491e+05} +- equation: A1CH3 + H => A1CH2 + H2 # Reaction 199 + rate-constant: {A: 6.47, b: 3.98, Ea: 3384.32} +- equation: A1CH3 + OH => A1CH2 + H2O # Reaction 200 + rate-constant: {A: 1.62e+13, b: 0.0, Ea: 2770.08} +- equation: A1CH3 + CH3 => A1CH2 + CH4 # Reaction 201 + rate-constant: {A: 4.22e+14, b: 0.0, Ea: 2.225621e+04} +- equation: C7H15 => C5H11 + C2H4 # Reaction 202 + rate-constant: {A: 1.89e+12, b: 0.02, Ea: 2.778442e+04} +- equation: C7H15 => C2H5 + C2H4 + C3H6 # Reaction 203 + rate-constant: {A: 7.73e+18, b: -1.75, Ea: 3.197419e+04} +- equation: C7H15 => C4H8 + N-C3H7 # Reaction 204 + rate-constant: {A: 2.53e+18, b: -1.65, Ea: 3.16826e+04} +- equation: C7H15 => C2H5 + C5H10 # Reaction 205 + rate-constant: {A: 2.49e+16, b: -1.18, Ea: 2.951721e+04} +- equation: N-C7H16 => C5H11 + C2H5 # Reaction 206 + rate-constant: {A: 8.1e+77, b: -17.62, Ea: 1.2039914e+05} +- equation: N-C7H16 => C2H5 + C2H4 + N-C3H7 # Reaction 207 + rate-constant: {A: 1.42e+78, b: -17.71, Ea: 1.2070029e+05} +- equation: N-C7H16 + H => C7H15 + H2 # Reaction 208 + rate-constant: {A: 1.75e+06, b: 2.6, Ea: 4361.85} +- equation: N-C7H16 + O => C7H15 + OH # Reaction 209 + rate-constant: {A: 1.72e+05, b: 2.81, Ea: 2260.99} +- equation: N-C7H16 + OH => C7H15 + H2O # Reaction 210 + rate-constant: {A: 7.4e+08, b: 1.5, Ea: 258.13} +- equation: N-C7H16 + CH3 => C7H15 + CH4 # Reaction 211 + rate-constant: {A: 1.46e+04, b: 2.57, Ea: 6933.56} +- equation: A1CHO => A1- + HCO # Reaction 212 + rate-constant: {A: 2.61e+15, b: 0.15, Ea: 8.054971e+04} +- equation: A1CHO + H => A1- + CO + H2 # Reaction 213 + rate-constant: {A: 2.05e+09, b: 1.16, Ea: 2404.4} +- equation: A1CHO + CH3 => A1- + CO + CH4 # Reaction 214 + rate-constant: {A: 2.72e+06, b: 1.77, Ea: 5920.17} +- equation: A1C2H* + C2H2 <=> A2- # Reaction 215 + rate-constant: {A: 1.34e+04, b: 2.5, Ea: 1283.46} +- equation: A1C2H* + C2H4 <=> A2 + H # Reaction 216 + rate-constant: {A: 3.62e+28, b: -4.24, Ea: 2.386472e+04} +- equation: A1C2H <=> A1C2H* + H # Reaction 217 + rate-constant: {A: 2.1e+60, b: -12.4, Ea: 1.48076e+05} +- equation: A1C2H + H <=> A1C2H* + H2 # Reaction 218 + rate-constant: {A: 1.32e+08, b: 1.88, Ea: 1.682122e+04} +- equation: A1C2H + OH <=> A1C2H* + H2O # Reaction 219 + rate-constant: {A: 134.0, b: 3.33, Ea: 1455.54} +- equation: A1C2H2 <=> A1C2H + H # Reaction 220 + rate-constant: {A: 1.34e+17, b: -0.86, Ea: 4.123805e+04} +- equation: A1C2H2 + C2H2 <=> A2 + H # Reaction 221 + rate-constant: {A: 7.091e+13, b: -0.26, Ea: 7002.87} +- equation: A2 <=> A2- + H # Reaction 222 + rate-constant: {A: 8.6e+60, b: -12.48, Ea: 1.48076e+05} +- equation: A2 + H <=> A2- + H2 # Reaction 223 + rate-constant: {A: 2.65e+08, b: 1.87, Ea: 1.709608e+04} +- equation: A2 + OH <=> A2- + H2O # Reaction 224 + rate-constant: {A: 963.0, b: 3.02, Ea: 4373.8} diff --git a/samples/python/AVBP/inputs/Lu.cti b/samples/python/AVBP/inputs/Lu.cti new file mode 100755 index 00000000000..66a81d9203c --- /dev/null +++ b/samples/python/AVBP/inputs/Lu.cti @@ -0,0 +1,1351 @@ +""" + A 30-species skeletal mechanism based on GRI3.0 + + by Tianfeng Lu + Email: tlu@engr.uconn.edu + + Reference: + Tianfeng Lu and Chung K. Law, + "A criterion based on computational singular perturbation + for the identification of quasi steady state species: + A reduced mechanism for methane oxidation with NO chemistry," + Combustion and Flame, Vol.154 No.4 pp.761774, 2008. + + +""" + +units(length='cm', time='s', quantity='mol', act_energy='cal/mol') + +ideal_gas(name='gas', + elements="O H C N Ar", + species="""H2 H O O2 OH H2O HO2 + H2O2 C CH CH2 CH2(S) CH3 CH4 + CO CO2 HCO CH2O CH2OH CH3O CH3OH + C2H2 C2H3 C2H4 C2H5 C2H6 HCCO CH2CO + CH2CHO N2""", + reactions='all', + transport='Mix', + initial_state=state(temperature=300.0, pressure=OneAtm)) + +#------------------------------------------------------------------------------- +# Species data +#------------------------------------------------------------------------------- + +species(name=u'H2', + atoms='H:2', + thermo=(NASA([200.00, 1000.00], + [ 2.34433112E+00, 7.98052075E-03, -1.94781510E-05, + 2.01572094E-08, -7.37611761E-12, -9.17935173E+02, + 6.83010238E-01]), + NASA([1000.00, 3500.00], + [ 3.33727920E+00, -4.94024731E-05, 4.99456778E-07, + -1.79566394E-10, 2.00255376E-14, -9.50158922E+02, + -3.20502331E+00])), + transport=gas_transport(geom='linear', + diam=2.92, + well_depth=38.0, + polar=0.79, + rot_relax=280.0), + note=u'TPIS78') + +species(name=u'H', + atoms='H:1', + thermo=(NASA([200.00, 1000.00], + [ 2.50000000E+00, 7.05332819E-13, -1.99591964E-15, + 2.30081632E-18, -9.27732332E-22, 2.54736599E+04, + -4.46682853E-01]), + NASA([1000.00, 3500.00], + [ 2.50000001E+00, -2.30842973E-11, 1.61561948E-14, + -4.73515235E-18, 4.98197357E-22, 2.54736599E+04, + -4.46682914E-01])), + transport=gas_transport(geom='atom', + diam=2.05, + well_depth=145.0), + note=u'L7/88') + +species(name=u'O', + atoms='O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.16826710E+00, -3.27931884E-03, 6.64306396E-06, + -6.12806624E-09, 2.11265971E-12, 2.91222592E+04, + 2.05193346E+00]), + NASA([1000.00, 3500.00], + [ 2.56942078E+00, -8.59741137E-05, 4.19484589E-08, + -1.00177799E-11, 1.22833691E-15, 2.92175791E+04, + 4.78433864E+00])), + transport=gas_transport(geom='atom', + diam=2.75, + well_depth=80.0), + note=u'L1/90') + +species(name=u'O2', + atoms='O:2', + thermo=(NASA([200.00, 1000.00], + [ 3.78245636E+00, -2.99673416E-03, 9.84730201E-06, + -9.68129509E-09, 3.24372837E-12, -1.06394356E+03, + 3.65767573E+00]), + NASA([1000.00, 3500.00], + [ 3.28253784E+00, 1.48308754E-03, -7.57966669E-07, + 2.09470555E-10, -2.16717794E-14, -1.08845772E+03, + 5.45323129E+00])), + transport=gas_transport(geom='linear', + diam=3.458, + well_depth=107.4, + polar=1.6, + rot_relax=3.8), + note=u'TPIS89') + +species(name=u'OH', + atoms='H:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.99201543E+00, -2.40131752E-03, 4.61793841E-06, + -3.88113333E-09, 1.36411470E-12, 3.61508056E+03, + -1.03925458E-01]), + NASA([1000.00, 3500.00], + [ 3.09288767E+00, 5.48429716E-04, 1.26505228E-07, + -8.79461556E-11, 1.17412376E-14, 3.85865700E+03, + 4.47669610E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note=u'RUS78') + +species(name=u'H2O', + atoms='H:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19864056E+00, -2.03643410E-03, 6.52040211E-06, + -5.48797062E-09, 1.77197817E-12, -3.02937267E+04, + -8.49032208E-01]), + NASA([1000.00, 3500.00], + [ 3.03399249E+00, 2.17691804E-03, -1.64072518E-07, + -9.70419870E-11, 1.68200992E-14, -3.00042971E+04, + 4.96677010E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.605, + well_depth=572.4, + dipole=1.844, + rot_relax=4.0), + note=u'L8/89') + +species(name=u'HO2', + atoms='H:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30179801E+00, -4.74912051E-03, 2.11582891E-05, + -2.42763894E-08, 9.29225124E-12, 2.94808040E+02, + 3.71666245E+00]), + NASA([1000.00, 3500.00], + [ 4.01721090E+00, 2.23982013E-03, -6.33658150E-07, + 1.14246370E-10, -1.07908535E-14, 1.11856713E+02, + 3.78510215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=1.0), + note=u'L5/89') + +species(name=u'H2O2', + atoms='H:2 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.27611269E+00, -5.42822417E-04, 1.67335701E-05, + -2.15770813E-08, 8.62454363E-12, -1.77025821E+04, + 3.43505074E+00]), + NASA([1000.00, 3500.00], + [ 4.16500285E+00, 4.90831694E-03, -1.90139225E-06, + 3.71185986E-10, -2.87908305E-14, -1.78617877E+04, + 2.91615662E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=3.8), + note=u'L7/88') + +species(name=u'C', + atoms='C:1', + thermo=(NASA([200.00, 1000.00], + [ 2.55423955E+00, -3.21537724E-04, 7.33792245E-07, + -7.32234889E-10, 2.66521446E-13, 8.54438832E+04, + 4.53130848E+00]), + NASA([1000.00, 3500.00], + [ 2.49266888E+00, 4.79889284E-05, -7.24335020E-08, + 3.74291029E-11, -4.87277893E-15, 8.54512953E+04, + 4.80150373E+00])), + transport=gas_transport(geom='atom', + diam=3.298, + well_depth=71.4), + note=u'L11/88') + +species(name=u'CH', + atoms='H:1 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.48981665E+00, 3.23835541E-04, -1.68899065E-06, + 3.16217327E-09, -1.40609067E-12, 7.07972934E+04, + 2.08401108E+00]), + NASA([1000.00, 3500.00], + [ 2.87846473E+00, 9.70913681E-04, 1.44445655E-07, + -1.30687849E-10, 1.76079383E-14, 7.10124364E+04, + 5.48497999E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note=u'TPIS79') + +species(name=u'CH2', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.76267867E+00, 9.68872143E-04, 2.79489841E-06, + -3.85091153E-09, 1.68741719E-12, 4.60040401E+04, + 1.56253185E+00]), + NASA([1000.00, 3500.00], + [ 2.87410113E+00, 3.65639292E-03, -1.40894597E-06, + 2.60179549E-10, -1.87727567E-14, 4.62636040E+04, + 6.17119324E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'LS/93') + +species(name=u'CH2(S)', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19860411E+00, -2.36661419E-03, 8.23296220E-06, + -6.68815981E-09, 1.94314737E-12, 5.04968163E+04, + -7.69118967E-01]), + NASA([1000.00, 3500.00], + [ 2.29203842E+00, 4.65588637E-03, -2.01191947E-06, + 4.17906000E-10, -3.39716365E-14, 5.09259997E+04, + 8.62650169E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'LS/93') + +species(name=u'CH3', + atoms='H:3 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.67359040E+00, 2.01095175E-03, 5.73021856E-06, + -6.87117425E-09, 2.54385734E-12, 1.64449988E+04, + 1.60456433E+00]), + NASA([1000.00, 3500.00], + [ 2.28571772E+00, 7.23990037E-03, -2.98714348E-06, + 5.95684644E-10, -4.67154394E-14, 1.67755843E+04, + 8.48007179E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'L11/89') + +species(name=u'CH4', + atoms='H:4 C:1', + thermo=(NASA([200.00, 1000.00], + [ 5.14987613E+00, -1.36709788E-02, 4.91800599E-05, + -4.84743026E-08, 1.66693956E-11, -1.02466476E+04, + -4.64130376E+00]), + NASA([1000.00, 3500.00], + [ 7.48514950E-02, 1.33909467E-02, -5.73285809E-06, + 1.22292535E-09, -1.01815230E-13, -9.46834459E+03, + 1.84373180E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.746, + well_depth=141.4, + polar=2.6, + rot_relax=13.0), + note=u'L8/88') + +species(name=u'CO', + atoms='C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.57953347E+00, -6.10353680E-04, 1.01681433E-06, + 9.07005884E-10, -9.04424499E-13, -1.43440860E+04, + 3.50840928E+00]), + NASA([1000.00, 3500.00], + [ 2.71518561E+00, 2.06252743E-03, -9.98825771E-07, + 2.30053008E-10, -2.03647716E-14, -1.41518724E+04, + 7.81868772E+00])), + transport=gas_transport(geom='linear', + diam=3.65, + well_depth=98.1, + polar=1.95, + rot_relax=1.8), + note=u'TPIS79') + +species(name=u'CO2', + atoms='C:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 2.35677352E+00, 8.98459677E-03, -7.12356269E-06, + 2.45919022E-09, -1.43699548E-13, -4.83719697E+04, + 9.90105222E+00]), + NASA([1000.00, 3500.00], + [ 3.85746029E+00, 4.41437026E-03, -2.21481404E-06, + 5.23490188E-10, -4.72084164E-14, -4.87591660E+04, + 2.27163806E+00])), + transport=gas_transport(geom='linear', + diam=3.763, + well_depth=244.0, + polar=2.65, + rot_relax=2.1), + note=u'L7/88') + +species(name=u'HCO', + atoms='H:1 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.22118584E+00, -3.24392532E-03, 1.37799446E-05, + -1.33144093E-08, 4.33768865E-12, 3.83956496E+03, + 3.39437243E+00]), + NASA([1000.00, 3500.00], + [ 2.77217438E+00, 4.95695526E-03, -2.48445613E-06, + 5.89161778E-10, -5.33508711E-14, 4.01191815E+03, + 9.79834492E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0), + note=u'L12/89') + +species(name=u'CH2O', + atoms='H:2 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.79372315E+00, -9.90833369E-03, 3.73220008E-05, + -3.79285261E-08, 1.31772652E-11, -1.43089567E+04, + 6.02812900E-01]), + NASA([1000.00, 3500.00], + [ 1.76069008E+00, 9.20000082E-03, -4.42258813E-06, + 1.00641212E-09, -8.83855640E-14, -1.39958323E+04, + 1.36563230E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0, + rot_relax=2.0), + note=u'L8/88') + +species(name=u'CH2OH', + atoms='H:3 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.86388918E+00, 5.59672304E-03, 5.93271791E-06, + -1.04532012E-08, 4.36967278E-12, -3.19391367E+03, + 5.47302243E+00]), + NASA([1000.00, 3500.00], + [ 3.69266569E+00, 8.64576797E-03, -3.75101120E-06, + 7.87234636E-10, -6.48554201E-14, -3.24250627E+03, + 5.81043215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.69, + well_depth=417.0, + dipole=1.7, + rot_relax=2.0), + note=u'GUNL93') + +species(name=u'CH3O', + atoms='H:3 C:1 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.10620400E+00, 7.21659500E-03, 5.33847200E-06, + -7.37763600E-09, 2.07561000E-12, 9.78601100E+02, + 1.31521770E+01]), + NASA([1000.00, 3000.00], + [ 3.77079900E+00, 7.87149700E-03, -2.65638400E-06, + 3.94443100E-10, -2.11261600E-14, 1.27832520E+02, + 2.92957500E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.69, + well_depth=417.0, + dipole=1.7, + rot_relax=2.0), + note=u'121686') + +species(name=u'CH3OH', + atoms='H:4 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 5.71539582E+00, -1.52309129E-02, 6.52441155E-05, + -7.10806889E-08, 2.61352698E-11, -2.56427656E+04, + -1.50409823E+00]), + NASA([1000.00, 3500.00], + [ 1.78970791E+00, 1.40938292E-02, -6.36500835E-06, + 1.38171085E-09, -1.17060220E-13, -2.53748747E+04, + 1.45023623E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.626, + well_depth=481.8, + rot_relax=1.0), + note=u'L8/88') + +species(name=u'C2H2', + atoms='H:2 C:2', + thermo=(NASA([200.00, 1000.00], + [ 8.08681094E-01, 2.33615629E-02, -3.55171815E-05, + 2.80152437E-08, -8.50072974E-12, 2.64289807E+04, + 1.39397051E+01]), + NASA([1000.00, 3500.00], + [ 4.14756964E+00, 5.96166664E-03, -2.37294852E-06, + 4.67412171E-10, -3.61235213E-14, 2.59359992E+04, + -1.23028121E+00])), + transport=gas_transport(geom='linear', + diam=4.1, + well_depth=209.0, + rot_relax=2.5), + note=u'L1/91') + +species(name=u'C2H3', + atoms='H:3 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.21246645E+00, 1.51479162E-03, 2.59209412E-05, + -3.57657847E-08, 1.47150873E-11, 3.48598468E+04, + 8.51054025E+00]), + NASA([1000.00, 3500.00], + [ 3.01672400E+00, 1.03302292E-02, -4.68082349E-06, + 1.01763288E-09, -8.62607041E-14, 3.46128739E+04, + 7.78732378E+00])), + transport=gas_transport(geom='nonlinear', + diam=4.1, + well_depth=209.0, + rot_relax=1.0), + note=u'L2/92') + +species(name=u'C2H4', + atoms='H:4 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.95920148E+00, -7.57052247E-03, 5.70990292E-05, + -6.91588753E-08, 2.69884373E-11, 5.08977593E+03, + 4.09733096E+00]), + NASA([1000.00, 3500.00], + [ 2.03611116E+00, 1.46454151E-02, -6.71077915E-06, + 1.47222923E-09, -1.25706061E-13, 4.93988614E+03, + 1.03053693E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.971, + well_depth=280.8, + rot_relax=1.5), + note=u'L1/91') + +species(name=u'C2H5', + atoms='H:5 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30646568E+00, -4.18658892E-03, 4.97142807E-05, + -5.99126606E-08, 2.30509004E-11, 1.28416265E+04, + 4.70720924E+00]), + NASA([1000.00, 3500.00], + [ 1.95465642E+00, 1.73972722E-02, -7.98206668E-06, + 1.75217689E-09, -1.49641576E-13, 1.28575200E+04, + 1.34624343E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note=u'L12/92') + +species(name=u'C2H6', + atoms='H:6 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.29142492E+00, -5.50154270E-03, 5.99438288E-05, + -7.08466285E-08, 2.68685771E-11, -1.15222055E+04, + 2.66682316E+00]), + NASA([1000.00, 3500.00], + [ 1.07188150E+00, 2.16852677E-02, -1.00256067E-05, + 2.21412001E-09, -1.90002890E-13, -1.14263932E+04, + 1.51156107E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note=u'L8/88') + +species(name=u'HCCO', + atoms='H:1 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.25172140E+00, 1.76550210E-02, -2.37291010E-05, + 1.72757590E-08, -5.06648110E-12, 2.00594490E+04, + 1.24904170E+01]), + NASA([1000.00, 4000.00], + [ 5.62820580E+00, 4.08534010E-03, -1.59345470E-06, + 2.86260520E-10, -1.94078320E-14, 1.93272150E+04, + -3.93025950E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.5, + well_depth=150.0, + rot_relax=1.0), + note=u'SRIC91') + +species(name=u'CH2CO', + atoms='H:2 C:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 2.13583630E+00, 1.81188721E-02, -1.73947474E-05, + 9.34397568E-09, -2.01457615E-12, -7.04291804E+03, + 1.22156480E+01]), + NASA([1000.00, 3500.00], + [ 4.51129732E+00, 9.00359745E-03, -4.16939635E-06, + 9.23345882E-10, -7.94838201E-14, -7.55105311E+03, + 6.32247205E-01])), + transport=gas_transport(geom='nonlinear', + diam=3.97, + well_depth=436.0, + rot_relax=2.0), + note=u'L5/90') + +species(name=u'CH2CHO', + atoms='H:3 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 3.40906200E+00, 1.07385740E-02, 1.89149200E-06, + -7.15858300E-09, 2.86738500E-12, 1.52147660E+03, + 9.55829000E+00]), + NASA([1000.00, 5000.00], + [ 5.97567000E+00, 8.13059100E-03, -2.74362400E-06, + 4.07030400E-10, -2.17601700E-14, 4.90321800E+02, + -5.04525100E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.97, + well_depth=436.0, + rot_relax=2.0), + note=u'SAND86') + +species(name=u'N2', + atoms='N:2', + thermo=(NASA([300.00, 1000.00], + [ 3.29867700E+00, 1.40824040E-03, -3.96322200E-06, + 5.64151500E-09, -2.44485400E-12, -1.02089990E+03, + 3.95037200E+00]), + NASA([1000.00, 5000.00], + [ 2.92664000E+00, 1.48797680E-03, -5.68476000E-07, + 1.00970380E-10, -6.75335100E-15, -9.22797700E+02, + 5.98052800E+00])), + transport=gas_transport(geom='linear', + diam=3.621, + well_depth=97.53, + polar=1.76, + rot_relax=4.0), + note=u'121286') + +#------------------------------------------------------------------------------- +# Reaction data +#------------------------------------------------------------------------------- +# R1 + +# Reaction 1 +three_body_reaction('2 O + M <=> O2 + M', [1.200000e+17, -1.0, 0.0], + efficiencies='CO2:3.6 CO:1.75 H2:2.4 H2O:15.4 CH4:2.0 C2H6:3.0') +# R2 + +# Reaction 2 +three_body_reaction('O + H + M <=> OH + M', [5.000000e+17, -1.0, 0.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0') +# R3 + +# Reaction 3 +reaction('O + H2 <=> H + OH', [3.870000e+04, 2.7, 6260.0]) +# R4 + +# Reaction 4 +reaction('O + HO2 <=> OH + O2', [2.000000e+13, 0.0, 0.0]) +# R5 + +# Reaction 5 +reaction('O + H2O2 <=> OH + HO2', [9.630000e+06, 2.0, 4000.0]) +# R6 + +# Reaction 6 +reaction('O + CH <=> H + CO', [5.700000e+13, 0.0, 0.0]) +# R7 + +# Reaction 7 +reaction('O + CH2 <=> H + HCO', [8.000000e+13, 0.0, 0.0]) +# R8 + +# Reaction 8 +reaction('O + CH2(S) <=> H2 + CO', [1.500000e+13, 0.0, 0.0]) +# R9 + +# Reaction 9 +reaction('O + CH2(S) <=> H + HCO', [1.500000e+13, 0.0, 0.0]) +# R10 + +# Reaction 10 +reaction('O + CH3 <=> H + CH2O', [5.060000e+13, 0.0, 0.0]) +# R11 + +# Reaction 11 +reaction('O + CH4 <=> OH + CH3', [1.020000e+09, 1.5, 8600.0]) +# R12 + +# Reaction 12 +falloff_reaction('O + CO (+ M) <=> CO2 (+ M)', + kf=[1.800000e+10, 0.0, 2385.0], + kf0=[6.020000e+14, 0.0, 3000.0], + efficiencies='CO2:3.5 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0 O2:6.0') +# R13 + +# Reaction 13 +reaction('O + HCO <=> OH + CO', [3.000000e+13, 0.0, 0.0]) +# R14 + +# Reaction 14 +reaction('O + HCO <=> H + CO2', [3.000000e+13, 0.0, 0.0]) +# R15 + +# Reaction 15 +reaction('O + CH2O <=> OH + HCO', [3.900000e+13, 0.0, 3540.0]) +# R16 + +# Reaction 16 +reaction('O + CH2OH <=> OH + CH2O', [1.000000e+13, 0.0, 0.0]) +# R17 + +# Reaction 17 +reaction('O + CH3O <=> OH + CH2O', [1.000000e+13, 0.0, 0.0]) +# R18 + +# Reaction 18 +reaction('O + CH3OH <=> OH + CH2OH', [3.880000e+05, 2.5, 3100.0]) +# R19 + +# Reaction 19 +reaction('O + CH3OH <=> OH + CH3O', [1.300000e+05, 2.5, 5000.0]) +# R20 + +# Reaction 20 +reaction('O + C2H2 <=> H + HCCO', [1.350000e+07, 2.0, 1900.0]) +# R21 + +# Reaction 21 +reaction('O + C2H2 <=> CO + CH2', [6.940000e+06, 2.0, 1900.0]) +# R22 + +# Reaction 22 +reaction('O + C2H3 <=> H + CH2CO', [3.000000e+13, 0.0, 0.0]) +# R23 + +# Reaction 23 +reaction('O + C2H4 <=> CH3 + HCO', [1.250000e+07, 1.83, 220.0]) +# R24 + +# Reaction 24 +reaction('O + C2H5 <=> CH3 + CH2O', [2.240000e+13, 0.0, 0.0]) +# R25 + +# Reaction 25 +reaction('O + C2H6 <=> OH + C2H5', [8.980000e+07, 1.92, 5690.0]) +# R26 + +# Reaction 26 +reaction('O + HCCO <=> H + 2 CO', [1.000000e+14, 0.0, 0.0]) +# R27 + +# Reaction 27 +reaction('O + CH2CO <=> OH + HCCO', [1.000000e+13, 0.0, 8000.0]) +# R28 + +# Reaction 28 +reaction('O + CH2CO <=> CH2 + CO2', [1.750000e+12, 0.0, 1350.0]) +# R29 + +# Reaction 29 +reaction('O2 + CO <=> O + CO2', [2.500000e+12, 0.0, 47800.0]) +# R30 + +# Reaction 30 +reaction('O2 + CH2O <=> HO2 + HCO', [1.000000e+14, 0.0, 40000.0]) +# R31 + +# Reaction 31 +three_body_reaction('H + O2 + M <=> HO2 + M', [2.800000e+18, -0.86, 0.0], + efficiencies='CO2:1.5 CO:0.75 H2O:0.0 C2H6:1.5 N2:0.0 O2:0.0') +# R32 + +# Reaction 32 +reaction('H + 2 O2 <=> HO2 + O2', [2.080000e+19, -1.24, 0.0]) +# R33 + +# Reaction 33 +reaction('H + O2 + H2O <=> HO2 + H2O', [1.126000e+19, -0.76, 0.0]) +# R34 + +# Reaction 34 +reaction('H + O2 + N2 <=> HO2 + N2', [2.600000e+19, -1.24, 0.0]) +# R35 + +# Reaction 35 +reaction('H + O2 <=> O + OH', [2.650000e+16, -0.6707, 17041.0]) +# R36 + +# Reaction 36 +three_body_reaction('2 H + M <=> H2 + M', [1.000000e+18, -1.0, 0.0], + efficiencies='H2:0.0 C2H6:3.0 H2O:0.0 CO2:0.0 CH4:2.0') +# R37 + +# Reaction 37 +reaction('2 H + H2 <=> 2 H2', [9.000000e+16, -0.6, 0.0]) +# R38 + +# Reaction 38 +reaction('2 H + H2O <=> H2 + H2O', [6.000000e+19, -1.25, 0.0]) +# R39 + +# Reaction 39 +reaction('2 H + CO2 <=> H2 + CO2', [5.500000e+20, -2.0, 0.0]) +# R40 + +# Reaction 40 +three_body_reaction('H + OH + M <=> H2O + M', [2.200000e+22, -2.0, 0.0], + efficiencies='H2:0.73 C2H6:3.0 H2O:3.65 CH4:2.0') +# R41 + +# Reaction 41 +reaction('H + HO2 <=> O + H2O', [3.970000e+12, 0.0, 671.0]) +# R42 + +# Reaction 42 +reaction('H + HO2 <=> O2 + H2', [4.480000e+13, 0.0, 1068.0]) +# R43 + +# Reaction 43 +reaction('H + HO2 <=> 2 OH', [8.400000e+13, 0.0, 635.0]) +# R44 + +# Reaction 44 +reaction('H + H2O2 <=> HO2 + H2', [1.210000e+07, 2.0, 5200.0]) +# R45 + +# Reaction 45 +reaction('H + H2O2 <=> OH + H2O', [1.000000e+13, 0.0, 3600.0]) +# R46 + +# Reaction 46 +reaction('H + CH <=> C + H2', [1.650000e+14, 0.0, 0.0]) +# R47 + +# Reaction 47 +falloff_reaction('H + CH2 (+ M) <=> CH3 (+ M)', + kf=[6.000000e+14, 0.0, 0.0], + kf0=[1.040000e+26, -2.76, 1600.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.562, T3=91.0, T1=5836.0, T2=8552.0)) +# R48 + +# Reaction 48 +reaction('H + CH2(S) <=> CH + H2', [3.000000e+13, 0.0, 0.0]) +# R49 + +# Reaction 49 +falloff_reaction('H + CH3 (+ M) <=> CH4 (+ M)', + kf=[1.390000e+16, -0.534, 536.0], + kf0=[2.620000e+33, -4.76, 2440.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:3.0 C2H6:3.0', + falloff=Troe(A=0.783, T3=74.0, T1=2941.0, T2=6964.0)) +# R50 + +# Reaction 50 +reaction('H + CH4 <=> CH3 + H2', [6.600000e+08, 1.62, 10840.0]) +# R51 + +# Reaction 51 +falloff_reaction('H + HCO (+ M) <=> CH2O (+ M)', + kf=[1.090000e+12, 0.48, -260.0], + kf0=[2.470000e+24, -2.57, 425.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7824, T3=271.0, T1=2755.0, T2=6570.0)) +# R52 + +# Reaction 52 +reaction('H + HCO <=> H2 + CO', [7.340000e+13, 0.0, 0.0]) +# R53 + +# Reaction 53 +falloff_reaction('H + CH2O (+ M) <=> CH2OH (+ M)', + kf=[5.400000e+11, 0.454, 3600.0], + kf0=[1.270000e+32, -4.82, 6530.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7187, T3=103.0, T1=1291.0, T2=4160.0)) +# R54 + +# Reaction 54 +falloff_reaction('H + CH2O (+ M) <=> CH3O (+ M)', + kf=[5.400000e+11, 0.454, 2600.0], + kf0=[2.200000e+30, -4.8, 5560.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.758, T3=94.0, T1=1555.0, T2=4200.0)) +# R55 + +# Reaction 55 +reaction('H + CH2O <=> HCO + H2', [5.740000e+07, 1.9, 2742.0]) +# R56 + +# Reaction 56 +falloff_reaction('H + CH2OH (+ M) <=> CH3OH (+ M)', + kf=[1.055000e+12, 0.5, 86.0], + kf0=[4.360000e+31, -4.65, 5080.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.6, T3=100.0, T1=90000.0, T2=10000.0)) +# R57 + +# Reaction 57 +reaction('H + CH2OH <=> H2 + CH2O', [2.000000e+13, 0.0, 0.0]) +# R58 + +# Reaction 58 +reaction('H + CH2OH <=> OH + CH3', [1.650000e+11, 0.65, -284.0]) +# R59 + +# Reaction 59 +reaction('H + CH2OH <=> CH2(S) + H2O', [3.280000e+13, -0.09, 610.0]) +# R60 + +# Reaction 60 +falloff_reaction('H + CH3O (+ M) <=> CH3OH (+ M)', + kf=[2.430000e+12, 0.515, 50.0], + kf0=[4.660000e+41, -7.44, 14080.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7, T3=100.0, T1=90000.0, T2=10000.0)) +# R61 + +# Reaction 61 +reaction('H + CH3O <=> H + CH2OH', [4.150000e+07, 1.63, 1924.0]) +# R62 + +# Reaction 62 +reaction('H + CH3O <=> H2 + CH2O', [2.000000e+13, 0.0, 0.0]) +# R63 + +# Reaction 63 +reaction('H + CH3O <=> OH + CH3', [1.500000e+12, 0.5, -110.0]) +# R64 + +# Reaction 64 +reaction('H + CH3O <=> CH2(S) + H2O', [2.620000e+14, -0.23, 1070.0]) +# R65 + +# Reaction 65 +reaction('H + CH3OH <=> CH2OH + H2', [1.700000e+07, 2.1, 4870.0]) +# R66 + +# Reaction 66 +reaction('H + CH3OH <=> CH3O + H2', [4.200000e+06, 2.1, 4870.0]) +# R67 + +# Reaction 67 +falloff_reaction('H + C2H2 (+ M) <=> C2H3 (+ M)', + kf=[5.600000e+12, 0.0, 2400.0], + kf0=[3.800000e+40, -7.27, 7220.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7507, T3=98.5, T1=1302.0, T2=4167.0)) +# R68 + +# Reaction 68 +falloff_reaction('H + C2H3 (+ M) <=> C2H4 (+ M)', + kf=[6.080000e+12, 0.27, 280.0], + kf0=[1.400000e+30, -3.86, 3320.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.782, T3=207.5, T1=2663.0, T2=6095.0)) +# R69 + +# Reaction 69 +reaction('H + C2H3 <=> H2 + C2H2', [3.000000e+13, 0.0, 0.0]) +# R70 + +# Reaction 70 +falloff_reaction('H + C2H4 (+ M) <=> C2H5 (+ M)', + kf=[5.400000e+11, 0.454, 1820.0], + kf0=[6.000000e+41, -7.62, 6970.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.9753, T3=210.0, T1=984.0, T2=4374.0)) +# R71 + +# Reaction 71 +reaction('H + C2H4 <=> C2H3 + H2', [1.325000e+06, 2.53, 12240.0]) +# R72 + +# Reaction 72 +falloff_reaction('H + C2H5 (+ M) <=> C2H6 (+ M)', + kf=[5.210000e+17, -0.99, 1580.0], + kf0=[1.990000e+41, -7.08, 6685.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.8422, T3=125.0, T1=2219.0, T2=6882.0)) +# R73 + +# Reaction 73 +reaction('H + C2H5 <=> H2 + C2H4', [2.000000e+12, 0.0, 0.0]) +# R74 + +# Reaction 74 +reaction('H + C2H6 <=> C2H5 + H2', [1.150000e+08, 1.9, 7530.0]) +# R75 + +# Reaction 75 +reaction('H + HCCO <=> CH2(S) + CO', [1.000000e+14, 0.0, 0.0]) +# R76 + +# Reaction 76 +reaction('H + CH2CO <=> HCCO + H2', [5.000000e+13, 0.0, 8000.0]) +# R77 + +# Reaction 77 +reaction('H + CH2CO <=> CH3 + CO', [1.130000e+13, 0.0, 3428.0]) +# R78 + +# Reaction 78 +falloff_reaction('H2 + CO (+ M) <=> CH2O (+ M)', + kf=[4.300000e+07, 1.5, 79600.0], + kf0=[5.070000e+27, -3.42, 84350.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.932, T3=197.0, T1=1540.0, T2=10300.0)) +# R79 + +# Reaction 79 +reaction('OH + H2 <=> H + H2O', [2.160000e+08, 1.51, 3430.0]) +# R80 + +# Reaction 80 +falloff_reaction('2 OH (+ M) <=> H2O2 (+ M)', + kf=[7.400000e+13, -0.37, 0.0], + kf0=[2.300000e+18, -0.9, -1700.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7346, T3=94.0, T1=1756.0, T2=5182.0)) +# R81 + +# Reaction 81 +reaction('2 OH <=> O + H2O', [3.570000e+04, 2.4, -2110.0]) +# R82 + +# Reaction 82 +reaction('OH + HO2 <=> O2 + H2O', [1.450000e+13, 0.0, -500.0], + options='duplicate') +# R83 + +# Reaction 83 +reaction('OH + H2O2 <=> HO2 + H2O', [2.000000e+12, 0.0, 427.0], + options='duplicate') +# R84 + +# Reaction 84 +reaction('OH + H2O2 <=> HO2 + H2O', [1.700000e+18, 0.0, 29410.0], + options='duplicate') +# R85 + +# Reaction 85 +reaction('OH + C <=> H + CO', [5.000000e+13, 0.0, 0.0]) +# R86 + +# Reaction 86 +reaction('OH + CH <=> H + HCO', [3.000000e+13, 0.0, 0.0]) +# R87 + +# Reaction 87 +reaction('OH + CH2 <=> H + CH2O', [2.000000e+13, 0.0, 0.0]) +# R88 + +# Reaction 88 +reaction('OH + CH2 <=> CH + H2O', [1.130000e+07, 2.0, 3000.0]) +# R89 + +# Reaction 89 +reaction('OH + CH2(S) <=> H + CH2O', [3.000000e+13, 0.0, 0.0]) +# R90 + +# Reaction 90 +falloff_reaction('OH + CH3 (+ M) <=> CH3OH (+ M)', + kf=[2.790000e+18, -1.43, 1330.0], + kf0=[4.000000e+36, -5.92, 3140.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.412, T3=195.0, T1=5900.0, T2=6394.0)) +# R91 + +# Reaction 91 +reaction('OH + CH3 <=> CH2 + H2O', [5.600000e+07, 1.6, 5420.0]) +# R92 + +# Reaction 92 +reaction('OH + CH3 <=> CH2(S) + H2O', [6.440000e+17, -1.34, 1417.0]) +# R93 + +# Reaction 93 +reaction('OH + CH4 <=> CH3 + H2O', [1.000000e+08, 1.6, 3120.0]) +# R94 + +# Reaction 94 +reaction('OH + CO <=> H + CO2', [4.760000e+07, 1.228, 70.0]) +# R95 + +# Reaction 95 +reaction('OH + HCO <=> H2O + CO', [5.000000e+13, 0.0, 0.0]) +# R96 + +# Reaction 96 +reaction('OH + CH2O <=> HCO + H2O', [3.430000e+09, 1.18, -447.0]) +# R97 + +# Reaction 97 +reaction('OH + CH2OH <=> H2O + CH2O', [5.000000e+12, 0.0, 0.0]) +# R98 + +# Reaction 98 +reaction('OH + CH3O <=> H2O + CH2O', [5.000000e+12, 0.0, 0.0]) +# R99 + +# Reaction 99 +reaction('OH + CH3OH <=> CH2OH + H2O', [1.440000e+06, 2.0, -840.0]) +# R100 + +# Reaction 100 +reaction('OH + CH3OH <=> CH3O + H2O', [6.300000e+06, 2.0, 1500.0]) +# R101 + +# Reaction 101 +reaction('OH + C2H2 <=> H + CH2CO', [2.180000e-04, 4.5, -1000.0]) +# R102 + +# Reaction 102 +reaction('OH + C2H2 <=> CH3 + CO', [4.830000e-04, 4.0, -2000.0]) +# R103 + +# Reaction 103 +reaction('OH + C2H3 <=> H2O + C2H2', [5.000000e+12, 0.0, 0.0]) +# R104 + +# Reaction 104 +reaction('OH + C2H4 <=> C2H3 + H2O', [3.600000e+06, 2.0, 2500.0]) +# R105 + +# Reaction 105 +reaction('OH + C2H6 <=> C2H5 + H2O', [3.540000e+06, 2.12, 870.0]) +# R106 + +# Reaction 106 +reaction('OH + CH2CO <=> HCCO + H2O', [7.500000e+12, 0.0, 2000.0]) +# R107 + +# Reaction 107 +reaction('2 HO2 <=> O2 + H2O2', [1.300000e+11, 0.0, -1630.0], + options='duplicate') +# R108 + +# Reaction 108 +reaction('2 HO2 <=> O2 + H2O2', [4.200000e+14, 0.0, 12000.0], + options='duplicate') +# R109 + +# Reaction 109 +reaction('HO2 + CH2 <=> OH + CH2O', [2.000000e+13, 0.0, 0.0]) +# R110 + +# Reaction 110 +reaction('HO2 + CH3 <=> O2 + CH4', [1.000000e+12, 0.0, 0.0]) +# R111 + +# Reaction 111 +reaction('HO2 + CH3 <=> OH + CH3O', [3.780000e+13, 0.0, 0.0]) +# R112 + +# Reaction 112 +reaction('HO2 + CO <=> OH + CO2', [1.500000e+14, 0.0, 23600.0]) +# R113 + +# Reaction 113 +reaction('HO2 + CH2O <=> HCO + H2O2', [5.600000e+06, 2.0, 12000.0]) +# R114 + +# Reaction 114 +reaction('C + O2 <=> O + CO', [5.800000e+13, 0.0, 576.0]) +# R115 + +# Reaction 115 +reaction('C + CH3 <=> H + C2H2', [5.000000e+13, 0.0, 0.0]) +# R116 + +# Reaction 116 +reaction('CH + O2 <=> O + HCO', [6.710000e+13, 0.0, 0.0]) +# R117 + +# Reaction 117 +reaction('CH + H2 <=> H + CH2', [1.080000e+14, 0.0, 3110.0]) +# R118 + +# Reaction 118 +reaction('CH + H2O <=> H + CH2O', [5.710000e+12, 0.0, -755.0]) +# R119 + +# Reaction 119 +# reaction('CH + CH2 <=> H + C2H2', [4.000000e+13, 0.0, 0.0]) +# R120 + +# Reaction 120 +reaction('CH + CH3 <=> H + C2H3', [3.000000e+13, 0.0, 0.0]) +# R121 + +# Reaction 121 +reaction('CH + CH4 <=> H + C2H4', [6.000000e+13, 0.0, 0.0]) +# R122 + +# Reaction 122 +falloff_reaction('CH + CO (+ M) <=> HCCO (+ M)', + kf=[5.000000e+13, 0.0, 0.0], + kf0=[2.690000e+28, -3.74, 1936.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.5757, T3=237.0, T1=1652.0, T2=5069.0)) +# R123 + +# Reaction 123 +reaction('CH + CO2 <=> HCO + CO', [1.900000e+14, 0.0, 15792.0]) +# R124 + +# Reaction 124 +reaction('CH + CH2O <=> H + CH2CO', [9.460000e+13, 0.0, -515.0]) +# R125 + +# Reaction 125 +# reaction('CH + HCCO <=> CO + C2H2', [5.000000e+13, 0.0, 0.0]) +# R126 + +# Reaction 126 +reaction('CH2 + O2 => OH + H + CO', [5.000000e+12, 0.0, 1500.0]) +# R127 + +# Reaction 127 +reaction('CH2 + H2 <=> H + CH3', [5.000000e+05, 2.0, 7230.0]) +# R128 + +# Reaction 128 +# reaction('2 CH2 <=> H2 + C2H2', [1.600000e+15, 0.0, 11944.0]) +# R129 + +# Reaction 129 +reaction('CH2 + CH3 <=> H + C2H4', [4.000000e+13, 0.0, 0.0]) +# R130 + +# Reaction 130 +reaction('CH2 + CH4 <=> 2 CH3', [2.460000e+06, 2.0, 8270.0]) +# R131 + +# Reaction 131 +falloff_reaction('CH2 + CO (+ M) <=> CH2CO (+ M)', + kf=[8.100000e+11, 0.5, 4510.0], + kf0=[2.690000e+33, -5.11, 7095.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.5907, T3=275.0, T1=1226.0, T2=5185.0)) +# R132 + +# Reaction 132 +# reaction('CH2 + HCCO <=> C2H3 + CO', [3.000000e+13, 0.0, 0.0]) +# R133 + +# Reaction 133 +reaction('CH2(S) + N2 <=> CH2 + N2', [1.500000e+13, 0.0, 600.0]) +# R134 + +# Reaction 134 +reaction('CH2(S) + O2 <=> H + OH + CO', [2.800000e+13, 0.0, 0.0]) +# R135 + +# Reaction 135 +reaction('CH2(S) + O2 <=> CO + H2O', [1.200000e+13, 0.0, 0.0]) +# R136 + +# Reaction 136 +reaction('CH2(S) + H2 <=> CH3 + H', [7.000000e+13, 0.0, 0.0]) +# R137 + +# Reaction 137 +falloff_reaction('CH2(S) + H2O (+ M) <=> CH3OH (+ M)', + kf=[4.820000e+17, -1.16, 1145.0], + kf0=[1.880000e+38, -6.36, 5040.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.6027, T3=208.0, T1=3922.0, T2=10180.0)) +# R138 + +# Reaction 138 +reaction('CH2(S) + H2O <=> CH2 + H2O', [3.000000e+13, 0.0, 0.0]) +# R139 + +# Reaction 139 +reaction('CH2(S) + CH3 <=> H + C2H4', [1.200000e+13, 0.0, -570.0]) +# R140 + +# Reaction 140 +reaction('CH2(S) + CH4 <=> 2 CH3', [1.600000e+13, 0.0, -570.0]) +# R141 + +# Reaction 141 +reaction('CH2(S) + CO <=> CH2 + CO', [9.000000e+12, 0.0, 0.0]) +# R142 + +# Reaction 142 +reaction('CH2(S) + CO2 <=> CH2 + CO2', [7.000000e+12, 0.0, 0.0]) +# R143 + +# Reaction 143 +reaction('CH2(S) + CO2 <=> CO + CH2O', [1.400000e+13, 0.0, 0.0]) +# R144 + +# Reaction 144 +reaction('CH2(S) + C2H6 <=> CH3 + C2H5', [4.000000e+13, 0.0, -550.0]) +# R145 + +# Reaction 145 +reaction('CH3 + O2 <=> O + CH3O', [3.560000e+13, 0.0, 30480.0]) +# R146 + +# Reaction 146 +reaction('CH3 + O2 <=> OH + CH2O', [2.310000e+12, 0.0, 20315.0]) +# R147 + +# Reaction 147 +reaction('CH3 + H2O2 <=> HO2 + CH4', [2.450000e+04, 2.47, 5180.0]) +# R148 + +# Reaction 148 +falloff_reaction('2 CH3 (+ M) <=> C2H6 (+ M)', + kf=[6.770000e+16, -1.18, 654.0], + kf0=[3.400000e+41, -7.03, 2762.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.619, T3=73.2, T1=1180.0, T2=9999.0)) +# R149 + +# Reaction 149 +reaction('2 CH3 <=> H + C2H5', [6.840000e+12, 0.1, 10600.0]) +# R150 + +# Reaction 150 +reaction('CH3 + HCO <=> CH4 + CO', [2.648000e+13, 0.0, 0.0]) +# R151 + +# Reaction 151 +reaction('CH3 + CH2O <=> HCO + CH4', [3.320000e+03, 2.81, 5860.0]) +# R152 + +# Reaction 152 +reaction('CH3 + CH3OH <=> CH2OH + CH4', [3.000000e+07, 1.5, 9940.0]) +# R153 + +# Reaction 153 +reaction('CH3 + CH3OH <=> CH3O + CH4', [1.000000e+07, 1.5, 9940.0]) +# R154 + +# Reaction 154 +reaction('CH3 + C2H4 <=> C2H3 + CH4', [2.270000e+05, 2.0, 9200.0]) +# R155 + +# Reaction 155 +reaction('CH3 + C2H6 <=> C2H5 + CH4', [6.140000e+06, 1.74, 10450.0]) +# R156 + +# Reaction 156 +reaction('HCO + H2O <=> H + CO + H2O', [1.500000e+18, -1.0, 17000.0]) +# R157 + +# Reaction 157 +three_body_reaction('HCO + M <=> H + CO + M', [1.870000e+17, -1.0, 17000.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:0.0 CH4:2.0 C2H6:3.0') +# R158 + +# Reaction 158 +reaction('HCO + O2 <=> HO2 + CO', [1.345000e+13, 0.0, 400.0]) +# R159 + +# Reaction 159 +reaction('CH2OH + O2 <=> HO2 + CH2O', [1.800000e+13, 0.0, 900.0]) +# R160 + +# Reaction 160 +reaction('CH3O + O2 <=> HO2 + CH2O', [4.280000e-13, 7.6, -3530.0]) +# R161 + +# Reaction 161 +reaction('C2H3 + O2 <=> HCO + CH2O', [4.580000e+16, -1.39, 1015.0]) +# R162 + +# Reaction 162 +falloff_reaction('C2H4 (+ M) <=> H2 + C2H2 (+ M)', + kf=[8.000000e+12, 0.44, 86770.0], + kf0=[1.580000e+51, -9.3, 97800.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7345, T3=180.0, T1=1035.0, T2=5417.0)) +# R163 + +# Reaction 163 +reaction('C2H5 + O2 <=> HO2 + C2H4', [8.400000e+11, 0.0, 3875.0]) +# R164 + +# Reaction 164 +reaction('HCCO + O2 <=> OH + 2 CO', [3.200000e+12, 0.0, 854.0]) +# R165 + +# Reaction 165 +# reaction('2 HCCO <=> 2 CO + C2H2', [1.000000e+13, 0.0, 0.0]) +# R166 + +# Reaction 166 +reaction('O + CH3 => H + H2 + CO', [3.370000e+13, 0.0, 0.0]) +# R167 + +# Reaction 167 +reaction('O + C2H4 <=> H + CH2CHO', [6.700000e+06, 1.83, 220.0]) +# R168 + +# Reaction 168 +reaction('OH + HO2 <=> O2 + H2O', [5.000000e+15, 0.0, 17330.0], + options='duplicate') +# R169 + +# Reaction 169 +reaction('OH + CH3 => H2 + CH2O', [8.000000e+09, 0.5, -1755.0]) +# R170 + +# Reaction 170 +falloff_reaction('CH + H2 (+ M) <=> CH3 (+ M)', + kf=[1.970000e+12, 0.43, -370.0], + kf0=[4.820000e+25, -2.8, 590.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.578, T3=122.0, T1=2535.0, T2=9365.0)) +# R171 + +# Reaction 171 +reaction('CH2 + O2 => 2 H + CO2', [5.800000e+12, 0.0, 1500.0]) +# R172 + +# Reaction 172 +reaction('CH2 + O2 <=> O + CH2O', [2.400000e+12, 0.0, 1500.0]) +# R173 + +# Reaction 173 +# reaction('CH2 + CH2 => 2 H + C2H2', [2.000000e+14, 0.0, 10989.0]) +# R174 + +# Reaction 174 +reaction('CH2(S) + H2O => H2 + CH2O', [6.820000e+10, 0.25, -935.0]) +# R175 + +# Reaction 175 +reaction('C2H3 + O2 <=> O + CH2CHO', [3.030000e+11, 0.29, 11.0]) +# R176 + +# Reaction 176 +reaction('C2H3 + O2 <=> HO2 + C2H2', [1.337000e+06, 1.61, -384.0]) +# R177 + +# Reaction 177 +falloff_reaction('H + CH2CO (+ M) <=> CH2CHO (+ M)', + kf=[4.865000e+11, 0.422, -1755.0], + kf0=[1.012000e+42, -7.63, 3854.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.465, T3=201.0, T1=1773.0, T2=5333.0)) +# R178 + +# Reaction 178 +reaction('O + CH2CHO => H + CH2 + CO2', [1.500000e+14, 0.0, 0.0]) +# R179 + +# Reaction 179 +reaction('O2 + CH2CHO => OH + CO + CH2O', [1.810000e+10, 0.0, 0.0]) +# R180 + +# Reaction 180 +reaction('O2 + CH2CHO => OH + 2 HCO', [2.350000e+10, 0.0, 0.0]) +# R181 + +# Reaction 181 +reaction('H + CH2CHO <=> CH3 + HCO', [2.200000e+13, 0.0, 0.0]) +# R182 + +# Reaction 182 +reaction('H + CH2CHO <=> CH2CO + H2', [1.100000e+13, 0.0, 0.0]) +# R183 + +# Reaction 183 +reaction('OH + CH2CHO <=> H2O + CH2CO', [1.200000e+13, 0.0, 0.0]) +# R184 + +# Reaction 184 +# reaction('OH + CH2CHO <=> HCO + CH2OH', [3.010000e+13, 0.0, 0.0]) diff --git a/samples/python/AVBP/inputs/Lu.yaml b/samples/python/AVBP/inputs/Lu.yaml new file mode 100644 index 00000000000..3dcf578a23c --- /dev/null +++ b/samples/python/AVBP/inputs/Lu.yaml @@ -0,0 +1,997 @@ +description: |- + "" + +generator: cti2yaml +cantera-version: 3.0.0 +date: Tue, 26 Dec 2023 00:54:57 +0100 +input-files: [Lu.cti] + +units: {length: cm, quantity: mol, activation-energy: cal/mol} + +phases: +- name: gas + thermo: ideal-gas + elements: [O, H, C, N, Ar] + species: [H2, H, O, O2, OH, H2O, HO2, H2O2, C, CH, CH2, CH2(S), CH3, CH4, + CO, CO2, HCO, CH2O, CH2OH, CH3O, CH3OH, C2H2, C2H3, C2H4, C2H5, C2H6, + HCCO, CH2CO, CH2CHO, N2] + kinetics: gas + reactions: all + transport: mixture-averaged + state: + T: 300.0 + P: 1.01325e+05 + +species: +- name: H2 + composition: {H: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.34433112, 7.98052075e-03, -1.9478151e-05, 2.01572094e-08, -7.37611761e-12, + -917.935173, 0.683010238] + - [3.3372792, -4.94024731e-05, 4.99456778e-07, -1.79566394e-10, 2.00255376e-14, + -950.158922, -3.20502331] + transport: + model: gas + geometry: linear + diameter: 2.92 + well-depth: 38.0 + polarizability: 0.79 + rotational-relaxation: 280.0 + note: TPIS78 +- name: H + composition: {H: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18, -9.27732332e-22, + 2.54736599e+04, -0.446682853] + - [2.50000001, -2.30842973e-11, 1.61561948e-14, -4.73515235e-18, 4.98197357e-22, + 2.54736599e+04, -0.446682914] + transport: + model: gas + geometry: atom + diameter: 2.05 + well-depth: 145.0 + note: L7/88 +- name: O + composition: {O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.1682671, -3.27931884e-03, 6.64306396e-06, -6.12806624e-09, 2.11265971e-12, + 2.91222592e+04, 2.05193346] + - [2.56942078, -8.59741137e-05, 4.19484589e-08, -1.00177799e-11, 1.22833691e-15, + 2.92175791e+04, 4.78433864] + transport: + model: gas + geometry: atom + diameter: 2.75 + well-depth: 80.0 + note: L1/90 +- name: O2 + composition: {O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.78245636, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09, 3.24372837e-12, + -1063.94356, 3.65767573] + - [3.28253784, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10, -2.16717794e-14, + -1088.45772, 5.45323129] + transport: + model: gas + geometry: linear + diameter: 3.458 + well-depth: 107.4 + polarizability: 1.6 + rotational-relaxation: 3.8 + note: TPIS89 +- name: OH + composition: {H: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.99201543, -2.40131752e-03, 4.61793841e-06, -3.88113333e-09, 1.3641147e-12, + 3615.08056, -0.103925458] + - [3.09288767, 5.48429716e-04, 1.26505228e-07, -8.79461556e-11, 1.17412376e-14, + 3858.657, 4.4766961] + transport: + model: gas + geometry: linear + diameter: 2.75 + well-depth: 80.0 + note: RUS78 +- name: H2O + composition: {H: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19864056, -2.0364341e-03, 6.52040211e-06, -5.48797062e-09, 1.77197817e-12, + -3.02937267e+04, -0.849032208] + - [3.03399249, 2.17691804e-03, -1.64072518e-07, -9.7041987e-11, 1.68200992e-14, + -3.00042971e+04, 4.9667701] + transport: + model: gas + geometry: nonlinear + diameter: 2.605 + well-depth: 572.4 + dipole: 1.844 + rotational-relaxation: 4.0 + note: L8/89 +- name: HO2 + composition: {H: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30179801, -4.74912051e-03, 2.11582891e-05, -2.42763894e-08, 9.29225124e-12, + 294.80804, 3.71666245] + - [4.0172109, 2.23982013e-03, -6.3365815e-07, 1.1424637e-10, -1.07908535e-14, + 111.856713, 3.78510215] + transport: + model: gas + geometry: nonlinear + diameter: 3.458 + well-depth: 107.4 + rotational-relaxation: 1.0 + note: L5/89 +- name: H2O2 + composition: {H: 2, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.27611269, -5.42822417e-04, 1.67335701e-05, -2.15770813e-08, 8.62454363e-12, + -1.77025821e+04, 3.43505074] + - [4.16500285, 4.90831694e-03, -1.90139225e-06, 3.71185986e-10, -2.87908305e-14, + -1.78617877e+04, 2.91615662] + transport: + model: gas + geometry: nonlinear + diameter: 3.458 + well-depth: 107.4 + rotational-relaxation: 3.8 + note: L7/88 +- name: C + composition: {C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.55423955, -3.21537724e-04, 7.33792245e-07, -7.32234889e-10, 2.66521446e-13, + 8.54438832e+04, 4.53130848] + - [2.49266888, 4.79889284e-05, -7.2433502e-08, 3.74291029e-11, -4.87277893e-15, + 8.54512953e+04, 4.80150373] + transport: + model: gas + geometry: atom + diameter: 3.298 + well-depth: 71.4 + note: L11/88 +- name: CH + composition: {H: 1, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.48981665, 3.23835541e-04, -1.68899065e-06, 3.16217327e-09, -1.40609067e-12, + 7.07972934e+04, 2.08401108] + - [2.87846473, 9.70913681e-04, 1.44445655e-07, -1.30687849e-10, 1.76079383e-14, + 7.10124364e+04, 5.48497999] + transport: + model: gas + geometry: linear + diameter: 2.75 + well-depth: 80.0 + note: TPIS79 +- name: CH2 + composition: {H: 2, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.76267867, 9.68872143e-04, 2.79489841e-06, -3.85091153e-09, 1.68741719e-12, + 4.60040401e+04, 1.56253185] + - [2.87410113, 3.65639292e-03, -1.40894597e-06, 2.60179549e-10, -1.87727567e-14, + 4.6263604e+04, 6.17119324] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 +- name: CH2(S) + composition: {H: 2, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19860411, -2.36661419e-03, 8.2329622e-06, -6.68815981e-09, 1.94314737e-12, + 5.04968163e+04, -0.769118967] + - [2.29203842, 4.65588637e-03, -2.01191947e-06, 4.17906e-10, -3.39716365e-14, + 5.09259997e+04, 8.62650169] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 +- name: CH3 + composition: {H: 3, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.6735904, 2.01095175e-03, 5.73021856e-06, -6.87117425e-09, 2.54385734e-12, + 1.64449988e+04, 1.60456433] + - [2.28571772, 7.23990037e-03, -2.98714348e-06, 5.95684644e-10, -4.67154394e-14, + 1.67755843e+04, 8.48007179] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: L11/89 +- name: CH4 + composition: {H: 4, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.14987613, -0.0136709788, 4.91800599e-05, -4.84743026e-08, 1.66693956e-11, + -1.02466476e+04, -4.64130376] + - [0.074851495, 0.0133909467, -5.73285809e-06, 1.22292535e-09, -1.0181523e-13, + -9468.34459, 18.437318] + transport: + model: gas + geometry: nonlinear + diameter: 3.746 + well-depth: 141.4 + polarizability: 2.6 + rotational-relaxation: 13.0 + note: L8/88 +- name: CO + composition: {C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.57953347, -6.1035368e-04, 1.01681433e-06, 9.07005884e-10, -9.04424499e-13, + -1.4344086e+04, 3.50840928] + - [2.71518561, 2.06252743e-03, -9.98825771e-07, 2.30053008e-10, -2.03647716e-14, + -1.41518724e+04, 7.81868772] + transport: + model: gas + geometry: linear + diameter: 3.65 + well-depth: 98.1 + polarizability: 1.95 + rotational-relaxation: 1.8 + note: TPIS79 +- name: CO2 + composition: {C: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.35677352, 8.98459677e-03, -7.12356269e-06, 2.45919022e-09, -1.43699548e-13, + -4.83719697e+04, 9.90105222] + - [3.85746029, 4.41437026e-03, -2.21481404e-06, 5.23490188e-10, -4.72084164e-14, + -4.8759166e+04, 2.27163806] + transport: + model: gas + geometry: linear + diameter: 3.763 + well-depth: 244.0 + polarizability: 2.65 + rotational-relaxation: 2.1 + note: L7/88 +- name: HCO + composition: {H: 1, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.22118584, -3.24392532e-03, 1.37799446e-05, -1.33144093e-08, 4.33768865e-12, + 3839.56496, 3.39437243] + - [2.77217438, 4.95695526e-03, -2.48445613e-06, 5.89161778e-10, -5.33508711e-14, + 4011.91815, 9.79834492] + transport: + model: gas + geometry: nonlinear + diameter: 3.59 + well-depth: 498.0 + note: L12/89 +- name: CH2O + composition: {H: 2, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.79372315, -9.90833369e-03, 3.73220008e-05, -3.79285261e-08, 1.31772652e-11, + -1.43089567e+04, 0.6028129] + - [1.76069008, 9.20000082e-03, -4.42258813e-06, 1.00641212e-09, -8.8385564e-14, + -1.39958323e+04, 13.656323] + transport: + model: gas + geometry: nonlinear + diameter: 3.59 + well-depth: 498.0 + rotational-relaxation: 2.0 + note: L8/88 +- name: CH2OH + composition: {H: 3, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.86388918, 5.59672304e-03, 5.93271791e-06, -1.04532012e-08, 4.36967278e-12, + -3193.91367, 5.47302243] + - [3.69266569, 8.64576797e-03, -3.7510112e-06, 7.87234636e-10, -6.48554201e-14, + -3242.50627, 5.81043215] + transport: + model: gas + geometry: nonlinear + diameter: 3.69 + well-depth: 417.0 + dipole: 1.7 + rotational-relaxation: 2.0 + note: GUNL93 +- name: CH3O + composition: {H: 3, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [2.106204, 7.216595e-03, 5.338472e-06, -7.377636e-09, 2.07561e-12, + 978.6011, 13.152177] + - [3.770799, 7.871497e-03, -2.656384e-06, 3.944431e-10, -2.112616e-14, + 127.83252, 2.929575] + transport: + model: gas + geometry: nonlinear + diameter: 3.69 + well-depth: 417.0 + dipole: 1.7 + rotational-relaxation: 2.0 + note: '121686' +- name: CH3OH + composition: {H: 4, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.71539582, -0.0152309129, 6.52441155e-05, -7.10806889e-08, 2.61352698e-11, + -2.56427656e+04, -1.50409823] + - [1.78970791, 0.0140938292, -6.36500835e-06, 1.38171085e-09, -1.1706022e-13, + -2.53748747e+04, 14.5023623] + transport: + model: gas + geometry: nonlinear + diameter: 3.626 + well-depth: 481.8 + rotational-relaxation: 1.0 + note: L8/88 +- name: C2H2 + composition: {H: 2, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [0.808681094, 0.0233615629, -3.55171815e-05, 2.80152437e-08, -8.50072974e-12, + 2.64289807e+04, 13.9397051] + - [4.14756964, 5.96166664e-03, -2.37294852e-06, 4.67412171e-10, -3.61235213e-14, + 2.59359992e+04, -1.23028121] + transport: + model: gas + geometry: linear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 2.5 + note: L1/91 +- name: C2H3 + composition: {H: 3, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.21246645, 1.51479162e-03, 2.59209412e-05, -3.57657847e-08, 1.47150873e-11, + 3.48598468e+04, 8.51054025] + - [3.016724, 0.0103302292, -4.68082349e-06, 1.01763288e-09, -8.62607041e-14, + 3.46128739e+04, 7.78732378] + transport: + model: gas + geometry: nonlinear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 1.0 + note: L2/92 +- name: C2H4 + composition: {H: 4, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.95920148, -7.57052247e-03, 5.70990292e-05, -6.91588753e-08, 2.69884373e-11, + 5089.77593, 4.09733096] + - [2.03611116, 0.0146454151, -6.71077915e-06, 1.47222923e-09, -1.25706061e-13, + 4939.88614, 10.3053693] + transport: + model: gas + geometry: nonlinear + diameter: 3.971 + well-depth: 280.8 + rotational-relaxation: 1.5 + note: L1/91 +- name: C2H5 + composition: {H: 5, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30646568, -4.18658892e-03, 4.97142807e-05, -5.99126606e-08, 2.30509004e-11, + 1.28416265e+04, 4.70720924] + - [1.95465642, 0.0173972722, -7.98206668e-06, 1.75217689e-09, -1.49641576e-13, + 1.285752e+04, 13.4624343] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L12/92 +- name: C2H6 + composition: {H: 6, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.29142492, -5.5015427e-03, 5.99438288e-05, -7.08466285e-08, 2.68685771e-11, + -1.15222055e+04, 2.66682316] + - [1.0718815, 0.0216852677, -1.00256067e-05, 2.21412001e-09, -1.9000289e-13, + -1.14263932e+04, 15.1156107] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L8/88 +- name: HCCO + composition: {H: 1, C: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 4000.0] + data: + - [2.2517214, 0.017655021, -2.3729101e-05, 1.7275759e-08, -5.0664811e-12, + 2.0059449e+04, 12.490417] + - [5.6282058, 4.0853401e-03, -1.5934547e-06, 2.8626052e-10, -1.9407832e-14, + 1.9327215e+04, -3.9302595] + transport: + model: gas + geometry: nonlinear + diameter: 2.5 + well-depth: 150.0 + rotational-relaxation: 1.0 + note: SRIC91 +- name: CH2CO + composition: {H: 2, C: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.1358363, 0.0181188721, -1.73947474e-05, 9.34397568e-09, -2.01457615e-12, + -7042.91804, 12.215648] + - [4.51129732, 9.00359745e-03, -4.16939635e-06, 9.23345882e-10, -7.94838201e-14, + -7551.05311, 0.632247205] + transport: + model: gas + geometry: nonlinear + diameter: 3.97 + well-depth: 436.0 + rotational-relaxation: 2.0 + note: L5/90 +- name: CH2CHO + composition: {H: 3, C: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.409062, 0.010738574, 1.891492e-06, -7.158583e-09, 2.867385e-12, + 1521.4766, 9.55829] + - [5.97567, 8.130591e-03, -2.743624e-06, 4.070304e-10, -2.176017e-14, + 490.3218, -5.045251] + transport: + model: gas + geometry: nonlinear + diameter: 3.97 + well-depth: 436.0 + rotational-relaxation: 2.0 + note: SAND86 +- name: N2 + composition: {N: 2} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12, + -1020.8999, 3.950372] + - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15, + -922.7977, 5.980528] + transport: + model: gas + geometry: linear + diameter: 3.621 + well-depth: 97.53 + polarizability: 1.76 + rotational-relaxation: 4.0 + note: '121286' + +reactions: +- equation: 2 O + M <=> O2 + M # Reaction 1 + type: three-body + rate-constant: {A: 1.2e+17, b: -1.0, Ea: 0.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.4, H2O: 15.4, CH4: 2.0, C2H6: 3.0} +- equation: O + H + M <=> OH + M # Reaction 2 + type: three-body + rate-constant: {A: 5.0e+17, b: -1.0, Ea: 0.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: O + H2 <=> H + OH # Reaction 3 + rate-constant: {A: 3.87e+04, b: 2.7, Ea: 6260.0} +- equation: O + HO2 <=> OH + O2 # Reaction 4 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: O + H2O2 <=> OH + HO2 # Reaction 5 + rate-constant: {A: 9.63e+06, b: 2.0, Ea: 4000.0} +- equation: O + CH <=> H + CO # Reaction 6 + rate-constant: {A: 5.7e+13, b: 0.0, Ea: 0.0} +- equation: O + CH2 <=> H + HCO # Reaction 7 + rate-constant: {A: 8.0e+13, b: 0.0, Ea: 0.0} +- equation: O + CH2(S) <=> H2 + CO # Reaction 8 + rate-constant: {A: 1.5e+13, b: 0.0, Ea: 0.0} +- equation: O + CH2(S) <=> H + HCO # Reaction 9 + rate-constant: {A: 1.5e+13, b: 0.0, Ea: 0.0} +- equation: O + CH3 <=> H + CH2O # Reaction 10 + rate-constant: {A: 5.06e+13, b: 0.0, Ea: 0.0} +- equation: O + CH4 <=> OH + CH3 # Reaction 11 + rate-constant: {A: 1.02e+09, b: 1.5, Ea: 8600.0} +- equation: O + CO (+ M) <=> CO2 (+ M) # Reaction 12 + type: falloff + low-P-rate-constant: {A: 6.02e+14, b: 0.0, Ea: 3000.0} + high-P-rate-constant: {A: 1.8e+10, b: 0.0, Ea: 2385.0} + efficiencies: {CO2: 3.5, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0, + O2: 6.0} +- equation: O + HCO <=> OH + CO # Reaction 13 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: O + HCO <=> H + CO2 # Reaction 14 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: O + CH2O <=> OH + HCO # Reaction 15 + rate-constant: {A: 3.9e+13, b: 0.0, Ea: 3540.0} +- equation: O + CH2OH <=> OH + CH2O # Reaction 16 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: O + CH3O <=> OH + CH2O # Reaction 17 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: O + CH3OH <=> OH + CH2OH # Reaction 18 + rate-constant: {A: 3.88e+05, b: 2.5, Ea: 3100.0} +- equation: O + CH3OH <=> OH + CH3O # Reaction 19 + rate-constant: {A: 1.3e+05, b: 2.5, Ea: 5000.0} +- equation: O + C2H2 <=> H + HCCO # Reaction 20 + rate-constant: {A: 1.35e+07, b: 2.0, Ea: 1900.0} +- equation: O + C2H2 <=> CO + CH2 # Reaction 21 + rate-constant: {A: 6.94e+06, b: 2.0, Ea: 1900.0} +- equation: O + C2H3 <=> H + CH2CO # Reaction 22 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: O + C2H4 <=> CH3 + HCO # Reaction 23 + rate-constant: {A: 1.25e+07, b: 1.83, Ea: 220.0} +- equation: O + C2H5 <=> CH3 + CH2O # Reaction 24 + rate-constant: {A: 2.24e+13, b: 0.0, Ea: 0.0} +- equation: O + C2H6 <=> OH + C2H5 # Reaction 25 + rate-constant: {A: 8.98e+07, b: 1.92, Ea: 5690.0} +- equation: O + HCCO <=> H + 2 CO # Reaction 26 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: O + CH2CO <=> OH + HCCO # Reaction 27 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 8000.0} +- equation: O + CH2CO <=> CH2 + CO2 # Reaction 28 + rate-constant: {A: 1.75e+12, b: 0.0, Ea: 1350.0} +- equation: O2 + CO <=> O + CO2 # Reaction 29 + rate-constant: {A: 2.5e+12, b: 0.0, Ea: 4.78e+04} +- equation: O2 + CH2O <=> HO2 + HCO # Reaction 30 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 4.0e+04} +- equation: H + O2 + M <=> HO2 + M # Reaction 31 + type: three-body + rate-constant: {A: 2.8e+18, b: -0.86, Ea: 0.0} + efficiencies: {CO2: 1.5, CO: 0.75, H2O: 0.0, C2H6: 1.5, N2: 0.0, O2: 0.0} +- equation: H + 2 O2 <=> HO2 + O2 # Reaction 32 + rate-constant: {A: 2.08e+19, b: -1.24, Ea: 0.0} +- equation: H + O2 + H2O <=> HO2 + H2O # Reaction 33 + rate-constant: {A: 1.126e+19, b: -0.76, Ea: 0.0} +- equation: H + O2 + N2 <=> HO2 + N2 # Reaction 34 + rate-constant: {A: 2.6e+19, b: -1.24, Ea: 0.0} +- equation: H + O2 <=> O + OH # Reaction 35 + rate-constant: {A: 2.65e+16, b: -0.6707, Ea: 1.7041e+04} +- equation: 2 H + M <=> H2 + M # Reaction 36 + type: three-body + rate-constant: {A: 1.0e+18, b: -1.0, Ea: 0.0} + efficiencies: {H2: 0.0, C2H6: 3.0, H2O: 0.0, CO2: 0.0, CH4: 2.0} +- equation: 2 H + H2 <=> 2 H2 # Reaction 37 + rate-constant: {A: 9.0e+16, b: -0.6, Ea: 0.0} +- equation: 2 H + H2O <=> H2 + H2O # Reaction 38 + rate-constant: {A: 6.0e+19, b: -1.25, Ea: 0.0} +- equation: 2 H + CO2 <=> H2 + CO2 # Reaction 39 + rate-constant: {A: 5.5e+20, b: -2.0, Ea: 0.0} +- equation: H + OH + M <=> H2O + M # Reaction 40 + type: three-body + rate-constant: {A: 2.2e+22, b: -2.0, Ea: 0.0} + efficiencies: {H2: 0.73, C2H6: 3.0, H2O: 3.65, CH4: 2.0} +- equation: H + HO2 <=> O + H2O # Reaction 41 + rate-constant: {A: 3.97e+12, b: 0.0, Ea: 671.0} +- equation: H + HO2 <=> O2 + H2 # Reaction 42 + rate-constant: {A: 4.48e+13, b: 0.0, Ea: 1068.0} +- equation: H + HO2 <=> 2 OH # Reaction 43 + rate-constant: {A: 8.4e+13, b: 0.0, Ea: 635.0} +- equation: H + H2O2 <=> HO2 + H2 # Reaction 44 + rate-constant: {A: 1.21e+07, b: 2.0, Ea: 5200.0} +- equation: H + H2O2 <=> OH + H2O # Reaction 45 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 3600.0} +- equation: H + CH <=> C + H2 # Reaction 46 + rate-constant: {A: 1.65e+14, b: 0.0, Ea: 0.0} +- equation: H + CH2 (+ M) <=> CH3 (+ M) # Reaction 47 + type: falloff + low-P-rate-constant: {A: 1.04e+26, b: -2.76, Ea: 1600.0} + high-P-rate-constant: {A: 6.0e+14, b: 0.0, Ea: 0.0} + Troe: {A: 0.562, T3: 91.0, T1: 5836.0, T2: 8552.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH2(S) <=> CH + H2 # Reaction 48 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: H + CH3 (+ M) <=> CH4 (+ M) # Reaction 49 + type: falloff + low-P-rate-constant: {A: 2.62e+33, b: -4.76, Ea: 2440.0} + high-P-rate-constant: {A: 1.39e+16, b: -0.534, Ea: 536.0} + Troe: {A: 0.783, T3: 74.0, T1: 2941.0, T2: 6964.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 3.0, C2H6: 3.0} +- equation: H + CH4 <=> CH3 + H2 # Reaction 50 + rate-constant: {A: 6.6e+08, b: 1.62, Ea: 1.084e+04} +- equation: H + HCO (+ M) <=> CH2O (+ M) # Reaction 51 + type: falloff + low-P-rate-constant: {A: 2.47e+24, b: -2.57, Ea: 425.0} + high-P-rate-constant: {A: 1.09e+12, b: 0.48, Ea: -260.0} + Troe: {A: 0.7824, T3: 271.0, T1: 2755.0, T2: 6570.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + HCO <=> H2 + CO # Reaction 52 + rate-constant: {A: 7.34e+13, b: 0.0, Ea: 0.0} +- equation: H + CH2O (+ M) <=> CH2OH (+ M) # Reaction 53 + type: falloff + low-P-rate-constant: {A: 1.27e+32, b: -4.82, Ea: 6530.0} + high-P-rate-constant: {A: 5.4e+11, b: 0.454, Ea: 3600.0} + Troe: {A: 0.7187, T3: 103.0, T1: 1291.0, T2: 4160.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH2O (+ M) <=> CH3O (+ M) # Reaction 54 + type: falloff + low-P-rate-constant: {A: 2.2e+30, b: -4.8, Ea: 5560.0} + high-P-rate-constant: {A: 5.4e+11, b: 0.454, Ea: 2600.0} + Troe: {A: 0.758, T3: 94.0, T1: 1555.0, T2: 4200.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH2O <=> HCO + H2 # Reaction 55 + rate-constant: {A: 5.74e+07, b: 1.9, Ea: 2742.0} +- equation: H + CH2OH (+ M) <=> CH3OH (+ M) # Reaction 56 + type: falloff + low-P-rate-constant: {A: 4.36e+31, b: -4.65, Ea: 5080.0} + high-P-rate-constant: {A: 1.055e+12, b: 0.5, Ea: 86.0} + Troe: {A: 0.6, T3: 100.0, T1: 9.0e+04, T2: 1.0e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH2OH <=> H2 + CH2O # Reaction 57 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: H + CH2OH <=> OH + CH3 # Reaction 58 + rate-constant: {A: 1.65e+11, b: 0.65, Ea: -284.0} +- equation: H + CH2OH <=> CH2(S) + H2O # Reaction 59 + rate-constant: {A: 3.28e+13, b: -0.09, Ea: 610.0} +- equation: H + CH3O (+ M) <=> CH3OH (+ M) # Reaction 60 + type: falloff + low-P-rate-constant: {A: 4.66e+41, b: -7.44, Ea: 1.408e+04} + high-P-rate-constant: {A: 2.43e+12, b: 0.515, Ea: 50.0} + Troe: {A: 0.7, T3: 100.0, T1: 9.0e+04, T2: 1.0e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH3O <=> H + CH2OH # Reaction 61 + rate-constant: {A: 4.15e+07, b: 1.63, Ea: 1924.0} +- equation: H + CH3O <=> H2 + CH2O # Reaction 62 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: H + CH3O <=> OH + CH3 # Reaction 63 + rate-constant: {A: 1.5e+12, b: 0.5, Ea: -110.0} +- equation: H + CH3O <=> CH2(S) + H2O # Reaction 64 + rate-constant: {A: 2.62e+14, b: -0.23, Ea: 1070.0} +- equation: H + CH3OH <=> CH2OH + H2 # Reaction 65 + rate-constant: {A: 1.7e+07, b: 2.1, Ea: 4870.0} +- equation: H + CH3OH <=> CH3O + H2 # Reaction 66 + rate-constant: {A: 4.2e+06, b: 2.1, Ea: 4870.0} +- equation: H + C2H2 (+ M) <=> C2H3 (+ M) # Reaction 67 + type: falloff + low-P-rate-constant: {A: 3.8e+40, b: -7.27, Ea: 7220.0} + high-P-rate-constant: {A: 5.6e+12, b: 0.0, Ea: 2400.0} + Troe: {A: 0.7507, T3: 98.5, T1: 1302.0, T2: 4167.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + C2H3 (+ M) <=> C2H4 (+ M) # Reaction 68 + type: falloff + low-P-rate-constant: {A: 1.4e+30, b: -3.86, Ea: 3320.0} + high-P-rate-constant: {A: 6.08e+12, b: 0.27, Ea: 280.0} + Troe: {A: 0.782, T3: 207.5, T1: 2663.0, T2: 6095.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + C2H3 <=> H2 + C2H2 # Reaction 69 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: H + C2H4 (+ M) <=> C2H5 (+ M) # Reaction 70 + type: falloff + low-P-rate-constant: {A: 6.0e+41, b: -7.62, Ea: 6970.0} + high-P-rate-constant: {A: 5.4e+11, b: 0.454, Ea: 1820.0} + Troe: {A: 0.9753, T3: 210.0, T1: 984.0, T2: 4374.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + C2H4 <=> C2H3 + H2 # Reaction 71 + rate-constant: {A: 1.325e+06, b: 2.53, Ea: 1.224e+04} +- equation: H + C2H5 (+ M) <=> C2H6 (+ M) # Reaction 72 + type: falloff + low-P-rate-constant: {A: 1.99e+41, b: -7.08, Ea: 6685.0} + high-P-rate-constant: {A: 5.21e+17, b: -0.99, Ea: 1580.0} + Troe: {A: 0.8422, T3: 125.0, T1: 2219.0, T2: 6882.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + C2H5 <=> H2 + C2H4 # Reaction 73 + rate-constant: {A: 2.0e+12, b: 0.0, Ea: 0.0} +- equation: H + C2H6 <=> C2H5 + H2 # Reaction 74 + rate-constant: {A: 1.15e+08, b: 1.9, Ea: 7530.0} +- equation: H + HCCO <=> CH2(S) + CO # Reaction 75 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: H + CH2CO <=> HCCO + H2 # Reaction 76 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 8000.0} +- equation: H + CH2CO <=> CH3 + CO # Reaction 77 + rate-constant: {A: 1.13e+13, b: 0.0, Ea: 3428.0} +- equation: H2 + CO (+ M) <=> CH2O (+ M) # Reaction 78 + type: falloff + low-P-rate-constant: {A: 5.07e+27, b: -3.42, Ea: 8.435e+04} + high-P-rate-constant: {A: 4.3e+07, b: 1.5, Ea: 7.96e+04} + Troe: {A: 0.932, T3: 197.0, T1: 1540.0, T2: 1.03e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: OH + H2 <=> H + H2O # Reaction 79 + rate-constant: {A: 2.16e+08, b: 1.51, Ea: 3430.0} +- equation: 2 OH (+ M) <=> H2O2 (+ M) # Reaction 80 + type: falloff + low-P-rate-constant: {A: 2.3e+18, b: -0.9, Ea: -1700.0} + high-P-rate-constant: {A: 7.4e+13, b: -0.37, Ea: 0.0} + Troe: {A: 0.7346, T3: 94.0, T1: 1756.0, T2: 5182.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: 2 OH <=> O + H2O # Reaction 81 + rate-constant: {A: 3.57e+04, b: 2.4, Ea: -2110.0} +- equation: OH + HO2 <=> O2 + H2O # Reaction 82 + rate-constant: {A: 1.45e+13, b: 0.0, Ea: -500.0} + duplicate: true +- equation: OH + H2O2 <=> HO2 + H2O # Reaction 83 + rate-constant: {A: 2.0e+12, b: 0.0, Ea: 427.0} + duplicate: true +- equation: OH + H2O2 <=> HO2 + H2O # Reaction 84 + rate-constant: {A: 1.7e+18, b: 0.0, Ea: 2.941e+04} + duplicate: true +- equation: OH + C <=> H + CO # Reaction 85 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH <=> H + HCO # Reaction 86 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH2 <=> H + CH2O # Reaction 87 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH2 <=> CH + H2O # Reaction 88 + rate-constant: {A: 1.13e+07, b: 2.0, Ea: 3000.0} +- equation: OH + CH2(S) <=> H + CH2O # Reaction 89 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH3 (+ M) <=> CH3OH (+ M) # Reaction 90 + type: falloff + low-P-rate-constant: {A: 4.0e+36, b: -5.92, Ea: 3140.0} + high-P-rate-constant: {A: 2.79e+18, b: -1.43, Ea: 1330.0} + Troe: {A: 0.412, T3: 195.0, T1: 5900.0, T2: 6394.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: OH + CH3 <=> CH2 + H2O # Reaction 91 + rate-constant: {A: 5.6e+07, b: 1.6, Ea: 5420.0} +- equation: OH + CH3 <=> CH2(S) + H2O # Reaction 92 + rate-constant: {A: 6.44e+17, b: -1.34, Ea: 1417.0} +- equation: OH + CH4 <=> CH3 + H2O # Reaction 93 + rate-constant: {A: 1.0e+08, b: 1.6, Ea: 3120.0} +- equation: OH + CO <=> H + CO2 # Reaction 94 + rate-constant: {A: 4.76e+07, b: 1.228, Ea: 70.0} +- equation: OH + HCO <=> H2O + CO # Reaction 95 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH2O <=> HCO + H2O # Reaction 96 + rate-constant: {A: 3.43e+09, b: 1.18, Ea: -447.0} +- equation: OH + CH2OH <=> H2O + CH2O # Reaction 97 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0} +- equation: OH + CH3O <=> H2O + CH2O # Reaction 98 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0} +- equation: OH + CH3OH <=> CH2OH + H2O # Reaction 99 + rate-constant: {A: 1.44e+06, b: 2.0, Ea: -840.0} +- equation: OH + CH3OH <=> CH3O + H2O # Reaction 100 + rate-constant: {A: 6.3e+06, b: 2.0, Ea: 1500.0} +- equation: OH + C2H2 <=> H + CH2CO # Reaction 101 + rate-constant: {A: 2.18e-04, b: 4.5, Ea: -1000.0} +- equation: OH + C2H2 <=> CH3 + CO # Reaction 102 + rate-constant: {A: 4.83e-04, b: 4.0, Ea: -2000.0} +- equation: OH + C2H3 <=> H2O + C2H2 # Reaction 103 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0} +- equation: OH + C2H4 <=> C2H3 + H2O # Reaction 104 + rate-constant: {A: 3.6e+06, b: 2.0, Ea: 2500.0} +- equation: OH + C2H6 <=> C2H5 + H2O # Reaction 105 + rate-constant: {A: 3.54e+06, b: 2.12, Ea: 870.0} +- equation: OH + CH2CO <=> HCCO + H2O # Reaction 106 + rate-constant: {A: 7.5e+12, b: 0.0, Ea: 2000.0} +- equation: 2 HO2 <=> O2 + H2O2 # Reaction 107 + rate-constant: {A: 1.3e+11, b: 0.0, Ea: -1630.0} + duplicate: true +- equation: 2 HO2 <=> O2 + H2O2 # Reaction 108 + rate-constant: {A: 4.2e+14, b: 0.0, Ea: 1.2e+04} + duplicate: true +- equation: HO2 + CH2 <=> OH + CH2O # Reaction 109 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: HO2 + CH3 <=> O2 + CH4 # Reaction 110 + rate-constant: {A: 1.0e+12, b: 0.0, Ea: 0.0} +- equation: HO2 + CH3 <=> OH + CH3O # Reaction 111 + rate-constant: {A: 3.78e+13, b: 0.0, Ea: 0.0} +- equation: HO2 + CO <=> OH + CO2 # Reaction 112 + rate-constant: {A: 1.5e+14, b: 0.0, Ea: 2.36e+04} +- equation: HO2 + CH2O <=> HCO + H2O2 # Reaction 113 + rate-constant: {A: 5.6e+06, b: 2.0, Ea: 1.2e+04} +- equation: C + O2 <=> O + CO # Reaction 114 + rate-constant: {A: 5.8e+13, b: 0.0, Ea: 576.0} +- equation: C + CH3 <=> H + C2H2 # Reaction 115 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: CH + O2 <=> O + HCO # Reaction 116 + rate-constant: {A: 6.71e+13, b: 0.0, Ea: 0.0} +- equation: CH + H2 <=> H + CH2 # Reaction 117 + rate-constant: {A: 1.08e+14, b: 0.0, Ea: 3110.0} +- equation: CH + H2O <=> H + CH2O # Reaction 118 + rate-constant: {A: 5.71e+12, b: 0.0, Ea: -755.0} +- equation: CH + CH3 <=> H + C2H3 # Reaction 119 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: CH + CH4 <=> H + C2H4 # Reaction 120 + rate-constant: {A: 6.0e+13, b: 0.0, Ea: 0.0} +- equation: CH + CO (+ M) <=> HCCO (+ M) # Reaction 121 + type: falloff + low-P-rate-constant: {A: 2.69e+28, b: -3.74, Ea: 1936.0} + high-P-rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} + Troe: {A: 0.5757, T3: 237.0, T1: 1652.0, T2: 5069.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: CH + CO2 <=> HCO + CO # Reaction 122 + rate-constant: {A: 1.9e+14, b: 0.0, Ea: 1.5792e+04} +- equation: CH + CH2O <=> H + CH2CO # Reaction 123 + rate-constant: {A: 9.46e+13, b: 0.0, Ea: -515.0} +- equation: CH2 + O2 => OH + H + CO # Reaction 124 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 1500.0} +- equation: CH2 + H2 <=> H + CH3 # Reaction 125 + rate-constant: {A: 5.0e+05, b: 2.0, Ea: 7230.0} +- equation: CH2 + CH3 <=> H + C2H4 # Reaction 126 + rate-constant: {A: 4.0e+13, b: 0.0, Ea: 0.0} +- equation: CH2 + CH4 <=> 2 CH3 # Reaction 127 + rate-constant: {A: 2.46e+06, b: 2.0, Ea: 8270.0} +- equation: CH2 + CO (+ M) <=> CH2CO (+ M) # Reaction 128 + type: falloff + low-P-rate-constant: {A: 2.69e+33, b: -5.11, Ea: 7095.0} + high-P-rate-constant: {A: 8.1e+11, b: 0.5, Ea: 4510.0} + Troe: {A: 0.5907, T3: 275.0, T1: 1226.0, T2: 5185.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: CH2(S) + N2 <=> CH2 + N2 # Reaction 129 + rate-constant: {A: 1.5e+13, b: 0.0, Ea: 600.0} +- equation: CH2(S) + O2 <=> H + OH + CO # Reaction 130 + rate-constant: {A: 2.8e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + O2 <=> CO + H2O # Reaction 131 + rate-constant: {A: 1.2e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + H2 <=> CH3 + H # Reaction 132 + rate-constant: {A: 7.0e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + H2O (+ M) <=> CH3OH (+ M) # Reaction 133 + type: falloff + low-P-rate-constant: {A: 1.88e+38, b: -6.36, Ea: 5040.0} + high-P-rate-constant: {A: 4.82e+17, b: -1.16, Ea: 1145.0} + Troe: {A: 0.6027, T3: 208.0, T1: 3922.0, T2: 1.018e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: CH2(S) + H2O <=> CH2 + H2O # Reaction 134 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + CH3 <=> H + C2H4 # Reaction 135 + rate-constant: {A: 1.2e+13, b: 0.0, Ea: -570.0} +- equation: CH2(S) + CH4 <=> 2 CH3 # Reaction 136 + rate-constant: {A: 1.6e+13, b: 0.0, Ea: -570.0} +- equation: CH2(S) + CO <=> CH2 + CO # Reaction 137 + rate-constant: {A: 9.0e+12, b: 0.0, Ea: 0.0} +- equation: CH2(S) + CO2 <=> CH2 + CO2 # Reaction 138 + rate-constant: {A: 7.0e+12, b: 0.0, Ea: 0.0} +- equation: CH2(S) + CO2 <=> CO + CH2O # Reaction 139 + rate-constant: {A: 1.4e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + C2H6 <=> CH3 + C2H5 # Reaction 140 + rate-constant: {A: 4.0e+13, b: 0.0, Ea: -550.0} +- equation: CH3 + O2 <=> O + CH3O # Reaction 141 + rate-constant: {A: 3.56e+13, b: 0.0, Ea: 3.048e+04} +- equation: CH3 + O2 <=> OH + CH2O # Reaction 142 + rate-constant: {A: 2.31e+12, b: 0.0, Ea: 2.0315e+04} +- equation: CH3 + H2O2 <=> HO2 + CH4 # Reaction 143 + rate-constant: {A: 2.45e+04, b: 2.47, Ea: 5180.0} +- equation: 2 CH3 (+ M) <=> C2H6 (+ M) # Reaction 144 + type: falloff + low-P-rate-constant: {A: 3.4e+41, b: -7.03, Ea: 2762.0} + high-P-rate-constant: {A: 6.77e+16, b: -1.18, Ea: 654.0} + Troe: {A: 0.619, T3: 73.2, T1: 1180.0, T2: 9999.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: 2 CH3 <=> H + C2H5 # Reaction 145 + rate-constant: {A: 6.84e+12, b: 0.1, Ea: 1.06e+04} +- equation: CH3 + HCO <=> CH4 + CO # Reaction 146 + rate-constant: {A: 2.648e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + CH2O <=> HCO + CH4 # Reaction 147 + rate-constant: {A: 3320.0, b: 2.81, Ea: 5860.0} +- equation: CH3 + CH3OH <=> CH2OH + CH4 # Reaction 148 + rate-constant: {A: 3.0e+07, b: 1.5, Ea: 9940.0} +- equation: CH3 + CH3OH <=> CH3O + CH4 # Reaction 149 + rate-constant: {A: 1.0e+07, b: 1.5, Ea: 9940.0} +- equation: CH3 + C2H4 <=> C2H3 + CH4 # Reaction 150 + rate-constant: {A: 2.27e+05, b: 2.0, Ea: 9200.0} +- equation: CH3 + C2H6 <=> C2H5 + CH4 # Reaction 151 + rate-constant: {A: 6.14e+06, b: 1.74, Ea: 1.045e+04} +- equation: HCO + H2O <=> H + CO + H2O # Reaction 152 + rate-constant: {A: 1.5e+18, b: -1.0, Ea: 1.7e+04} +- equation: HCO + M <=> H + CO + M # Reaction 153 + type: three-body + rate-constant: {A: 1.87e+17, b: -1.0, Ea: 1.7e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 0.0, CH4: 2.0, C2H6: 3.0} +- equation: HCO + O2 <=> HO2 + CO # Reaction 154 + rate-constant: {A: 1.345e+13, b: 0.0, Ea: 400.0} +- equation: CH2OH + O2 <=> HO2 + CH2O # Reaction 155 + rate-constant: {A: 1.8e+13, b: 0.0, Ea: 900.0} +- equation: CH3O + O2 <=> HO2 + CH2O # Reaction 156 + rate-constant: {A: 4.28e-13, b: 7.6, Ea: -3530.0} +- equation: C2H3 + O2 <=> HCO + CH2O # Reaction 157 + rate-constant: {A: 4.58e+16, b: -1.39, Ea: 1015.0} +- equation: C2H4 (+ M) <=> H2 + C2H2 (+ M) # Reaction 158 + type: falloff + low-P-rate-constant: {A: 1.58e+51, b: -9.3, Ea: 9.78e+04} + high-P-rate-constant: {A: 8.0e+12, b: 0.44, Ea: 8.677e+04} + Troe: {A: 0.7345, T3: 180.0, T1: 1035.0, T2: 5417.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H5 + O2 <=> HO2 + C2H4 # Reaction 159 + rate-constant: {A: 8.4e+11, b: 0.0, Ea: 3875.0} +- equation: HCCO + O2 <=> OH + 2 CO # Reaction 160 + rate-constant: {A: 3.2e+12, b: 0.0, Ea: 854.0} +- equation: O + CH3 => H + H2 + CO # Reaction 161 + rate-constant: {A: 3.37e+13, b: 0.0, Ea: 0.0} +- equation: O + C2H4 <=> H + CH2CHO # Reaction 162 + rate-constant: {A: 6.7e+06, b: 1.83, Ea: 220.0} +- equation: OH + HO2 <=> O2 + H2O # Reaction 163 + rate-constant: {A: 5.0e+15, b: 0.0, Ea: 1.733e+04} + duplicate: true +- equation: OH + CH3 => H2 + CH2O # Reaction 164 + rate-constant: {A: 8.0e+09, b: 0.5, Ea: -1755.0} +- equation: CH + H2 (+ M) <=> CH3 (+ M) # Reaction 165 + type: falloff + low-P-rate-constant: {A: 4.82e+25, b: -2.8, Ea: 590.0} + high-P-rate-constant: {A: 1.97e+12, b: 0.43, Ea: -370.0} + Troe: {A: 0.578, T3: 122.0, T1: 2535.0, T2: 9365.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: CH2 + O2 => 2 H + CO2 # Reaction 166 + rate-constant: {A: 5.8e+12, b: 0.0, Ea: 1500.0} +- equation: CH2 + O2 <=> O + CH2O # Reaction 167 + rate-constant: {A: 2.4e+12, b: 0.0, Ea: 1500.0} +- equation: CH2(S) + H2O => H2 + CH2O # Reaction 168 + rate-constant: {A: 6.82e+10, b: 0.25, Ea: -935.0} +- equation: C2H3 + O2 <=> O + CH2CHO # Reaction 169 + rate-constant: {A: 3.03e+11, b: 0.29, Ea: 11.0} +- equation: C2H3 + O2 <=> HO2 + C2H2 # Reaction 170 + rate-constant: {A: 1.337e+06, b: 1.61, Ea: -384.0} +- equation: H + CH2CO (+ M) <=> CH2CHO (+ M) # Reaction 171 + type: falloff + low-P-rate-constant: {A: 1.012e+42, b: -7.63, Ea: 3854.0} + high-P-rate-constant: {A: 4.865e+11, b: 0.422, Ea: -1755.0} + Troe: {A: 0.465, T3: 201.0, T1: 1773.0, T2: 5333.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: O + CH2CHO => H + CH2 + CO2 # Reaction 172 + rate-constant: {A: 1.5e+14, b: 0.0, Ea: 0.0} +- equation: O2 + CH2CHO => OH + CO + CH2O # Reaction 173 + rate-constant: {A: 1.81e+10, b: 0.0, Ea: 0.0} +- equation: O2 + CH2CHO => OH + 2 HCO # Reaction 174 + rate-constant: {A: 2.35e+10, b: 0.0, Ea: 0.0} +- equation: H + CH2CHO <=> CH3 + HCO # Reaction 175 + rate-constant: {A: 2.2e+13, b: 0.0, Ea: 0.0} +- equation: H + CH2CHO <=> CH2CO + H2 # Reaction 176 + rate-constant: {A: 1.1e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH2CHO <=> H2O + CH2CO # Reaction 177 + rate-constant: {A: 1.2e+13, b: 0.0, Ea: 0.0} diff --git a/samples/python/AVBP/inputs/Lu_ARC.cti b/samples/python/AVBP/inputs/Lu_ARC.cti new file mode 100755 index 00000000000..d31c4b10100 --- /dev/null +++ b/samples/python/AVBP/inputs/Lu_ARC.cti @@ -0,0 +1,1338 @@ +#--------------------------------------------------------------------------- +# CTI File converted from Solution Object +#--------------------------------------------------------------------------- +units(length='cm', time='s', quantity='mol', act_energy='cal/mol') + +ideal_gas(name = "gas", + elements = "N O H C", + species = """H2 H O O2 OH H2O HO2 H2O2 CH3 CH4 CO CO2 CH2O + CH3OH C2H2 C2H4 C2H6 CH2CO N2""", +# species_qss = """ C CH CH2 CH2(S) HCO CH2OH CH3O C2H3 C2H5 +# HCCO CH2CHO """, + reactions = "all", + kinetics = "custom", + initial_state = state(temperature = 3.000000E+02, pressure= 1.013250E+05) ) +#------------------------------------------------------------------------------- +# Species data +#------------------------------------------------------------------------------- + +species(name='H2', + atoms='H:2', + thermo=(NASA([200.00, 1000.00], + [ 2.34433112E+00, 7.98052075E-03, -1.94781510E-05, + 2.01572094E-08, -7.37611761E-12, -9.17935173E+02, + 6.83010238E-01]), + NASA([1000.00, 3500.00], + [ 3.33727920E+00, -4.94024731E-05, 4.99456778E-07, + -1.79566394E-10, 2.00255376E-14, -9.50158922E+02, + -3.20502331E+00])), + transport=gas_transport(geom='linear', + diam=2.92, + well_depth=38.0, + polar=0.79, + rot_relax=280.0), + note=u'TPIS78') + +species(name='H', + atoms='H:1', + thermo=(NASA([200.00, 1000.00], + [ 2.50000000E+00, 7.05332819E-13, -1.99591964E-15, + 2.30081632E-18, -9.27732332E-22, 2.54736599E+04, + -4.46682853E-01]), + NASA([1000.00, 3500.00], + [ 2.50000001E+00, -2.30842973E-11, 1.61561948E-14, + -4.73515235E-18, 4.98197357E-22, 2.54736599E+04, + -4.46682914E-01])), + transport=gas_transport(geom='atom', + diam=2.05, + well_depth=145.0), + note=u'L7/88') + +species(name='O', + atoms='O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.16826710E+00, -3.27931884E-03, 6.64306396E-06, + -6.12806624E-09, 2.11265971E-12, 2.91222592E+04, + 2.05193346E+00]), + NASA([1000.00, 3500.00], + [ 2.56942078E+00, -8.59741137E-05, 4.19484589E-08, + -1.00177799E-11, 1.22833691E-15, 2.92175791E+04, + 4.78433864E+00])), + transport=gas_transport(geom='atom', + diam=2.75, + well_depth=80.0), + note=u'L1/90') + +species(name='O2', + atoms='O:2', + thermo=(NASA([200.00, 1000.00], + [ 3.78245636E+00, -2.99673416E-03, 9.84730201E-06, + -9.68129509E-09, 3.24372837E-12, -1.06394356E+03, + 3.65767573E+00]), + NASA([1000.00, 3500.00], + [ 3.28253784E+00, 1.48308754E-03, -7.57966669E-07, + 2.09470555E-10, -2.16717794E-14, -1.08845772E+03, + 5.45323129E+00])), + transport=gas_transport(geom='linear', + diam=3.458, + well_depth=107.4, + polar=1.6, + rot_relax=3.8), + note=u'TPIS89') + +species(name='OH', + atoms='H:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.99201543E+00, -2.40131752E-03, 4.61793841E-06, + -3.88113333E-09, 1.36411470E-12, 3.61508056E+03, + -1.03925458E-01]), + NASA([1000.00, 3500.00], + [ 3.09288767E+00, 5.48429716E-04, 1.26505228E-07, + -8.79461556E-11, 1.17412376E-14, 3.85865700E+03, + 4.47669610E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note='RUS78') + +species(name='H2O', + atoms='H:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19864056E+00, -2.03643410E-03, 6.52040211E-06, + -5.48797062E-09, 1.77197817E-12, -3.02937267E+04, + -8.49032208E-01]), + NASA([1000.00, 3500.00], + [ 3.03399249E+00, 2.17691804E-03, -1.64072518E-07, + -9.70419870E-11, 1.68200992E-14, -3.00042971E+04, + 4.96677010E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.605, + well_depth=572.4, + dipole=1.844, + rot_relax=4.0), + note='L8/89') + +species(name='HO2', + atoms='H:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30179801E+00, -4.74912051E-03, 2.11582891E-05, + -2.42763894E-08, 9.29225124E-12, 2.94808040E+02, + 3.71666245E+00]), + NASA([1000.00, 3500.00], + [ 4.01721090E+00, 2.23982013E-03, -6.33658150E-07, + 1.14246370E-10, -1.07908535E-14, 1.11856713E+02, + 3.78510215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=1.0), + note='L5/89') + +species(name='H2O2', + atoms='H:2 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.27611269E+00, -5.42822417E-04, 1.67335701E-05, + -2.15770813E-08, 8.62454363E-12, -1.77025821E+04, + 3.43505074E+00]), + NASA([1000.00, 3500.00], + [ 4.16500285E+00, 4.90831694E-03, -1.90139225E-06, + 3.71185986E-10, -2.87908305E-14, -1.78617877E+04, + 2.91615662E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=3.8), + note='L7/88') + +species(name='C', + atoms='C:1', + thermo=(NASA([200.00, 1000.00], + [ 2.55423955E+00, -3.21537724E-04, 7.33792245E-07, + -7.32234889E-10, 2.66521446E-13, 8.54438832E+04, + 4.53130848E+00]), + NASA([1000.00, 3500.00], + [ 2.49266888E+00, 4.79889284E-05, -7.24335020E-08, + 3.74291029E-11, -4.87277893E-15, 8.54512953E+04, + 4.80150373E+00])), + transport=gas_transport(geom='atom', + diam=3.298, + well_depth=71.4), + note='L11/88') + +species(name='CH', + atoms='H:1 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.48981665E+00, 3.23835541E-04, -1.68899065E-06, + 3.16217327E-09, -1.40609067E-12, 7.07972934E+04, + 2.08401108E+00]), + NASA([1000.00, 3500.00], + [ 2.87846473E+00, 9.70913681E-04, 1.44445655E-07, + -1.30687849E-10, 1.76079383E-14, 7.10124364E+04, + 5.48497999E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note='TPIS79') + +species(name='CH2', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.76267867E+00, 9.68872143E-04, 2.79489841E-06, + -3.85091153E-09, 1.68741719E-12, 4.60040401E+04, + 1.56253185E+00]), + NASA([1000.00, 3500.00], + [ 2.87410113E+00, 3.65639292E-03, -1.40894597E-06, + 2.60179549E-10, -1.87727567E-14, 4.62636040E+04, + 6.17119324E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note='LS/93') + +species(name='CH2(S)', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19860411E+00, -2.36661419E-03, 8.23296220E-06, + -6.68815981E-09, 1.94314737E-12, 5.04968163E+04, + -7.69118967E-01]), + NASA([1000.00, 3500.00], + [ 2.29203842E+00, 4.65588637E-03, -2.01191947E-06, + 4.17906000E-10, -3.39716365E-14, 5.09259997E+04, + 8.62650169E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note='LS/93') + +species(name='CH3', + atoms='H:3 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.67359040E+00, 2.01095175E-03, 5.73021856E-06, + -6.87117425E-09, 2.54385734E-12, 1.64449988E+04, + 1.60456433E+00]), + NASA([1000.00, 3500.00], + [ 2.28571772E+00, 7.23990037E-03, -2.98714348E-06, + 5.95684644E-10, -4.67154394E-14, 1.67755843E+04, + 8.48007179E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note='L11/89') + +species(name='CH4', + atoms='H:4 C:1', + thermo=(NASA([200.00, 1000.00], + [ 5.14987613E+00, -1.36709788E-02, 4.91800599E-05, + -4.84743026E-08, 1.66693956E-11, -1.02466476E+04, + -4.64130376E+00]), + NASA([1000.00, 3500.00], + [ 7.48514950E-02, 1.33909467E-02, -5.73285809E-06, + 1.22292535E-09, -1.01815230E-13, -9.46834459E+03, + 1.84373180E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.746, + well_depth=141.4, + polar=2.6, + rot_relax=13.0), + note='L8/88') + +species(name='CO', + atoms='C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.57953347E+00, -6.10353680E-04, 1.01681433E-06, + 9.07005884E-10, -9.04424499E-13, -1.43440860E+04, + 3.50840928E+00]), + NASA([1000.00, 3500.00], + [ 2.71518561E+00, 2.06252743E-03, -9.98825771E-07, + 2.30053008E-10, -2.03647716E-14, -1.41518724E+04, + 7.81868772E+00])), + transport=gas_transport(geom='linear', + diam=3.65, + well_depth=98.1, + polar=1.95, + rot_relax=1.8), + note='TPIS79') + +species(name='CO2', + atoms='C:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 2.35677352E+00, 8.98459677E-03, -7.12356269E-06, + 2.45919022E-09, -1.43699548E-13, -4.83719697E+04, + 9.90105222E+00]), + NASA([1000.00, 3500.00], + [ 3.85746029E+00, 4.41437026E-03, -2.21481404E-06, + 5.23490188E-10, -4.72084164E-14, -4.87591660E+04, + 2.27163806E+00])), + transport=gas_transport(geom='linear', + diam=3.763, + well_depth=244.0, + polar=2.65, + rot_relax=2.1), + note='L7/88') + +species(name='HCO', + atoms='H:1 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.22118584E+00, -3.24392532E-03, 1.37799446E-05, + -1.33144093E-08, 4.33768865E-12, 3.83956496E+03, + 3.39437243E+00]), + NASA([1000.00, 3500.00], + [ 2.77217438E+00, 4.95695526E-03, -2.48445613E-06, + 5.89161778E-10, -5.33508711E-14, 4.01191815E+03, + 9.79834492E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0), + note='L12/89') + +species(name='CH2O', + atoms='H:2 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.79372315E+00, -9.90833369E-03, 3.73220008E-05, + -3.79285261E-08, 1.31772652E-11, -1.43089567E+04, + 6.02812900E-01]), + NASA([1000.00, 3500.00], + [ 1.76069008E+00, 9.20000082E-03, -4.42258813E-06, + 1.00641212E-09, -8.83855640E-14, -1.39958323E+04, + 1.36563230E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0, + rot_relax=2.0), + note='L8/88') + +species(name='CH2OH', + atoms='H:3 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.86388918E+00, 5.59672304E-03, 5.93271791E-06, + -1.04532012E-08, 4.36967278E-12, -3.19391367E+03, + 5.47302243E+00]), + NASA([1000.00, 3500.00], + [ 3.69266569E+00, 8.64576797E-03, -3.75101120E-06, + 7.87234636E-10, -6.48554201E-14, -3.24250627E+03, + 5.81043215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.69, + well_depth=417.0, + dipole=1.7, + rot_relax=2.0), + note='GUNL93') + +species(name='CH3O', + atoms='H:3 C:1 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.10620400E+00, 7.21659500E-03, 5.33847200E-06, + -7.37763600E-09, 2.07561000E-12, 9.78601100E+02, + 1.31521770E+01]), + NASA([1000.00, 3000.00], + [ 3.77079900E+00, 7.87149700E-03, -2.65638400E-06, + 3.94443100E-10, -2.11261600E-14, 1.27832520E+02, + 2.92957500E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.69, + well_depth=417.0, + dipole=1.7, + rot_relax=2.0), + note='121686') + +species(name='CH3OH', + atoms='H:4 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 5.71539582E+00, -1.52309129E-02, 6.52441155E-05, + -7.10806889E-08, 2.61352698E-11, -2.56427656E+04, + -1.50409823E+00]), + NASA([1000.00, 3500.00], + [ 1.78970791E+00, 1.40938292E-02, -6.36500835E-06, + 1.38171085E-09, -1.17060220E-13, -2.53748747E+04, + 1.45023623E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.626, + well_depth=481.8, + rot_relax=1.0), + note='L8/88') + +species(name='C2H2', + atoms='H:2 C:2', + thermo=(NASA([200.00, 1000.00], + [ 8.08681094E-01, 2.33615629E-02, -3.55171815E-05, + 2.80152437E-08, -8.50072974E-12, 2.64289807E+04, + 1.39397051E+01]), + NASA([1000.00, 3500.00], + [ 4.14756964E+00, 5.96166664E-03, -2.37294852E-06, + 4.67412171E-10, -3.61235213E-14, 2.59359992E+04, + -1.23028121E+00])), + transport=gas_transport(geom='linear', + diam=4.1, + well_depth=209.0, + rot_relax=2.5), + note='L1/91') + +species(name='C2H3', + atoms='H:3 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.21246645E+00, 1.51479162E-03, 2.59209412E-05, + -3.57657847E-08, 1.47150873E-11, 3.48598468E+04, + 8.51054025E+00]), + NASA([1000.00, 3500.00], + [ 3.01672400E+00, 1.03302292E-02, -4.68082349E-06, + 1.01763288E-09, -8.62607041E-14, 3.46128739E+04, + 7.78732378E+00])), + transport=gas_transport(geom='nonlinear', + diam=4.1, + well_depth=209.0, + rot_relax=1.0), + note='L2/92') + +species(name='C2H4', + atoms='H:4 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.95920148E+00, -7.57052247E-03, 5.70990292E-05, + -6.91588753E-08, 2.69884373E-11, 5.08977593E+03, + 4.09733096E+00]), + NASA([1000.00, 3500.00], + [ 2.03611116E+00, 1.46454151E-02, -6.71077915E-06, + 1.47222923E-09, -1.25706061E-13, 4.93988614E+03, + 1.03053693E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.971, + well_depth=280.8, + rot_relax=1.5), + note='L1/91') + +species(name='C2H5', + atoms='H:5 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30646568E+00, -4.18658892E-03, 4.97142807E-05, + -5.99126606E-08, 2.30509004E-11, 1.28416265E+04, + 4.70720924E+00]), + NASA([1000.00, 3500.00], + [ 1.95465642E+00, 1.73972722E-02, -7.98206668E-06, + 1.75217689E-09, -1.49641576E-13, 1.28575200E+04, + 1.34624343E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note='L12/92') + +species(name='C2H6', + atoms='H:6 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.29142492E+00, -5.50154270E-03, 5.99438288E-05, + -7.08466285E-08, 2.68685771E-11, -1.15222055E+04, + 2.66682316E+00]), + NASA([1000.00, 3500.00], + [ 1.07188150E+00, 2.16852677E-02, -1.00256067E-05, + 2.21412001E-09, -1.90002890E-13, -1.14263932E+04, + 1.51156107E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note='L8/88') + +species(name='HCCO', + atoms='H:1 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.25172140E+00, 1.76550210E-02, -2.37291010E-05, + 1.72757590E-08, -5.06648110E-12, 2.00594490E+04, + 1.24904170E+01]), + NASA([1000.00, 4000.00], + [ 5.62820580E+00, 4.08534010E-03, -1.59345470E-06, + 2.86260520E-10, -1.94078320E-14, 1.93272150E+04, + -3.93025950E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.5, + well_depth=150.0, + rot_relax=1.0), + note='SRIC91') + +species(name='CH2CO', + atoms='H:2 C:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 2.13583630E+00, 1.81188721E-02, -1.73947474E-05, + 9.34397568E-09, -2.01457615E-12, -7.04291804E+03, + 1.22156480E+01]), + NASA([1000.00, 3500.00], + [ 4.51129732E+00, 9.00359745E-03, -4.16939635E-06, + 9.23345882E-10, -7.94838201E-14, -7.55105311E+03, + 6.32247205E-01])), + transport=gas_transport(geom='nonlinear', + diam=3.97, + well_depth=436.0, + rot_relax=2.0), + note='L5/90') + +species(name='CH2CHO', + atoms='H:3 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 3.40906200E+00, 1.07385740E-02, 1.89149200E-06, + -7.15858300E-09, 2.86738500E-12, 1.52147660E+03, + 9.55829000E+00]), + NASA([1000.00, 5000.00], + [ 5.97567000E+00, 8.13059100E-03, -2.74362400E-06, + 4.07030400E-10, -2.17601700E-14, 4.90321800E+02, + -5.04525100E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.97, + well_depth=436.0, + rot_relax=2.0), + note='SAND86') + +species(name='N2', + atoms='N:2', + thermo=(NASA([300.00, 1000.00], + [ 3.29867700E+00, 1.40824040E-03, -3.96322200E-06, + 5.64151500E-09, -2.44485400E-12, -1.02089990E+03, + 3.95037200E+00]), + NASA([1000.00, 5000.00], + [ 2.92664000E+00, 1.48797680E-03, -5.68476000E-07, + 1.00970380E-10, -6.75335100E-15, -9.22797700E+02, + 5.98052800E+00])), + transport=gas_transport(geom='linear', + diam=3.621, + well_depth=97.53, + polar=1.76, + rot_relax=4.0), + note='121286') + +#------------------------------------------------------------------------------- +# Reaction data +#------------------------------------------------------------------------------- + +# Dummy Reaction +reaction('O + H2 <=> H + OH', [0.0, 0.0, 0.0]) + +## Reaction 1 +#three_body_reaction('2 O + M <=> O2 + M', [1.200000e+17, -1.0, 0.0], +# efficiencies='CO2:3.6 CO:1.75 H2:2.4 H2O:15.4 CH4:2.0 C2H6:3.0') + +## Reaction 2 +#three_body_reaction('O + H + M <=> OH + M', [5.000000e+17, -1.0, 0.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0') + +## Reaction 3 +#reaction('O + H2 <=> H + OH', [3.870000e+04, 2.7, 6260.0]) +## R4 +# + +## Reaction 4 +#reaction('O + HO2 <=> OH + O2', [2.000000e+13, 0.0, 0.0]) +## R5 +# +## Reaction 5 +#reaction('O + H2O2 <=> OH + HO2', [9.630000e+06, 2.0, 4000.0]) +## R6 +# +## Reaction 6 +#reaction('O + CH <=> H + CO', [5.700000e+13, 0.0, 0.0]) +## R7 +# +## Reaction 7 +#reaction('O + CH2 <=> H + HCO', [8.000000e+13, 0.0, 0.0]) +## R8 +# +## Reaction 8 +#reaction('O + CH2(S) <=> H2 + CO', [1.500000e+13, 0.0, 0.0]) +## R9 +# +## Reaction 9 +#reaction('O + CH2(S) <=> H + HCO', [1.500000e+13, 0.0, 0.0]) +## R10 +# +## Reaction 10 +#reaction('O + CH3 <=> H + CH2O', [5.060000e+13, 0.0, 0.0]) +## R11 +# +## Reaction 11 +#reaction('O + CH4 <=> OH + CH3', [1.020000e+09, 1.5, 8600.0]) +## R12 +# +## Reaction 12 +#falloff_reaction('O + CO (+ M) <=> CO2 (+ M)', +# kf=[1.800000e+10, 0.0, 2385.0], +# kf0=[6.020000e+14, 0.0, 3000.0], +# efficiencies='CO2:3.5 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0 O2:6.0') +## R13 +# +## Reaction 13 +#reaction('O + HCO <=> OH + CO', [3.000000e+13, 0.0, 0.0]) +## R14 +# +## Reaction 14 +#reaction('O + HCO <=> H + CO2', [3.000000e+13, 0.0, 0.0]) +## R15 +# +## Reaction 15 +#reaction('O + CH2O <=> OH + HCO', [3.900000e+13, 0.0, 3540.0]) +## R16 +# +## Reaction 16 +#reaction('O + CH2OH <=> OH + CH2O', [1.000000e+13, 0.0, 0.0]) +## R17 +# +## Reaction 17 +#reaction('O + CH3O <=> OH + CH2O', [1.000000e+13, 0.0, 0.0]) +## R18 +# +## Reaction 18 +#reaction('O + CH3OH <=> OH + CH2OH', [3.880000e+05, 2.5, 3100.0]) +## R19 +# +## Reaction 19 +#reaction('O + CH3OH <=> OH + CH3O', [1.300000e+05, 2.5, 5000.0]) +## R20 +# +## Reaction 20 +#reaction('O + C2H2 <=> H + HCCO', [1.350000e+07, 2.0, 1900.0]) +## R21 +# +## Reaction 21 +#reaction('O + C2H2 <=> CO + CH2', [6.940000e+06, 2.0, 1900.0]) +## R22 +# +## Reaction 22 +#reaction('O + C2H3 <=> H + CH2CO', [3.000000e+13, 0.0, 0.0]) +## R23 +# +## Reaction 23 +#reaction('O + C2H4 <=> CH3 + HCO', [1.250000e+07, 1.83, 220.0]) +## R24 +# +## Reaction 24 +#reaction('O + C2H5 <=> CH3 + CH2O', [2.240000e+13, 0.0, 0.0]) +## R25 +# +## Reaction 25 +#reaction('O + C2H6 <=> OH + C2H5', [8.980000e+07, 1.92, 5690.0]) +## R26 +# +## Reaction 26 +#reaction('O + HCCO <=> H + 2 CO', [1.000000e+14, 0.0, 0.0]) +## R27 +# +## Reaction 27 +#reaction('O + CH2CO <=> OH + HCCO', [1.000000e+13, 0.0, 8000.0]) +## R28 +# +## Reaction 28 +#reaction('O + CH2CO <=> CH2 + CO2', [1.750000e+12, 0.0, 1350.0]) +## R29 +# +## Reaction 29 +#reaction('O2 + CO <=> O + CO2', [2.500000e+12, 0.0, 47800.0]) +## R30 +# +## Reaction 30 +#reaction('O2 + CH2O <=> HO2 + HCO', [1.000000e+14, 0.0, 40000.0]) +## R31 +# +## Reaction 31 +#three_body_reaction('H + O2 + M <=> HO2 + M', [2.800000e+18, -0.86, 0.0], +# efficiencies='CO2:1.5 CO:0.75 H2O:0.0 C2H6:1.5 N2:0.0 O2:0.0') +## R32 +# +## Reaction 32 +#reaction('H + 2 O2 <=> HO2 + O2', [2.080000e+19, -1.24, 0.0]) +## R33 +# +## Reaction 33 +#reaction('H + O2 + H2O <=> HO2 + H2O', [1.126000e+19, -0.76, 0.0]) +## R34 +# +## Reaction 34 +#reaction('H + O2 + N2 <=> HO2 + N2', [2.600000e+19, -1.24, 0.0]) +## R35 +# +## Reaction 35 +#reaction('H + O2 <=> O + OH', [2.650000e+16, -0.6707, 17041.0]) +## R36 +# +## Reaction 36 +#three_body_reaction('2 H + M <=> H2 + M', [1.000000e+18, -1.0, 0.0], +# efficiencies='H2:0.0 C2H6:3.0 H2O:0.0 CO2:0.0 CH4:2.0') +## R37 +# +## Reaction 37 +#reaction('2 H + H2 <=> 2 H2', [9.000000e+16, -0.6, 0.0]) +## R38 +# +## Reaction 38 +#reaction('2 H + H2O <=> H2 + H2O', [6.000000e+19, -1.25, 0.0]) +## R39 +# +## Reaction 39 +#reaction('2 H + CO2 <=> H2 + CO2', [5.500000e+20, -2.0, 0.0]) +## R40 +# +## Reaction 40 +#three_body_reaction('H + OH + M <=> H2O + M', [2.200000e+22, -2.0, 0.0], +# efficiencies='H2:0.73 C2H6:3.0 H2O:3.65 CH4:2.0') +## R41 +# +## Reaction 41 +#reaction('H + HO2 <=> O + H2O', [3.970000e+12, 0.0, 671.0]) +## R42 +# +## Reaction 42 +#reaction('H + HO2 <=> O2 + H2', [4.480000e+13, 0.0, 1068.0]) +## R43 +# +## Reaction 43 +#reaction('H + HO2 <=> 2 OH', [8.400000e+13, 0.0, 635.0]) +## R44 +# +## Reaction 44 +#reaction('H + H2O2 <=> HO2 + H2', [1.210000e+07, 2.0, 5200.0]) +## R45 +# +## Reaction 45 +#reaction('H + H2O2 <=> OH + H2O', [1.000000e+13, 0.0, 3600.0]) +## R46 +# +## Reaction 46 +#reaction('H + CH <=> C + H2', [1.650000e+14, 0.0, 0.0]) +## R47 +# +## Reaction 47 +#falloff_reaction('H + CH2 (+ M) <=> CH3 (+ M)', +# kf=[6.000000e+14, 0.0, 0.0], +# kf0=[1.040000e+26, -2.76, 1600.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.562, T3=91.0, T1=5836.0, T2=8552.0)) +## R48 +# +## Reaction 48 +#reaction('H + CH2(S) <=> CH + H2', [3.000000e+13, 0.0, 0.0]) +## R49 +# +## Reaction 49 +#falloff_reaction('H + CH3 (+ M) <=> CH4 (+ M)', +# kf=[1.390000e+16, -0.534, 536.0], +# kf0=[2.620000e+33, -4.76, 2440.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:3.0 C2H6:3.0', +# falloff=Troe(A=0.783, T3=74.0, T1=2941.0, T2=6964.0)) +## R50 +# +## Reaction 50 +#reaction('H + CH4 <=> CH3 + H2', [6.600000e+08, 1.62, 10840.0]) +## R51 +# +## Reaction 51 +#falloff_reaction('H + HCO (+ M) <=> CH2O (+ M)', +# kf=[1.090000e+12, 0.48, -260.0], +# kf0=[2.470000e+24, -2.57, 425.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7824, T3=271.0, T1=2755.0, T2=6570.0)) +## R52 +# +## Reaction 52 +#reaction('H + HCO <=> H2 + CO', [7.340000e+13, 0.0, 0.0]) +## R53 +# +## Reaction 53 +#falloff_reaction('H + CH2O (+ M) <=> CH2OH (+ M)', +# kf=[5.400000e+11, 0.454, 3600.0], +# kf0=[1.270000e+32, -4.82, 6530.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7187, T3=103.0, T1=1291.0, T2=4160.0)) +## R54 +# +## Reaction 54 +#falloff_reaction('H + CH2O (+ M) <=> CH3O (+ M)', +# kf=[5.400000e+11, 0.454, 2600.0], +# kf0=[2.200000e+30, -4.8, 5560.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.758, T3=94.0, T1=1555.0, T2=4200.0)) +## R55 +# +## Reaction 55 +#reaction('H + CH2O <=> HCO + H2', [5.740000e+07, 1.9, 2742.0]) +## R56 +# +## Reaction 56 +#falloff_reaction('H + CH2OH (+ M) <=> CH3OH (+ M)', +# kf=[1.055000e+12, 0.5, 86.0], +# kf0=[4.360000e+31, -4.65, 5080.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.6, T3=100.0, T1=90000.0, T2=10000.0)) +## R57 +# +## Reaction 57 +#reaction('H + CH2OH <=> H2 + CH2O', [2.000000e+13, 0.0, 0.0]) +## R58 +# +## Reaction 58 +#reaction('H + CH2OH <=> OH + CH3', [1.650000e+11, 0.65, -284.0]) +## R59 +# +## Reaction 59 +#reaction('H + CH2OH <=> CH2(S) + H2O', [3.280000e+13, -0.09, 610.0]) +## R60 +# +## Reaction 60 +#falloff_reaction('H + CH3O (+ M) <=> CH3OH (+ M)', +# kf=[2.430000e+12, 0.515, 50.0], +# kf0=[4.660000e+41, -7.44, 14080.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7, T3=100.0, T1=90000.0, T2=10000.0)) +## R61 +# +## Reaction 61 +#reaction('H + CH3O <=> H + CH2OH', [4.150000e+07, 1.63, 1924.0]) +## R62 +# +## Reaction 62 +#reaction('H + CH3O <=> H2 + CH2O', [2.000000e+13, 0.0, 0.0]) +## R63 +# +## Reaction 63 +#reaction('H + CH3O <=> OH + CH3', [1.500000e+12, 0.5, -110.0]) +## R64 +# +## Reaction 64 +#reaction('H + CH3O <=> CH2(S) + H2O', [2.620000e+14, -0.23, 1070.0]) +## R65 +# +## Reaction 65 +#reaction('H + CH3OH <=> CH2OH + H2', [1.700000e+07, 2.1, 4870.0]) +## R66 +# +## Reaction 66 +#reaction('H + CH3OH <=> CH3O + H2', [4.200000e+06, 2.1, 4870.0]) +## R67 +# +## Reaction 67 +#falloff_reaction('H + C2H2 (+ M) <=> C2H3 (+ M)', +# kf=[5.600000e+12, 0.0, 2400.0], +# kf0=[3.800000e+40, -7.27, 7220.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7507, T3=98.5, T1=1302.0, T2=4167.0)) +## R68 +# +## Reaction 68 +#falloff_reaction('H + C2H3 (+ M) <=> C2H4 (+ M)', +# kf=[6.080000e+12, 0.27, 280.0], +# kf0=[1.400000e+30, -3.86, 3320.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.782, T3=207.5, T1=2663.0, T2=6095.0)) +## R69 +# +## Reaction 69 +#reaction('H + C2H3 <=> H2 + C2H2', [3.000000e+13, 0.0, 0.0]) +## R70 +# +## Reaction 70 +#falloff_reaction('H + C2H4 (+ M) <=> C2H5 (+ M)', +# kf=[5.400000e+11, 0.454, 1820.0], +# kf0=[6.000000e+41, -7.62, 6970.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.9753, T3=210.0, T1=984.0, T2=4374.0)) +## R71 +# +## Reaction 71 +#reaction('H + C2H4 <=> C2H3 + H2', [1.325000e+06, 2.53, 12240.0]) +## R72 +# +## Reaction 72 +#falloff_reaction('H + C2H5 (+ M) <=> C2H6 (+ M)', +# kf=[5.210000e+17, -0.99, 1580.0], +# kf0=[1.990000e+41, -7.08, 6685.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.8422, T3=125.0, T1=2219.0, T2=6882.0)) +## R73 +# +## Reaction 73 +#reaction('H + C2H5 <=> H2 + C2H4', [2.000000e+12, 0.0, 0.0]) +## R74 +# +## Reaction 74 +#reaction('H + C2H6 <=> C2H5 + H2', [1.150000e+08, 1.9, 7530.0]) +## R75 +# +## Reaction 75 +#reaction('H + HCCO <=> CH2(S) + CO', [1.000000e+14, 0.0, 0.0]) +## R76 +# +## Reaction 76 +#reaction('H + CH2CO <=> HCCO + H2', [5.000000e+13, 0.0, 8000.0]) +## R77 +# +## Reaction 77 +#reaction('H + CH2CO <=> CH3 + CO', [1.130000e+13, 0.0, 3428.0]) +## R78 +# +## Reaction 78 +#falloff_reaction('H2 + CO (+ M) <=> CH2O (+ M)', +# kf=[4.300000e+07, 1.5, 79600.0], +# kf0=[5.070000e+27, -3.42, 84350.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.932, T3=197.0, T1=1540.0, T2=10300.0)) +## R79 +# +## Reaction 79 +#reaction('OH + H2 <=> H + H2O', [2.160000e+08, 1.51, 3430.0]) +## R80 +# +## Reaction 80 +#falloff_reaction('2 OH (+ M) <=> H2O2 (+ M)', +# kf=[7.400000e+13, -0.37, 0.0], +# kf0=[2.300000e+18, -0.9, -1700.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7346, T3=94.0, T1=1756.0, T2=5182.0)) +## R81 +# +## Reaction 81 +#reaction('2 OH <=> O + H2O', [3.570000e+04, 2.4, -2110.0]) +## R82 +# +## Reaction 82 +#reaction('OH + HO2 <=> O2 + H2O', [1.450000e+13, 0.0, -500.0], +# options='duplicate') +## R83 +# +## Reaction 83 +#reaction('OH + H2O2 <=> HO2 + H2O', [2.000000e+12, 0.0, 427.0], +# options='duplicate') +## R84 +# +## Reaction 84 +#reaction('OH + H2O2 <=> HO2 + H2O', [1.700000e+18, 0.0, 29410.0], +# options='duplicate') +## R85 +# +## Reaction 85 +#reaction('OH + C <=> H + CO', [5.000000e+13, 0.0, 0.0]) +## R86 +# +## Reaction 86 +#reaction('OH + CH <=> H + HCO', [3.000000e+13, 0.0, 0.0]) +## R87 +# +## Reaction 87 +#reaction('OH + CH2 <=> H + CH2O', [2.000000e+13, 0.0, 0.0]) +## R88 +# +## Reaction 88 +#reaction('OH + CH2 <=> CH + H2O', [1.130000e+07, 2.0, 3000.0]) +## R89 +# +## Reaction 89 +#reaction('OH + CH2(S) <=> H + CH2O', [3.000000e+13, 0.0, 0.0]) +## R90 +# +## Reaction 90 +#falloff_reaction('OH + CH3 (+ M) <=> CH3OH (+ M)', +# kf=[2.790000e+18, -1.43, 1330.0], +# kf0=[4.000000e+36, -5.92, 3140.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.412, T3=195.0, T1=5900.0, T2=6394.0)) +## R91 +# +## Reaction 91 +#reaction('OH + CH3 <=> CH2 + H2O', [5.600000e+07, 1.6, 5420.0]) +## R92 +# +## Reaction 92 +#reaction('OH + CH3 <=> CH2(S) + H2O', [6.440000e+17, -1.34, 1417.0]) +## R93 +# +## Reaction 93 +#reaction('OH + CH4 <=> CH3 + H2O', [1.000000e+08, 1.6, 3120.0]) +## R94 +# +## Reaction 94 +#reaction('OH + CO <=> H + CO2', [4.760000e+07, 1.228, 70.0]) +## R95 +# +## Reaction 95 +#reaction('OH + HCO <=> H2O + CO', [5.000000e+13, 0.0, 0.0]) +## R96 +# +## Reaction 96 +#reaction('OH + CH2O <=> HCO + H2O', [3.430000e+09, 1.18, -447.0]) +## R97 +# +## Reaction 97 +#reaction('OH + CH2OH <=> H2O + CH2O', [5.000000e+12, 0.0, 0.0]) +## R98 +# +## Reaction 98 +#reaction('OH + CH3O <=> H2O + CH2O', [5.000000e+12, 0.0, 0.0]) +## R99 +# +## Reaction 99 +#reaction('OH + CH3OH <=> CH2OH + H2O', [1.440000e+06, 2.0, -840.0]) +## R100 +# +## Reaction 100 +#reaction('OH + CH3OH <=> CH3O + H2O', [6.300000e+06, 2.0, 1500.0]) +## R101 +# +## Reaction 101 +#reaction('OH + C2H2 <=> H + CH2CO', [2.180000e-04, 4.5, -1000.0]) +## R102 +# +## Reaction 102 +#reaction('OH + C2H2 <=> CH3 + CO', [4.830000e-04, 4.0, -2000.0]) +## R103 +# +## Reaction 103 +#reaction('OH + C2H3 <=> H2O + C2H2', [5.000000e+12, 0.0, 0.0]) +## R104 +# +## Reaction 104 +#reaction('OH + C2H4 <=> C2H3 + H2O', [3.600000e+06, 2.0, 2500.0]) +## R105 +# +## Reaction 105 +#reaction('OH + C2H6 <=> C2H5 + H2O', [3.540000e+06, 2.12, 870.0]) +## R106 +# +## Reaction 106 +#reaction('OH + CH2CO <=> HCCO + H2O', [7.500000e+12, 0.0, 2000.0]) +## R107 +# +## Reaction 107 +#reaction('2 HO2 <=> O2 + H2O2', [1.300000e+11, 0.0, -1630.0], +# options='duplicate') +## R108 +# +## Reaction 108 +#reaction('2 HO2 <=> O2 + H2O2', [4.200000e+14, 0.0, 12000.0], +# options='duplicate') +## R109 +# +## Reaction 109 +#reaction('HO2 + CH2 <=> OH + CH2O', [2.000000e+13, 0.0, 0.0]) +## R110 +# +## Reaction 110 +#reaction('HO2 + CH3 <=> O2 + CH4', [1.000000e+12, 0.0, 0.0]) +## R111 +# +## Reaction 111 +#reaction('HO2 + CH3 <=> OH + CH3O', [3.780000e+13, 0.0, 0.0]) +## R112 +# +## Reaction 112 +#reaction('HO2 + CO <=> OH + CO2', [1.500000e+14, 0.0, 23600.0]) +## R113 +# +## Reaction 113 +#reaction('HO2 + CH2O <=> HCO + H2O2', [5.600000e+06, 2.0, 12000.0]) +## R114 +# +## Reaction 114 +#reaction('C + O2 <=> O + CO', [5.800000e+13, 0.0, 576.0]) +## R115 +# +## Reaction 115 +#reaction('C + CH3 <=> H + C2H2', [5.000000e+13, 0.0, 0.0]) +## R116 +# +## Reaction 116 +#reaction('CH + O2 <=> O + HCO', [6.710000e+13, 0.0, 0.0]) +## R117 +# +## Reaction 117 +#reaction('CH + H2 <=> H + CH2', [1.080000e+14, 0.0, 3110.0]) +## R118 +# +## Reaction 118 +#reaction('CH + H2O <=> H + CH2O', [5.710000e+12, 0.0, -755.0]) +## R119 +# +## Reaction 119 +## reaction('CH + CH2 <=> H + C2H2', [4.000000e+13, 0.0, 0.0]) +## R120 +# +## Reaction 120 +#reaction('CH + CH3 <=> H + C2H3', [3.000000e+13, 0.0, 0.0]) +## R121 +# +## Reaction 121 +#reaction('CH + CH4 <=> H + C2H4', [6.000000e+13, 0.0, 0.0]) +## R122 +# +## Reaction 122 +#falloff_reaction('CH + CO (+ M) <=> HCCO (+ M)', +# kf=[5.000000e+13, 0.0, 0.0], +# kf0=[2.690000e+28, -3.74, 1936.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.5757, T3=237.0, T1=1652.0, T2=5069.0)) +## R123 +# +## Reaction 123 +#reaction('CH + CO2 <=> HCO + CO', [1.900000e+14, 0.0, 15792.0]) +## R124 +# +## Reaction 124 +#reaction('CH + CH2O <=> H + CH2CO', [9.460000e+13, 0.0, -515.0]) +## R125 +# +## Reaction 125 +## reaction('CH + HCCO <=> CO + C2H2', [5.000000e+13, 0.0, 0.0]) +## R126 +# +## Reaction 126 +#reaction('CH2 + O2 => OH + H + CO', [5.000000e+12, 0.0, 1500.0]) +## R127 +# +## Reaction 127 +#reaction('CH2 + H2 <=> H + CH3', [5.000000e+05, 2.0, 7230.0]) +## R128 +# +## Reaction 128 +## reaction('2 CH2 <=> H2 + C2H2', [1.600000e+15, 0.0, 11944.0]) +## R129 +# +## Reaction 129 +#reaction('CH2 + CH3 <=> H + C2H4', [4.000000e+13, 0.0, 0.0]) +## R130 +# +## Reaction 130 +#reaction('CH2 + CH4 <=> 2 CH3', [2.460000e+06, 2.0, 8270.0]) +## R131 +# +## Reaction 131 +#falloff_reaction('CH2 + CO (+ M) <=> CH2CO (+ M)', +# kf=[8.100000e+11, 0.5, 4510.0], +# kf0=[2.690000e+33, -5.11, 7095.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.5907, T3=275.0, T1=1226.0, T2=5185.0)) +## R132 +# +## Reaction 132 +## reaction('CH2 + HCCO <=> C2H3 + CO', [3.000000e+13, 0.0, 0.0]) +## R133 +# +## Reaction 133 +#reaction('CH2(S) + N2 <=> CH2 + N2', [1.500000e+13, 0.0, 600.0]) +## R134 +# +## Reaction 134 +#reaction('CH2(S) + O2 <=> H + OH + CO', [2.800000e+13, 0.0, 0.0]) +## R135 +# +## Reaction 135 +#reaction('CH2(S) + O2 <=> CO + H2O', [1.200000e+13, 0.0, 0.0]) +## R136 +# +## Reaction 136 +#reaction('CH2(S) + H2 <=> CH3 + H', [7.000000e+13, 0.0, 0.0]) +## R137 +# +## Reaction 137 +#falloff_reaction('CH2(S) + H2O (+ M) <=> CH3OH (+ M)', +# kf=[4.820000e+17, -1.16, 1145.0], +# kf0=[1.880000e+38, -6.36, 5040.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.6027, T3=208.0, T1=3922.0, T2=10180.0)) +## R138 +# +## Reaction 138 +#reaction('CH2(S) + H2O <=> CH2 + H2O', [3.000000e+13, 0.0, 0.0]) +## R139 +# +## Reaction 139 +#reaction('CH2(S) + CH3 <=> H + C2H4', [1.200000e+13, 0.0, -570.0]) +## R140 +# +## Reaction 140 +#reaction('CH2(S) + CH4 <=> 2 CH3', [1.600000e+13, 0.0, -570.0]) +## R141 +# +## Reaction 141 +#reaction('CH2(S) + CO <=> CH2 + CO', [9.000000e+12, 0.0, 0.0]) +## R142 +# +## Reaction 142 +#reaction('CH2(S) + CO2 <=> CH2 + CO2', [7.000000e+12, 0.0, 0.0]) +## R143 +# +## Reaction 143 +#reaction('CH2(S) + CO2 <=> CO + CH2O', [1.400000e+13, 0.0, 0.0]) +## R144 +# +## Reaction 144 +#reaction('CH2(S) + C2H6 <=> CH3 + C2H5', [4.000000e+13, 0.0, -550.0]) +## R145 +# +## Reaction 145 +#reaction('CH3 + O2 <=> O + CH3O', [3.560000e+13, 0.0, 30480.0]) +## R146 +# +## Reaction 146 +#reaction('CH3 + O2 <=> OH + CH2O', [2.310000e+12, 0.0, 20315.0]) +## R147 +# +## Reaction 147 +#reaction('CH3 + H2O2 <=> HO2 + CH4', [2.450000e+04, 2.47, 5180.0]) +## R148 +# +## Reaction 148 +#falloff_reaction('2 CH3 (+ M) <=> C2H6 (+ M)', +# kf=[6.770000e+16, -1.18, 654.0], +# kf0=[3.400000e+41, -7.03, 2762.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.619, T3=73.2, T1=1180.0, T2=9999.0)) +## R149 +# +## Reaction 149 +#reaction('2 CH3 <=> H + C2H5', [6.840000e+12, 0.1, 10600.0]) +## R150 +# +## Reaction 150 +#reaction('CH3 + HCO <=> CH4 + CO', [2.648000e+13, 0.0, 0.0]) +## R151 +# +## Reaction 151 +#reaction('CH3 + CH2O <=> HCO + CH4', [3.320000e+03, 2.81, 5860.0]) +## R152 +# +## Reaction 152 +#reaction('CH3 + CH3OH <=> CH2OH + CH4', [3.000000e+07, 1.5, 9940.0]) +## R153 +# +## Reaction 153 +#reaction('CH3 + CH3OH <=> CH3O + CH4', [1.000000e+07, 1.5, 9940.0]) +## R154 +# +## Reaction 154 +#reaction('CH3 + C2H4 <=> C2H3 + CH4', [2.270000e+05, 2.0, 9200.0]) +## R155 +# +## Reaction 155 +#reaction('CH3 + C2H6 <=> C2H5 + CH4', [6.140000e+06, 1.74, 10450.0]) +## R156 +# +## Reaction 156 +#reaction('HCO + H2O <=> H + CO + H2O', [1.500000e+18, -1.0, 17000.0]) +## R157 +# +## Reaction 157 +#three_body_reaction('HCO + M <=> H + CO + M', [1.870000e+17, -1.0, 17000.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:0.0 CH4:2.0 C2H6:3.0') +## R158 +# +## Reaction 158 +#reaction('HCO + O2 <=> HO2 + CO', [1.345000e+13, 0.0, 400.0]) +## R159 +# +## Reaction 159 +#reaction('CH2OH + O2 <=> HO2 + CH2O', [1.800000e+13, 0.0, 900.0]) +## R160 +# +## Reaction 160 +#reaction('CH3O + O2 <=> HO2 + CH2O', [4.280000e-13, 7.6, -3530.0]) +## R161 +# +## Reaction 161 +#reaction('C2H3 + O2 <=> HCO + CH2O', [4.580000e+16, -1.39, 1015.0]) +## R162 +# +## Reaction 162 +#falloff_reaction('C2H4 (+ M) <=> H2 + C2H2 (+ M)', +# kf=[8.000000e+12, 0.44, 86770.0], +# kf0=[1.580000e+51, -9.3, 97800.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7345, T3=180.0, T1=1035.0, T2=5417.0)) +## R163 +# +## Reaction 163 +#reaction('C2H5 + O2 <=> HO2 + C2H4', [8.400000e+11, 0.0, 3875.0]) +## R164 +# +## Reaction 164 +#reaction('HCCO + O2 <=> OH + 2 CO', [3.200000e+12, 0.0, 854.0]) +## R165 +# +## Reaction 165 +## reaction('2 HCCO <=> 2 CO + C2H2', [1.000000e+13, 0.0, 0.0]) +## R166 +# +## Reaction 166 +#reaction('O + CH3 => H + H2 + CO', [3.370000e+13, 0.0, 0.0]) +## R167 +# +## Reaction 167 +#reaction('O + C2H4 <=> H + CH2CHO', [6.700000e+06, 1.83, 220.0]) +## R168 +# +## Reaction 168 +#reaction('OH + HO2 <=> O2 + H2O', [5.000000e+15, 0.0, 17330.0], +# options='duplicate') +## R169 +# +## Reaction 169 +#reaction('OH + CH3 => H2 + CH2O', [8.000000e+09, 0.5, -1755.0]) +## R170 +# +## Reaction 170 +#falloff_reaction('CH + H2 (+ M) <=> CH3 (+ M)', +# kf=[1.970000e+12, 0.43, -370.0], +# kf0=[4.820000e+25, -2.8, 590.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.578, T3=122.0, T1=2535.0, T2=9365.0)) +## R171 +# +## Reaction 171 +#reaction('CH2 + O2 => 2 H + CO2', [5.800000e+12, 0.0, 1500.0]) +## R172 +# +## Reaction 172 +#reaction('CH2 + O2 <=> O + CH2O', [2.400000e+12, 0.0, 1500.0]) +## R173 +# +## Reaction 173 +## reaction('CH2 + CH2 => 2 H + C2H2', [2.000000e+14, 0.0, 10989.0]) +## R174 +# +## Reaction 174 +#reaction('CH2(S) + H2O => H2 + CH2O', [6.820000e+10, 0.25, -935.0]) +## R175 +# +## Reaction 175 +#reaction('C2H3 + O2 <=> O + CH2CHO', [3.030000e+11, 0.29, 11.0]) +## R176 +# +## Reaction 176 +#reaction('C2H3 + O2 <=> HO2 + C2H2', [1.337000e+06, 1.61, -384.0]) +## R177 +# +## Reaction 177 +#falloff_reaction('H + CH2CO (+ M) <=> CH2CHO (+ M)', +# kf=[4.865000e+11, 0.422, -1755.0], +# kf0=[1.012000e+42, -7.63, 3854.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.465, T3=201.0, T1=1773.0, T2=5333.0)) +## R178 +# +## Reaction 178 +#reaction('O + CH2CHO => H + CH2 + CO2', [1.500000e+14, 0.0, 0.0]) +## R179 +# +## Reaction 179 +#reaction('O2 + CH2CHO => OH + CO + CH2O', [1.810000e+10, 0.0, 0.0]) +## R180 +# +## Reaction 180 +#reaction('O2 + CH2CHO => OH + 2 HCO', [2.350000e+10, 0.0, 0.0]) +## R181 +# +## Reaction 181 +#reaction('H + CH2CHO <=> CH3 + HCO', [2.200000e+13, 0.0, 0.0]) +## R182 +# +## Reaction 182 +#reaction('H + CH2CHO <=> CH2CO + H2', [1.100000e+13, 0.0, 0.0]) +## R183 +# +## Reaction 183 +#reaction('OH + CH2CHO <=> H2O + CH2CO', [1.200000e+13, 0.0, 0.0]) +## R184 +# +## Reaction 184 +## reaction('OH + CH2CHO <=> HCO + CH2OH', [3.010000e+13, 0.0, 0.0]) +# \ No newline at end of file diff --git a/samples/python/AVBP/inputs/Lu_ARC.f90 b/samples/python/AVBP/inputs/Lu_ARC.f90 new file mode 100755 index 00000000000..355e516069d --- /dev/null +++ b/samples/python/AVBP/inputs/Lu_ARC.f90 @@ -0,0 +1,2317 @@ +! +! A 15-step reduced mechanism based on GRI3.0 +! +! by Tianfeng Lu +! Email: tlu@engr.uconn.edu +! +! Reference: +! Tianfeng Lu and Chung K. Law, +! "A criterion based on computational singular perturbation +! for the identification of quasi steady state species: +! A reduced mechanism for methane oxidation with NO chemistry," +! Combustion and Flame, Vol.154 No.4 pp.761�774, 2008. +! +! SUBROUTINE CKWYP (P, T, Y, ICKWRK, RCKWRK, WDOT) + SUBROUTINE customkinetics(P, T, Y, WDOT) + IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! +! DIMENSION ICKWRK(*), RCKWRK(*), WDOT(*), Y(*) + PARAMETER (RU=8.314510D7, PATM=1.01325D6, SMALL = 1.D-200) + DIMENSION WDOT(19), Y(19) + DIMENSION TN(5), ROP(184), CTB(184) + DIMENSION RF(184), RB(184), RKLOW(22), XQ(11), C(19) + DIMENSION EQK(184), SMH(30), EG(30) + + ! Correction for units compatibility in Cantera + P = P*10.D0 +! +! CALL YTCP(P, T, Y, C) +! CALL RATT(T, RF, RB, RKLOW) +! CALL RATX(T, C, RF, RB, RKLOW) +! CALL QSSA(RF, RB, XQ) +! CALL RDOT(RF, RB, WDOT) +! END +! +! ----------------------------------------------------------------------! +! +! SUBROUTINE YTCP (P, T, Y, C) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION Y(*), C(*) +! +! +! convert Y to ! + + C(1) = Y(1)*4.96046521D-1 + C(2) = Y(2)*9.92093043D-1 + C(3) = Y(3)*6.25023433D-2 + C(4) = Y(4)*3.12511716D-2 + C(5) = Y(5)*5.87980383D-2 + C(6) = Y(6)*5.55082499D-2 + C(7) = Y(7)*3.02968146D-2 + C(8) = Y(8)*2.93990192D-2 + C(9) = Y(9)*6.65112065D-2 + C(10) = Y(10)*6.23323639D-2 + C(11) = Y(11)*3.57008335D-2 + C(12) = Y(12)*2.27221341D-2 + C(13) = Y(13)*3.33039255D-2 + C(14) = Y(14)*3.12086189D-2 + C(15) = Y(15)*3.84050525D-2 + C(16) = Y(16)*3.56453112D-2 + C(17) = Y(17)*3.32556033D-2 + C(18) = Y(18)*2.37882046D-2 + C(19) = Y(19)*3.56972032D-2 +! + SUM = 0.0 + DO K = 1, 19 + SUM = SUM + C(K) + ENDDO + SUM = P/(SUM*T*8.314510D7) +! + DO K = 1, 19 + C(K) = MAX(C(K),SMALL) * SUM + ENDDO +! END +! +! ----------------------------------------------------------------------! +! +! +! forward reaction rates +! +! SUBROUTINE RATT (T, RF, RB, RKLOW) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION RF(*), RB(*), RKLOW(*), EQK(184), SMH(30), EG(30) +! + ALOGT = LOG(T) + TI = 1.0D0/T + TI2 = TI*TI +! + RF(1) = 1.2D17*TI + RF(2) = 5.D17*TI + RF(3) = EXP(1.05635949D1 +2.7D0*ALOGT -3.15013634D3*TI) + RF(4) = 2.D13 + RF(5) = EXP(1.60803938D1 +2.D0*ALOGT -2.01286667D3*TI) + RF(6) = 5.7D13 + RF(7) = 8.D13 + RF(8) = 1.5D13 + RF(9) = 1.5D13 + RF(10) = 5.06D13 + RF(11) = EXP(2.07430685D1 +1.5D0*ALOGT -4.32766334D3*TI) + RF(12) = EXP(2.36136376D1 -1.20017175D3*TI) + RF(13) = 3.D13 + RF(14) = 3.D13 + RF(15) = EXP(3.12945828D1 -1.781387D3*TI) + RF(16) = 1.D13 + RF(17) = 1.D13 + RF(18) = EXP(1.28687606D1 +2.5D0*ALOGT -1.55997167D3*TI) + RF(19) = EXP(1.17752897D1 +2.5D0*ALOGT -2.51608334D3*TI) + TMP = EXP(2.D0*ALOGT -9.56111669D2*TI ) + RF(20) = 1.35D7 * TMP + RF(21) = 6.94D6 * TMP + RF(22) = 3.D13 + TMP = EXP(1.83D0*ALOGT -1.10707667D2*TI ) + RF(23) = 1.25D7 * TMP + RF(167) = 6.7D6 * TMP + RF(24) = 2.24D13 + RF(25) = EXP(1.83130955D1 +1.92D0*ALOGT -2.86330284D3*TI) + RF(26) = 1.D14 + TMP = EXP(-4.02573334D3*TI) + RF(27) = 1.D13 * TMP + RF(76) = 5.D13 * TMP + RF(28) = EXP(2.81906369D1 -6.79342501D2*TI) + RF(29) = EXP(2.85473118D1 -2.40537567D4*TI) + RF(30) = EXP(3.22361913D1 -2.01286667D4*TI) + RF(31) = EXP(4.24761511D1 -8.6D-1*ALOGT) + TMP = EXP(-1.24D0*ALOGT) + RF(32) = 2.08D19 * TMP + RF(34) = 2.6D19 * TMP + RF(33) = EXP(4.38677883D1 -7.6D-1*ALOGT) + RF(35) = EXP(3.78159211D1 -6.707D-1*ALOGT -8.57531523D3*TI) + RF(36) = 1.D18*TI + RF(37) = EXP(3.90385861D1 -6.D-1*ALOGT) + RF(38) = EXP(4.55408762D1 -1.25D0*ALOGT) + RF(39) = 5.5D20*TI2 + RF(40) = 2.2D22*TI2 + RF(41) = EXP(2.90097872D1 -3.37658384D2*TI) + RF(42) = EXP(3.14332293D1 -5.37435401D2*TI) + RF(43) = EXP(3.20618379D1 -3.19542584D2*TI) + RF(44) = EXP(1.6308716D1 +2.D0*ALOGT -2.61672667D3*TI) + RF(45) = EXP(2.99336062D1 -1.81158D3*TI) + RF(46) = 1.65D14 + RF(47) = 6.D14 + RF(48) = 3.D13 + RF(49) = EXP(3.71706652D1 -5.34D-1*ALOGT -2.69724134D2*TI) + RF(50) = EXP(2.03077504D1 +1.62D0*ALOGT -5.45486868D3*TI) + RF(51) = EXP(2.77171988D1 +4.8D-1*ALOGT +1.30836334D2*TI) + RF(52) = 7.34D13 + RF(53) = EXP(2.7014835D1 +4.54D-1*ALOGT -1.81158D3*TI) + RF(54) = EXP(2.7014835D1 +4.54D-1*ALOGT -1.30836334D3*TI) + RF(55) = EXP(1.78655549D1 +1.9D0*ALOGT -1.3798201D3*TI) + RF(56) = EXP(2.76845619D1 +5.D-1*ALOGT -4.32766334D1*TI) + RF(57) = 2.D13 + RF(58) = EXP(2.58292113D1 +6.5D-1*ALOGT +1.42913534D2*TI) + RF(59) = EXP(3.11214496D1 -9.D-2*ALOGT -3.06962167D2*TI) + RF(60) = EXP(2.85189124D1 +5.15D-1*ALOGT -2.51608334D1*TI) + RF(61) = EXP(1.7541204D1 +1.63D0*ALOGT -9.68188869D2*TI) + RF(62) = 2.D13 + RF(63) = EXP(2.80364862D1 +5.D-1*ALOGT +5.53538334D1*TI) + RF(64) = EXP(3.31993656D1 -2.3D-1*ALOGT -5.38441834D2*TI) + TMP = EXP(2.1D0*ALOGT -2.45066517D3*TI ) + RF(65) = 1.7D7 * TMP + RF(66) = 4.2D6 * TMP + RF(67) = EXP(2.93537877D1 -1.20772D3*TI) + RF(68) = EXP(2.94360258D1 +2.7D-1*ALOGT -1.40900667D2*TI) + RF(69) = 3.D13 + RF(70) = EXP(2.7014835D1 +4.54D-1*ALOGT -9.15854335D2*TI) + RF(71) = EXP(1.4096923D1 +2.53D0*ALOGT -6.15937201D3*TI) + RF(72) = EXP(4.07945264D1 -9.9D-1*ALOGT -7.95082335D2*TI) + RF(73) = 2.D12 + RF(74) = EXP(1.85604427D1 +1.9D0*ALOGT -3.78922151D3*TI) + RF(75) = 1.D14 + RF(77) = EXP(3.00558238D1 -1.72502674D3*TI) + RF(78) = EXP(1.75767107D1 +1.5D0*ALOGT -4.00560467D4*TI) + RF(79) = EXP(1.9190789D1 +1.51D0*ALOGT -1.72603317D3*TI) + RF(80) = EXP(3.19350862D1 -3.7D-1*ALOGT) + RF(81) = EXP(1.0482906D1 +2.4D0*ALOGT +1.06178717D3*TI) + RF(82) = EXP(3.03051698D1 +2.51608334D2*TI) + RF(83) = EXP(2.83241683D1 -2.14873517D2*TI) + RF(84) = EXP(4.19771599D1 -1.47996022D4*TI) + RF(85) = 5.D13 + RF(86) = 3.D13 + RF(87) = 2.D13 + RF(88) = EXP(1.62403133D1 +2.D0*ALOGT -1.50965D3*TI) + RF(89) = 3.D13 + RF(90) = EXP(4.24725733D1 -1.43D0*ALOGT -6.69278168D2*TI) + RF(91) = EXP(1.78408622D1 +1.6D0*ALOGT -2.72743434D3*TI) + RF(92) = EXP(4.10064751D1 -1.34D0*ALOGT -7.13058018D2*TI) + RF(93) = EXP(1.84206807D1 +1.6D0*ALOGT -1.570036D3*TI) + RF(94) = EXP(1.76783433D1 +1.228D0*ALOGT -3.52251667D1*TI) + RF(95) = 5.D13 + RF(96) = EXP(2.19558261D1 +1.18D0*ALOGT +2.2493785D2*TI) + RF(97) = 5.D12 + RF(98) = 5.D12 + RF(99) = EXP(1.41801537D1 +2.D0*ALOGT +4.22702001D2*TI) + RF(100) = EXP(1.56560602D1 +2.D0*ALOGT -7.54825001D2*TI) + RF(101) = EXP(-8.4310155D0 +4.5D0*ALOGT +5.03216668D2*TI) + RF(102) = EXP(-7.6354939D0 +4.D0*ALOGT +1.00643334D3*TI) + RF(103) = 5.D12 + RF(104) = EXP(1.50964444D1 +2.D0*ALOGT -1.25804167D3*TI) + RF(105) = EXP(1.50796373D1 +2.12D0*ALOGT -4.37798501D2*TI) + RF(106) = EXP(2.96459241D1 -1.00643334D3*TI) + RF(107) = EXP(2.55908003D1 +8.20243168D2*TI) + RF(108) = EXP(3.36712758D1 -6.03860001D3*TI) + RF(109) = 2.D13 + RF(110) = 1.D12 + RF(111) = 3.78D13 + RF(112) = EXP(3.26416564D1 -1.18759134D4*TI) + RF(113) = EXP(1.55382772D1 +2.D0*ALOGT -6.03860001D3*TI) + RF(114) = EXP(3.16914641D1 -2.89852801D2*TI) + RF(115) = 5.D13 + RF(116) = 6.71D13 + RF(117) = EXP(3.23131523D1 -1.56500384D3*TI) + RF(118) = EXP(2.93732401D1 +3.79928584D2*TI) + RF(119) = 4.D13 + RF(120) = 3.D13 + RF(121) = 6.D13 + RF(122) = 5.D13 + RF(123) = EXP(3.28780452D1 -7.94679762D3*TI) + RF(124) = EXP(3.21806786D1 +2.59156584D2*TI) + RF(125) = 5.D13 + TMP = EXP(-7.54825001D2*TI) + RF(126) = 5.D12 * TMP + RF(171) = 5.8D12 * TMP + RF(172) = 2.4D12 * TMP + RF(127) = EXP(1.31223634D1 +2.D0*ALOGT -3.63825651D3*TI) + RF(128) = EXP(3.500878D1 -6.01041988D3*TI) + RF(129) = 4.D13 + RF(130) = EXP(1.47156719D1 +2.D0*ALOGT -4.16160184D3*TI) + RF(131) = EXP(2.74203001D1 +5.D-1*ALOGT -2.26950717D3*TI) + RF(132) = 3.D13 + RF(133) = EXP(3.03390713D1 -3.01930001D2*TI) + RF(134) = 2.8D13 + RF(135) = 1.2D13 + RF(136) = 7.D13 + RF(137) = EXP(4.07167205D1 -1.16D0*ALOGT -5.76183084D2*TI) + RF(138) = 3.D13 + TMP = EXP(2.86833501D2*TI) + RF(139) = 1.2D13 * TMP + RF(140) = 1.6D13 * TMP + RF(141) = 9.D12 + RF(142) = 7.D12 + RF(143) = 1.4D13 + RF(144) = EXP(3.13199006D1 +2.76769167D2*TI) + RF(145) = EXP(3.12033668D1 -1.5338044D4*TI) + RF(146) = EXP(2.84682686D1 -1.02228466D4*TI) + RF(147) = EXP(1.01064284D1 +2.47D0*ALOGT -2.60666234D3*TI) + RF(148) = EXP(3.87538626D1 -1.18D0*ALOGT -3.29103701D2*TI) + RF(149) = EXP(2.95538088D1 +1.D-1*ALOGT -5.33409668D3*TI) + RF(150) = 2.648D13 + RF(151) = EXP(8.10772006D0 +2.81D0*ALOGT -2.94884967D3*TI) + TMP = EXP(1.5D0*ALOGT -5.00197368D3*TI) + RF(152) = 3.D7 * TMP + RF(153) = 1.D7 * TMP + RF(154) = EXP(1.23327053D1 +2.D0*ALOGT -4.62959334D3*TI) + RF(155) = EXP(1.56303353D1 +1.74D0*ALOGT -5.25861418D3*TI) + TMP = EXP(-1.D0*ALOGT -8.55468335D3*TI) + RF(156) = 1.5D18 * TMP + RF(157) = 1.87D17 * TMP + RF(158) = EXP(3.02300002D1 -2.01286667D2*TI) + RF(159) = EXP(3.05213929D1 -4.52895001D2*TI) + RF(160) = EXP(-2.84796532D1 +7.6D0*ALOGT +1.77635484D3*TI) + RF(161) = EXP(3.83630605D1 -1.39D0*ALOGT -5.10764918D2*TI) + RF(162) = EXP(2.97104627D1 +4.4D-1*ALOGT -4.36641103D4*TI) + RF(163) = EXP(2.74566677D1 -1.94996459D3*TI) + RF(164) = EXP(2.87941719D1 -4.29747034D2*TI) + RF(165) = 1.D13 + RF(166) = 3.37D13 + RF(168) = EXP(3.61482143D1 -8.72074485D3*TI) + RF(169) = EXP(2.28027074D1 +5.D-1*ALOGT +8.83145252D2*TI) + RF(170) = EXP(2.83090547D1 +4.3D-1*ALOGT +1.86190167D2*TI) + RF(173) = EXP(3.29293385D1 -5.52984796D3*TI) + RF(174) = EXP(2.49457104D1 +2.5D-1*ALOGT +4.70507584D2*TI) + RF(175) = EXP(2.64369986D1 +2.9D-1*ALOGT -5.53538334D0*TI) + RF(176) = EXP(1.41059389D1 +1.61D0*ALOGT +1.932352D2*TI) + RF(177) = EXP(2.69105027D1 +4.22D-1*ALOGT +8.83145252D2*TI) + RF(178) = 1.5D14 + RF(179) = 1.81D10 + RF(180) = 2.35D10 + RF(181) = 2.2D13 + RF(182) = 1.1D13 + RF(183) = 1.2D13 + RF(184) = 3.01D13 +! +! +! thermal data +! +! + TLOG = LOG(T) + TI = 1.0D0/T + TN(1) = TLOG - 1.0 + TN(2) = T + TN(3) = TN(2)*T + TN(4) = TN(3)*T + TN(5) = TN(4)*T +! + IF (T .GT. 1.D3) THEN +! + SMH(1) = -3.20502331D+00 + 9.50158922D+02*TI & + + 3.33727920D+00*TN(1) - 2.47012365D-05*TN(2) & + + 8.32427963D-08*TN(3) - 1.49638662D-11*TN(4) & + + 1.00127688D-15*TN(5) + SMH(2) = -4.46682914D-01 - 2.54736599D+04*TI & + + 2.50000001D+00*TN(1) - 1.15421486D-11*TN(2) & + + 2.69269913D-15*TN(3) - 3.94596029D-19*TN(4) & + + 2.49098679D-23*TN(5) + SMH(3) = 4.78433864D+00 - 2.92175791D+04*TI & + + 2.56942078D+00*TN(1) - 4.29870569D-05*TN(2) & + + 6.99140982D-09*TN(3) - 8.34814992D-13*TN(4) & + + 6.14168455D-17*TN(5) + SMH(4) = 5.45323129D+00 + 1.08845772D+03*TI & + + 3.28253784D+00*TN(1) + 7.41543770D-04*TN(2) & + - 1.26327778D-07*TN(3) + 1.74558796D-11*TN(4) & + - 1.08358897D-15*TN(5) + SMH(5) = 4.47669610D+00 - 3.85865700D+03*TI & + + 3.09288767D+00*TN(1) + 2.74214858D-04*TN(2) & + + 2.10842047D-08*TN(3) - 7.32884630D-12*TN(4) & + + 5.87061880D-16*TN(5) + SMH(6) = 4.96677010D+00 + 3.00042971D+04*TI & + + 3.03399249D+00*TN(1) + 1.08845902D-03*TN(2) & + - 2.73454197D-08*TN(3) - 8.08683225D-12*TN(4) & + + 8.41004960D-16*TN(5) + SMH(7) = 3.78510215D+00 - 1.11856713D+02*TI & + + 4.01721090D+00*TN(1) + 1.11991007D-03*TN(2) & + - 1.05609692D-07*TN(3) + 9.52053083D-12*TN(4) & + - 5.39542675D-16*TN(5) + SMH(8) = 2.91615662D+00 + 1.78617877D+04*TI & + + 4.16500285D+00*TN(1) + 2.45415847D-03*TN(2) & + - 3.16898708D-07*TN(3) + 3.09321655D-11*TN(4) & + - 1.43954153D-15*TN(5) + SMH(9) = 4.80150373D+00 - 8.54512953D+04*TI & + + 2.49266888D+00*TN(1) + 2.39944642D-05*TN(2) & + - 1.20722503D-08*TN(3) + 3.11909191D-12*TN(4) & + - 2.43638946D-16*TN(5) + SMH(10) = 5.48497999D+00 - 7.10124364D+04*TI & + + 2.87846473D+00*TN(1) + 4.85456841D-04*TN(2) & + + 2.40742758D-08*TN(3) - 1.08906541D-11*TN(4) & + + 8.80396915D-16*TN(5) + SMH(11) = 6.17119324D+00 - 4.62636040D+04*TI & + + 2.87410113D+00*TN(1) + 1.82819646D-03*TN(2) & + - 2.34824328D-07*TN(3) + 2.16816291D-11*TN(4) & + - 9.38637835D-16*TN(5) + SMH(12) = 8.62650169D+00 - 5.09259997D+04*TI & + + 2.29203842D+00*TN(1) + 2.32794319D-03*TN(2) & + - 3.35319912D-07*TN(3) + 3.48255000D-11*TN(4) & + - 1.69858183D-15*TN(5) + SMH(13) = 8.48007179D+00 - 1.67755843D+04*TI & + + 2.28571772D+00*TN(1) + 3.61995018D-03*TN(2) & + - 4.97857247D-07*TN(3) + 4.96403870D-11*TN(4) & + - 2.33577197D-15*TN(5) + SMH(14) = 1.84373180D+01 + 9.46834459D+03*TI & + + 7.48514950D-02*TN(1) + 6.69547335D-03*TN(2) & + - 9.55476348D-07*TN(3) + 1.01910446D-10*TN(4) & + - 5.09076150D-15*TN(5) + SMH(15) = 7.81868772D+00 + 1.41518724D+04*TI & + + 2.71518561D+00*TN(1) + 1.03126372D-03*TN(2) & + - 1.66470962D-07*TN(3) + 1.91710840D-11*TN(4) & + - 1.01823858D-15*TN(5) + SMH(16) = 2.27163806D+00 + 4.87591660D+04*TI & + + 3.85746029D+00*TN(1) + 2.20718513D-03*TN(2) & + - 3.69135673D-07*TN(3) + 4.36241823D-11*TN(4) & + - 2.36042082D-15*TN(5) + SMH(17) = 9.79834492D+00 - 4.01191815D+03*TI & + + 2.77217438D+00*TN(1) + 2.47847763D-03*TN(2) & + - 4.14076022D-07*TN(3) + 4.90968148D-11*TN(4) & + - 2.66754356D-15*TN(5) + SMH(18) = 1.36563230D+01 + 1.39958323D+04*TI & + + 1.76069008D+00*TN(1) + 4.60000041D-03*TN(2) & + - 7.37098022D-07*TN(3) + 8.38676767D-11*TN(4) & + - 4.41927820D-15*TN(5) + SMH(19) = 5.81043215D+00 + 3.24250627D+03*TI & + + 3.69266569D+00*TN(1) + 4.32288399D-03*TN(2) & + - 6.25168533D-07*TN(3) + 6.56028863D-11*TN(4) & + - 3.24277101D-15*TN(5) + SMH(20) = 2.92957500D+00 - 1.27832520D+02*TI & + + 3.77079900D+00*TN(1) + 3.93574850D-03*TN(2) & + - 4.42730667D-07*TN(3) + 3.28702583D-11*TN(4) & + - 1.05630800D-15*TN(5) + + SMH(21) = 1.45023623D+01 + 2.53748747D+04*TI & + + 1.78970791D+00*TN(1) + 7.04691460D-03*TN(2) & + - 1.06083472D-06*TN(3) + 1.15142571D-10*TN(4) & + - 5.85301100D-15*TN(5) + SMH(22) = -1.23028121D+00 - 2.59359992D+04*TI & + + 4.14756964D+00*TN(1) + 2.98083332D-03*TN(2) & + - 3.95491420D-07*TN(3) + 3.89510143D-11*TN(4) & + - 1.80617607D-15*TN(5) + SMH(23) = 7.78732378D+00 - 3.46128739D+04*TI & + + 3.01672400D+00*TN(1) + 5.16511460D-03*TN(2) & + - 7.80137248D-07*TN(3) + 8.48027400D-11*TN(4) & + - 4.31303520D-15*TN(5) + SMH(24) = 1.03053693D+01 - 4.93988614D+03*TI & + + 2.03611116D+00*TN(1) + 7.32270755D-03*TN(2) & + - 1.11846319D-06*TN(3) + 1.22685769D-10*TN(4) & + - 6.28530305D-15*TN(5) + SMH(25) = 1.34624343D+01 - 1.28575200D+04*TI & + + 1.95465642D+00*TN(1) + 8.69863610D-03*TN(2) & + - 1.33034445D-06*TN(3) + 1.46014741D-10*TN(4) & + - 7.48207880D-15*TN(5) + SMH(26) = 1.51156107D+01 + 1.14263932D+04*TI & + + 1.07188150D+00*TN(1) + 1.08426339D-02*TN(2) & + - 1.67093445D-06*TN(3) + 1.84510001D-10*TN(4) & + - 9.50014450D-15*TN(5) + SMH(27) = -3.93025950D+00 - 1.93272150D+04*TI & + + 5.62820580D+00*TN(1) + 2.04267005D-03*TN(2) & + - 2.65575783D-07*TN(3) + 2.38550433D-11*TN(4) & + - 9.70391600D-16*TN(5) + SMH(28) = 6.32247205D-01 + 7.55105311D+03*TI & + + 4.51129732D+00*TN(1) + 4.50179872D-03*TN(2) & + - 6.94899392D-07*TN(3) + 7.69454902D-11*TN(4) & + - 3.97419100D-15*TN(5) + SMH(29) = -5.04525100D+00 - 4.90321800D+02*TI & + + 5.97567000D+00*TN(1) + 4.06529550D-03*TN(2) & + - 4.57270667D-07*TN(3) + 3.39192000D-11*TN(4) & + - 1.08800850D-15*TN(5) +! + ELSE +! + SMH(1) = 6.83010238D-01 + 9.17935173D+02*TI & + + 2.34433112D+00*TN(1) + 3.99026037D-03*TN(2) & + - 3.24635850D-06*TN(3) + 1.67976745D-09*TN(4) & + - 3.68805881D-13*TN(5) + SMH(2) = -4.46682853D-01 - 2.54736599D+04*TI & + + 2.50000000D+00*TN(1) + 3.52666409D-13*TN(2) & + - 3.32653273D-16*TN(3) + 1.91734693D-19*TN(4) & + - 4.63866166D-23*TN(5) + SMH(3) = 2.05193346D+00 - 2.91222592D+04*TI & + + 3.16826710D+00*TN(1) - 1.63965942D-03*TN(2) & + + 1.10717733D-06*TN(3) - 5.10672187D-10*TN(4) & + + 1.05632986D-13*TN(5) + SMH(4) = 3.65767573D+00 + 1.06394356D+03*TI & + + 3.78245636D+00*TN(1) - 1.49836708D-03*TN(2) & + + 1.64121700D-06*TN(3) - 8.06774591D-10*TN(4) & + + 1.62186419D-13*TN(5) + SMH(5) = -1.03925458D-01 - 3.61508056D+03*TI & + + 3.99201543D+00*TN(1) - 1.20065876D-03*TN(2) & + + 7.69656402D-07*TN(3) - 3.23427778D-10*TN(4) & + + 6.82057350D-14*TN(5) + SMH(6) = -8.49032208D-01 + 3.02937267D+04*TI & + + 4.19864056D+00*TN(1) - 1.01821705D-03*TN(2) & + + 1.08673369D-06*TN(3) - 4.57330885D-10*TN(4) & + + 8.85989085D-14*TN(5) + SMH(7) = 3.71666245D+00 - 2.94808040D+02*TI & + + 4.30179801D+00*TN(1) - 2.37456025D-03*TN(2) & + + 3.52638152D-06*TN(3) - 2.02303245D-09*TN(4) & + + 4.64612562D-13*TN(5) + SMH(8) = 3.43505074D+00 + 1.77025821D+04*TI & + + 4.27611269D+00*TN(1) - 2.71411208D-04*TN(2) & + + 2.78892835D-06*TN(3) - 1.79809011D-09*TN(4) & + + 4.31227182D-13*TN(5) + SMH(9) = 4.53130848D+00 - 8.54438832D+04*TI & + + 2.55423955D+00*TN(1) - 1.60768862D-04*TN(2) & + + 1.22298708D-07*TN(3) - 6.10195741D-11*TN(4) & + + 1.33260723D-14*TN(5) + SMH(10) = 2.08401108D+00 - 7.07972934D+04*TI & + + 3.48981665D+00*TN(1) + 1.61917771D-04*TN(2) & + - 2.81498442D-07*TN(3) + 2.63514439D-10*TN(4) & + - 7.03045335D-14*TN(5) + SMH(11) = 1.56253185D+00 - 4.60040401D+04*TI & + + 3.76267867D+00*TN(1) + 4.84436072D-04*TN(2) & + + 4.65816402D-07*TN(3) - 3.20909294D-10*TN(4) & + + 8.43708595D-14*TN(5) + SMH(12) = -7.69118967D-01 - 5.04968163D+04*TI & + + 4.19860411D+00*TN(1) - 1.18330710D-03*TN(2) & + + 1.37216037D-06*TN(3) - 5.57346651D-10*TN(4) & + + 9.71573685D-14*TN(5) + SMH(13) = 1.60456433D+00 - 1.64449988D+04*TI & + + 3.67359040D+00*TN(1) + 1.00547588D-03*TN(2) & + + 9.55036427D-07*TN(3) - 5.72597854D-10*TN(4) & + + 1.27192867D-13*TN(5) + SMH(14) = -4.64130376D+00 + 1.02466476D+04*TI & + + 5.14987613D+00*TN(1) - 6.83548940D-03*TN(2) & + + 8.19667665D-06*TN(3) - 4.03952522D-09*TN(4) & + + 8.33469780D-13*TN(5) + SMH(15) = 3.50840928D+00 + 1.43440860D+04*TI & + + 3.57953347D+00*TN(1) - 3.05176840D-04*TN(2) & + + 1.69469055D-07*TN(3) + 7.55838237D-11*TN(4) & + - 4.52212249D-14*TN(5) + SMH(16) = 9.90105222D+00 + 4.83719697D+04*TI & + + 2.35677352D+00*TN(1) + 4.49229839D-03*TN(2) & + - 1.18726045D-06*TN(3) + 2.04932518D-10*TN(4) & + - 7.18497740D-15*TN(5) + SMH(17) = 3.39437243D+00 - 3.83956496D+03*TI & + + 4.22118584D+00*TN(1) - 1.62196266D-03*TN(2) & + + 2.29665743D-06*TN(3) - 1.10953411D-09*TN(4) & + + 2.16884433D-13*TN(5) + SMH(18) = 6.02812900D-01 + 1.43089567D+04*TI & + + 4.79372315D+00*TN(1) - 4.95416685D-03*TN(2) & + + 6.22033347D-06*TN(3) - 3.16071051D-09*TN(4) & + + 6.58863260D-13*TN(5) + SMH(19) = 5.47302243D+00 + 3.19391367D+03*TI & + + 3.86388918D+00*TN(1) + 2.79836152D-03*TN(2) & + + 9.88786318D-07*TN(3) - 8.71100100D-10*TN(4) & + + 2.18483639D-13*TN(5) + SMH(20) = 1.31521770D+01 - 9.78601100D+02*TI & + + 2.10620400D+00*TN(1) + 3.60829750D-03*TN(2) & + + 8.89745333D-07*TN(3) - 6.14803000D-10*TN(4) & + + 1.03780500D-13*TN(5) + SMH(21) = -1.50409823D+00 + 2.56427656D+04*TI & + + 5.71539582D+00*TN(1) - 7.61545645D-03*TN(2) & + + 1.08740193D-05*TN(3) - 5.92339074D-09*TN(4) & + + 1.30676349D-12*TN(5) + SMH(22) = 1.39397051D+01 - 2.64289807D+04*TI & + + 8.08681094D-01*TN(1) + 1.16807815D-02*TN(2) & + - 5.91953025D-06*TN(3) + 2.33460364D-09*TN(4) & + - 4.25036487D-13*TN(5) + SMH(23) = 8.51054025D+00 - 3.48598468D+04*TI & + + 3.21246645D+00*TN(1) + 7.57395810D-04*TN(2) & + + 4.32015687D-06*TN(3) - 2.98048206D-09*TN(4) & + + 7.35754365D-13*TN(5) + SMH(24) = 4.09733096D+00 - 5.08977593D+03*TI & + + 3.95920148D+00*TN(1) - 3.78526124D-03*TN(2) & + + 9.51650487D-06*TN(3) - 5.76323961D-09*TN(4) & + + 1.34942187D-12*TN(5) + SMH(25) = 4.70720924D+00 - 1.28416265D+04*TI & + + 4.30646568D+00*TN(1) - 2.09329446D-03*TN(2) & + + 8.28571345D-06*TN(3) - 4.99272172D-09*TN(4) & + + 1.15254502D-12*TN(5) + SMH(26) = 2.66682316D+00 + 1.15222055D+04*TI & + + 4.29142492D+00*TN(1) - 2.75077135D-03*TN(2) & + + 9.99063813D-06*TN(3) - 5.90388571D-09*TN(4) & + + 1.34342886D-12*TN(5) + SMH(27) = 1.24904170D+01 - 2.00594490D+04*TI & + + 2.25172140D+00*TN(1) + 8.82751050D-03*TN(2) & + - 3.95485017D-06*TN(3) + 1.43964658D-09*TN(4) & + - 2.53324055D-13*TN(5) + SMH(28) = 1.22156480D+01 + 7.04291804D+03*TI & + + 2.13583630D+00*TN(1) + 9.05943605D-03*TN(2) & + - 2.89912457D-06*TN(3) + 7.78664640D-10*TN(4) & + - 1.00728807D-13*TN(5) + SMH(29) = 9.55829000D+00 - 1.52147660D+03*TI & + + 3.40906200D+00*TN(1) + 5.36928700D-03*TN(2) & + + 3.15248667D-07*TN(3) - 5.96548583D-10*TN(4) & + + 1.43369250D-13*TN(5) + ENDIF +! CALL RDSMH (T, SMH) +! +! equilibrium constants +! + DO N = 1, 29 + EG(N) = EXP(SMH(N)) + ENDDO +! + PFAC = PATM / (RU*T) + PFAC2 = PFAC*PFAC + PFAC3 = PFAC2*PFAC +! + EQK(1)=EG(4)/EG(3)/EG(3)/PFAC + EQK(2)=EG(5)/EG(2)/EG(3)/PFAC + EQK(3)=EG(2)*EG(5)/EG(1)/EG(3) + EQK(4)=EG(4)*EG(5)/EG(3)/EG(7) + EQK(5)=EG(5)*EG(7)/EG(3)/EG(8) + EQK(6)=EG(2)*EG(15)/EG(3)/EG(10) + EQK(7)=EG(2)*EG(17)/EG(3)/EG(11) + EQK(8)=EG(1)*EG(15)/EG(3)/EG(12) + EQK(9)=EG(2)*EG(17)/EG(3)/EG(12) + EQK(10)=EG(2)*EG(18)/EG(3)/EG(13) + EQK(11)=EG(5)*EG(13)/EG(3)/EG(14) + EQK(12)=EG(16)/EG(3)/EG(15)/PFAC + EQK(13)=EG(5)*EG(15)/EG(3)/EG(17) + EQK(14)=EG(2)*EG(16)/EG(3)/EG(17) + EQK(15)=EG(5)*EG(17)/EG(3)/EG(18) + EQK(16)=EG(5)*EG(18)/EG(3)/EG(19) + EQK(17)=EG(5)*EG(18)/EG(3)/EG(20) + EQK(18)=EG(5)*EG(19)/EG(3)/EG(21) + EQK(19)=EG(5)*EG(20)/EG(3)/EG(21) + EQK(20)=EG(2)*EG(27)/EG(3)/EG(22) + EQK(21)=EG(11)*EG(15)/EG(3)/EG(22) + EQK(22)=EG(2)*EG(28)/EG(3)/EG(23) + EQK(23)=EG(13)*EG(17)/EG(3)/EG(24) + EQK(24)=EG(13)*EG(18)/EG(3)/EG(25) + EQK(25)=EG(5)*EG(25)/EG(3)/EG(26) + EQK(26)=EG(2)*EG(15)*EG(15)/EG(3)/EG(27)*PFAC + EQK(27)=EG(5)*EG(27)/EG(3)/EG(28) + EQK(28)=EG(11)*EG(16)/EG(3)/EG(28) + EQK(29)=EG(3)*EG(16)/EG(4)/EG(15) + EQK(30)=EG(7)*EG(17)/EG(4)/EG(18) + EQK(31)=EG(7)/EG(2)/EG(4)/PFAC + EQK(32)=EQK(31) + EQK(33)=EQK(31) + EQK(34)=EQK(31) + EQK(35)=EG(3)*EG(5)/EG(2)/EG(4) + EQK(36)=EG(1)/EG(2)/EG(2)/PFAC + EQK(37)=EQK(36) + EQK(38)=EQK(36) + EQK(39)=EQK(36) + EQK(40)=EG(6)/EG(2)/EG(5)/PFAC + EQK(41)=EG(3)*EG(6)/EG(2)/EG(7) + EQK(42)=EG(1)*EG(4)/EG(2)/EG(7) + EQK(43)=EG(5)*EG(5)/EG(2)/EG(7) + EQK(44)=EG(1)*EG(7)/EG(2)/EG(8) + EQK(45)=EG(5)*EG(6)/EG(2)/EG(8) + EQK(46)=EG(1)*EG(9)/EG(2)/EG(10) + EQK(47)=EG(13)/EG(2)/EG(11)/PFAC + EQK(48)=EG(1)*EG(10)/EG(2)/EG(12) + EQK(49)=EG(14)/EG(2)/EG(13)/PFAC + EQK(50)=EG(1)*EG(13)/EG(2)/EG(14) + EQK(51)=EG(18)/EG(2)/EG(17)/PFAC + EQK(52)=EG(1)*EG(15)/EG(2)/EG(17) + EQK(53)=EG(19)/EG(2)/EG(18)/PFAC + EQK(54)=EG(20)/EG(2)/EG(18)/PFAC + EQK(55)=EG(1)*EG(17)/EG(2)/EG(18) + EQK(56)=EG(21)/EG(2)/EG(19)/PFAC + EQK(57)=EG(1)*EG(18)/EG(2)/EG(19) + EQK(58)=EG(5)*EG(13)/EG(2)/EG(19) + EQK(59)=EG(6)*EG(12)/EG(2)/EG(19) + EQK(60)=EG(21)/EG(2)/EG(20)/PFAC + EQK(61)=EG(19)/EG(20) + EQK(62)=EG(1)*EG(18)/EG(2)/EG(20) + EQK(63)=EG(5)*EG(13)/EG(2)/EG(20) + EQK(64)=EG(6)*EG(12)/EG(2)/EG(20) + EQK(65)=EG(1)*EG(19)/EG(2)/EG(21) + EQK(66)=EG(1)*EG(20)/EG(2)/EG(21) + EQK(67)=EG(23)/EG(2)/EG(22)/PFAC + EQK(68)=EG(24)/EG(2)/EG(23)/PFAC + EQK(69)=EG(1)*EG(22)/EG(2)/EG(23) + EQK(70)=EG(25)/EG(2)/EG(24)/PFAC + EQK(71)=EG(1)*EG(23)/EG(2)/EG(24) + EQK(72)=EG(26)/EG(2)/EG(25)/PFAC + EQK(73)=EG(1)*EG(24)/EG(2)/EG(25) + EQK(74)=EG(1)*EG(25)/EG(2)/EG(26) + EQK(75)=EG(12)*EG(15)/EG(2)/EG(27) + EQK(76)=EG(1)*EG(27)/EG(2)/EG(28) + EQK(77)=EG(13)*EG(15)/EG(2)/EG(28) + EQK(78)=EG(18)/EG(1)/EG(15)/PFAC + EQK(79)=EG(2)*EG(6)/EG(1)/EG(5) + EQK(80)=EG(8)/EG(5)/EG(5)/PFAC + EQK(81)=EG(3)*EG(6)/EG(5)/EG(5) + EQK(82)=EG(4)*EG(6)/EG(5)/EG(7) + EQK(168)=EQK(82) + EQK(83)=EG(6)*EG(7)/EG(5)/EG(8) + EQK(84)=EQK(83) + EQK(85)=EG(2)*EG(15)/EG(5)/EG(9) + EQK(86)=EG(2)*EG(17)/EG(5)/EG(10) + EQK(87)=EG(2)*EG(18)/EG(5)/EG(11) + EQK(88)=EG(6)*EG(10)/EG(5)/EG(11) + EQK(89)=EG(2)*EG(18)/EG(5)/EG(12) + EQK(90)=EG(21)/EG(5)/EG(13)/PFAC + EQK(91)=EG(6)*EG(11)/EG(5)/EG(13) + EQK(92)=EG(6)*EG(12)/EG(5)/EG(13) + EQK(93)=EG(6)*EG(13)/EG(5)/EG(14) + EQK(94)=EG(2)*EG(16)/EG(5)/EG(15) + EQK(95)=EG(6)*EG(15)/EG(5)/EG(17) + EQK(96)=EG(6)*EG(17)/EG(5)/EG(18) + EQK(97)=EG(6)*EG(18)/EG(5)/EG(19) + EQK(98)=EG(6)*EG(18)/EG(5)/EG(20) + EQK(99)=EG(6)*EG(19)/EG(5)/EG(21) + EQK(100)=EG(6)*EG(20)/EG(5)/EG(21) + EQK(101)=EG(2)*EG(28)/EG(5)/EG(22) + EQK(102)=EG(13)*EG(15)/EG(5)/EG(22) + EQK(103)=EG(6)*EG(22)/EG(5)/EG(23) + EQK(104)=EG(6)*EG(23)/EG(5)/EG(24) + EQK(105)=EG(6)*EG(25)/EG(5)/EG(26) + EQK(106)=EG(6)*EG(27)/EG(5)/EG(28) + EQK(107)=EG(4)*EG(8)/EG(7)/EG(7) + EQK(108)=EQK(107) + EQK(109)=EG(5)*EG(18)/EG(7)/EG(11) + EQK(110)=EG(4)*EG(14)/EG(7)/EG(13) + EQK(111)=EG(5)*EG(20)/EG(7)/EG(13) + EQK(112)=EG(5)*EG(16)/EG(7)/EG(15) + EQK(113)=EG(8)*EG(17)/EG(7)/EG(18) + EQK(114)=EG(3)*EG(15)/EG(4)/EG(9) + EQK(115)=EG(2)*EG(22)/EG(9)/EG(13) + EQK(116)=EG(3)*EG(17)/EG(4)/EG(10) + EQK(117)=EG(2)*EG(11)/EG(1)/EG(10) + EQK(118)=EG(2)*EG(18)/EG(6)/EG(10) + EQK(119)=EG(2)*EG(22)/EG(10)/EG(11) + EQK(120)=EG(2)*EG(23)/EG(10)/EG(13) + EQK(121)=EG(2)*EG(24)/EG(10)/EG(14) + EQK(122)=EG(27)/EG(10)/EG(15)/PFAC + EQK(123)=EG(15)*EG(17)/EG(10)/EG(16) + EQK(124)=EG(2)*EG(28)/EG(10)/EG(18) + EQK(125)=EG(15)*EG(22)/EG(10)/EG(27) + EQK(127)=EG(2)*EG(13)/EG(1)/EG(11) + EQK(128)=EG(1)*EG(22)/EG(11)/EG(11) + EQK(129)=EG(2)*EG(24)/EG(11)/EG(13) + EQK(130)=EG(13)*EG(13)/EG(11)/EG(14) + EQK(131)=EG(28)/EG(11)/EG(15)/PFAC + EQK(132)=EG(15)*EG(23)/EG(11)/EG(27) + EQK(133)=EG(11)/EG(12) + EQK(138)=EQK(133) + EQK(141)=EQK(133) + EQK(142)=EQK(133) + EQK(134)=EG(2)*EG(5)*EG(15)/EG(4)/EG(12)*PFAC + EQK(135)=EG(6)*EG(15)/EG(4)/EG(12) + EQK(136)=EG(2)*EG(13)/EG(1)/EG(12) + EQK(137)=EG(21)/EG(6)/EG(12)/PFAC + EQK(139)=EG(2)*EG(24)/EG(12)/EG(13) + EQK(140)=EG(13)*EG(13)/EG(12)/EG(14) + EQK(143)=EG(15)*EG(18)/EG(12)/EG(16) + EQK(144)=EG(13)*EG(25)/EG(12)/EG(26) + EQK(145)=EG(3)*EG(20)/EG(4)/EG(13) + EQK(146)=EG(5)*EG(18)/EG(4)/EG(13) + EQK(147)=EG(7)*EG(14)/EG(8)/EG(13) + EQK(148)=EG(26)/EG(13)/EG(13)/PFAC + EQK(149)=EG(2)*EG(25)/EG(13)/EG(13) + EQK(150)=EG(14)*EG(15)/EG(13)/EG(17) + EQK(151)=EG(14)*EG(17)/EG(13)/EG(18) + EQK(152)=EG(14)*EG(19)/EG(13)/EG(21) + EQK(153)=EG(14)*EG(20)/EG(13)/EG(21) + EQK(154)=EG(14)*EG(23)/EG(13)/EG(24) + EQK(155)=EG(14)*EG(25)/EG(13)/EG(26) + EQK(156)=EG(2)*EG(15)/EG(17)*PFAC + EQK(157)=EQK(156) + EQK(158)=EG(7)*EG(15)/EG(4)/EG(17) + EQK(159)=EG(7)*EG(18)/EG(4)/EG(19) + EQK(160)=EG(7)*EG(18)/EG(4)/EG(20) + EQK(161)=EG(17)*EG(18)/EG(4)/EG(23) + EQK(162)=EG(1)*EG(22)/EG(24)*PFAC + EQK(163)=EG(7)*EG(24)/EG(4)/EG(25) + EQK(164)=EG(5)*EG(15)*EG(15)/EG(4)/EG(27)*PFAC + EQK(165)=EG(15)*EG(15)*EG(22)/EG(27)/EG(27)*PFAC + EQK(167)=EG(2)*EG(29)/EG(3)/EG(24) + EQK(170)=EG(13)/EG(1)/EG(10)/PFAC + EQK(172)=EG(3)*EG(18)/EG(4)/EG(11) + EQK(175)=EG(3)*EG(29)/EG(4)/EG(23) + EQK(176)=EG(7)*EG(22)/EG(4)/EG(23) + EQK(177)=EG(29)/EG(2)/EG(28)/PFAC + EQK(181)=EG(13)*EG(17)/EG(2)/EG(29) + EQK(182)=EG(1)*EG(28)/EG(2)/EG(29) + EQK(183)=EG(6)*EG(28)/EG(5)/EG(29) + EQK(184)=EG(17)*EG(19)/EG(5)/EG(29) +! +! +! ! Compute reverse reaction rates +! +! PARAMETER (SMALL = 1.D-200) +! + RB(1) = RF(1) / MAX(EQK(1),SMALL) + RB(2) = RF(2) / MAX(EQK(2),SMALL) + RB(3) = RF(3) / MAX(EQK(3),SMALL) + RB(4) = RF(4) / MAX(EQK(4),SMALL) + RB(5) = RF(5) / MAX(EQK(5),SMALL) + RB(6) = RF(6) / MAX(EQK(6),SMALL) + RB(7) = RF(7) / MAX(EQK(7),SMALL) + RB(8) = RF(8) / MAX(EQK(8),SMALL) + RB(9) = RF(9) / MAX(EQK(9),SMALL) + RB(10) = RF(10) / MAX(EQK(10),SMALL) + RB(11) = RF(11) / MAX(EQK(11),SMALL) + RB(12) = RF(12) / MAX(EQK(12),SMALL) + RB(13) = RF(13) / MAX(EQK(13),SMALL) + RB(14) = RF(14) / MAX(EQK(14),SMALL) + RB(15) = RF(15) / MAX(EQK(15),SMALL) + RB(16) = RF(16) / MAX(EQK(16),SMALL) + RB(17) = RF(17) / MAX(EQK(17),SMALL) + RB(18) = RF(18) / MAX(EQK(18),SMALL) + RB(19) = RF(19) / MAX(EQK(19),SMALL) + RB(20) = RF(20) / MAX(EQK(20),SMALL) + RB(21) = RF(21) / MAX(EQK(21),SMALL) + RB(22) = RF(22) / MAX(EQK(22),SMALL) + RB(23) = RF(23) / MAX(EQK(23),SMALL) + RB(24) = RF(24) / MAX(EQK(24),SMALL) + RB(25) = RF(25) / MAX(EQK(25),SMALL) + RB(26) = RF(26) / MAX(EQK(26),SMALL) + RB(27) = RF(27) / MAX(EQK(27),SMALL) + RB(28) = RF(28) / MAX(EQK(28),SMALL) + RB(29) = RF(29) / MAX(EQK(29),SMALL) + RB(30) = RF(30) / MAX(EQK(30),SMALL) + RB(31) = RF(31) / MAX(EQK(31),SMALL) + RB(32) = RF(32) / MAX(EQK(32),SMALL) + RB(33) = RF(33) / MAX(EQK(33),SMALL) + RB(34) = RF(34) / MAX(EQK(34),SMALL) + RB(35) = RF(35) / MAX(EQK(35),SMALL) + RB(36) = RF(36) / MAX(EQK(36),SMALL) + RB(37) = RF(37) / MAX(EQK(37),SMALL) + + RB(38) = RF(38) / MAX(EQK(38),SMALL) + RB(39) = RF(39) / MAX(EQK(39),SMALL) + RB(40) = RF(40) / MAX(EQK(40),SMALL) + RB(41) = RF(41) / MAX(EQK(41),SMALL) + RB(42) = RF(42) / MAX(EQK(42),SMALL) + RB(43) = RF(43) / MAX(EQK(43),SMALL) + RB(44) = RF(44) / MAX(EQK(44),SMALL) + RB(45) = RF(45) / MAX(EQK(45),SMALL) + RB(46) = RF(46) / MAX(EQK(46),SMALL) + RB(47) = RF(47) / MAX(EQK(47),SMALL) + RB(48) = RF(48) / MAX(EQK(48),SMALL) + RB(49) = RF(49) / MAX(EQK(49),SMALL) + RB(50) = RF(50) / MAX(EQK(50),SMALL) + RB(51) = RF(51) / MAX(EQK(51),SMALL) + RB(52) = RF(52) / MAX(EQK(52),SMALL) + RB(53) = RF(53) / MAX(EQK(53),SMALL) + RB(54) = RF(54) / MAX(EQK(54),SMALL) + RB(55) = RF(55) / MAX(EQK(55),SMALL) + RB(56) = RF(56) / MAX(EQK(56),SMALL) + RB(57) = RF(57) / MAX(EQK(57),SMALL) + RB(58) = RF(58) / MAX(EQK(58),SMALL) + RB(59) = RF(59) / MAX(EQK(59),SMALL) + RB(60) = RF(60) / MAX(EQK(60),SMALL) + RB(61) = RF(61) / MAX(EQK(61),SMALL) + RB(62) = RF(62) / MAX(EQK(62),SMALL) + RB(63) = RF(63) / MAX(EQK(63),SMALL) + RB(64) = RF(64) / MAX(EQK(64),SMALL) + RB(65) = RF(65) / MAX(EQK(65),SMALL) + RB(66) = RF(66) / MAX(EQK(66),SMALL) + RB(67) = RF(67) / MAX(EQK(67),SMALL) + RB(68) = RF(68) / MAX(EQK(68),SMALL) + RB(69) = RF(69) / MAX(EQK(69),SMALL) + RB(70) = RF(70) / MAX(EQK(70),SMALL) + RB(71) = RF(71) / MAX(EQK(71),SMALL) + RB(72) = RF(72) / MAX(EQK(72),SMALL) + RB(73) = RF(73) / MAX(EQK(73),SMALL) + RB(74) = RF(74) / MAX(EQK(74),SMALL) + RB(75) = RF(75) / MAX(EQK(75),SMALL) + RB(76) = RF(76) / MAX(EQK(76),SMALL) + RB(77) = RF(77) / MAX(EQK(77),SMALL) + RB(78) = RF(78) / MAX(EQK(78),SMALL) + RB(79) = RF(79) / MAX(EQK(79),SMALL) + RB(80) = RF(80) / MAX(EQK(80),SMALL) + RB(81) = RF(81) / MAX(EQK(81),SMALL) + RB(82) = RF(82) / MAX(EQK(82),SMALL) + RB(83) = RF(83) / MAX(EQK(83),SMALL) + RB(84) = RF(84) / MAX(EQK(84),SMALL) + RB(85) = RF(85) / MAX(EQK(85),SMALL) + RB(86) = RF(86) / MAX(EQK(86),SMALL) + RB(87) = RF(87) / MAX(EQK(87),SMALL) + RB(88) = RF(88) / MAX(EQK(88),SMALL) + RB(89) = RF(89) / MAX(EQK(89),SMALL) + RB(90) = RF(90) / MAX(EQK(90),SMALL) + RB(91) = RF(91) / MAX(EQK(91),SMALL) + RB(92) = RF(92) / MAX(EQK(92),SMALL) + RB(93) = RF(93) / MAX(EQK(93),SMALL) + RB(94) = RF(94) / MAX(EQK(94),SMALL) + RB(95) = RF(95) / MAX(EQK(95),SMALL) + RB(96) = RF(96) / MAX(EQK(96),SMALL) + RB(97) = RF(97) / MAX(EQK(97),SMALL) + RB(98) = RF(98) / MAX(EQK(98),SMALL) + RB(99) = RF(99) / MAX(EQK(99),SMALL) + RB(100) = RF(100) / MAX(EQK(100),SMALL) + RB(101) = RF(101) / MAX(EQK(101),SMALL) + RB(102) = RF(102) / MAX(EQK(102),SMALL) + RB(103) = RF(103) / MAX(EQK(103),SMALL) + RB(104) = RF(104) / MAX(EQK(104),SMALL) + RB(105) = RF(105) / MAX(EQK(105),SMALL) + RB(106) = RF(106) / MAX(EQK(106),SMALL) + RB(107) = RF(107) / MAX(EQK(107),SMALL) + RB(108) = RF(108) / MAX(EQK(108),SMALL) + RB(109) = RF(109) / MAX(EQK(109),SMALL) + RB(110) = RF(110) / MAX(EQK(110),SMALL) + RB(111) = RF(111) / MAX(EQK(111),SMALL) + RB(112) = RF(112) / MAX(EQK(112),SMALL) + RB(113) = RF(113) / MAX(EQK(113),SMALL) + RB(114) = RF(114) / MAX(EQK(114),SMALL) + RB(115) = RF(115) / MAX(EQK(115),SMALL) + RB(116) = RF(116) / MAX(EQK(116),SMALL) + RB(117) = RF(117) / MAX(EQK(117),SMALL) + RB(118) = RF(118) / MAX(EQK(118),SMALL) + RB(119) = RF(119) / MAX(EQK(119),SMALL) + RB(120) = RF(120) / MAX(EQK(120),SMALL) + RB(121) = RF(121) / MAX(EQK(121),SMALL) + RB(122) = RF(122) / MAX(EQK(122),SMALL) + RB(123) = RF(123) / MAX(EQK(123),SMALL) + RB(124) = RF(124) / MAX(EQK(124),SMALL) + RB(125) = RF(125) / MAX(EQK(125),SMALL) + RB(126) = 0.0 + RB(127) = RF(127) / MAX(EQK(127),SMALL) + RB(128) = RF(128) / MAX(EQK(128),SMALL) + RB(129) = RF(129) / MAX(EQK(129),SMALL) + RB(130) = RF(130) / MAX(EQK(130),SMALL) + RB(131) = RF(131) / MAX(EQK(131),SMALL) + RB(132) = RF(132) / MAX(EQK(132),SMALL) + RB(133) = RF(133) / MAX(EQK(133),SMALL) + RB(134) = RF(134) / MAX(EQK(134),SMALL) + RB(135) = RF(135) / MAX(EQK(135),SMALL) + RB(136) = RF(136) / MAX(EQK(136),SMALL) + RB(137) = RF(137) / MAX(EQK(137),SMALL) + RB(138) = RF(138) / MAX(EQK(138),SMALL) + RB(139) = RF(139) / MAX(EQK(139),SMALL) + RB(140) = RF(140) / MAX(EQK(140),SMALL) + RB(141) = RF(141) / MAX(EQK(141),SMALL) + RB(142) = RF(142) / MAX(EQK(142),SMALL) + RB(143) = RF(143) / MAX(EQK(143),SMALL) + RB(144) = RF(144) / MAX(EQK(144),SMALL) + RB(145) = RF(145) / MAX(EQK(145),SMALL) + RB(146) = RF(146) / MAX(EQK(146),SMALL) + RB(147) = RF(147) / MAX(EQK(147),SMALL) + RB(148) = RF(148) / MAX(EQK(148),SMALL) + RB(149) = RF(149) / MAX(EQK(149),SMALL) + RB(150) = RF(150) / MAX(EQK(150),SMALL) + RB(151) = RF(151) / MAX(EQK(151),SMALL) + RB(152) = RF(152) / MAX(EQK(152),SMALL) + RB(153) = RF(153) / MAX(EQK(153),SMALL) + RB(154) = RF(154) / MAX(EQK(154),SMALL) + RB(155) = RF(155) / MAX(EQK(155),SMALL) + RB(156) = RF(156) / MAX(EQK(156),SMALL) + RB(157) = RF(157) / MAX(EQK(157),SMALL) + RB(158) = RF(158) / MAX(EQK(158),SMALL) + RB(159) = RF(159) / MAX(EQK(159),SMALL) + RB(160) = RF(160) / MAX(EQK(160),SMALL) + RB(161) = RF(161) / MAX(EQK(161),SMALL) + RB(162) = RF(162) / MAX(EQK(162),SMALL) + RB(163) = RF(163) / MAX(EQK(163),SMALL) + RB(164) = RF(164) / MAX(EQK(164),SMALL) + RB(165) = RF(165) / MAX(EQK(165),SMALL) + RB(166) = 0.0 + RB(167) = RF(167) / MAX(EQK(167),SMALL) + RB(168) = RF(168) / MAX(EQK(168),SMALL) + RB(169) = 0.0 + RB(170) = RF(170) / MAX(EQK(170),SMALL) + RB(171) = 0.0 + RB(172) = RF(172) / MAX(EQK(172),SMALL) + RB(173) = 0.0 + RB(174) = 0.0 + RB(175) = RF(175) / MAX(EQK(175),SMALL) + RB(176) = RF(176) / MAX(EQK(176),SMALL) + RB(177) = RF(177) / MAX(EQK(177),SMALL) + RB(178) = 0.0 + RB(179) = 0.0 + RB(180) = 0.0 + RB(181) = RF(181) / MAX(EQK(181),SMALL) + RB(182) = RF(182) / MAX(EQK(182),SMALL) + RB(183) = RF(183) / MAX(EQK(183),SMALL) + RB(184) = RF(184) / MAX(EQK(184),SMALL) +! +! +! rates at low pressure limit +! + RKLOW(1) = EXP(3.40312786D1 -1.50965D3/T) + RKLOW(2) = EXP(5.99064331D1 -2.76D0*ALOGT -8.05146668D2/T) + RKLOW(3) = EXP(7.69484824D1 -4.76D0*ALOGT -1.22784867D3/T) + RKLOW(4) = EXP(5.61662604D1 -2.57D0*ALOGT -2.13867084D2/T) + RKLOW(5) = EXP(7.39217399D1 -4.82D0*ALOGT -3.28600484D3/T) + RKLOW(6) = EXP(6.98660102D1 -4.8D0*ALOGT -2.79788467D3/T) + RKLOW(7) = EXP(7.28526099D1 -4.65D0*ALOGT -2.55634067D3/T) + RKLOW(8) = EXP(9.59450043D1 -7.44D0*ALOGT -7.08529068D3/T) + RKLOW(9) = EXP(9.34384048D1 -7.27D0*ALOGT -3.63322434D3/T) + RKLOW(10) = EXP(6.9414025D1 -3.86D0*ALOGT -1.67067934D3/T) + RKLOW(11) = EXP(9.61977483D1 -7.62D0*ALOGT -3.50742017D3/T) + RKLOW(12) = EXP(9.50941235D1 -7.08D0*ALOGT -3.36400342D3/T) + RKLOW(13) = EXP(6.37931383D1 -3.42D0*ALOGT -4.24463259D4/T) + RKLOW(14) = EXP(4.22794408D1 -9.D-1*ALOGT +8.55468335D2/T) + RKLOW(15) = EXP(8.42793577D1 -5.92D0*ALOGT -1.58010034D3/T) + RKLOW(16) = EXP(6.54619238D1 -3.74D0*ALOGT -9.74227469D2/T) + RKLOW(17) = EXP(7.69748493D1 -5.11D0*ALOGT -3.57032226D3/T) + RKLOW(18) = EXP(8.81295053D1 -6.36D0*ALOGT -2.536212D3/T) + RKLOW(19) = EXP(9.56297642D1 -7.03D0*ALOGT -1.38988444D3/T) + RKLOW(20) = EXP(1.17889265D2 -9.3D0*ALOGT -4.92145901D4/T) + RKLOW(21) = EXP(5.91374013D1 -2.8D0*ALOGT -2.96897834D2/T) + RKLOW(22) = EXP(9.67205025D1 -7.63D0*ALOGT -1.93939704D3/T) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! third-body concentrations +! ! +! SUBROUTINE RATX (T, C, RF, RB, RKLOW) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! PARAMETER (SMALL = 1.D-200) +! DIMENSION C(*), RF(*), RB(*), RKLOW(*) +! + ALOGT = LOG(T) + CTOT = 0.0 + DO K = 1, 19 + CTOT = CTOT + C(K) + ENDDO +! + CTB(1) = CTOT + 1.4D0*C(1) + 1.44D1*C(6) + C(10) + 7.5D-1*C(11) & + + 2.6D0*C(12) + 2.D0*C(17) + CTB(2) = CTOT + C(1) + 5.D0*C(6) + C(10) + 5.D-1*C(11) + C(12) & + + 2.D0*C(17) + CTB(47) = CTB(2) + CTB(51) = CTB(2) + CTB(53) = CTB(2) + CTB(54) = CTB(2) + CTB(56) = CTB(2) + CTB(60) = CTB(2) + CTB(67) = CTB(2) + CTB(68) = CTB(2) + CTB(70) = CTB(2) + CTB(72) = CTB(2) + CTB(78) = CTB(2) + CTB(80) = CTB(2) + CTB(90) = CTB(2) + CTB(122) = CTB(2) + CTB(131) = CTB(2) + CTB(137) = CTB(2) + CTB(148) = CTB(2) + CTB(162) = CTB(2) + CTB(170) = CTB(2) + CTB(177) = CTB(2) + CTB(12) = CTOT + C(1) + 5.D0*C(4) + 5.D0*C(6) + C(10) & + + 5.D-1*C(11) + 2.5D0*C(12) + 2.D0*C(17) + CTB(31) = CTOT - C(4) - C(6) - 2.5D-1*C(11) + 5.D-1*C(12) & + + 5.D-1*C(17) - C(19) + CTB(36) = CTOT - C(1) - C(6) + C(10) - C(12) + 2.D0*C(17) + CTB(40) = CTOT - 2.7D-1*C(1) + 2.65D0*C(6) + C(10) + 2.D0*C(17) + CTB(49) = CTOT + C(1) + 5.D0*C(6) + 2.D0*C(10) + 5.D-1*C(11) & + + C(12) + 2.D0*C(17) + CTB(157) = CTOT + C(1) - C(6) + C(10) + 5.D-1*C(11) + C(12) & + + 2.D0*C(17) +! +! +! fall-off reactions +! +! + PR = RKLOW(1) * CTB(12) / RF(12) + PCOR = PR / (1.0 + PR) + RF(12) = RF(12) * PCOR + RB(12) = RB(12) * PCOR +! + PR = RKLOW(2) * CTB(47) / RF(47) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.38D-1*EXP(-T/9.1D1) + 5.62D-1*EXP(-T/5.836D3)& + + EXP(-8.552D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(47) = RF(47) * PCOR + RB(47) = RB(47) * PCOR +! + PR = RKLOW(3) * CTB(49) / RF(49) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.17D-1*EXP(-T/7.4D1) + 7.83D-1*EXP(-T/2.941D3)& + + EXP(-6.964D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(49) = RF(49) * PCOR + RB(49) = RB(49) * PCOR +! + PR = RKLOW(4) * CTB(51) / RF(51) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.176D-1*EXP(-T/2.71D2) + 7.824D-1*EXP(-T/2.755D3)& + + EXP(-6.57D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(51) = RF(51) * PCOR + RB(51) = RB(51) * PCOR + + PR = RKLOW(5) * CTB(53) / RF(53) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.813D-1*EXP(-T/1.03D2) + 7.187D-1*EXP(-T/1.291D3)& + + EXP(-4.16D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(53) = RF(53) * PCOR + RB(53) = RB(53) * PCOR + + PR = RKLOW(6) * CTB(54) / RF(54) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.42D-1*EXP(-T/9.4D1) + 7.58D-1*EXP(-T/1.555D3)& + + EXP(-4.2D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(54) = RF(54) * PCOR + RB(54) = RB(54) * PCOR + + PR = RKLOW(7) * CTB(56) / RF(56) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.D-1*EXP(-T/1.D2) + 6.D-1*EXP(-T/9.D4)& + + EXP(-1.D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(56) = RF(56) * PCOR + RB(56) = RB(56) * PCOR + + PR = RKLOW(8) * CTB(60) / RF(60) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.D-1*EXP(-T/1.D2) + 7.D-1*EXP(-T/9.D4)& + + EXP(-1.D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(60) = RF(60) * PCOR + RB(60) = RB(60) * PCOR + + PR = RKLOW(9) * CTB(67) / RF(67) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.493D-1*EXP(-T/9.85D1) + 7.507D-1*EXP(-T/1.302D3)& + + EXP(-4.167D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(67) = RF(67) * PCOR + RB(67) = RB(67) * PCOR + + PR = RKLOW(10) * CTB(68) / RF(68) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.18D-1*EXP(-T/2.075D2) + 7.82D-1*EXP(-T/2.663D3)& + + EXP(-6.095D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(68) = RF(68) * PCOR + RB(68) = RB(68) * PCOR + + PR = RKLOW(11) * CTB(70) / RF(70) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.47D-2*EXP(-T/2.1D2) + 9.753D-1*EXP(-T/9.84D2)& + + EXP(-4.374D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(70) = RF(70) * PCOR + RB(70) = RB(70) * PCOR + + PR = RKLOW(12) * CTB(72) / RF(72) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 1.578D-1*EXP(-T/1.25D2) + 8.422D-1*EXP(-T/2.219D3)& + + EXP(-6.882D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(72) = RF(72) * PCOR + RB(72) = RB(72) * PCOR + + PR = RKLOW(13) * CTB(78) / RF(78) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 6.8D-2*EXP(-T/1.97D2) + 9.32D-1*EXP(-T/1.54D3)& + + EXP(-1.03D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(78) = RF(78) * PCOR + RB(78) = RB(78) * PCOR + + PR = RKLOW(14) * CTB(80) / RF(80) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.654D-1*EXP(-T/9.4D1) + 7.346D-1*EXP(-T/1.756D3)& + + EXP(-5.182D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(80) = RF(80) * PCOR + RB(80) = RB(80) * PCOR + + PR = RKLOW(15) * CTB(90) / RF(90) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 5.88D-1*EXP(-T/1.95D2) + 4.12D-1*EXP(-T/5.9D3)& + + EXP(-6.394D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(90) = RF(90) * PCOR + RB(90) = RB(90) * PCOR + + PR = RKLOW(16) * CTB(122) / RF(122) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.243D-1*EXP(-T/2.37D2) + 5.757D-1*EXP(-T/1.652D3)& + + EXP(-5.069D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(122) = RF(122) * PCOR + RB(122) = RB(122) * PCOR + + PR = RKLOW(17) * CTB(131) / RF(131) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.093D-1*EXP(-T/2.75D2) + 5.907D-1*EXP(-T/1.226D3)& + + EXP(-5.185D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(131) = RF(131) * PCOR + RB(131) = RB(131) * PCOR + + PR = RKLOW(18) * CTB(137) / RF(137) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.973D-1*EXP(-T/2.08D2) + 6.027D-1*EXP(-T/3.922D3)& + + EXP(-1.018D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(137) = RF(137) * PCOR + RB(137) = RB(137) * PCOR + + PR = RKLOW(19) * CTB(148) / RF(148) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.81D-1*EXP(-T/7.32D1) + 6.19D-1*EXP(-T/1.18D3)& + + EXP(-9.999D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(148) = RF(148) * PCOR + RB(148) = RB(148) * PCOR + + PR = RKLOW(20) * CTB(162) / RF(162) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.655D-1*EXP(-T/1.8D2) + 7.345D-1*EXP(-T/1.035D3)& + + EXP(-5.417D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(162) = RF(162) * PCOR + RB(162) = RB(162) * PCOR + + PR = RKLOW(21) * CTB(170) / RF(170) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.22D-1*EXP(-T/1.22D2) + 5.78D-1*EXP(-T/2.535D3)& + + EXP(-9.365D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(170) = RF(170) * PCOR + RB(170) = RB(170) * PCOR + + PR = RKLOW(22) * CTB(177) / RF(177) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 5.35D-1*EXP(-T/2.01D2) + 4.65D-1*EXP(-T/1.773D3)& + + EXP(-5.333D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(177) = RF(177) * PCOR + RB(177) = RB(177) * PCOR + + RF(1) = RF(1)*CTB(1)*C(3)*C(3) + RF(2) = RF(2)*CTB(2)*C(3)*C(2) + RF(3) = RF(3)*C(3)*C(1) + RF(4) = RF(4)*C(3)*C(7) + RF(5) = RF(5)*C(3)*C(8) + RF(6) = RF(6)*C(3) + RF(7) = RF(7)*C(3) + RF(8) = RF(8)*C(3) + RF(9) = RF(9)*C(3) + RF(10) = RF(10)*C(3)*C(9) + RF(11) = RF(11)*C(3)*C(10) + RF(12) = RF(12)*C(3)*C(11) + RF(13) = RF(13)*C(3) + RF(14) = RF(14)*C(3) + RF(15) = RF(15)*C(3)*C(13) + RF(16) = RF(16)*C(3) + RF(17) = RF(17)*C(3) + RF(18) = RF(18)*C(3)*C(14) + RF(19) = RF(19)*C(3)*C(14) + RF(20) = RF(20)*C(3)*C(15) + RF(21) = RF(21)*C(3)*C(15) + RF(22) = RF(22)*C(3) + RF(23) = RF(23)*C(3)*C(16) + RF(24) = RF(24)*C(3) + RF(25) = RF(25)*C(3)*C(17) + RF(26) = RF(26)*C(3) + RF(27) = RF(27)*C(3)*C(18) + RF(28) = RF(28)*C(3)*C(18) + RF(29) = RF(29)*C(4)*C(11) + RF(30) = RF(30)*C(4)*C(13) + RF(31) = RF(31)*CTB(31)*C(2)*C(4) + RF(32) = RF(32)*C(2)*C(4)*C(4) + RF(33) = RF(33)*C(2)*C(4)*C(6) + RF(34) = RF(34)*C(2)*C(4)*C(19) + RF(35) = RF(35)*C(2)*C(4) + RF(36) = RF(36)*CTB(36)*C(2)*C(2) + RF(37) = RF(37)*C(2)*C(2)*C(1) + RF(38) = RF(38)*C(2)*C(2)*C(6) + RF(39) = RF(39)*C(2)*C(2)*C(12) + RF(40) = RF(40)*CTB(40)*C(2)*C(5) + RF(41) = RF(41)*C(2)*C(7) + RF(42) = RF(42)*C(2)*C(7) + RF(43) = RF(43)*C(2)*C(7) + RF(44) = RF(44)*C(2)*C(8) + RF(45) = RF(45)*C(2)*C(8) + RF(46) = RF(46)*C(2) + RF(47) = RF(47)*C(2) + RF(48) = RF(48)*C(2) + RF(49) = RF(49)*C(2)*C(9) + RF(50) = RF(50)*C(2)*C(10) + RF(51) = RF(51)*C(2) + RF(52) = RF(52)*C(2) + RF(53) = RF(53)*C(2)*C(13) + RF(54) = RF(54)*C(2)*C(13) + RF(55) = RF(55)*C(2)*C(13) + RF(56) = RF(56)*C(2) + RF(57) = RF(57)*C(2) + RF(58) = RF(58)*C(2) + RF(59) = RF(59)*C(2) + RF(60) = RF(60)*C(2) + RF(61) = RF(61)*C(2) + RF(62) = RF(62)*C(2) + RF(63) = RF(63)*C(2) + RF(64) = RF(64)*C(2) + RF(65) = RF(65)*C(2)*C(14) + RF(66) = RF(66)*C(2)*C(14) + RF(67) = RF(67)*C(2)*C(15) + RF(68) = RF(68)*C(2) + RF(69) = RF(69)*C(2) + RF(70) = RF(70)*C(2)*C(16) + RF(71) = RF(71)*C(2)*C(16) + RF(72) = RF(72)*C(2) + RF(73) = RF(73)*C(2) + RF(74) = RF(74)*C(2)*C(17) + RF(75) = RF(75)*C(2) + RF(76) = RF(76)*C(2)*C(18) + RF(77) = RF(77)*C(2)*C(18) + RF(78) = RF(78)*C(1)*C(11) + RF(79) = RF(79)*C(5)*C(1) + RF(80) = RF(80)*C(5)*C(5) + RF(81) = RF(81)*C(5)*C(5) + RF(82) = RF(82)*C(5)*C(7) + RF(83) = RF(83)*C(5)*C(8) + RF(84) = RF(84)*C(5)*C(8) + RF(85) = RF(85)*C(5) + RF(86) = RF(86)*C(5) + RF(87) = RF(87)*C(5) + RF(88) = RF(88)*C(5) + RF(89) = RF(89)*C(5) + RF(90) = RF(90)*C(5)*C(9) + RF(91) = RF(91)*C(5)*C(9) + RF(92) = RF(92)*C(5)*C(9) + RF(93) = RF(93)*C(5)*C(10) + RF(94) = RF(94)*C(5)*C(11) + RF(95) = RF(95)*C(5) + RF(96) = RF(96)*C(5)*C(13) + RF(97) = RF(97)*C(5) + RF(98) = RF(98)*C(5) + RF(99) = RF(99)*C(5)*C(14) + RF(100) = RF(100)*C(5)*C(14) + RF(101) = RF(101)*C(5)*C(15) + RF(102) = RF(102)*C(5)*C(15) + RF(103) = RF(103)*C(5) + RF(104) = RF(104)*C(5)*C(16) + RF(105) = RF(105)*C(5)*C(17) + RF(106) = RF(106)*C(5)*C(18) + RF(107) = RF(107)*C(7)*C(7) + RF(108) = RF(108)*C(7)*C(7) + RF(109) = RF(109)*C(7) + RF(110) = RF(110)*C(7)*C(9) + RF(111) = RF(111)*C(7)*C(9) + RF(112) = RF(112)*C(7)*C(11) + RF(113) = RF(113)*C(7)*C(13) + RF(114) = RF(114)*C(4) + RF(115) = RF(115)*C(9) + RF(116) = RF(116)*C(4) + RF(117) = RF(117)*C(1) + RF(118) = RF(118)*C(6) + RF(120) = RF(120)*C(9) + RF(121) = RF(121)*C(10) + RF(122) = RF(122)*C(11) + RF(123) = RF(123)*C(12) + RF(124) = RF(124)*C(13) + RF(126) = RF(126)*C(4) + RF(127) = RF(127)*C(1) + RF(129) = RF(129)*C(9) + RF(130) = RF(130)*C(10) + RF(131) = RF(131)*C(11) + RF(133) = RF(133)*C(19) + RF(134) = RF(134)*C(4) + RF(135) = RF(135)*C(4) + RF(136) = RF(136)*C(1) + RF(137) = RF(137)*C(6) + RF(138) = RF(138)*C(6) + RF(139) = RF(139)*C(9) + RF(140) = RF(140)*C(10) + RF(141) = RF(141)*C(11) + RF(142) = RF(142)*C(12) + RF(143) = RF(143)*C(12) + RF(144) = RF(144)*C(17) + RF(145) = RF(145)*C(9)*C(4) + RF(146) = RF(146)*C(9)*C(4) + RF(147) = RF(147)*C(9)*C(8) + RF(148) = RF(148)*C(9)*C(9) + RF(149) = RF(149)*C(9)*C(9) + RF(150) = RF(150)*C(9) + RF(151) = RF(151)*C(9)*C(13) + RF(152) = RF(152)*C(9)*C(14) + RF(153) = RF(153)*C(9)*C(14) + RF(154) = RF(154)*C(9)*C(16) + RF(155) = RF(155)*C(9)*C(17) + RF(156) = RF(156)*C(6) + RF(157) = RF(157)*CTB(157) + RF(158) = RF(158)*C(4) + RF(159) = RF(159)*C(4) + RF(160) = RF(160)*C(4) + RF(161) = RF(161)*C(4) + RF(162) = RF(162)*C(16) + RF(163) = RF(163)*C(4) + RF(164) = RF(164)*C(4) + RF(166) = RF(166)*C(3)*C(9) + RF(167) = RF(167)*C(3)*C(16) + RF(168) = RF(168)*C(5)*C(7) + RF(169) = RF(169)*C(5)*C(9) + RF(170) = RF(170)*C(1) + RF(171) = RF(171)*C(4) + RF(172) = RF(172)*C(4) + RF(174) = RF(174)*C(6) + RF(175) = RF(175)*C(4) + RF(176) = RF(176)*C(4) + RF(177) = RF(177)*C(2)*C(18) + RF(178) = RF(178)*C(3) + RF(179) = RF(179)*C(4) + RF(180) = RF(180)*C(4) + RF(181) = RF(181)*C(2) + RF(182) = RF(182)*C(2) + RF(183) = RF(183)*C(5) + RF(184) = RF(184)*C(5) + RB(1) = RB(1)*CTB(1)*C(4) + RB(2) = RB(2)*CTB(2)*C(5) + RB(3) = RB(3)*C(2)*C(5) + RB(4) = RB(4)*C(5)*C(4) + RB(5) = RB(5)*C(5)*C(7) + RB(6) = RB(6)*C(2)*C(11) + RB(7) = RB(7)*C(2) + RB(8) = RB(8)*C(1)*C(11) + RB(9) = RB(9)*C(2) + RB(10) = RB(10)*C(2)*C(13) + RB(11) = RB(11)*C(5)*C(9) + RB(12) = RB(12)*C(12) + RB(13) = RB(13)*C(5)*C(11) + RB(14) = RB(14)*C(2)*C(12) + RB(15) = RB(15)*C(5) + RB(16) = RB(16)*C(5)*C(13) + RB(17) = RB(17)*C(5)*C(13) + RB(18) = RB(18)*C(5) + RB(19) = RB(19)*C(5) + RB(20) = RB(20)*C(2) + RB(21) = RB(21)*C(11) + RB(22) = RB(22)*C(2)*C(18) + RB(23) = RB(23)*C(9) + RB(24) = RB(24)*C(9)*C(13) + RB(25) = RB(25)*C(5) + RB(26) = RB(26)*C(2)*C(11)*C(11) + RB(27) = RB(27)*C(5) + RB(28) = RB(28)*C(12) + RB(29) = RB(29)*C(3)*C(12) + RB(30) = RB(30)*C(7) + RB(31) = RB(31)*CTB(31)*C(7) + RB(32) = RB(32)*C(7)*C(4) + RB(33) = RB(33)*C(7)*C(6) + RB(34) = RB(34)*C(7)*C(19) + RB(35) = RB(35)*C(3)*C(5) + RB(36) = RB(36)*CTB(36)*C(1) + RB(37) = RB(37)*C(1)*C(1) + RB(38) = RB(38)*C(1)*C(6) + RB(39) = RB(39)*C(1)*C(12) + RB(40) = RB(40)*CTB(40)*C(6) + RB(41) = RB(41)*C(3)*C(6) + RB(42) = RB(42)*C(4)*C(1) + RB(43) = RB(43)*C(5)*C(5) + RB(44) = RB(44)*C(7)*C(1) + RB(45) = RB(45)*C(5)*C(6) + RB(46) = RB(46)*C(1) + RB(47) = RB(47)*C(9) + RB(48) = RB(48)*C(1) + RB(49) = RB(49)*C(10) + RB(50) = RB(50)*C(9)*C(1) + RB(51) = RB(51)*C(13) + RB(52) = RB(52)*C(1)*C(11) + RB(55) = RB(55)*C(1) + RB(56) = RB(56)*C(14) + RB(57) = RB(57)*C(1)*C(13) + RB(58) = RB(58)*C(5)*C(9) + RB(59) = RB(59)*C(6) + RB(60) = RB(60)*C(14) + RB(61) = RB(61)*C(2) + RB(62) = RB(62)*C(1)*C(13) + RB(63) = RB(63)*C(5)*C(9) + RB(64) = RB(64)*C(6) + RB(65) = RB(65)*C(1) + RB(66) = RB(66)*C(1) + RB(68) = RB(68)*C(16) + RB(69) = RB(69)*C(1)*C(15) + RB(71) = RB(71)*C(1) + RB(72) = RB(72)*C(17) + RB(73) = RB(73)*C(1)*C(16) + RB(74) = RB(74)*C(1) + RB(75) = RB(75)*C(11) + RB(76) = RB(76)*C(1) + RB(77) = RB(77)*C(9)*C(11) + RB(78) = RB(78)*C(13) + RB(79) = RB(79)*C(2)*C(6) + RB(80) = RB(80)*C(8) + RB(81) = RB(81)*C(3)*C(6) + RB(82) = RB(82)*C(4)*C(6) + RB(83) = RB(83)*C(7)*C(6) + RB(84) = RB(84)*C(7)*C(6) + RB(85) = RB(85)*C(2)*C(11) + RB(86) = RB(86)*C(2) + RB(87) = RB(87)*C(2)*C(13) + RB(88) = RB(88)*C(6) + RB(89) = RB(89)*C(2)*C(13) + RB(90) = RB(90)*C(14) + RB(91) = RB(91)*C(6) + RB(92) = RB(92)*C(6) + RB(93) = RB(93)*C(9)*C(6) + RB(94) = RB(94)*C(2)*C(12) + RB(95) = RB(95)*C(6)*C(11) + RB(96) = RB(96)*C(6) + RB(97) = RB(97)*C(6)*C(13) + RB(98) = RB(98)*C(6)*C(13) + RB(99) = RB(99)*C(6) + RB(100) = RB(100)*C(6) + RB(101) = RB(101)*C(2)*C(18) + RB(102) = RB(102)*C(9)*C(11) + RB(103) = RB(103)*C(6)*C(15) + RB(104) = RB(104)*C(6) + RB(105) = RB(105)*C(6) + RB(106) = RB(106)*C(6) + RB(107) = RB(107)*C(4)*C(8) + RB(108) = RB(108)*C(4)*C(8) + RB(109) = RB(109)*C(5)*C(13) + RB(110) = RB(110)*C(4)*C(10) + RB(111) = RB(111)*C(5) + RB(112) = RB(112)*C(5)*C(12) + RB(113) = RB(113)*C(8) + RB(114) = RB(114)*C(3)*C(11) + RB(115) = RB(115)*C(2)*C(15) + RB(116) = RB(116)*C(3) + RB(117) = RB(117)*C(2) + RB(118) = RB(118)*C(2)*C(13) + RB(119) = RB(119)*C(2)*C(15) + RB(120) = RB(120)*C(2) + RB(121) = RB(121)*C(2)*C(16) + RB(123) = RB(123)*C(11) + RB(124) = RB(124)*C(2)*C(18) + RB(125) = RB(125)*C(11)*C(15) + RB(127) = RB(127)*C(2)*C(9) + RB(128) = RB(128)*C(1)*C(15) + RB(129) = RB(129)*C(2)*C(16) + RB(130) = RB(130)*C(9)*C(9) + RB(131) = RB(131)*C(18) + RB(132) = RB(132)*C(11) + RB(133) = RB(133)*C(19) + RB(134) = RB(134)*C(2)*C(5)*C(11) + RB(135) = RB(135)*C(11)*C(6) + RB(136) = RB(136)*C(9)*C(2) + RB(137) = RB(137)*C(14) + RB(138) = RB(138)*C(6) + RB(139) = RB(139)*C(2)*C(16) + RB(140) = RB(140)*C(9)*C(9) + RB(141) = RB(141)*C(11) + RB(142) = RB(142)*C(12) + RB(143) = RB(143)*C(11)*C(13) + RB(144) = RB(144)*C(9) + RB(145) = RB(145)*C(3) + RB(146) = RB(146)*C(5)*C(13) + RB(147) = RB(147)*C(7)*C(10) + RB(148) = RB(148)*C(17) + RB(149) = RB(149)*C(2) + RB(150) = RB(150)*C(10)*C(11) + RB(151) = RB(151)*C(10) + RB(152) = RB(152)*C(10) + RB(153) = RB(153)*C(10) + RB(154) = RB(154)*C(10) + RB(155) = RB(155)*C(10) + RB(156) = RB(156)*C(2)*C(11)*C(6) + RB(157) = RB(157)*CTB(157)*C(2)*C(11) + RB(158) = RB(158)*C(7)*C(11) + RB(159) = RB(159)*C(7)*C(13) + RB(160) = RB(160)*C(7)*C(13) + RB(161) = RB(161)*C(13) + RB(162) = RB(162)*C(1)*C(15) + RB(163) = RB(163)*C(7)*C(16) + RB(164) = RB(164)*C(5)*C(11)*C(11) + RB(165) = RB(165)*C(11)*C(11)*C(15) + RB(167) = RB(167)*C(2) + RB(168) = RB(168)*C(4)*C(6) + RB(170) = RB(170)*C(9) + RB(172) = RB(172)*C(3)*C(13) + RB(175) = RB(175)*C(3) + RB(176) = RB(176)*C(7)*C(15) + RB(181) = RB(181)*C(9) + RB(182) = RB(182)*C(18)*C(1) + RB(183) = RB(183)*C(6)*C(18) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! solving QSS species concentration +! ------------------------------------------- +! +! SUBROUTINE QSSA(RF, RB, XQ) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! PARAMETER (SMALL = 1.D-200) +! DIMENSION RF(*), RB(*), XQ(*) +! + RF(119) = 0.D0 + RF(125) = 0.D0 + RF(128) = 0.D0 + RF(132) = 0.D0 + RF(165) = 0.D0 + RF(173) = 0.D0 + RB(180) = 0.D0 + RB(184) = 0.D0 + +! C + DEN = +RF( 85) +RF(114) +RF(115) +RB( 46) + A1_0 = ( +RB( 85) +RB(114) +RB(115) )/MAX(DEN, SMALL) + A1_2 = ( +RF( 46) )/MAX(DEN, SMALL) +! CH + DEN = +RF( 6) +RF( 46) +RF( 86) +RF(116) +RF(117) & + +RF(118) +RF(120) +RF(121) +RF(122) +RF(123) +RF(124) & + +RF(170) +RB( 48) +RB( 88) + A2_0 = ( +RB( 6) +RB(118) +RB(119) +RB(121) +RB(124) & + +RB(125) +RB(170) )/MAX(DEN, SMALL) + A2_1 = ( +RB( 46) )/MAX(DEN, SMALL) + A2_3 = ( +RF( 88) +RB(117) )/MAX(DEN, SMALL) + A2_4 = ( +RF( 48) )/MAX(DEN, SMALL) + A2_5 = ( +RB( 86) +RB(116) +RB(123) )/MAX(DEN, SMALL) + A2_8 = ( +RB(120) )/MAX(DEN, SMALL) + + A2_10 = ( +RB(122) )/MAX(DEN, SMALL) +! CH2 + DEN = +RF( 7) +RF( 47) +RF( 87) +RF( 88) +RF(109) & + +RF(126) +RF(127) +RF(129) +RF(130) +RF(131) +RF(171) & + +RF(172) +RB( 21) +RB( 28) +RB( 91) +RB(117) +RB(133) & + +RB(138) +RB(141) +RB(142) +RB(178) + A3_0 = ( +RF( 21) +RF( 28) +RB( 47) +RB( 87) +RF( 91) & + +RB(109) +RB(119) +RB(126) +RB(127) +RB(128) +RB(128) & + +RB(129) +RB(130) +RB(131) +RB(171) +RB(172) +RB(173) & + +RB(173) )/MAX(DEN, SMALL) + A3_2 = ( +RB( 88) +RF(117) )/MAX(DEN, SMALL) + A3_4 = ( +RF(133) +RF(138) +RF(141) +RF(142) )/MAX(DEN, SMALL) + A3_5 = ( +RB( 7) )/MAX(DEN, SMALL) + A3_8 = ( +RB(132) )/MAX(DEN, SMALL) + A3_11 = ( +RF(178) )/MAX(DEN, SMALL) +! CH2(S) + DEN = +RF( 8) +RF( 9) +RF( 48) +RF( 89) +RF(133) & + +RF(134) +RF(135) +RF(136) +RF(137) +RF(138) +RF(139) & + +RF(140) +RF(141) +RF(142) +RF(143) +RF(144) +RF(174) & + +RB( 59) +RB( 64) +RB( 75) +RB( 92) + A4_0 = ( +RB( 8) +RB( 89) +RF( 92) +RB(134) +RB(135) & + +RB(136) +RB(137) +RB(139) +RB(140) +RB(143) +RB(174) )& + /MAX(DEN, SMALL) + A4_2 = ( +RB( 48) )/MAX(DEN, SMALL) + A4_3 = ( +RB(133) +RB(138) +RB(141) +RB(142) )/MAX(DEN, SMALL) + A4_5 = ( +RB( 9) )/MAX(DEN, SMALL) + A4_6 = ( +RF( 59) )/MAX(DEN, SMALL) + A4_7 = ( +RF( 64) )/MAX(DEN, SMALL) + A4_9 = ( +RB(144) )/MAX(DEN, SMALL) + A4_10 = ( +RF( 75) )/MAX(DEN, SMALL) +! HCO + DEN = +RF( 13) +RF( 14) +RF( 51) +RF( 52) +RF( 95) & + +RF(150) +RF(156) +RF(157) +RF(158) +RB( 7) +RB( 9) & + +RB( 15) +RB( 23) +RB( 30) +RB( 55) +RB( 86) +RB( 96) & + +RB(113) +RB(116) +RB(123) +RB(151) +RB(161) +RB(181) + A5_0 = ( +RB( 13) +RB( 14) +RF( 15) +RF( 23) +RF( 30) & + +RB( 51) +RB( 52) +RF( 55) +RB( 95) +RF( 96) +RF(113) & + +RB(150) +RF(151) +RB(156) +RB(157) +RB(158) )/MAX(DEN, SMALL) + A5_2 = ( +RF( 86) +RF(116) +RF(123) )/MAX(DEN, SMALL) + A5_3 = ( +RF( 7) )/MAX(DEN, SMALL) + A5_4 = ( +RF( 9) )/MAX(DEN, SMALL) + A5_8 = ( +RF(161) )/MAX(DEN, SMALL) + A5_11 = ( +RF(180) +RF(180) +RF(181) +RF(184) )/MAX(DEN, SMALL) +! CH2OH + DEN = +RF( 16) +RF( 56) +RF( 57) +RF( 58) +RF( 59) & + +RF( 97) +RF(159) +RB( 18) +RB( 53) +RB( 61) +RB( 65) & + +RB( 99) +RB(152) + A6_0 = ( +RB( 16) +RF( 18) +RF( 53) +RB( 56) +RB( 57) & + +RB( 58) +RF( 65) +RB( 97) +RF( 99) +RF(152) +RB(159) )& + /MAX(DEN, SMALL) + A6_4 = ( +RB( 59) )/MAX(DEN, SMALL) + A6_7 = ( +RF( 61) )/MAX(DEN, SMALL) + A6_11 = ( +RF(184) )/MAX(DEN, SMALL) +! CH3O + DEN = +RF( 17) +RF( 60) +RF( 61) +RF( 62) +RF( 63) & + +RF( 64) +RF( 98) +RF(160) +RB( 19) +RB( 54) +RB( 66) & + +RB(100) +RB(111) +RB(145) +RB(153) + A7_0 = ( +RB( 17) +RF( 19) +RF( 54) +RB( 60) +RB( 62) & + +RB( 63) +RF( 66) +RB( 98) +RF(100) +RF(111) +RF(145) & + +RF(153) +RB(160) )/MAX(DEN, SMALL) + A7_4 = ( +RB( 64) )/MAX(DEN, SMALL) + A7_6 = ( +RB( 61) )/MAX(DEN, SMALL) +! C2H3 + DEN = +RF( 22) +RF( 68) +RF( 69) +RF(103) +RF(161) & + +RF(175) +RF(176) +RB( 67) +RB( 71) +RB(104) +RB(120) & + +RB(132) +RB(154) + A8_0 = ( +RB( 22) +RF( 67) +RB( 68) +RB( 69) +RF( 71) & + +RB(103) +RF(104) +RF(154) +RB(176) )/MAX(DEN, SMALL) + A8_2 = ( +RF(120) )/MAX(DEN, SMALL) + A8_5 = ( +RB(161) )/MAX(DEN, SMALL) + A8_11 = ( +RB(175) )/MAX(DEN, SMALL) +! C2H5 + DEN = +RF( 24) +RF( 72) +RF( 73) +RF(163) +RB( 25) & + +RB( 70) +RB( 74) +RB(105) +RB(144) +RB(149) +RB(155) + A9_0 = ( +RB( 24) +RF( 25) +RF( 70) +RB( 72) +RB( 73) & + +RF( 74) +RF(105) +RF(149) +RF(155) +RB(163) )/MAX(DEN, SMALL) + A9_4 = ( +RF(144) )/MAX(DEN, SMALL) +! HCCO + DEN = +RF( 26) +RF( 75) +RF(164) +RB( 20) +RB( 27) & + +RB( 76) +RB(106) +RB(122) + A10_0 = ( +RF( 20) +RB( 26) +RF( 27) +RF( 76) +RF(106) & + +RB(125) +RB(164) +RB(165) +RB(165) )/MAX(DEN, SMALL) + A10_2 = ( +RF(122) )/MAX(DEN, SMALL) + A10_4 = ( +RB( 75) )/MAX(DEN, SMALL) + A10_8 = ( +RB(132) )/MAX(DEN, SMALL) +! CH2CHO + DEN = +RF(178) +RF(179) +RF(180) +RF(181) +RF(182) & + +RF(183) +RF(184) +RB(167) +RB(175) +RB(177) + A11_0 = ( +RF(167) +RF(177) +RB(179) +RB(182) +RB(183) )& + /MAX(DEN, SMALL) + A11_5 = ( +RB(181) )/MAX(DEN, SMALL) + A11_8 = ( +RF(175) )/MAX(DEN, SMALL) +! + A2_0 = A2_0 + A2_1*A1_0 + DEN = 1 -A2_1*A1_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A2_10 = A2_10/MAX(DEN, SMALL) + A2_8 = A2_8/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_9*A9_0 + DEN = 1 -A4_9*A9_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A4_10 = A4_10/MAX(DEN, SMALL) + A4_7 = A4_7/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_11*A11_0 + A5_8 = A5_8 + A5_11*A11_8 + DEN = 1 -A5_11*A11_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A5_3 = A5_3/MAX(DEN, SMALL) + A5_8 = A5_8/MAX(DEN, SMALL) + A3_0 = A3_0 + A3_11*A11_0 + A3_5 = A3_5 + A3_11*A11_5 + A3_8 = A3_8 + A3_11*A11_8 + A6_0 = A6_0 + A6_11*A11_0 + A6_5 = A6_11*A11_5 + A6_8 = A6_11*A11_8 + A8_0 = A8_0 + A8_11*A11_0 + A8_5 = A8_5 + A8_11*A11_5 + DEN = 1 -A8_11*A11_8 + A8_0 = A8_0/MAX(DEN, SMALL) + A8_2 = A8_2/MAX(DEN, SMALL) + A8_5 = A8_5/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_8*A8_0 + A2_5 = A2_5 + A2_8*A8_5 + DEN = 1 -A2_8*A8_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A2_10 = A2_10/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_8*A8_0 + A5_2 = A5_2 + A5_8*A8_2 + DEN = 1 -A5_8*A8_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A5_3 = A5_3/MAX(DEN, SMALL) + A3_0 = A3_0 + A3_8*A8_0 + A3_2 = A3_2 + A3_8*A8_2 + A3_5 = A3_5 + A3_8*A8_5 + A6_0 = A6_0 + A6_8*A8_0 + A6_2 = A6_8*A8_2 + A6_5 = A6_5 + A6_8*A8_5 + A10_0 = A10_0 + A10_8*A8_0 + A10_2 = A10_2 + A10_8*A8_2 + A10_5 = A10_8*A8_5 + A4_0 = A4_0 + A4_7*A7_0 + A4_6 = A4_6 + A4_7*A7_6 + DEN = 1 -A4_7*A7_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A4_10 = A4_10/MAX(DEN, SMALL) + A6_0 = A6_0 + A6_7*A7_0 + A6_4 = A6_4 + A6_7*A7_4 + DEN = 1 -A6_7*A7_6 + A6_0 = A6_0/MAX(DEN, SMALL) + A6_4 = A6_4/MAX(DEN, SMALL) + A6_2 = A6_2/MAX(DEN, SMALL) + A6_5 = A6_5/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_10*A10_0 + A4_2 = A4_2 + A4_10*A10_2 + A4_5 = A4_5 + A4_10*A10_5 + DEN = 1 -A4_10*A10_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_10*A10_0 + A2_4 = A2_4 + A2_10*A10_4 + A2_5 = A2_5 + A2_10*A10_5 + DEN = 1 -A2_10*A10_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_6*A6_0 + A4_2 = A4_2 + A4_6*A6_2 + A4_5 = A4_5 + A4_6*A6_5 + DEN = 1 -A4_6*A6_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_3*A3_0 + A4_2 = A4_2 + A4_3*A3_2 + A4_5 = A4_5 + A4_3*A3_5 + DEN = 1 -A4_3*A3_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_3*A3_0 + A2_4 = A2_4 + A2_3*A3_4 + A2_5 = A2_5 + A2_3*A3_5 + DEN = 1 -A2_3*A3_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_3*A3_0 + A5_4 = A5_4 + A5_3*A3_4 + A5_2 = A5_2 + A5_3*A3_2 + DEN = 1 -A5_3*A3_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_5*A5_0 + A4_2 = A4_2 + A4_5*A5_2 + DEN = 1 -A4_5*A5_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_5*A5_0 + A2_4 = A2_4 + A2_5*A5_4 + DEN = 1 -A2_5*A5_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_2*A2_0 + DEN = 1 -A4_2*A2_4 + A4_0 = A4_0/MAX(DEN, SMALL) + XQ(4) = A4_0 + XQ(2) = A2_0 +A2_4*XQ(4) + XQ(5) = A5_0 +A5_4*XQ(4) +A5_2*XQ(2) + XQ(3) = A3_0 +A3_4*XQ(4) +A3_2*XQ(2) +A3_5*XQ(5) + XQ(6) = A6_0 +A6_4*XQ(4) +A6_2*XQ(2) +A6_5*XQ(5) + XQ(10) = A10_0 +A10_4*XQ(4) +A10_2*XQ(2) +A10_5*XQ(5) + XQ(7) = A7_0 +A7_4*XQ(4) +A7_6*XQ(6) + XQ(8) = A8_0 +A8_2*XQ(2) +A8_5*XQ(5) + XQ(11) = A11_0 +A11_5*XQ(5) +A11_8*XQ(8) + XQ(9) = A9_0 +A9_4*XQ(4) + XQ(1) = A1_0 +A1_2*XQ(2) +! +! +! --------------------------------------------- +! +! update rates of reactions involving QSS species +! + RF( 6) = RF( 6)*XQ( 2) + RF( 7) = RF( 7)*XQ( 3) + RB( 7) = RB( 7)*XQ( 5) + RF( 8) = RF( 8)*XQ( 4) + RF( 9) = RF( 9)*XQ( 4) + RB( 9) = RB( 9)*XQ( 5) + RF( 13) = RF( 13)*XQ( 5) + RF( 14) = RF( 14)*XQ( 5) + RB( 15) = RB( 15)*XQ( 5) + RF( 16) = RF( 16)*XQ( 6) + RF( 17) = RF( 17)*XQ( 7) + RB( 18) = RB( 18)*XQ( 6) + RB( 19) = RB( 19)*XQ( 7) + RB( 20) = RB( 20)*XQ(10) + RB( 21) = RB( 21)*XQ( 3) + RF( 22) = RF( 22)*XQ( 8) + RB( 23) = RB( 23)*XQ( 5) + RF( 24) = RF( 24)*XQ( 9) + RB( 25) = RB( 25)*XQ( 9) + RF( 26) = RF( 26)*XQ(10) + RB( 27) = RB( 27)*XQ(10) + RB( 28) = RB( 28)*XQ( 3) + RB( 30) = RB( 30)*XQ( 5) + RF( 46) = RF( 46)*XQ( 2) + RB( 46) = RB( 46)*XQ( 1) + RF( 47) = RF( 47)*XQ( 3) + RF( 48) = RF( 48)*XQ( 4) + RB( 48) = RB( 48)*XQ( 2) + RF( 51) = RF( 51)*XQ( 5) + RF( 52) = RF( 52)*XQ( 5) + RB( 53) = RB( 53)*XQ( 6) + RB( 54) = RB( 54)*XQ( 7) + RB( 55) = RB( 55)*XQ( 5) + RF( 56) = RF( 56)*XQ( 6) + RF( 57) = RF( 57)*XQ( 6) + RF( 58) = RF( 58)*XQ( 6) + RF( 59) = RF( 59)*XQ( 6) + RB( 59) = RB( 59)*XQ( 4) + RF( 60) = RF( 60)*XQ( 7) + RF( 61) = RF( 61)*XQ( 7) + RB( 61) = RB( 61)*XQ( 6) + RF( 62) = RF( 62)*XQ( 7) + RF( 63) = RF( 63)*XQ( 7) + RF( 64) = RF( 64)*XQ( 7) + RB( 64) = RB( 64)*XQ( 4) + RB( 65) = RB( 65)*XQ( 6) + RB( 66) = RB( 66)*XQ( 7) + RB( 67) = RB( 67)*XQ( 8) + RF( 68) = RF( 68)*XQ( 8) + RF( 69) = RF( 69)*XQ( 8) + RB( 70) = RB( 70)*XQ( 9) + RB( 71) = RB( 71)*XQ( 8) + RF( 72) = RF( 72)*XQ( 9) + RF( 73) = RF( 73)*XQ( 9) + RB( 74) = RB( 74)*XQ( 9) + RF( 75) = RF( 75)*XQ(10) + RB( 75) = RB( 75)*XQ( 4) + RB( 76) = RB( 76)*XQ(10) + RF( 85) = RF( 85)*XQ( 1) + RF( 86) = RF( 86)*XQ( 2) + RB( 86) = RB( 86)*XQ( 5) + RF( 87) = RF( 87)*XQ( 3) + RF( 88) = RF( 88)*XQ( 3) + RB( 88) = RB( 88)*XQ( 2) + RF( 89) = RF( 89)*XQ( 4) + RB( 91) = RB( 91)*XQ( 3) + RB( 92) = RB( 92)*XQ( 4) + RF( 95) = RF( 95)*XQ( 5) + RB( 96) = RB( 96)*XQ( 5) + RF( 97) = RF( 97)*XQ( 6) + RF( 98) = RF( 98)*XQ( 7) + RB( 99) = RB( 99)*XQ( 6) + RB(100) = RB(100)*XQ( 7) + RF(103) = RF(103)*XQ( 8) + RB(104) = RB(104)*XQ( 8) + RB(105) = RB(105)*XQ( 9) + RB(106) = RB(106)*XQ(10) + RF(109) = RF(109)*XQ( 3) + RB(111) = RB(111)*XQ( 7) + RB(113) = RB(113)*XQ( 5) + RF(114) = RF(114)*XQ( 1) + RF(115) = RF(115)*XQ( 1) + RF(116) = RF(116)*XQ( 2) + RB(116) = RB(116)*XQ( 5) + RF(117) = RF(117)*XQ( 2) + RB(117) = RB(117)*XQ( 3) + RF(118) = RF(118)*XQ( 2) + RF(120) = RF(120)*XQ( 2) + RB(120) = RB(120)*XQ( 8) + RF(121) = RF(121)*XQ( 2) + RF(122) = RF(122)*XQ( 2) + RB(122) = RB(122)*XQ(10) + RF(123) = RF(123)*XQ( 2) + RB(123) = RB(123)*XQ( 5) + RF(124) = RF(124)*XQ( 2) + RF(126) = RF(126)*XQ( 3) + RF(127) = RF(127)*XQ( 3) + RF(129) = RF(129)*XQ( 3) + RF(130) = RF(130)*XQ( 3) + RF(131) = RF(131)*XQ( 3) + RB(132) = RB(132)*XQ( 8) + RF(133) = RF(133)*XQ( 4) + RB(133) = RB(133)*XQ( 3) + RF(134) = RF(134)*XQ( 4) + RF(135) = RF(135)*XQ( 4) + RF(136) = RF(136)*XQ( 4) + RF(137) = RF(137)*XQ( 4) + RF(138) = RF(138)*XQ( 4) + RB(138) = RB(138)*XQ( 3) + RF(139) = RF(139)*XQ( 4) + RF(140) = RF(140)*XQ( 4) + RF(141) = RF(141)*XQ( 4) + RB(141) = RB(141)*XQ( 3) + RF(142) = RF(142)*XQ( 4) + RB(142) = RB(142)*XQ( 3) + RF(143) = RF(143)*XQ( 4) + RF(144) = RF(144)*XQ( 4) + RB(144) = RB(144)*XQ( 9) + RB(145) = RB(145)*XQ( 7) + RB(149) = RB(149)*XQ( 9) + RF(150) = RF(150)*XQ( 5) + RB(151) = RB(151)*XQ( 5) + RB(152) = RB(152)*XQ( 6) + RB(153) = RB(153)*XQ( 7) + RB(154) = RB(154)*XQ( 8) + RB(155) = RB(155)*XQ( 9) + RF(156) = RF(156)*XQ( 5) + RF(157) = RF(157)*XQ( 5) + RF(158) = RF(158)*XQ( 5) + RF(159) = RF(159)*XQ( 6) + RF(160) = RF(160)*XQ( 7) + RF(161) = RF(161)*XQ( 8) + RB(161) = RB(161)*XQ( 5) + RF(163) = RF(163)*XQ( 9) + RF(164) = RF(164)*XQ(10) + RB(167) = RB(167)*XQ(11) + RF(170) = RF(170)*XQ( 2) + RF(171) = RF(171)*XQ( 3) + RF(172) = RF(172)*XQ( 3) + RF(174) = RF(174)*XQ( 4) + RF(175) = RF(175)*XQ( 8) + RB(175) = RB(175)*XQ(11) + RF(176) = RF(176)*XQ( 8) + RB(177) = RB(177)*XQ(11) + RF(178) = RF(178)*XQ(11) + RB(178) = RB(178)*XQ( 3) + RF(179) = RF(179)*XQ(11) + RF(180) = RF(180)*XQ(11) + RF(181) = RF(181)*XQ(11) + RB(181) = RB(181)*XQ( 5) + RF(182) = RF(182)*XQ(11) + RF(183) = RF(183)*XQ(11) + RF(184) = RF(184)*XQ(11) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! ! ompute WDOT +! +! SUBROUTINE RDOT(RF, RB, WDOT) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION RF(*), RB(*), WDOT(*), ROP(184) +! + DO I = 1, 184 + ROP(I) = RF(I) - RB(I) + ENDDO +! +! H2 + WDOT( 1) = -ROP( 3) +ROP( 8) +ROP( 36) +ROP( 37) & + +ROP( 38) +ROP( 39) +ROP( 42) +ROP( 44) & + +ROP( 46) +ROP( 48) +ROP( 50) +ROP( 52) & + +ROP( 55) +ROP( 57) +ROP( 62) +ROP( 65) & + +ROP( 66) +ROP( 69) +ROP( 71) +ROP( 73) & + +ROP( 74) +ROP( 76) -ROP( 78) -ROP( 79) & + -ROP(117) -ROP(127) +ROP(128) -ROP(136) & + +ROP(162) +ROP(166) +ROP(169) -ROP(170) & + +ROP(174) +ROP(182) +! H + WDOT( 2) = -ROP( 2) +ROP( 3) +ROP( 6) -ROP( 7) & + -2*ROP( 8) -ROP( 9) +ROP( 10) +ROP( 14) & + -ROP( 17) +ROP( 19) +ROP( 20) +2*ROP( 21) & + -ROP( 24) +ROP( 25) +ROP( 26) +2*ROP( 28) & + -ROP( 31) -ROP( 32) -ROP( 33) -ROP( 34) & + -ROP( 35) -2*ROP( 36) -2*ROP( 37) -2*ROP( 38) & + -2*ROP( 39) -ROP( 40) -ROP( 41) -ROP( 42) & + -ROP( 43) -ROP( 44) -ROP( 45) -ROP( 46) & + -3*ROP( 47) -3*ROP( 48) -ROP( 49) -ROP( 50) & + -ROP( 51) -ROP( 52) -ROP( 53) -ROP( 55) & + -ROP( 56) -ROP( 57) -ROP( 58) +ROP( 59) & + -2*ROP( 60) -ROP( 61) -2*ROP( 62) -2*ROP( 63) & + -ROP( 65) -2*ROP( 68) -2*ROP( 69) -2*ROP( 72) & + -2*ROP( 73) +ROP( 75) -ROP( 76) -ROP( 77) & + +ROP( 79) +ROP( 85) +ROP( 86) -ROP( 87) & + -2*ROP( 88) -ROP( 89) +2*ROP( 91) +2*ROP( 92) & + +ROP( 94) -ROP( 98) +ROP(100) +ROP(101) & + -ROP(103) +ROP(104) +ROP(105) -2*ROP(109) & + +ROP(111) +ROP(115) +3*ROP(117) +ROP(118) & + -ROP(119) +2*ROP(120) +ROP(121) +ROP(124) & + -ROP(126) -ROP(127) -4*ROP(128) -ROP(129) & + -2*ROP(130) -2*ROP(131) -ROP(132) -ROP(134) & + -2*ROP(135) -ROP(136) -2*ROP(137) -ROP(139) & + -2*ROP(140) -2*ROP(143) -ROP(144) +ROP(145) & + +2*ROP(149) +ROP(153) +ROP(154) +ROP(155) & + +ROP(156) +ROP(157) -ROP(160) -ROP(161) & + -ROP(163) +ROP(166) +2*ROP(167) -2*ROP(172) & + -2*ROP(173) -2*ROP(174) -ROP(176) +2*ROP(178) & + -ROP(179) -ROP(180) -2*ROP(181) -2*ROP(182) & + -ROP(183) -ROP(184) +! O + WDOT( 3) = -2*ROP( 1) -ROP( 2) -ROP( 3) -ROP( 4) & + -ROP( 5) -2*ROP( 6) -ROP( 7) -ROP( 8) & + -ROP( 9) -ROP( 10) -ROP( 11) -ROP( 12) & + -ROP( 13) -ROP( 14) -ROP( 15) -ROP( 16) & + -ROP( 17) -ROP( 18) -ROP( 19) -ROP( 20) & + -ROP( 21) -2*ROP( 22) -ROP( 23) -ROP( 24) & + -ROP( 25) -ROP( 26) -ROP( 27) -ROP( 28) & + +ROP( 29) +ROP( 35) +ROP( 41) +ROP( 48) & + +ROP( 67) -ROP( 68) -ROP( 69) +ROP( 71) & + +ROP( 81) -ROP( 85) -ROP( 86) +ROP( 88) & + -ROP(103) +ROP(104) -ROP(115) -ROP(117) & + -ROP(118) -ROP(119) -ROP(121) -ROP(122) & + -ROP(123) -ROP(124) -ROP(125) +ROP(132) & + +ROP(145) +ROP(154) -ROP(161) -ROP(166) & + -ROP(167) -ROP(170) +ROP(172) -ROP(176) & + -ROP(178) +! O2 + WDOT( 4) = +ROP( 1) +ROP( 4) +2*ROP( 6) +ROP( 8) & + +ROP( 13) +ROP( 14) -ROP( 15) +ROP( 16) & + -ROP( 18) -ROP( 20) -ROP( 21) +ROP( 22) & + -ROP( 23) +ROP( 26) -ROP( 27) -ROP( 28) & + -ROP( 29) -2*ROP( 30) -ROP( 31) -ROP( 32) & + -ROP( 33) -ROP( 34) -ROP( 35) +ROP( 42) & + +ROP( 46) +ROP( 47) -ROP( 48) +ROP( 51) & + +ROP( 52) -ROP( 53) -ROP( 55) +ROP( 56) & + +ROP( 57) +ROP( 58) -ROP( 61) -ROP( 64) & + -ROP( 65) -ROP( 67) +ROP( 68) +ROP( 69) & + -ROP( 71) -ROP( 76) +ROP( 82) +ROP( 85) & + +ROP( 86) +ROP( 87) -ROP( 88) +ROP( 89) & + -ROP( 91) -ROP( 92) +ROP( 95) -ROP( 96) & + +ROP( 97) -ROP( 99) +ROP(103) -ROP(104) & + -ROP(106) +ROP(107) +ROP(108) +ROP(109) & + +ROP(110) -ROP(113) +ROP(115) +ROP(117) & + +2*ROP(118) +3*ROP(119) +ROP(120) +2*ROP(121) & + +ROP(122) +ROP(123) +2*ROP(124) +3*ROP(125) & + +ROP(127) +2*ROP(128) +ROP(129) +ROP(130) & + +ROP(131) +ROP(132) +ROP(136) +ROP(137) & + +ROP(139) +ROP(140) +ROP(143) +ROP(144) & + -ROP(145) -ROP(146) +ROP(150) -ROP(151) & + -ROP(152) -ROP(154) +ROP(156) +ROP(157) & + -ROP(160) -ROP(161) -ROP(163) +2*ROP(165) & + +ROP(168) +2*ROP(170) +2*ROP(173) +ROP(174) & + -ROP(178) -ROP(179) -3*ROP(180) -ROP(181) & + -2*ROP(184) +! OH + WDOT( 5) = +ROP( 2) +ROP( 3) +ROP( 4) +ROP( 5) & + +ROP( 11) +ROP( 13) +ROP( 15) +ROP( 16) & + +ROP( 17) +ROP( 18) +ROP( 19) +ROP( 20) & + +ROP( 25) -ROP( 26) +2*ROP( 27) +ROP( 35) & + -ROP( 40) +2*ROP( 43) +ROP( 45) +ROP( 58) & + +ROP( 63) -ROP( 75) +ROP( 76) -ROP( 79) & + -2*ROP( 80) -2*ROP( 81) -ROP( 82) -ROP( 83) & + -ROP( 84) -ROP( 85) -ROP( 86) -ROP( 87) & + -ROP( 88) -ROP( 89) -ROP( 90) -ROP( 91) & + -ROP( 92) -ROP( 93) -ROP( 94) -ROP( 95) & + -ROP( 96) -ROP( 97) -ROP( 98) -ROP( 99) & + -ROP(100) -ROP(101) -ROP(102) -ROP(103) & + -ROP(104) -ROP(105) +ROP(109) +ROP(111) & + +ROP(112) +ROP(122) -ROP(125) +ROP(126) & + -ROP(132) +ROP(134) +ROP(146) -2*ROP(165) & + -ROP(168) -ROP(169) +ROP(179) +ROP(180) & + -ROP(183) -ROP(184) +! H2O + WDOT( 6) = +ROP( 40) +ROP( 41) +ROP( 45) +ROP( 59) & + +ROP( 64) +ROP( 79) +ROP( 81) +ROP( 82) & + +ROP( 83) +ROP( 84) +ROP( 88) +ROP( 91) & + +ROP( 92) +ROP( 93) +ROP( 95) +ROP( 96) & + +ROP( 97) +ROP( 98) +ROP( 99) +ROP(100) & + +ROP(103) +ROP(104) +ROP(105) +ROP(106) & + -ROP(118) +ROP(135) -ROP(137) +ROP(168) & + -ROP(174) +ROP(183) +! HO2 + WDOT( 7) = -ROP( 4) +ROP( 5) -ROP( 6) +ROP( 7) & + +ROP( 9) -ROP( 13) -ROP( 14) +ROP( 15) & + -ROP( 16) +ROP( 18) +ROP( 23) +2*ROP( 30) & + +ROP( 31) +ROP( 32) +ROP( 33) +ROP( 34) & + -ROP( 41) -ROP( 42) -ROP( 43) +ROP( 44) & + -ROP( 46) +ROP( 48) -ROP( 51) -ROP( 52) & + +ROP( 53) +ROP( 55) -ROP( 56) -ROP( 57) & + -ROP( 58) -ROP( 59) +ROP( 61) +ROP( 65) & + -ROP( 82) +ROP( 83) +ROP( 84) +ROP( 88) & + -ROP( 95) +ROP( 96) -ROP( 97) +ROP( 99) & + -2*ROP(107) -2*ROP(108) -ROP(109) -ROP(110) & + -ROP(111) -ROP(112) -ROP(117) -ROP(118) & + -ROP(119) -ROP(120) -ROP(121) -ROP(122) & + -ROP(124) -ROP(125) +ROP(147) -ROP(150) & + +ROP(151) +ROP(152) -ROP(156) -ROP(157) & + +ROP(160) +ROP(161) +ROP(163) -ROP(168) & + -ROP(170) +ROP(176) +2*ROP(180) +ROP(181) & + +2*ROP(184) +! H2O2 + WDOT( 8) = -ROP( 5) -ROP( 44) -ROP( 45) +ROP( 80) & + -ROP( 83) -ROP( 84) +ROP(107) +ROP(108) & + +ROP(113) -ROP(147) +! CH3 + WDOT( 9) = -ROP( 10) +ROP( 11) +ROP( 23) +ROP( 24) & + +ROP( 47) -ROP( 49) +ROP( 50) +ROP( 58) & + +ROP( 63) +ROP( 77) -ROP( 90) -ROP( 91) & + -ROP( 92) +ROP( 93) +ROP(102) -ROP(110) & + -ROP(111) -ROP(115) -ROP(120) +ROP(127) & + -ROP(129) +2*ROP(130) +ROP(136) -ROP(139) & + +2*ROP(140) +ROP(144) -ROP(145) -ROP(146) & + -ROP(147) -2*ROP(148) -2*ROP(149) -ROP(150) & + -ROP(151) -ROP(152) -ROP(153) -ROP(154) & + -ROP(155) -ROP(166) -ROP(169) +ROP(170) & + +ROP(181) +! CH4 + WDOT(10) = -ROP( 11) +ROP( 49) -ROP( 50) -ROP( 93) & + +ROP(110) -ROP(121) -ROP(130) -ROP(140) & + +ROP(147) +ROP(150) +ROP(151) +ROP(152) & + +ROP(153) +ROP(154) +ROP(155) +! CO + WDOT(11) = +ROP( 7) +ROP( 8) +ROP( 9) -ROP( 12) & + -ROP( 14) +ROP( 15) +2*ROP( 20) +ROP( 21) & + +ROP( 23) +2*ROP( 27) -ROP( 29) +ROP( 30) & + +ROP( 48) -ROP( 51) +ROP( 55) -ROP( 75) & + +2*ROP( 76) +ROP( 77) -ROP( 78) +ROP( 88) & + -ROP( 94) +ROP( 96) +ROP(102) +2*ROP(106) & + -ROP(112) +ROP(113) -ROP(115) -ROP(117) & + -ROP(118) -ROP(119) -ROP(120) -ROP(121) & + +ROP(123) -ROP(124) -2*ROP(125) +ROP(126) & + -ROP(131) -ROP(132) +ROP(134) +ROP(135) & + +ROP(143) +ROP(151) +ROP(161) -2*ROP(165) & + +ROP(166) -ROP(170) +ROP(179) +2*ROP(180) & + +ROP(181) +ROP(184) +! CO2 + WDOT(12) = -ROP( 7) -ROP( 8) -ROP( 9) +ROP( 12) & + +ROP( 14) +ROP( 21) +2*ROP( 28) +ROP( 29) & + -ROP( 47) -ROP( 48) +ROP( 59) +ROP( 64) & + +ROP( 75) -ROP( 87) -ROP( 88) -ROP( 89) & + +ROP( 91) +ROP( 92) +ROP( 94) -ROP(109) & + +ROP(112) +ROP(117) -ROP(119) -ROP(123) & + -ROP(126) -ROP(127) -2*ROP(128) -ROP(129) & + -ROP(130) -ROP(131) -ROP(132) -ROP(134) & + -ROP(135) -ROP(136) -ROP(137) -ROP(139) & + -ROP(140) -2*ROP(143) -ROP(144) -ROP(172) & + -2*ROP(173) -ROP(174) +2*ROP(178) +! CH2O + WDOT(13) = +ROP( 10) -ROP( 15) +ROP( 18) +ROP( 19) & + +ROP( 24) -ROP( 30) +ROP( 51) -ROP( 55) & + -ROP( 56) -ROP( 58) -ROP( 59) -ROP( 60) & + -ROP( 63) -ROP( 64) +ROP( 65) +ROP( 66) & + +ROP( 78) +ROP( 87) +ROP( 89) -ROP( 96) & + +ROP( 99) +ROP(100) +ROP(109) +ROP(111) & + -ROP(113) +ROP(118) -ROP(124) +ROP(143) & + +ROP(145) +ROP(146) -ROP(151) +ROP(152) & + +ROP(153) +ROP(161) +ROP(169) +ROP(172) & + +ROP(174) +ROP(179) +ROP(184) +! CH3OH + WDOT(14) = -ROP( 18) -ROP( 19) +ROP( 56) +ROP( 60) & + -ROP( 65) -ROP( 66) +ROP( 90) -ROP( 99) & + -ROP(100) +ROP(137) -ROP(152) -ROP(153) +! C2H2 + WDOT(15) = -ROP( 20) -ROP( 21) -ROP( 67) +ROP( 69) & + -ROP(101) -ROP(102) +ROP(103) +ROP(115) & + +ROP(119) +ROP(125) +ROP(128) +ROP(162) & + +ROP(165) +ROP(173) +ROP(176) +! C2H4 + WDOT(16) = -ROP( 23) -ROP( 24) +ROP( 25) +ROP( 68) & + -ROP( 71) -ROP( 72) +ROP( 74) -ROP(104) & + +ROP(105) +ROP(121) +ROP(129) +ROP(139) & + +ROP(144) +ROP(149) -ROP(154) +ROP(155) & + -ROP(162) -ROP(167) +! C2H6 + WDOT(17) = -ROP( 25) +ROP( 72) -ROP( 74) -ROP(105) & + -ROP(144) +ROP(148) -ROP(155) +! CH2CO + WDOT(18) = -ROP( 27) -ROP( 28) +ROP( 67) -ROP( 68) & + -ROP( 69) +ROP( 71) -ROP( 76) -ROP( 77) & + +ROP(101) -ROP(103) +ROP(104) -ROP(106) & + +ROP(120) +ROP(124) +ROP(131) +ROP(132) & + +ROP(154) -ROP(161) +ROP(167) -ROP(176) & + -ROP(178) -ROP(179) -ROP(180) -ROP(181) & + -ROP(184) +! N2 + WDOT(19) = 0.0 + + ! Correction for unit compatibility in Cantera + WDOT(1:19) = WDOT(1:19)*1D6 + + RETURN + END \ No newline at end of file diff --git a/samples/python/AVBP/inputs/Lu_ARC.yaml b/samples/python/AVBP/inputs/Lu_ARC.yaml new file mode 100644 index 00000000000..91213b6c00c --- /dev/null +++ b/samples/python/AVBP/inputs/Lu_ARC.yaml @@ -0,0 +1,2230 @@ +units: {length: cm, quantity: mol, activation-energy: cal/mol} +solution: + generator: Cantera SolutionArray + cantera-version: 3.0.0 + git-commit: "'c4e2732'" + date: Tue Dec 19 21:16:13 2023 + reactants: + size: 1 + type: inlet + points: 1 + mass-flux: 0.3218542195132330 + temperature: 300.0 + pressure: 1.0e+05 + mass-fractions: + O2: 0.2201412376866278 + CH4: 0.05518666598235154 + N2: 0.7246720963310207 + flame: + CH2O: [2.512053803898528e-13, 5.963718667192086e-13, 4.060244108455286e-12, + 5.156316656302329e-11, 3.017932821671933e-10, 2.142704546543387e-09, + 1.568562522811727e-08, 5.473619662708908e-08, 2.178288436068591e-07, + 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[grid, velocity, T, D, H2, H, O, O2, OH, H2O, HO2, H2O2, CH3, CH4, CO, + CO2, CH2O, CH3OH, C2H2, C2H4, C2H6, CH2CO, N2] + products: + type: outlet + size: 0 + points: 1 +description: | + --------------------------------------------------------------------------- + CTI File converted from Solution Object + --------------------------------------------------------------------------- +generator: cti2yaml +cantera-version: 3.0.0 +date: Tue, 19 Dec 2023 20:13:38 +0100 +input-files: [Lu_ARC.cti] +phases: + - name: gas + thermo: ideal-gas + elements: [N, O, H, C] + species: [H2, H, O, O2, OH, H2O, HO2, H2O2, CH3, CH4, CO, CO2, CH2O, CH3OH, C2H2, + C2H4, C2H6, CH2CO, N2] + kinetics: custom + reactions: all + state: + T: 300.0 + P: 1.01325e+05 +species: + - name: H2 + composition: + H: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.34433112, 7.98052075e-03, -1.9478151e-05, 2.01572094e-08, + -7.37611761e-12, -917.935173, 0.683010238] + - [3.3372792, 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4.78433864] + transport: + model: gas + geometry: atom + diameter: 2.75 + well-depth: 80.0 + note: L1/90 + - name: O2 + composition: + O: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.78245636, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09, + 3.24372837e-12, -1063.94356, 3.65767573] + - [3.28253784, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10, + -2.16717794e-14, -1088.45772, 5.45323129] + transport: + model: gas + geometry: linear + diameter: 3.458 + well-depth: 107.4 + polarizability: 1.6 + rotational-relaxation: 3.8 + note: TPIS89 + - name: OH + composition: + H: 1 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.99201543, -2.40131752e-03, 4.61793841e-06, -3.88113333e-09, + 1.3641147e-12, 3615.08056, -0.103925458] + - [3.09288767, 5.48429716e-04, 1.26505228e-07, -8.79461556e-11, + 1.17412376e-14, 3858.657, 4.4766961] + transport: + model: gas + geometry: linear + diameter: 2.75 + well-depth: 80.0 + note: RUS78 + - name: H2O + composition: + H: 2 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19864056, -2.0364341e-03, 6.52040211e-06, -5.48797062e-09, + 1.77197817e-12, -3.02937267e+04, -0.849032208] + - [3.03399249, 2.17691804e-03, -1.64072518e-07, -9.7041987e-11, + 1.68200992e-14, -3.00042971e+04, 4.9667701] + transport: + model: gas + geometry: nonlinear + diameter: 2.605 + well-depth: 572.4 + dipole: 1.844 + rotational-relaxation: 4.0 + note: L8/89 + - name: HO2 + composition: + H: 1 + O: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30179801, -4.74912051e-03, 2.11582891e-05, -2.42763894e-08, + 9.29225124e-12, 294.80804, 3.71666245] + - [4.0172109, 2.23982013e-03, -6.3365815e-07, 1.1424637e-10, + -1.07908535e-14, 111.856713, 3.78510215] + transport: + model: gas + geometry: nonlinear + diameter: 3.458 + well-depth: 107.4 + rotational-relaxation: 1.0 + note: L5/89 + - name: H2O2 + composition: + H: 2 + O: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.27611269, -5.42822417e-04, 1.67335701e-05, -2.15770813e-08, + 8.62454363e-12, -1.77025821e+04, 3.43505074] + - [4.16500285, 4.90831694e-03, -1.90139225e-06, 3.71185986e-10, + -2.87908305e-14, -1.78617877e+04, 2.91615662] + transport: + model: gas + geometry: nonlinear + diameter: 3.458 + well-depth: 107.4 + rotational-relaxation: 3.8 + note: L7/88 + - name: C + composition: + C: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.55423955, -3.21537724e-04, 7.33792245e-07, -7.32234889e-10, + 2.66521446e-13, 8.54438832e+04, 4.53130848] + - [2.49266888, 4.79889284e-05, -7.2433502e-08, 3.74291029e-11, + -4.87277893e-15, 8.54512953e+04, 4.80150373] + transport: + model: gas + geometry: atom + diameter: 3.298 + well-depth: 71.4 + note: L11/88 + - name: CH + composition: + H: 1 + C: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.48981665, 3.23835541e-04, -1.68899065e-06, 3.16217327e-09, + -1.40609067e-12, 7.07972934e+04, 2.08401108] + - [2.87846473, 9.70913681e-04, 1.44445655e-07, -1.30687849e-10, + 1.76079383e-14, 7.10124364e+04, 5.48497999] + transport: + model: gas + geometry: linear + diameter: 2.75 + well-depth: 80.0 + note: TPIS79 + - name: CH2 + composition: + H: 2 + C: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.76267867, 9.68872143e-04, 2.79489841e-06, -3.85091153e-09, + 1.68741719e-12, 4.60040401e+04, 1.56253185] + - [2.87410113, 3.65639292e-03, -1.40894597e-06, 2.60179549e-10, + -1.87727567e-14, 4.6263604e+04, 6.17119324] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 + - name: CH2(S) + composition: + H: 2 + C: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19860411, -2.36661419e-03, 8.2329622e-06, -6.68815981e-09, + 1.94314737e-12, 5.04968163e+04, -0.769118967] + - [2.29203842, 4.65588637e-03, -2.01191947e-06, 4.17906e-10, + -3.39716365e-14, 5.09259997e+04, 8.62650169] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 + - name: CH3 + composition: + H: 3 + C: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.6735904, 2.01095175e-03, 5.73021856e-06, -6.87117425e-09, + 2.54385734e-12, 1.64449988e+04, 1.60456433] + - [2.28571772, 7.23990037e-03, -2.98714348e-06, 5.95684644e-10, + -4.67154394e-14, 1.67755843e+04, 8.48007179] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: L11/89 + - name: CH4 + composition: + H: 4 + C: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.14987613, -0.0136709788, 4.91800599e-05, -4.84743026e-08, + 1.66693956e-11, -1.02466476e+04, -4.64130376] + - [0.074851495, 0.0133909467, -5.73285809e-06, 1.22292535e-09, + -1.0181523e-13, -9468.34459, 18.437318] + transport: + model: gas + geometry: nonlinear + diameter: 3.746 + well-depth: 141.4 + polarizability: 2.6 + rotational-relaxation: 13.0 + note: L8/88 + - name: CO + composition: + C: 1 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.57953347, -6.1035368e-04, 1.01681433e-06, 9.07005884e-10, + -9.04424499e-13, -1.4344086e+04, 3.50840928] + - [2.71518561, 2.06252743e-03, -9.98825771e-07, 2.30053008e-10, + -2.03647716e-14, -1.41518724e+04, 7.81868772] + transport: + model: gas + geometry: linear + diameter: 3.65 + well-depth: 98.1 + polarizability: 1.95 + rotational-relaxation: 1.8 + note: TPIS79 + - name: CO2 + composition: + C: 1 + O: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.35677352, 8.98459677e-03, -7.12356269e-06, 2.45919022e-09, + -1.43699548e-13, -4.83719697e+04, 9.90105222] + - [3.85746029, 4.41437026e-03, -2.21481404e-06, 5.23490188e-10, + -4.72084164e-14, -4.8759166e+04, 2.27163806] + transport: + model: gas + geometry: linear + diameter: 3.763 + well-depth: 244.0 + polarizability: 2.65 + rotational-relaxation: 2.1 + note: L7/88 + - name: HCO + composition: + H: 1 + C: 1 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.22118584, -3.24392532e-03, 1.37799446e-05, -1.33144093e-08, + 4.33768865e-12, 3839.56496, 3.39437243] + - [2.77217438, 4.95695526e-03, -2.48445613e-06, 5.89161778e-10, + -5.33508711e-14, 4011.91815, 9.79834492] + transport: + model: gas + geometry: nonlinear + diameter: 3.59 + well-depth: 498.0 + note: L12/89 + - name: CH2O + composition: + H: 2 + C: 1 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.79372315, -9.90833369e-03, 3.73220008e-05, -3.79285261e-08, + 1.31772652e-11, -1.43089567e+04, 0.6028129] + - [1.76069008, 9.20000082e-03, -4.42258813e-06, 1.00641212e-09, + -8.8385564e-14, -1.39958323e+04, 13.656323] + transport: + model: gas + geometry: nonlinear + diameter: 3.59 + well-depth: 498.0 + rotational-relaxation: 2.0 + note: L8/88 + - name: CH2OH + composition: + H: 3 + C: 1 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.86388918, 5.59672304e-03, 5.93271791e-06, -1.04532012e-08, + 4.36967278e-12, -3193.91367, 5.47302243] + - [3.69266569, 8.64576797e-03, -3.7510112e-06, 7.87234636e-10, + -6.48554201e-14, -3242.50627, 5.81043215] + transport: + model: gas + geometry: nonlinear + diameter: 3.69 + well-depth: 417.0 + dipole: 1.7 + rotational-relaxation: 2.0 + note: GUNL93 + - name: CH3O + composition: + H: 3 + C: 1 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [2.106204, 7.216595e-03, 5.338472e-06, -7.377636e-09, 2.07561e-12, + 978.6011, 13.152177] + - [3.770799, 7.871497e-03, -2.656384e-06, 3.944431e-10, -2.112616e-14, + 127.83252, 2.929575] + transport: + model: gas + geometry: nonlinear + diameter: 3.69 + well-depth: 417.0 + dipole: 1.7 + rotational-relaxation: 2.0 + note: 121686 + - name: CH3OH + composition: + H: 4 + C: 1 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.71539582, -0.0152309129, 6.52441155e-05, -7.10806889e-08, + 2.61352698e-11, -2.56427656e+04, -1.50409823] + - [1.78970791, 0.0140938292, -6.36500835e-06, 1.38171085e-09, + -1.1706022e-13, -2.53748747e+04, 14.5023623] + transport: + model: gas + geometry: nonlinear + diameter: 3.626 + well-depth: 481.8 + rotational-relaxation: 1.0 + note: L8/88 + - name: C2H2 + composition: + H: 2 + C: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [0.808681094, 0.0233615629, -3.55171815e-05, 2.80152437e-08, + -8.50072974e-12, 2.64289807e+04, 13.9397051] + - [4.14756964, 5.96166664e-03, -2.37294852e-06, 4.67412171e-10, + -3.61235213e-14, 2.59359992e+04, -1.23028121] + transport: + model: gas + geometry: linear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 2.5 + note: L1/91 + - name: C2H3 + composition: + H: 3 + C: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.21246645, 1.51479162e-03, 2.59209412e-05, -3.57657847e-08, + 1.47150873e-11, 3.48598468e+04, 8.51054025] + - [3.016724, 0.0103302292, -4.68082349e-06, 1.01763288e-09, -8.62607041e-14, + 3.46128739e+04, 7.78732378] + transport: + model: gas + geometry: nonlinear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 1.0 + note: L2/92 + - name: C2H4 + composition: + H: 4 + C: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.95920148, -7.57052247e-03, 5.70990292e-05, -6.91588753e-08, + 2.69884373e-11, 5089.77593, 4.09733096] + - [2.03611116, 0.0146454151, -6.71077915e-06, 1.47222923e-09, + -1.25706061e-13, 4939.88614, 10.3053693] + transport: + model: gas + geometry: nonlinear + diameter: 3.971 + well-depth: 280.8 + rotational-relaxation: 1.5 + note: L1/91 + - name: C2H5 + composition: + H: 5 + C: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30646568, -4.18658892e-03, 4.97142807e-05, -5.99126606e-08, + 2.30509004e-11, 1.28416265e+04, 4.70720924] + - [1.95465642, 0.0173972722, -7.98206668e-06, 1.75217689e-09, + -1.49641576e-13, 1.285752e+04, 13.4624343] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L12/92 + - name: C2H6 + composition: + H: 6 + C: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.29142492, -5.5015427e-03, 5.99438288e-05, -7.08466285e-08, + 2.68685771e-11, -1.15222055e+04, 2.66682316] + - [1.0718815, 0.0216852677, -1.00256067e-05, 2.21412001e-09, -1.9000289e-13, + -1.14263932e+04, 15.1156107] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L8/88 + - name: HCCO + composition: + H: 1 + C: 2 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 4000.0] + data: + - [2.2517214, 0.017655021, -2.3729101e-05, 1.7275759e-08, -5.0664811e-12, + 2.0059449e+04, 12.490417] + - [5.6282058, 4.0853401e-03, -1.5934547e-06, 2.8626052e-10, -1.9407832e-14, + 1.9327215e+04, -3.9302595] + transport: + model: gas + geometry: nonlinear + diameter: 2.5 + well-depth: 150.0 + rotational-relaxation: 1.0 + note: SRIC91 + - name: CH2CO + composition: + H: 2 + C: 2 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.1358363, 0.0181188721, -1.73947474e-05, 9.34397568e-09, + -2.01457615e-12, -7042.91804, 12.215648] + - [4.51129732, 9.00359745e-03, -4.16939635e-06, 9.23345882e-10, + -7.94838201e-14, -7551.05311, 0.632247205] + transport: + model: gas + geometry: nonlinear + diameter: 3.97 + well-depth: 436.0 + rotational-relaxation: 2.0 + note: L5/90 + - name: CH2CHO + composition: + H: 3 + C: 2 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.409062, 0.010738574, 1.891492e-06, -7.158583e-09, 2.867385e-12, + 1521.4766, 9.55829] + - [5.97567, 8.130591e-03, -2.743624e-06, 4.070304e-10, -2.176017e-14, + 490.3218, -5.045251] + transport: + model: gas + geometry: nonlinear + diameter: 3.97 + well-depth: 436.0 + rotational-relaxation: 2.0 + note: SAND86 + - name: N2 + composition: + N: 2 + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12, + -1020.8999, 3.950372] + - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15, + -922.7977, 5.980528] + transport: + model: gas + geometry: linear + diameter: 3.621 + well-depth: 97.53 + polarizability: 1.76 + rotational-relaxation: 4.0 + note: 121286 +reactions: + - equation: O + H2 <=> H + OH + rate-constant: + A: 0.0 + b: 0.0 + Ea: 0.0 diff --git a/samples/python/AVBP/inputs/T_vs_x.dat b/samples/python/AVBP/inputs/T_vs_x.dat new file mode 100644 index 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-c customkinetics.f90 -g -fPIC -o customkinetics.o + gfortran -shared -o customkinetics.so customkinetics.o + \ No newline at end of file diff --git a/samples/python/AVBP/mech_lib/customkinetics.f90 b/samples/python/AVBP/mech_lib/customkinetics.f90 new file mode 100755 index 00000000000..355e516069d --- /dev/null +++ b/samples/python/AVBP/mech_lib/customkinetics.f90 @@ -0,0 +1,2317 @@ +! +! A 15-step reduced mechanism based on GRI3.0 +! +! by Tianfeng Lu +! Email: tlu@engr.uconn.edu +! +! Reference: +! Tianfeng Lu and Chung K. Law, +! "A criterion based on computational singular perturbation +! for the identification of quasi steady state species: +! A reduced mechanism for methane oxidation with NO chemistry," +! Combustion and Flame, Vol.154 No.4 pp.761�774, 2008. +! +! SUBROUTINE CKWYP (P, T, Y, ICKWRK, RCKWRK, WDOT) + SUBROUTINE customkinetics(P, T, Y, WDOT) + IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! +! DIMENSION ICKWRK(*), RCKWRK(*), WDOT(*), Y(*) + PARAMETER (RU=8.314510D7, PATM=1.01325D6, SMALL = 1.D-200) + DIMENSION WDOT(19), Y(19) + DIMENSION TN(5), ROP(184), CTB(184) + DIMENSION RF(184), RB(184), RKLOW(22), XQ(11), C(19) + DIMENSION EQK(184), SMH(30), EG(30) + + ! Correction for units compatibility in Cantera + P = P*10.D0 +! +! CALL YTCP(P, T, Y, C) +! CALL RATT(T, RF, RB, RKLOW) +! CALL RATX(T, C, RF, RB, RKLOW) +! CALL QSSA(RF, RB, XQ) +! CALL RDOT(RF, RB, WDOT) +! END +! +! ----------------------------------------------------------------------! +! +! SUBROUTINE YTCP (P, T, Y, C) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION Y(*), C(*) +! +! +! convert Y to ! + + C(1) = Y(1)*4.96046521D-1 + C(2) = Y(2)*9.92093043D-1 + C(3) = Y(3)*6.25023433D-2 + C(4) = Y(4)*3.12511716D-2 + C(5) = Y(5)*5.87980383D-2 + C(6) = Y(6)*5.55082499D-2 + C(7) = Y(7)*3.02968146D-2 + C(8) = Y(8)*2.93990192D-2 + C(9) = Y(9)*6.65112065D-2 + C(10) = Y(10)*6.23323639D-2 + C(11) = Y(11)*3.57008335D-2 + C(12) = Y(12)*2.27221341D-2 + C(13) = Y(13)*3.33039255D-2 + C(14) = Y(14)*3.12086189D-2 + C(15) = Y(15)*3.84050525D-2 + C(16) = Y(16)*3.56453112D-2 + C(17) = Y(17)*3.32556033D-2 + C(18) = Y(18)*2.37882046D-2 + C(19) = Y(19)*3.56972032D-2 +! + SUM = 0.0 + DO K = 1, 19 + SUM = SUM + C(K) + ENDDO + SUM = P/(SUM*T*8.314510D7) +! + DO K = 1, 19 + C(K) = MAX(C(K),SMALL) * SUM + ENDDO +! END +! +! ----------------------------------------------------------------------! +! +! +! forward reaction rates +! +! SUBROUTINE RATT (T, RF, RB, RKLOW) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION RF(*), RB(*), RKLOW(*), EQK(184), SMH(30), EG(30) +! + ALOGT = LOG(T) + TI = 1.0D0/T + TI2 = TI*TI +! + RF(1) = 1.2D17*TI + RF(2) = 5.D17*TI + RF(3) = EXP(1.05635949D1 +2.7D0*ALOGT -3.15013634D3*TI) + RF(4) = 2.D13 + RF(5) = EXP(1.60803938D1 +2.D0*ALOGT -2.01286667D3*TI) + RF(6) = 5.7D13 + RF(7) = 8.D13 + RF(8) = 1.5D13 + RF(9) = 1.5D13 + RF(10) = 5.06D13 + RF(11) = EXP(2.07430685D1 +1.5D0*ALOGT -4.32766334D3*TI) + RF(12) = EXP(2.36136376D1 -1.20017175D3*TI) + RF(13) = 3.D13 + RF(14) = 3.D13 + RF(15) = EXP(3.12945828D1 -1.781387D3*TI) + RF(16) = 1.D13 + RF(17) = 1.D13 + RF(18) = EXP(1.28687606D1 +2.5D0*ALOGT -1.55997167D3*TI) + RF(19) = EXP(1.17752897D1 +2.5D0*ALOGT -2.51608334D3*TI) + TMP = EXP(2.D0*ALOGT -9.56111669D2*TI ) + RF(20) = 1.35D7 * TMP + RF(21) = 6.94D6 * TMP + RF(22) = 3.D13 + TMP = EXP(1.83D0*ALOGT -1.10707667D2*TI ) + RF(23) = 1.25D7 * TMP + RF(167) = 6.7D6 * TMP + RF(24) = 2.24D13 + RF(25) = EXP(1.83130955D1 +1.92D0*ALOGT -2.86330284D3*TI) + RF(26) = 1.D14 + TMP = EXP(-4.02573334D3*TI) + RF(27) = 1.D13 * TMP + RF(76) = 5.D13 * TMP + RF(28) = EXP(2.81906369D1 -6.79342501D2*TI) + RF(29) = EXP(2.85473118D1 -2.40537567D4*TI) + RF(30) = EXP(3.22361913D1 -2.01286667D4*TI) + RF(31) = EXP(4.24761511D1 -8.6D-1*ALOGT) + TMP = EXP(-1.24D0*ALOGT) + RF(32) = 2.08D19 * TMP + RF(34) = 2.6D19 * TMP + RF(33) = EXP(4.38677883D1 -7.6D-1*ALOGT) + RF(35) = EXP(3.78159211D1 -6.707D-1*ALOGT -8.57531523D3*TI) + RF(36) = 1.D18*TI + RF(37) = EXP(3.90385861D1 -6.D-1*ALOGT) + RF(38) = EXP(4.55408762D1 -1.25D0*ALOGT) + RF(39) = 5.5D20*TI2 + RF(40) = 2.2D22*TI2 + RF(41) = EXP(2.90097872D1 -3.37658384D2*TI) + RF(42) = EXP(3.14332293D1 -5.37435401D2*TI) + RF(43) = EXP(3.20618379D1 -3.19542584D2*TI) + RF(44) = EXP(1.6308716D1 +2.D0*ALOGT -2.61672667D3*TI) + RF(45) = EXP(2.99336062D1 -1.81158D3*TI) + RF(46) = 1.65D14 + RF(47) = 6.D14 + RF(48) = 3.D13 + RF(49) = EXP(3.71706652D1 -5.34D-1*ALOGT -2.69724134D2*TI) + RF(50) = EXP(2.03077504D1 +1.62D0*ALOGT -5.45486868D3*TI) + RF(51) = EXP(2.77171988D1 +4.8D-1*ALOGT +1.30836334D2*TI) + RF(52) = 7.34D13 + RF(53) = EXP(2.7014835D1 +4.54D-1*ALOGT -1.81158D3*TI) + RF(54) = EXP(2.7014835D1 +4.54D-1*ALOGT -1.30836334D3*TI) + RF(55) = EXP(1.78655549D1 +1.9D0*ALOGT -1.3798201D3*TI) + RF(56) = EXP(2.76845619D1 +5.D-1*ALOGT -4.32766334D1*TI) + RF(57) = 2.D13 + RF(58) = EXP(2.58292113D1 +6.5D-1*ALOGT +1.42913534D2*TI) + RF(59) = EXP(3.11214496D1 -9.D-2*ALOGT -3.06962167D2*TI) + RF(60) = EXP(2.85189124D1 +5.15D-1*ALOGT -2.51608334D1*TI) + RF(61) = EXP(1.7541204D1 +1.63D0*ALOGT -9.68188869D2*TI) + RF(62) = 2.D13 + RF(63) = EXP(2.80364862D1 +5.D-1*ALOGT +5.53538334D1*TI) + RF(64) = EXP(3.31993656D1 -2.3D-1*ALOGT -5.38441834D2*TI) + TMP = EXP(2.1D0*ALOGT -2.45066517D3*TI ) + RF(65) = 1.7D7 * TMP + RF(66) = 4.2D6 * TMP + RF(67) = EXP(2.93537877D1 -1.20772D3*TI) + RF(68) = EXP(2.94360258D1 +2.7D-1*ALOGT -1.40900667D2*TI) + RF(69) = 3.D13 + RF(70) = EXP(2.7014835D1 +4.54D-1*ALOGT -9.15854335D2*TI) + RF(71) = EXP(1.4096923D1 +2.53D0*ALOGT -6.15937201D3*TI) + RF(72) = EXP(4.07945264D1 -9.9D-1*ALOGT -7.95082335D2*TI) + RF(73) = 2.D12 + RF(74) = EXP(1.85604427D1 +1.9D0*ALOGT -3.78922151D3*TI) + RF(75) = 1.D14 + RF(77) = EXP(3.00558238D1 -1.72502674D3*TI) + RF(78) = EXP(1.75767107D1 +1.5D0*ALOGT -4.00560467D4*TI) + RF(79) = EXP(1.9190789D1 +1.51D0*ALOGT -1.72603317D3*TI) + RF(80) = EXP(3.19350862D1 -3.7D-1*ALOGT) + RF(81) = EXP(1.0482906D1 +2.4D0*ALOGT +1.06178717D3*TI) + RF(82) = EXP(3.03051698D1 +2.51608334D2*TI) + RF(83) = EXP(2.83241683D1 -2.14873517D2*TI) + RF(84) = EXP(4.19771599D1 -1.47996022D4*TI) + RF(85) = 5.D13 + RF(86) = 3.D13 + RF(87) = 2.D13 + RF(88) = EXP(1.62403133D1 +2.D0*ALOGT -1.50965D3*TI) + RF(89) = 3.D13 + RF(90) = EXP(4.24725733D1 -1.43D0*ALOGT -6.69278168D2*TI) + RF(91) = EXP(1.78408622D1 +1.6D0*ALOGT -2.72743434D3*TI) + RF(92) = EXP(4.10064751D1 -1.34D0*ALOGT -7.13058018D2*TI) + RF(93) = EXP(1.84206807D1 +1.6D0*ALOGT -1.570036D3*TI) + RF(94) = EXP(1.76783433D1 +1.228D0*ALOGT -3.52251667D1*TI) + RF(95) = 5.D13 + RF(96) = EXP(2.19558261D1 +1.18D0*ALOGT +2.2493785D2*TI) + RF(97) = 5.D12 + RF(98) = 5.D12 + RF(99) = EXP(1.41801537D1 +2.D0*ALOGT +4.22702001D2*TI) + RF(100) = EXP(1.56560602D1 +2.D0*ALOGT -7.54825001D2*TI) + RF(101) = EXP(-8.4310155D0 +4.5D0*ALOGT +5.03216668D2*TI) + RF(102) = EXP(-7.6354939D0 +4.D0*ALOGT +1.00643334D3*TI) + RF(103) = 5.D12 + RF(104) = EXP(1.50964444D1 +2.D0*ALOGT -1.25804167D3*TI) + RF(105) = EXP(1.50796373D1 +2.12D0*ALOGT -4.37798501D2*TI) + RF(106) = EXP(2.96459241D1 -1.00643334D3*TI) + RF(107) = EXP(2.55908003D1 +8.20243168D2*TI) + RF(108) = EXP(3.36712758D1 -6.03860001D3*TI) + RF(109) = 2.D13 + RF(110) = 1.D12 + RF(111) = 3.78D13 + RF(112) = EXP(3.26416564D1 -1.18759134D4*TI) + RF(113) = EXP(1.55382772D1 +2.D0*ALOGT -6.03860001D3*TI) + RF(114) = EXP(3.16914641D1 -2.89852801D2*TI) + RF(115) = 5.D13 + RF(116) = 6.71D13 + RF(117) = EXP(3.23131523D1 -1.56500384D3*TI) + RF(118) = EXP(2.93732401D1 +3.79928584D2*TI) + RF(119) = 4.D13 + RF(120) = 3.D13 + RF(121) = 6.D13 + RF(122) = 5.D13 + RF(123) = EXP(3.28780452D1 -7.94679762D3*TI) + RF(124) = EXP(3.21806786D1 +2.59156584D2*TI) + RF(125) = 5.D13 + TMP = EXP(-7.54825001D2*TI) + RF(126) = 5.D12 * TMP + RF(171) = 5.8D12 * TMP + RF(172) = 2.4D12 * TMP + RF(127) = EXP(1.31223634D1 +2.D0*ALOGT -3.63825651D3*TI) + RF(128) = EXP(3.500878D1 -6.01041988D3*TI) + RF(129) = 4.D13 + RF(130) = EXP(1.47156719D1 +2.D0*ALOGT -4.16160184D3*TI) + RF(131) = EXP(2.74203001D1 +5.D-1*ALOGT -2.26950717D3*TI) + RF(132) = 3.D13 + RF(133) = EXP(3.03390713D1 -3.01930001D2*TI) + RF(134) = 2.8D13 + RF(135) = 1.2D13 + RF(136) = 7.D13 + RF(137) = EXP(4.07167205D1 -1.16D0*ALOGT -5.76183084D2*TI) + RF(138) = 3.D13 + TMP = EXP(2.86833501D2*TI) + RF(139) = 1.2D13 * TMP + RF(140) = 1.6D13 * TMP + RF(141) = 9.D12 + RF(142) = 7.D12 + RF(143) = 1.4D13 + RF(144) = EXP(3.13199006D1 +2.76769167D2*TI) + RF(145) = EXP(3.12033668D1 -1.5338044D4*TI) + RF(146) = EXP(2.84682686D1 -1.02228466D4*TI) + RF(147) = EXP(1.01064284D1 +2.47D0*ALOGT -2.60666234D3*TI) + RF(148) = EXP(3.87538626D1 -1.18D0*ALOGT -3.29103701D2*TI) + RF(149) = EXP(2.95538088D1 +1.D-1*ALOGT -5.33409668D3*TI) + RF(150) = 2.648D13 + RF(151) = EXP(8.10772006D0 +2.81D0*ALOGT -2.94884967D3*TI) + TMP = EXP(1.5D0*ALOGT -5.00197368D3*TI) + RF(152) = 3.D7 * TMP + RF(153) = 1.D7 * TMP + RF(154) = EXP(1.23327053D1 +2.D0*ALOGT -4.62959334D3*TI) + RF(155) = EXP(1.56303353D1 +1.74D0*ALOGT -5.25861418D3*TI) + TMP = EXP(-1.D0*ALOGT -8.55468335D3*TI) + RF(156) = 1.5D18 * TMP + RF(157) = 1.87D17 * TMP + RF(158) = EXP(3.02300002D1 -2.01286667D2*TI) + RF(159) = EXP(3.05213929D1 -4.52895001D2*TI) + RF(160) = EXP(-2.84796532D1 +7.6D0*ALOGT +1.77635484D3*TI) + RF(161) = EXP(3.83630605D1 -1.39D0*ALOGT -5.10764918D2*TI) + RF(162) = EXP(2.97104627D1 +4.4D-1*ALOGT -4.36641103D4*TI) + RF(163) = EXP(2.74566677D1 -1.94996459D3*TI) + RF(164) = EXP(2.87941719D1 -4.29747034D2*TI) + RF(165) = 1.D13 + RF(166) = 3.37D13 + RF(168) = EXP(3.61482143D1 -8.72074485D3*TI) + RF(169) = EXP(2.28027074D1 +5.D-1*ALOGT +8.83145252D2*TI) + RF(170) = EXP(2.83090547D1 +4.3D-1*ALOGT +1.86190167D2*TI) + RF(173) = EXP(3.29293385D1 -5.52984796D3*TI) + RF(174) = EXP(2.49457104D1 +2.5D-1*ALOGT +4.70507584D2*TI) + RF(175) = EXP(2.64369986D1 +2.9D-1*ALOGT -5.53538334D0*TI) + RF(176) = EXP(1.41059389D1 +1.61D0*ALOGT +1.932352D2*TI) + RF(177) = EXP(2.69105027D1 +4.22D-1*ALOGT +8.83145252D2*TI) + RF(178) = 1.5D14 + RF(179) = 1.81D10 + RF(180) = 2.35D10 + RF(181) = 2.2D13 + RF(182) = 1.1D13 + RF(183) = 1.2D13 + RF(184) = 3.01D13 +! +! +! thermal data +! +! + TLOG = LOG(T) + TI = 1.0D0/T + TN(1) = TLOG - 1.0 + TN(2) = T + TN(3) = TN(2)*T + TN(4) = TN(3)*T + TN(5) = TN(4)*T +! + IF (T .GT. 1.D3) THEN +! + SMH(1) = -3.20502331D+00 + 9.50158922D+02*TI & + + 3.33727920D+00*TN(1) - 2.47012365D-05*TN(2) & + + 8.32427963D-08*TN(3) - 1.49638662D-11*TN(4) & + + 1.00127688D-15*TN(5) + SMH(2) = -4.46682914D-01 - 2.54736599D+04*TI & + + 2.50000001D+00*TN(1) - 1.15421486D-11*TN(2) & + + 2.69269913D-15*TN(3) - 3.94596029D-19*TN(4) & + + 2.49098679D-23*TN(5) + SMH(3) = 4.78433864D+00 - 2.92175791D+04*TI & + + 2.56942078D+00*TN(1) - 4.29870569D-05*TN(2) & + + 6.99140982D-09*TN(3) - 8.34814992D-13*TN(4) & + + 6.14168455D-17*TN(5) + SMH(4) = 5.45323129D+00 + 1.08845772D+03*TI & + + 3.28253784D+00*TN(1) + 7.41543770D-04*TN(2) & + - 1.26327778D-07*TN(3) + 1.74558796D-11*TN(4) & + - 1.08358897D-15*TN(5) + SMH(5) = 4.47669610D+00 - 3.85865700D+03*TI & + + 3.09288767D+00*TN(1) + 2.74214858D-04*TN(2) & + + 2.10842047D-08*TN(3) - 7.32884630D-12*TN(4) & + + 5.87061880D-16*TN(5) + SMH(6) = 4.96677010D+00 + 3.00042971D+04*TI & + + 3.03399249D+00*TN(1) + 1.08845902D-03*TN(2) & + - 2.73454197D-08*TN(3) - 8.08683225D-12*TN(4) & + + 8.41004960D-16*TN(5) + SMH(7) = 3.78510215D+00 - 1.11856713D+02*TI & + + 4.01721090D+00*TN(1) + 1.11991007D-03*TN(2) & + - 1.05609692D-07*TN(3) + 9.52053083D-12*TN(4) & + - 5.39542675D-16*TN(5) + SMH(8) = 2.91615662D+00 + 1.78617877D+04*TI & + + 4.16500285D+00*TN(1) + 2.45415847D-03*TN(2) & + - 3.16898708D-07*TN(3) + 3.09321655D-11*TN(4) & + - 1.43954153D-15*TN(5) + SMH(9) = 4.80150373D+00 - 8.54512953D+04*TI & + + 2.49266888D+00*TN(1) + 2.39944642D-05*TN(2) & + - 1.20722503D-08*TN(3) + 3.11909191D-12*TN(4) & + - 2.43638946D-16*TN(5) + SMH(10) = 5.48497999D+00 - 7.10124364D+04*TI & + + 2.87846473D+00*TN(1) + 4.85456841D-04*TN(2) & + + 2.40742758D-08*TN(3) - 1.08906541D-11*TN(4) & + + 8.80396915D-16*TN(5) + SMH(11) = 6.17119324D+00 - 4.62636040D+04*TI & + + 2.87410113D+00*TN(1) + 1.82819646D-03*TN(2) & + - 2.34824328D-07*TN(3) + 2.16816291D-11*TN(4) & + - 9.38637835D-16*TN(5) + SMH(12) = 8.62650169D+00 - 5.09259997D+04*TI & + + 2.29203842D+00*TN(1) + 2.32794319D-03*TN(2) & + - 3.35319912D-07*TN(3) + 3.48255000D-11*TN(4) & + - 1.69858183D-15*TN(5) + SMH(13) = 8.48007179D+00 - 1.67755843D+04*TI & + + 2.28571772D+00*TN(1) + 3.61995018D-03*TN(2) & + - 4.97857247D-07*TN(3) + 4.96403870D-11*TN(4) & + - 2.33577197D-15*TN(5) + SMH(14) = 1.84373180D+01 + 9.46834459D+03*TI & + + 7.48514950D-02*TN(1) + 6.69547335D-03*TN(2) & + - 9.55476348D-07*TN(3) + 1.01910446D-10*TN(4) & + - 5.09076150D-15*TN(5) + SMH(15) = 7.81868772D+00 + 1.41518724D+04*TI & + + 2.71518561D+00*TN(1) + 1.03126372D-03*TN(2) & + - 1.66470962D-07*TN(3) + 1.91710840D-11*TN(4) & + - 1.01823858D-15*TN(5) + SMH(16) = 2.27163806D+00 + 4.87591660D+04*TI & + + 3.85746029D+00*TN(1) + 2.20718513D-03*TN(2) & + - 3.69135673D-07*TN(3) + 4.36241823D-11*TN(4) & + - 2.36042082D-15*TN(5) + SMH(17) = 9.79834492D+00 - 4.01191815D+03*TI & + + 2.77217438D+00*TN(1) + 2.47847763D-03*TN(2) & + - 4.14076022D-07*TN(3) + 4.90968148D-11*TN(4) & + - 2.66754356D-15*TN(5) + SMH(18) = 1.36563230D+01 + 1.39958323D+04*TI & + + 1.76069008D+00*TN(1) + 4.60000041D-03*TN(2) & + - 7.37098022D-07*TN(3) + 8.38676767D-11*TN(4) & + - 4.41927820D-15*TN(5) + SMH(19) = 5.81043215D+00 + 3.24250627D+03*TI & + + 3.69266569D+00*TN(1) + 4.32288399D-03*TN(2) & + - 6.25168533D-07*TN(3) + 6.56028863D-11*TN(4) & + - 3.24277101D-15*TN(5) + SMH(20) = 2.92957500D+00 - 1.27832520D+02*TI & + + 3.77079900D+00*TN(1) + 3.93574850D-03*TN(2) & + - 4.42730667D-07*TN(3) + 3.28702583D-11*TN(4) & + - 1.05630800D-15*TN(5) + + SMH(21) = 1.45023623D+01 + 2.53748747D+04*TI & + + 1.78970791D+00*TN(1) + 7.04691460D-03*TN(2) & + - 1.06083472D-06*TN(3) + 1.15142571D-10*TN(4) & + - 5.85301100D-15*TN(5) + SMH(22) = -1.23028121D+00 - 2.59359992D+04*TI & + + 4.14756964D+00*TN(1) + 2.98083332D-03*TN(2) & + - 3.95491420D-07*TN(3) + 3.89510143D-11*TN(4) & + - 1.80617607D-15*TN(5) + SMH(23) = 7.78732378D+00 - 3.46128739D+04*TI & + + 3.01672400D+00*TN(1) + 5.16511460D-03*TN(2) & + - 7.80137248D-07*TN(3) + 8.48027400D-11*TN(4) & + - 4.31303520D-15*TN(5) + SMH(24) = 1.03053693D+01 - 4.93988614D+03*TI & + + 2.03611116D+00*TN(1) + 7.32270755D-03*TN(2) & + - 1.11846319D-06*TN(3) + 1.22685769D-10*TN(4) & + - 6.28530305D-15*TN(5) + SMH(25) = 1.34624343D+01 - 1.28575200D+04*TI & + + 1.95465642D+00*TN(1) + 8.69863610D-03*TN(2) & + - 1.33034445D-06*TN(3) + 1.46014741D-10*TN(4) & + - 7.48207880D-15*TN(5) + SMH(26) = 1.51156107D+01 + 1.14263932D+04*TI & + + 1.07188150D+00*TN(1) + 1.08426339D-02*TN(2) & + - 1.67093445D-06*TN(3) + 1.84510001D-10*TN(4) & + - 9.50014450D-15*TN(5) + SMH(27) = -3.93025950D+00 - 1.93272150D+04*TI & + + 5.62820580D+00*TN(1) + 2.04267005D-03*TN(2) & + - 2.65575783D-07*TN(3) + 2.38550433D-11*TN(4) & + - 9.70391600D-16*TN(5) + SMH(28) = 6.32247205D-01 + 7.55105311D+03*TI & + + 4.51129732D+00*TN(1) + 4.50179872D-03*TN(2) & + - 6.94899392D-07*TN(3) + 7.69454902D-11*TN(4) & + - 3.97419100D-15*TN(5) + SMH(29) = -5.04525100D+00 - 4.90321800D+02*TI & + + 5.97567000D+00*TN(1) + 4.06529550D-03*TN(2) & + - 4.57270667D-07*TN(3) + 3.39192000D-11*TN(4) & + - 1.08800850D-15*TN(5) +! + ELSE +! + SMH(1) = 6.83010238D-01 + 9.17935173D+02*TI & + + 2.34433112D+00*TN(1) + 3.99026037D-03*TN(2) & + - 3.24635850D-06*TN(3) + 1.67976745D-09*TN(4) & + - 3.68805881D-13*TN(5) + SMH(2) = -4.46682853D-01 - 2.54736599D+04*TI & + + 2.50000000D+00*TN(1) + 3.52666409D-13*TN(2) & + - 3.32653273D-16*TN(3) + 1.91734693D-19*TN(4) & + - 4.63866166D-23*TN(5) + SMH(3) = 2.05193346D+00 - 2.91222592D+04*TI & + + 3.16826710D+00*TN(1) - 1.63965942D-03*TN(2) & + + 1.10717733D-06*TN(3) - 5.10672187D-10*TN(4) & + + 1.05632986D-13*TN(5) + SMH(4) = 3.65767573D+00 + 1.06394356D+03*TI & + + 3.78245636D+00*TN(1) - 1.49836708D-03*TN(2) & + + 1.64121700D-06*TN(3) - 8.06774591D-10*TN(4) & + + 1.62186419D-13*TN(5) + SMH(5) = -1.03925458D-01 - 3.61508056D+03*TI & + + 3.99201543D+00*TN(1) - 1.20065876D-03*TN(2) & + + 7.69656402D-07*TN(3) - 3.23427778D-10*TN(4) & + + 6.82057350D-14*TN(5) + SMH(6) = -8.49032208D-01 + 3.02937267D+04*TI & + + 4.19864056D+00*TN(1) - 1.01821705D-03*TN(2) & + + 1.08673369D-06*TN(3) - 4.57330885D-10*TN(4) & + + 8.85989085D-14*TN(5) + SMH(7) = 3.71666245D+00 - 2.94808040D+02*TI & + + 4.30179801D+00*TN(1) - 2.37456025D-03*TN(2) & + + 3.52638152D-06*TN(3) - 2.02303245D-09*TN(4) & + + 4.64612562D-13*TN(5) + SMH(8) = 3.43505074D+00 + 1.77025821D+04*TI & + + 4.27611269D+00*TN(1) - 2.71411208D-04*TN(2) & + + 2.78892835D-06*TN(3) - 1.79809011D-09*TN(4) & + + 4.31227182D-13*TN(5) + SMH(9) = 4.53130848D+00 - 8.54438832D+04*TI & + + 2.55423955D+00*TN(1) - 1.60768862D-04*TN(2) & + + 1.22298708D-07*TN(3) - 6.10195741D-11*TN(4) & + + 1.33260723D-14*TN(5) + SMH(10) = 2.08401108D+00 - 7.07972934D+04*TI & + + 3.48981665D+00*TN(1) + 1.61917771D-04*TN(2) & + - 2.81498442D-07*TN(3) + 2.63514439D-10*TN(4) & + - 7.03045335D-14*TN(5) + SMH(11) = 1.56253185D+00 - 4.60040401D+04*TI & + + 3.76267867D+00*TN(1) + 4.84436072D-04*TN(2) & + + 4.65816402D-07*TN(3) - 3.20909294D-10*TN(4) & + + 8.43708595D-14*TN(5) + SMH(12) = -7.69118967D-01 - 5.04968163D+04*TI & + + 4.19860411D+00*TN(1) - 1.18330710D-03*TN(2) & + + 1.37216037D-06*TN(3) - 5.57346651D-10*TN(4) & + + 9.71573685D-14*TN(5) + SMH(13) = 1.60456433D+00 - 1.64449988D+04*TI & + + 3.67359040D+00*TN(1) + 1.00547588D-03*TN(2) & + + 9.55036427D-07*TN(3) - 5.72597854D-10*TN(4) & + + 1.27192867D-13*TN(5) + SMH(14) = -4.64130376D+00 + 1.02466476D+04*TI & + + 5.14987613D+00*TN(1) - 6.83548940D-03*TN(2) & + + 8.19667665D-06*TN(3) - 4.03952522D-09*TN(4) & + + 8.33469780D-13*TN(5) + SMH(15) = 3.50840928D+00 + 1.43440860D+04*TI & + + 3.57953347D+00*TN(1) - 3.05176840D-04*TN(2) & + + 1.69469055D-07*TN(3) + 7.55838237D-11*TN(4) & + - 4.52212249D-14*TN(5) + SMH(16) = 9.90105222D+00 + 4.83719697D+04*TI & + + 2.35677352D+00*TN(1) + 4.49229839D-03*TN(2) & + - 1.18726045D-06*TN(3) + 2.04932518D-10*TN(4) & + - 7.18497740D-15*TN(5) + SMH(17) = 3.39437243D+00 - 3.83956496D+03*TI & + + 4.22118584D+00*TN(1) - 1.62196266D-03*TN(2) & + + 2.29665743D-06*TN(3) - 1.10953411D-09*TN(4) & + + 2.16884433D-13*TN(5) + SMH(18) = 6.02812900D-01 + 1.43089567D+04*TI & + + 4.79372315D+00*TN(1) - 4.95416685D-03*TN(2) & + + 6.22033347D-06*TN(3) - 3.16071051D-09*TN(4) & + + 6.58863260D-13*TN(5) + SMH(19) = 5.47302243D+00 + 3.19391367D+03*TI & + + 3.86388918D+00*TN(1) + 2.79836152D-03*TN(2) & + + 9.88786318D-07*TN(3) - 8.71100100D-10*TN(4) & + + 2.18483639D-13*TN(5) + SMH(20) = 1.31521770D+01 - 9.78601100D+02*TI & + + 2.10620400D+00*TN(1) + 3.60829750D-03*TN(2) & + + 8.89745333D-07*TN(3) - 6.14803000D-10*TN(4) & + + 1.03780500D-13*TN(5) + SMH(21) = -1.50409823D+00 + 2.56427656D+04*TI & + + 5.71539582D+00*TN(1) - 7.61545645D-03*TN(2) & + + 1.08740193D-05*TN(3) - 5.92339074D-09*TN(4) & + + 1.30676349D-12*TN(5) + SMH(22) = 1.39397051D+01 - 2.64289807D+04*TI & + + 8.08681094D-01*TN(1) + 1.16807815D-02*TN(2) & + - 5.91953025D-06*TN(3) + 2.33460364D-09*TN(4) & + - 4.25036487D-13*TN(5) + SMH(23) = 8.51054025D+00 - 3.48598468D+04*TI & + + 3.21246645D+00*TN(1) + 7.57395810D-04*TN(2) & + + 4.32015687D-06*TN(3) - 2.98048206D-09*TN(4) & + + 7.35754365D-13*TN(5) + SMH(24) = 4.09733096D+00 - 5.08977593D+03*TI & + + 3.95920148D+00*TN(1) - 3.78526124D-03*TN(2) & + + 9.51650487D-06*TN(3) - 5.76323961D-09*TN(4) & + + 1.34942187D-12*TN(5) + SMH(25) = 4.70720924D+00 - 1.28416265D+04*TI & + + 4.30646568D+00*TN(1) - 2.09329446D-03*TN(2) & + + 8.28571345D-06*TN(3) - 4.99272172D-09*TN(4) & + + 1.15254502D-12*TN(5) + SMH(26) = 2.66682316D+00 + 1.15222055D+04*TI & + + 4.29142492D+00*TN(1) - 2.75077135D-03*TN(2) & + + 9.99063813D-06*TN(3) - 5.90388571D-09*TN(4) & + + 1.34342886D-12*TN(5) + SMH(27) = 1.24904170D+01 - 2.00594490D+04*TI & + + 2.25172140D+00*TN(1) + 8.82751050D-03*TN(2) & + - 3.95485017D-06*TN(3) + 1.43964658D-09*TN(4) & + - 2.53324055D-13*TN(5) + SMH(28) = 1.22156480D+01 + 7.04291804D+03*TI & + + 2.13583630D+00*TN(1) + 9.05943605D-03*TN(2) & + - 2.89912457D-06*TN(3) + 7.78664640D-10*TN(4) & + - 1.00728807D-13*TN(5) + SMH(29) = 9.55829000D+00 - 1.52147660D+03*TI & + + 3.40906200D+00*TN(1) + 5.36928700D-03*TN(2) & + + 3.15248667D-07*TN(3) - 5.96548583D-10*TN(4) & + + 1.43369250D-13*TN(5) + ENDIF +! CALL RDSMH (T, SMH) +! +! equilibrium constants +! + DO N = 1, 29 + EG(N) = EXP(SMH(N)) + ENDDO +! + PFAC = PATM / (RU*T) + PFAC2 = PFAC*PFAC + PFAC3 = PFAC2*PFAC +! + EQK(1)=EG(4)/EG(3)/EG(3)/PFAC + EQK(2)=EG(5)/EG(2)/EG(3)/PFAC + EQK(3)=EG(2)*EG(5)/EG(1)/EG(3) + EQK(4)=EG(4)*EG(5)/EG(3)/EG(7) + EQK(5)=EG(5)*EG(7)/EG(3)/EG(8) + EQK(6)=EG(2)*EG(15)/EG(3)/EG(10) + EQK(7)=EG(2)*EG(17)/EG(3)/EG(11) + EQK(8)=EG(1)*EG(15)/EG(3)/EG(12) + EQK(9)=EG(2)*EG(17)/EG(3)/EG(12) + EQK(10)=EG(2)*EG(18)/EG(3)/EG(13) + EQK(11)=EG(5)*EG(13)/EG(3)/EG(14) + EQK(12)=EG(16)/EG(3)/EG(15)/PFAC + EQK(13)=EG(5)*EG(15)/EG(3)/EG(17) + EQK(14)=EG(2)*EG(16)/EG(3)/EG(17) + EQK(15)=EG(5)*EG(17)/EG(3)/EG(18) + EQK(16)=EG(5)*EG(18)/EG(3)/EG(19) + EQK(17)=EG(5)*EG(18)/EG(3)/EG(20) + EQK(18)=EG(5)*EG(19)/EG(3)/EG(21) + EQK(19)=EG(5)*EG(20)/EG(3)/EG(21) + EQK(20)=EG(2)*EG(27)/EG(3)/EG(22) + EQK(21)=EG(11)*EG(15)/EG(3)/EG(22) + EQK(22)=EG(2)*EG(28)/EG(3)/EG(23) + EQK(23)=EG(13)*EG(17)/EG(3)/EG(24) + EQK(24)=EG(13)*EG(18)/EG(3)/EG(25) + EQK(25)=EG(5)*EG(25)/EG(3)/EG(26) + EQK(26)=EG(2)*EG(15)*EG(15)/EG(3)/EG(27)*PFAC + EQK(27)=EG(5)*EG(27)/EG(3)/EG(28) + EQK(28)=EG(11)*EG(16)/EG(3)/EG(28) + EQK(29)=EG(3)*EG(16)/EG(4)/EG(15) + EQK(30)=EG(7)*EG(17)/EG(4)/EG(18) + EQK(31)=EG(7)/EG(2)/EG(4)/PFAC + EQK(32)=EQK(31) + EQK(33)=EQK(31) + EQK(34)=EQK(31) + EQK(35)=EG(3)*EG(5)/EG(2)/EG(4) + EQK(36)=EG(1)/EG(2)/EG(2)/PFAC + EQK(37)=EQK(36) + EQK(38)=EQK(36) + EQK(39)=EQK(36) + EQK(40)=EG(6)/EG(2)/EG(5)/PFAC + EQK(41)=EG(3)*EG(6)/EG(2)/EG(7) + EQK(42)=EG(1)*EG(4)/EG(2)/EG(7) + EQK(43)=EG(5)*EG(5)/EG(2)/EG(7) + EQK(44)=EG(1)*EG(7)/EG(2)/EG(8) + EQK(45)=EG(5)*EG(6)/EG(2)/EG(8) + EQK(46)=EG(1)*EG(9)/EG(2)/EG(10) + EQK(47)=EG(13)/EG(2)/EG(11)/PFAC + EQK(48)=EG(1)*EG(10)/EG(2)/EG(12) + EQK(49)=EG(14)/EG(2)/EG(13)/PFAC + EQK(50)=EG(1)*EG(13)/EG(2)/EG(14) + EQK(51)=EG(18)/EG(2)/EG(17)/PFAC + EQK(52)=EG(1)*EG(15)/EG(2)/EG(17) + EQK(53)=EG(19)/EG(2)/EG(18)/PFAC + EQK(54)=EG(20)/EG(2)/EG(18)/PFAC + EQK(55)=EG(1)*EG(17)/EG(2)/EG(18) + EQK(56)=EG(21)/EG(2)/EG(19)/PFAC + EQK(57)=EG(1)*EG(18)/EG(2)/EG(19) + EQK(58)=EG(5)*EG(13)/EG(2)/EG(19) + EQK(59)=EG(6)*EG(12)/EG(2)/EG(19) + EQK(60)=EG(21)/EG(2)/EG(20)/PFAC + EQK(61)=EG(19)/EG(20) + EQK(62)=EG(1)*EG(18)/EG(2)/EG(20) + EQK(63)=EG(5)*EG(13)/EG(2)/EG(20) + EQK(64)=EG(6)*EG(12)/EG(2)/EG(20) + EQK(65)=EG(1)*EG(19)/EG(2)/EG(21) + EQK(66)=EG(1)*EG(20)/EG(2)/EG(21) + EQK(67)=EG(23)/EG(2)/EG(22)/PFAC + EQK(68)=EG(24)/EG(2)/EG(23)/PFAC + EQK(69)=EG(1)*EG(22)/EG(2)/EG(23) + EQK(70)=EG(25)/EG(2)/EG(24)/PFAC + EQK(71)=EG(1)*EG(23)/EG(2)/EG(24) + EQK(72)=EG(26)/EG(2)/EG(25)/PFAC + EQK(73)=EG(1)*EG(24)/EG(2)/EG(25) + EQK(74)=EG(1)*EG(25)/EG(2)/EG(26) + EQK(75)=EG(12)*EG(15)/EG(2)/EG(27) + EQK(76)=EG(1)*EG(27)/EG(2)/EG(28) + EQK(77)=EG(13)*EG(15)/EG(2)/EG(28) + EQK(78)=EG(18)/EG(1)/EG(15)/PFAC + EQK(79)=EG(2)*EG(6)/EG(1)/EG(5) + EQK(80)=EG(8)/EG(5)/EG(5)/PFAC + EQK(81)=EG(3)*EG(6)/EG(5)/EG(5) + EQK(82)=EG(4)*EG(6)/EG(5)/EG(7) + EQK(168)=EQK(82) + EQK(83)=EG(6)*EG(7)/EG(5)/EG(8) + EQK(84)=EQK(83) + EQK(85)=EG(2)*EG(15)/EG(5)/EG(9) + EQK(86)=EG(2)*EG(17)/EG(5)/EG(10) + EQK(87)=EG(2)*EG(18)/EG(5)/EG(11) + EQK(88)=EG(6)*EG(10)/EG(5)/EG(11) + EQK(89)=EG(2)*EG(18)/EG(5)/EG(12) + EQK(90)=EG(21)/EG(5)/EG(13)/PFAC + EQK(91)=EG(6)*EG(11)/EG(5)/EG(13) + EQK(92)=EG(6)*EG(12)/EG(5)/EG(13) + EQK(93)=EG(6)*EG(13)/EG(5)/EG(14) + EQK(94)=EG(2)*EG(16)/EG(5)/EG(15) + EQK(95)=EG(6)*EG(15)/EG(5)/EG(17) + EQK(96)=EG(6)*EG(17)/EG(5)/EG(18) + EQK(97)=EG(6)*EG(18)/EG(5)/EG(19) + EQK(98)=EG(6)*EG(18)/EG(5)/EG(20) + EQK(99)=EG(6)*EG(19)/EG(5)/EG(21) + EQK(100)=EG(6)*EG(20)/EG(5)/EG(21) + EQK(101)=EG(2)*EG(28)/EG(5)/EG(22) + EQK(102)=EG(13)*EG(15)/EG(5)/EG(22) + EQK(103)=EG(6)*EG(22)/EG(5)/EG(23) + EQK(104)=EG(6)*EG(23)/EG(5)/EG(24) + EQK(105)=EG(6)*EG(25)/EG(5)/EG(26) + EQK(106)=EG(6)*EG(27)/EG(5)/EG(28) + EQK(107)=EG(4)*EG(8)/EG(7)/EG(7) + EQK(108)=EQK(107) + EQK(109)=EG(5)*EG(18)/EG(7)/EG(11) + EQK(110)=EG(4)*EG(14)/EG(7)/EG(13) + EQK(111)=EG(5)*EG(20)/EG(7)/EG(13) + EQK(112)=EG(5)*EG(16)/EG(7)/EG(15) + EQK(113)=EG(8)*EG(17)/EG(7)/EG(18) + EQK(114)=EG(3)*EG(15)/EG(4)/EG(9) + EQK(115)=EG(2)*EG(22)/EG(9)/EG(13) + EQK(116)=EG(3)*EG(17)/EG(4)/EG(10) + EQK(117)=EG(2)*EG(11)/EG(1)/EG(10) + EQK(118)=EG(2)*EG(18)/EG(6)/EG(10) + EQK(119)=EG(2)*EG(22)/EG(10)/EG(11) + EQK(120)=EG(2)*EG(23)/EG(10)/EG(13) + EQK(121)=EG(2)*EG(24)/EG(10)/EG(14) + EQK(122)=EG(27)/EG(10)/EG(15)/PFAC + EQK(123)=EG(15)*EG(17)/EG(10)/EG(16) + EQK(124)=EG(2)*EG(28)/EG(10)/EG(18) + EQK(125)=EG(15)*EG(22)/EG(10)/EG(27) + EQK(127)=EG(2)*EG(13)/EG(1)/EG(11) + EQK(128)=EG(1)*EG(22)/EG(11)/EG(11) + EQK(129)=EG(2)*EG(24)/EG(11)/EG(13) + EQK(130)=EG(13)*EG(13)/EG(11)/EG(14) + EQK(131)=EG(28)/EG(11)/EG(15)/PFAC + EQK(132)=EG(15)*EG(23)/EG(11)/EG(27) + EQK(133)=EG(11)/EG(12) + EQK(138)=EQK(133) + EQK(141)=EQK(133) + EQK(142)=EQK(133) + EQK(134)=EG(2)*EG(5)*EG(15)/EG(4)/EG(12)*PFAC + EQK(135)=EG(6)*EG(15)/EG(4)/EG(12) + EQK(136)=EG(2)*EG(13)/EG(1)/EG(12) + EQK(137)=EG(21)/EG(6)/EG(12)/PFAC + EQK(139)=EG(2)*EG(24)/EG(12)/EG(13) + EQK(140)=EG(13)*EG(13)/EG(12)/EG(14) + EQK(143)=EG(15)*EG(18)/EG(12)/EG(16) + EQK(144)=EG(13)*EG(25)/EG(12)/EG(26) + EQK(145)=EG(3)*EG(20)/EG(4)/EG(13) + EQK(146)=EG(5)*EG(18)/EG(4)/EG(13) + EQK(147)=EG(7)*EG(14)/EG(8)/EG(13) + EQK(148)=EG(26)/EG(13)/EG(13)/PFAC + EQK(149)=EG(2)*EG(25)/EG(13)/EG(13) + EQK(150)=EG(14)*EG(15)/EG(13)/EG(17) + EQK(151)=EG(14)*EG(17)/EG(13)/EG(18) + EQK(152)=EG(14)*EG(19)/EG(13)/EG(21) + EQK(153)=EG(14)*EG(20)/EG(13)/EG(21) + EQK(154)=EG(14)*EG(23)/EG(13)/EG(24) + EQK(155)=EG(14)*EG(25)/EG(13)/EG(26) + EQK(156)=EG(2)*EG(15)/EG(17)*PFAC + EQK(157)=EQK(156) + EQK(158)=EG(7)*EG(15)/EG(4)/EG(17) + EQK(159)=EG(7)*EG(18)/EG(4)/EG(19) + EQK(160)=EG(7)*EG(18)/EG(4)/EG(20) + EQK(161)=EG(17)*EG(18)/EG(4)/EG(23) + EQK(162)=EG(1)*EG(22)/EG(24)*PFAC + EQK(163)=EG(7)*EG(24)/EG(4)/EG(25) + EQK(164)=EG(5)*EG(15)*EG(15)/EG(4)/EG(27)*PFAC + EQK(165)=EG(15)*EG(15)*EG(22)/EG(27)/EG(27)*PFAC + EQK(167)=EG(2)*EG(29)/EG(3)/EG(24) + EQK(170)=EG(13)/EG(1)/EG(10)/PFAC + EQK(172)=EG(3)*EG(18)/EG(4)/EG(11) + EQK(175)=EG(3)*EG(29)/EG(4)/EG(23) + EQK(176)=EG(7)*EG(22)/EG(4)/EG(23) + EQK(177)=EG(29)/EG(2)/EG(28)/PFAC + EQK(181)=EG(13)*EG(17)/EG(2)/EG(29) + EQK(182)=EG(1)*EG(28)/EG(2)/EG(29) + EQK(183)=EG(6)*EG(28)/EG(5)/EG(29) + EQK(184)=EG(17)*EG(19)/EG(5)/EG(29) +! +! +! ! Compute reverse reaction rates +! +! PARAMETER (SMALL = 1.D-200) +! + RB(1) = RF(1) / MAX(EQK(1),SMALL) + RB(2) = RF(2) / MAX(EQK(2),SMALL) + RB(3) = RF(3) / MAX(EQK(3),SMALL) + RB(4) = RF(4) / MAX(EQK(4),SMALL) + RB(5) = RF(5) / MAX(EQK(5),SMALL) + RB(6) = RF(6) / MAX(EQK(6),SMALL) + RB(7) = RF(7) / MAX(EQK(7),SMALL) + RB(8) = RF(8) / MAX(EQK(8),SMALL) + RB(9) = RF(9) / MAX(EQK(9),SMALL) + RB(10) = RF(10) / MAX(EQK(10),SMALL) + RB(11) = RF(11) / MAX(EQK(11),SMALL) + RB(12) = RF(12) / MAX(EQK(12),SMALL) + RB(13) = RF(13) / MAX(EQK(13),SMALL) + RB(14) = RF(14) / MAX(EQK(14),SMALL) + RB(15) = RF(15) / MAX(EQK(15),SMALL) + RB(16) = RF(16) / MAX(EQK(16),SMALL) + RB(17) = RF(17) / MAX(EQK(17),SMALL) + RB(18) = RF(18) / MAX(EQK(18),SMALL) + RB(19) = RF(19) / MAX(EQK(19),SMALL) + RB(20) = RF(20) / MAX(EQK(20),SMALL) + RB(21) = RF(21) / MAX(EQK(21),SMALL) + RB(22) = RF(22) / MAX(EQK(22),SMALL) + RB(23) = RF(23) / MAX(EQK(23),SMALL) + RB(24) = RF(24) / MAX(EQK(24),SMALL) + RB(25) = RF(25) / MAX(EQK(25),SMALL) + RB(26) = RF(26) / MAX(EQK(26),SMALL) + RB(27) = RF(27) / MAX(EQK(27),SMALL) + RB(28) = RF(28) / MAX(EQK(28),SMALL) + RB(29) = RF(29) / MAX(EQK(29),SMALL) + RB(30) = RF(30) / MAX(EQK(30),SMALL) + RB(31) = RF(31) / MAX(EQK(31),SMALL) + RB(32) = RF(32) / MAX(EQK(32),SMALL) + RB(33) = RF(33) / MAX(EQK(33),SMALL) + RB(34) = RF(34) / MAX(EQK(34),SMALL) + RB(35) = RF(35) / MAX(EQK(35),SMALL) + RB(36) = RF(36) / MAX(EQK(36),SMALL) + RB(37) = RF(37) / MAX(EQK(37),SMALL) + + RB(38) = RF(38) / MAX(EQK(38),SMALL) + RB(39) = RF(39) / MAX(EQK(39),SMALL) + RB(40) = RF(40) / MAX(EQK(40),SMALL) + RB(41) = RF(41) / MAX(EQK(41),SMALL) + RB(42) = RF(42) / MAX(EQK(42),SMALL) + RB(43) = RF(43) / MAX(EQK(43),SMALL) + RB(44) = RF(44) / MAX(EQK(44),SMALL) + RB(45) = RF(45) / MAX(EQK(45),SMALL) + RB(46) = RF(46) / MAX(EQK(46),SMALL) + RB(47) = RF(47) / MAX(EQK(47),SMALL) + RB(48) = RF(48) / MAX(EQK(48),SMALL) + RB(49) = RF(49) / MAX(EQK(49),SMALL) + RB(50) = RF(50) / MAX(EQK(50),SMALL) + RB(51) = RF(51) / MAX(EQK(51),SMALL) + RB(52) = RF(52) / MAX(EQK(52),SMALL) + RB(53) = RF(53) / MAX(EQK(53),SMALL) + RB(54) = RF(54) / MAX(EQK(54),SMALL) + RB(55) = RF(55) / MAX(EQK(55),SMALL) + RB(56) = RF(56) / MAX(EQK(56),SMALL) + RB(57) = RF(57) / MAX(EQK(57),SMALL) + RB(58) = RF(58) / MAX(EQK(58),SMALL) + RB(59) = RF(59) / MAX(EQK(59),SMALL) + RB(60) = RF(60) / MAX(EQK(60),SMALL) + RB(61) = RF(61) / MAX(EQK(61),SMALL) + RB(62) = RF(62) / MAX(EQK(62),SMALL) + RB(63) = RF(63) / MAX(EQK(63),SMALL) + RB(64) = RF(64) / MAX(EQK(64),SMALL) + RB(65) = RF(65) / MAX(EQK(65),SMALL) + RB(66) = RF(66) / MAX(EQK(66),SMALL) + RB(67) = RF(67) / MAX(EQK(67),SMALL) + RB(68) = RF(68) / MAX(EQK(68),SMALL) + RB(69) = RF(69) / MAX(EQK(69),SMALL) + RB(70) = RF(70) / MAX(EQK(70),SMALL) + RB(71) = RF(71) / MAX(EQK(71),SMALL) + RB(72) = RF(72) / MAX(EQK(72),SMALL) + RB(73) = RF(73) / MAX(EQK(73),SMALL) + RB(74) = RF(74) / MAX(EQK(74),SMALL) + RB(75) = RF(75) / MAX(EQK(75),SMALL) + RB(76) = RF(76) / MAX(EQK(76),SMALL) + RB(77) = RF(77) / MAX(EQK(77),SMALL) + RB(78) = RF(78) / MAX(EQK(78),SMALL) + RB(79) = RF(79) / MAX(EQK(79),SMALL) + RB(80) = RF(80) / MAX(EQK(80),SMALL) + RB(81) = RF(81) / MAX(EQK(81),SMALL) + RB(82) = RF(82) / MAX(EQK(82),SMALL) + RB(83) = RF(83) / MAX(EQK(83),SMALL) + RB(84) = RF(84) / MAX(EQK(84),SMALL) + RB(85) = RF(85) / MAX(EQK(85),SMALL) + RB(86) = RF(86) / MAX(EQK(86),SMALL) + RB(87) = RF(87) / MAX(EQK(87),SMALL) + RB(88) = RF(88) / MAX(EQK(88),SMALL) + RB(89) = RF(89) / MAX(EQK(89),SMALL) + RB(90) = RF(90) / MAX(EQK(90),SMALL) + RB(91) = RF(91) / MAX(EQK(91),SMALL) + RB(92) = RF(92) / MAX(EQK(92),SMALL) + RB(93) = RF(93) / MAX(EQK(93),SMALL) + RB(94) = RF(94) / MAX(EQK(94),SMALL) + RB(95) = RF(95) / MAX(EQK(95),SMALL) + RB(96) = RF(96) / MAX(EQK(96),SMALL) + RB(97) = RF(97) / MAX(EQK(97),SMALL) + RB(98) = RF(98) / MAX(EQK(98),SMALL) + RB(99) = RF(99) / MAX(EQK(99),SMALL) + RB(100) = RF(100) / MAX(EQK(100),SMALL) + RB(101) = RF(101) / MAX(EQK(101),SMALL) + RB(102) = RF(102) / MAX(EQK(102),SMALL) + RB(103) = RF(103) / MAX(EQK(103),SMALL) + RB(104) = RF(104) / MAX(EQK(104),SMALL) + RB(105) = RF(105) / MAX(EQK(105),SMALL) + RB(106) = RF(106) / MAX(EQK(106),SMALL) + RB(107) = RF(107) / MAX(EQK(107),SMALL) + RB(108) = RF(108) / MAX(EQK(108),SMALL) + RB(109) = RF(109) / MAX(EQK(109),SMALL) + RB(110) = RF(110) / MAX(EQK(110),SMALL) + RB(111) = RF(111) / MAX(EQK(111),SMALL) + RB(112) = RF(112) / MAX(EQK(112),SMALL) + RB(113) = RF(113) / MAX(EQK(113),SMALL) + RB(114) = RF(114) / MAX(EQK(114),SMALL) + RB(115) = RF(115) / MAX(EQK(115),SMALL) + RB(116) = RF(116) / MAX(EQK(116),SMALL) + RB(117) = RF(117) / MAX(EQK(117),SMALL) + RB(118) = RF(118) / MAX(EQK(118),SMALL) + RB(119) = RF(119) / MAX(EQK(119),SMALL) + RB(120) = RF(120) / MAX(EQK(120),SMALL) + RB(121) = RF(121) / MAX(EQK(121),SMALL) + RB(122) = RF(122) / MAX(EQK(122),SMALL) + RB(123) = RF(123) / MAX(EQK(123),SMALL) + RB(124) = RF(124) / MAX(EQK(124),SMALL) + RB(125) = RF(125) / MAX(EQK(125),SMALL) + RB(126) = 0.0 + RB(127) = RF(127) / MAX(EQK(127),SMALL) + RB(128) = RF(128) / MAX(EQK(128),SMALL) + RB(129) = RF(129) / MAX(EQK(129),SMALL) + RB(130) = RF(130) / MAX(EQK(130),SMALL) + RB(131) = RF(131) / MAX(EQK(131),SMALL) + RB(132) = RF(132) / MAX(EQK(132),SMALL) + RB(133) = RF(133) / MAX(EQK(133),SMALL) + RB(134) = RF(134) / MAX(EQK(134),SMALL) + RB(135) = RF(135) / MAX(EQK(135),SMALL) + RB(136) = RF(136) / MAX(EQK(136),SMALL) + RB(137) = RF(137) / MAX(EQK(137),SMALL) + RB(138) = RF(138) / MAX(EQK(138),SMALL) + RB(139) = RF(139) / MAX(EQK(139),SMALL) + RB(140) = RF(140) / MAX(EQK(140),SMALL) + RB(141) = RF(141) / MAX(EQK(141),SMALL) + RB(142) = RF(142) / MAX(EQK(142),SMALL) + RB(143) = RF(143) / MAX(EQK(143),SMALL) + RB(144) = RF(144) / MAX(EQK(144),SMALL) + RB(145) = RF(145) / MAX(EQK(145),SMALL) + RB(146) = RF(146) / MAX(EQK(146),SMALL) + RB(147) = RF(147) / MAX(EQK(147),SMALL) + RB(148) = RF(148) / MAX(EQK(148),SMALL) + RB(149) = RF(149) / MAX(EQK(149),SMALL) + RB(150) = RF(150) / MAX(EQK(150),SMALL) + RB(151) = RF(151) / MAX(EQK(151),SMALL) + RB(152) = RF(152) / MAX(EQK(152),SMALL) + RB(153) = RF(153) / MAX(EQK(153),SMALL) + RB(154) = RF(154) / MAX(EQK(154),SMALL) + RB(155) = RF(155) / MAX(EQK(155),SMALL) + RB(156) = RF(156) / MAX(EQK(156),SMALL) + RB(157) = RF(157) / MAX(EQK(157),SMALL) + RB(158) = RF(158) / MAX(EQK(158),SMALL) + RB(159) = RF(159) / MAX(EQK(159),SMALL) + RB(160) = RF(160) / MAX(EQK(160),SMALL) + RB(161) = RF(161) / MAX(EQK(161),SMALL) + RB(162) = RF(162) / MAX(EQK(162),SMALL) + RB(163) = RF(163) / MAX(EQK(163),SMALL) + RB(164) = RF(164) / MAX(EQK(164),SMALL) + RB(165) = RF(165) / MAX(EQK(165),SMALL) + RB(166) = 0.0 + RB(167) = RF(167) / MAX(EQK(167),SMALL) + RB(168) = RF(168) / MAX(EQK(168),SMALL) + RB(169) = 0.0 + RB(170) = RF(170) / MAX(EQK(170),SMALL) + RB(171) = 0.0 + RB(172) = RF(172) / MAX(EQK(172),SMALL) + RB(173) = 0.0 + RB(174) = 0.0 + RB(175) = RF(175) / MAX(EQK(175),SMALL) + RB(176) = RF(176) / MAX(EQK(176),SMALL) + RB(177) = RF(177) / MAX(EQK(177),SMALL) + RB(178) = 0.0 + RB(179) = 0.0 + RB(180) = 0.0 + RB(181) = RF(181) / MAX(EQK(181),SMALL) + RB(182) = RF(182) / MAX(EQK(182),SMALL) + RB(183) = RF(183) / MAX(EQK(183),SMALL) + RB(184) = RF(184) / MAX(EQK(184),SMALL) +! +! +! rates at low pressure limit +! + RKLOW(1) = EXP(3.40312786D1 -1.50965D3/T) + RKLOW(2) = EXP(5.99064331D1 -2.76D0*ALOGT -8.05146668D2/T) + RKLOW(3) = EXP(7.69484824D1 -4.76D0*ALOGT -1.22784867D3/T) + RKLOW(4) = EXP(5.61662604D1 -2.57D0*ALOGT -2.13867084D2/T) + RKLOW(5) = EXP(7.39217399D1 -4.82D0*ALOGT -3.28600484D3/T) + RKLOW(6) = EXP(6.98660102D1 -4.8D0*ALOGT -2.79788467D3/T) + RKLOW(7) = EXP(7.28526099D1 -4.65D0*ALOGT -2.55634067D3/T) + RKLOW(8) = EXP(9.59450043D1 -7.44D0*ALOGT -7.08529068D3/T) + RKLOW(9) = EXP(9.34384048D1 -7.27D0*ALOGT -3.63322434D3/T) + RKLOW(10) = EXP(6.9414025D1 -3.86D0*ALOGT -1.67067934D3/T) + RKLOW(11) = EXP(9.61977483D1 -7.62D0*ALOGT -3.50742017D3/T) + RKLOW(12) = EXP(9.50941235D1 -7.08D0*ALOGT -3.36400342D3/T) + RKLOW(13) = EXP(6.37931383D1 -3.42D0*ALOGT -4.24463259D4/T) + RKLOW(14) = EXP(4.22794408D1 -9.D-1*ALOGT +8.55468335D2/T) + RKLOW(15) = EXP(8.42793577D1 -5.92D0*ALOGT -1.58010034D3/T) + RKLOW(16) = EXP(6.54619238D1 -3.74D0*ALOGT -9.74227469D2/T) + RKLOW(17) = EXP(7.69748493D1 -5.11D0*ALOGT -3.57032226D3/T) + RKLOW(18) = EXP(8.81295053D1 -6.36D0*ALOGT -2.536212D3/T) + RKLOW(19) = EXP(9.56297642D1 -7.03D0*ALOGT -1.38988444D3/T) + RKLOW(20) = EXP(1.17889265D2 -9.3D0*ALOGT -4.92145901D4/T) + RKLOW(21) = EXP(5.91374013D1 -2.8D0*ALOGT -2.96897834D2/T) + RKLOW(22) = EXP(9.67205025D1 -7.63D0*ALOGT -1.93939704D3/T) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! third-body concentrations +! ! +! SUBROUTINE RATX (T, C, RF, RB, RKLOW) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! PARAMETER (SMALL = 1.D-200) +! DIMENSION C(*), RF(*), RB(*), RKLOW(*) +! + ALOGT = LOG(T) + CTOT = 0.0 + DO K = 1, 19 + CTOT = CTOT + C(K) + ENDDO +! + CTB(1) = CTOT + 1.4D0*C(1) + 1.44D1*C(6) + C(10) + 7.5D-1*C(11) & + + 2.6D0*C(12) + 2.D0*C(17) + CTB(2) = CTOT + C(1) + 5.D0*C(6) + C(10) + 5.D-1*C(11) + C(12) & + + 2.D0*C(17) + CTB(47) = CTB(2) + CTB(51) = CTB(2) + CTB(53) = CTB(2) + CTB(54) = CTB(2) + CTB(56) = CTB(2) + CTB(60) = CTB(2) + CTB(67) = CTB(2) + CTB(68) = CTB(2) + CTB(70) = CTB(2) + CTB(72) = CTB(2) + CTB(78) = CTB(2) + CTB(80) = CTB(2) + CTB(90) = CTB(2) + CTB(122) = CTB(2) + CTB(131) = CTB(2) + CTB(137) = CTB(2) + CTB(148) = CTB(2) + CTB(162) = CTB(2) + CTB(170) = CTB(2) + CTB(177) = CTB(2) + CTB(12) = CTOT + C(1) + 5.D0*C(4) + 5.D0*C(6) + C(10) & + + 5.D-1*C(11) + 2.5D0*C(12) + 2.D0*C(17) + CTB(31) = CTOT - C(4) - C(6) - 2.5D-1*C(11) + 5.D-1*C(12) & + + 5.D-1*C(17) - C(19) + CTB(36) = CTOT - C(1) - C(6) + C(10) - C(12) + 2.D0*C(17) + CTB(40) = CTOT - 2.7D-1*C(1) + 2.65D0*C(6) + C(10) + 2.D0*C(17) + CTB(49) = CTOT + C(1) + 5.D0*C(6) + 2.D0*C(10) + 5.D-1*C(11) & + + C(12) + 2.D0*C(17) + CTB(157) = CTOT + C(1) - C(6) + C(10) + 5.D-1*C(11) + C(12) & + + 2.D0*C(17) +! +! +! fall-off reactions +! +! + PR = RKLOW(1) * CTB(12) / RF(12) + PCOR = PR / (1.0 + PR) + RF(12) = RF(12) * PCOR + RB(12) = RB(12) * PCOR +! + PR = RKLOW(2) * CTB(47) / RF(47) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.38D-1*EXP(-T/9.1D1) + 5.62D-1*EXP(-T/5.836D3)& + + EXP(-8.552D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(47) = RF(47) * PCOR + RB(47) = RB(47) * PCOR +! + PR = RKLOW(3) * CTB(49) / RF(49) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.17D-1*EXP(-T/7.4D1) + 7.83D-1*EXP(-T/2.941D3)& + + EXP(-6.964D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(49) = RF(49) * PCOR + RB(49) = RB(49) * PCOR +! + PR = RKLOW(4) * CTB(51) / RF(51) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.176D-1*EXP(-T/2.71D2) + 7.824D-1*EXP(-T/2.755D3)& + + EXP(-6.57D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(51) = RF(51) * PCOR + RB(51) = RB(51) * PCOR + + PR = RKLOW(5) * CTB(53) / RF(53) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.813D-1*EXP(-T/1.03D2) + 7.187D-1*EXP(-T/1.291D3)& + + EXP(-4.16D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(53) = RF(53) * PCOR + RB(53) = RB(53) * PCOR + + PR = RKLOW(6) * CTB(54) / RF(54) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.42D-1*EXP(-T/9.4D1) + 7.58D-1*EXP(-T/1.555D3)& + + EXP(-4.2D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(54) = RF(54) * PCOR + RB(54) = RB(54) * PCOR + + PR = RKLOW(7) * CTB(56) / RF(56) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.D-1*EXP(-T/1.D2) + 6.D-1*EXP(-T/9.D4)& + + EXP(-1.D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(56) = RF(56) * PCOR + RB(56) = RB(56) * PCOR + + PR = RKLOW(8) * CTB(60) / RF(60) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.D-1*EXP(-T/1.D2) + 7.D-1*EXP(-T/9.D4)& + + EXP(-1.D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(60) = RF(60) * PCOR + RB(60) = RB(60) * PCOR + + PR = RKLOW(9) * CTB(67) / RF(67) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.493D-1*EXP(-T/9.85D1) + 7.507D-1*EXP(-T/1.302D3)& + + EXP(-4.167D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(67) = RF(67) * PCOR + RB(67) = RB(67) * PCOR + + PR = RKLOW(10) * CTB(68) / RF(68) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.18D-1*EXP(-T/2.075D2) + 7.82D-1*EXP(-T/2.663D3)& + + EXP(-6.095D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(68) = RF(68) * PCOR + RB(68) = RB(68) * PCOR + + PR = RKLOW(11) * CTB(70) / RF(70) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.47D-2*EXP(-T/2.1D2) + 9.753D-1*EXP(-T/9.84D2)& + + EXP(-4.374D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(70) = RF(70) * PCOR + RB(70) = RB(70) * PCOR + + PR = RKLOW(12) * CTB(72) / RF(72) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 1.578D-1*EXP(-T/1.25D2) + 8.422D-1*EXP(-T/2.219D3)& + + EXP(-6.882D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(72) = RF(72) * PCOR + RB(72) = RB(72) * PCOR + + PR = RKLOW(13) * CTB(78) / RF(78) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 6.8D-2*EXP(-T/1.97D2) + 9.32D-1*EXP(-T/1.54D3)& + + EXP(-1.03D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(78) = RF(78) * PCOR + RB(78) = RB(78) * PCOR + + PR = RKLOW(14) * CTB(80) / RF(80) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.654D-1*EXP(-T/9.4D1) + 7.346D-1*EXP(-T/1.756D3)& + + EXP(-5.182D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(80) = RF(80) * PCOR + RB(80) = RB(80) * PCOR + + PR = RKLOW(15) * CTB(90) / RF(90) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 5.88D-1*EXP(-T/1.95D2) + 4.12D-1*EXP(-T/5.9D3)& + + EXP(-6.394D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(90) = RF(90) * PCOR + RB(90) = RB(90) * PCOR + + PR = RKLOW(16) * CTB(122) / RF(122) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.243D-1*EXP(-T/2.37D2) + 5.757D-1*EXP(-T/1.652D3)& + + EXP(-5.069D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(122) = RF(122) * PCOR + RB(122) = RB(122) * PCOR + + PR = RKLOW(17) * CTB(131) / RF(131) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.093D-1*EXP(-T/2.75D2) + 5.907D-1*EXP(-T/1.226D3)& + + EXP(-5.185D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(131) = RF(131) * PCOR + RB(131) = RB(131) * PCOR + + PR = RKLOW(18) * CTB(137) / RF(137) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.973D-1*EXP(-T/2.08D2) + 6.027D-1*EXP(-T/3.922D3)& + + EXP(-1.018D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(137) = RF(137) * PCOR + RB(137) = RB(137) * PCOR + + PR = RKLOW(19) * CTB(148) / RF(148) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.81D-1*EXP(-T/7.32D1) + 6.19D-1*EXP(-T/1.18D3)& + + EXP(-9.999D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(148) = RF(148) * PCOR + RB(148) = RB(148) * PCOR + + PR = RKLOW(20) * CTB(162) / RF(162) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.655D-1*EXP(-T/1.8D2) + 7.345D-1*EXP(-T/1.035D3)& + + EXP(-5.417D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(162) = RF(162) * PCOR + RB(162) = RB(162) * PCOR + + PR = RKLOW(21) * CTB(170) / RF(170) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.22D-1*EXP(-T/1.22D2) + 5.78D-1*EXP(-T/2.535D3)& + + EXP(-9.365D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(170) = RF(170) * PCOR + RB(170) = RB(170) * PCOR + + PR = RKLOW(22) * CTB(177) / RF(177) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 5.35D-1*EXP(-T/2.01D2) + 4.65D-1*EXP(-T/1.773D3)& + + EXP(-5.333D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(177) = RF(177) * PCOR + RB(177) = RB(177) * PCOR + + RF(1) = RF(1)*CTB(1)*C(3)*C(3) + RF(2) = RF(2)*CTB(2)*C(3)*C(2) + RF(3) = RF(3)*C(3)*C(1) + RF(4) = RF(4)*C(3)*C(7) + RF(5) = RF(5)*C(3)*C(8) + RF(6) = RF(6)*C(3) + RF(7) = RF(7)*C(3) + RF(8) = RF(8)*C(3) + RF(9) = RF(9)*C(3) + RF(10) = RF(10)*C(3)*C(9) + RF(11) = RF(11)*C(3)*C(10) + RF(12) = RF(12)*C(3)*C(11) + RF(13) = RF(13)*C(3) + RF(14) = RF(14)*C(3) + RF(15) = RF(15)*C(3)*C(13) + RF(16) = RF(16)*C(3) + RF(17) = RF(17)*C(3) + RF(18) = RF(18)*C(3)*C(14) + RF(19) = RF(19)*C(3)*C(14) + RF(20) = RF(20)*C(3)*C(15) + RF(21) = RF(21)*C(3)*C(15) + RF(22) = RF(22)*C(3) + RF(23) = RF(23)*C(3)*C(16) + RF(24) = RF(24)*C(3) + RF(25) = RF(25)*C(3)*C(17) + RF(26) = RF(26)*C(3) + RF(27) = RF(27)*C(3)*C(18) + RF(28) = RF(28)*C(3)*C(18) + RF(29) = RF(29)*C(4)*C(11) + RF(30) = RF(30)*C(4)*C(13) + RF(31) = RF(31)*CTB(31)*C(2)*C(4) + RF(32) = RF(32)*C(2)*C(4)*C(4) + RF(33) = RF(33)*C(2)*C(4)*C(6) + RF(34) = RF(34)*C(2)*C(4)*C(19) + RF(35) = RF(35)*C(2)*C(4) + RF(36) = RF(36)*CTB(36)*C(2)*C(2) + RF(37) = RF(37)*C(2)*C(2)*C(1) + RF(38) = RF(38)*C(2)*C(2)*C(6) + RF(39) = RF(39)*C(2)*C(2)*C(12) + RF(40) = RF(40)*CTB(40)*C(2)*C(5) + RF(41) = RF(41)*C(2)*C(7) + RF(42) = RF(42)*C(2)*C(7) + RF(43) = RF(43)*C(2)*C(7) + RF(44) = RF(44)*C(2)*C(8) + RF(45) = RF(45)*C(2)*C(8) + RF(46) = RF(46)*C(2) + RF(47) = RF(47)*C(2) + RF(48) = RF(48)*C(2) + RF(49) = RF(49)*C(2)*C(9) + RF(50) = RF(50)*C(2)*C(10) + RF(51) = RF(51)*C(2) + RF(52) = RF(52)*C(2) + RF(53) = RF(53)*C(2)*C(13) + RF(54) = RF(54)*C(2)*C(13) + RF(55) = RF(55)*C(2)*C(13) + RF(56) = RF(56)*C(2) + RF(57) = RF(57)*C(2) + RF(58) = RF(58)*C(2) + RF(59) = RF(59)*C(2) + RF(60) = RF(60)*C(2) + RF(61) = RF(61)*C(2) + RF(62) = RF(62)*C(2) + RF(63) = RF(63)*C(2) + RF(64) = RF(64)*C(2) + RF(65) = RF(65)*C(2)*C(14) + RF(66) = RF(66)*C(2)*C(14) + RF(67) = RF(67)*C(2)*C(15) + RF(68) = RF(68)*C(2) + RF(69) = RF(69)*C(2) + RF(70) = RF(70)*C(2)*C(16) + RF(71) = RF(71)*C(2)*C(16) + RF(72) = RF(72)*C(2) + RF(73) = RF(73)*C(2) + RF(74) = RF(74)*C(2)*C(17) + RF(75) = RF(75)*C(2) + RF(76) = RF(76)*C(2)*C(18) + RF(77) = RF(77)*C(2)*C(18) + RF(78) = RF(78)*C(1)*C(11) + RF(79) = RF(79)*C(5)*C(1) + RF(80) = RF(80)*C(5)*C(5) + RF(81) = RF(81)*C(5)*C(5) + RF(82) = RF(82)*C(5)*C(7) + RF(83) = RF(83)*C(5)*C(8) + RF(84) = RF(84)*C(5)*C(8) + RF(85) = RF(85)*C(5) + RF(86) = RF(86)*C(5) + RF(87) = RF(87)*C(5) + RF(88) = RF(88)*C(5) + RF(89) = RF(89)*C(5) + RF(90) = RF(90)*C(5)*C(9) + RF(91) = RF(91)*C(5)*C(9) + RF(92) = RF(92)*C(5)*C(9) + RF(93) = RF(93)*C(5)*C(10) + RF(94) = RF(94)*C(5)*C(11) + RF(95) = RF(95)*C(5) + RF(96) = RF(96)*C(5)*C(13) + RF(97) = RF(97)*C(5) + RF(98) = RF(98)*C(5) + RF(99) = RF(99)*C(5)*C(14) + RF(100) = RF(100)*C(5)*C(14) + RF(101) = RF(101)*C(5)*C(15) + RF(102) = RF(102)*C(5)*C(15) + RF(103) = RF(103)*C(5) + RF(104) = RF(104)*C(5)*C(16) + RF(105) = RF(105)*C(5)*C(17) + RF(106) = RF(106)*C(5)*C(18) + RF(107) = RF(107)*C(7)*C(7) + RF(108) = RF(108)*C(7)*C(7) + RF(109) = RF(109)*C(7) + RF(110) = RF(110)*C(7)*C(9) + RF(111) = RF(111)*C(7)*C(9) + RF(112) = RF(112)*C(7)*C(11) + RF(113) = RF(113)*C(7)*C(13) + RF(114) = RF(114)*C(4) + RF(115) = RF(115)*C(9) + RF(116) = RF(116)*C(4) + RF(117) = RF(117)*C(1) + RF(118) = RF(118)*C(6) + RF(120) = RF(120)*C(9) + RF(121) = RF(121)*C(10) + RF(122) = RF(122)*C(11) + RF(123) = RF(123)*C(12) + RF(124) = RF(124)*C(13) + RF(126) = RF(126)*C(4) + RF(127) = RF(127)*C(1) + RF(129) = RF(129)*C(9) + RF(130) = RF(130)*C(10) + RF(131) = RF(131)*C(11) + RF(133) = RF(133)*C(19) + RF(134) = RF(134)*C(4) + RF(135) = RF(135)*C(4) + RF(136) = RF(136)*C(1) + RF(137) = RF(137)*C(6) + RF(138) = RF(138)*C(6) + RF(139) = RF(139)*C(9) + RF(140) = RF(140)*C(10) + RF(141) = RF(141)*C(11) + RF(142) = RF(142)*C(12) + RF(143) = RF(143)*C(12) + RF(144) = RF(144)*C(17) + RF(145) = RF(145)*C(9)*C(4) + RF(146) = RF(146)*C(9)*C(4) + RF(147) = RF(147)*C(9)*C(8) + RF(148) = RF(148)*C(9)*C(9) + RF(149) = RF(149)*C(9)*C(9) + RF(150) = RF(150)*C(9) + RF(151) = RF(151)*C(9)*C(13) + RF(152) = RF(152)*C(9)*C(14) + RF(153) = RF(153)*C(9)*C(14) + RF(154) = RF(154)*C(9)*C(16) + RF(155) = RF(155)*C(9)*C(17) + RF(156) = RF(156)*C(6) + RF(157) = RF(157)*CTB(157) + RF(158) = RF(158)*C(4) + RF(159) = RF(159)*C(4) + RF(160) = RF(160)*C(4) + RF(161) = RF(161)*C(4) + RF(162) = RF(162)*C(16) + RF(163) = RF(163)*C(4) + RF(164) = RF(164)*C(4) + RF(166) = RF(166)*C(3)*C(9) + RF(167) = RF(167)*C(3)*C(16) + RF(168) = RF(168)*C(5)*C(7) + RF(169) = RF(169)*C(5)*C(9) + RF(170) = RF(170)*C(1) + RF(171) = RF(171)*C(4) + RF(172) = RF(172)*C(4) + RF(174) = RF(174)*C(6) + RF(175) = RF(175)*C(4) + RF(176) = RF(176)*C(4) + RF(177) = RF(177)*C(2)*C(18) + RF(178) = RF(178)*C(3) + RF(179) = RF(179)*C(4) + RF(180) = RF(180)*C(4) + RF(181) = RF(181)*C(2) + RF(182) = RF(182)*C(2) + RF(183) = RF(183)*C(5) + RF(184) = RF(184)*C(5) + RB(1) = RB(1)*CTB(1)*C(4) + RB(2) = RB(2)*CTB(2)*C(5) + RB(3) = RB(3)*C(2)*C(5) + RB(4) = RB(4)*C(5)*C(4) + RB(5) = RB(5)*C(5)*C(7) + RB(6) = RB(6)*C(2)*C(11) + RB(7) = RB(7)*C(2) + RB(8) = RB(8)*C(1)*C(11) + RB(9) = RB(9)*C(2) + RB(10) = RB(10)*C(2)*C(13) + RB(11) = RB(11)*C(5)*C(9) + RB(12) = RB(12)*C(12) + RB(13) = RB(13)*C(5)*C(11) + RB(14) = RB(14)*C(2)*C(12) + RB(15) = RB(15)*C(5) + RB(16) = RB(16)*C(5)*C(13) + RB(17) = RB(17)*C(5)*C(13) + RB(18) = RB(18)*C(5) + RB(19) = RB(19)*C(5) + RB(20) = RB(20)*C(2) + RB(21) = RB(21)*C(11) + RB(22) = RB(22)*C(2)*C(18) + RB(23) = RB(23)*C(9) + RB(24) = RB(24)*C(9)*C(13) + RB(25) = RB(25)*C(5) + RB(26) = RB(26)*C(2)*C(11)*C(11) + RB(27) = RB(27)*C(5) + RB(28) = RB(28)*C(12) + RB(29) = RB(29)*C(3)*C(12) + RB(30) = RB(30)*C(7) + RB(31) = RB(31)*CTB(31)*C(7) + RB(32) = RB(32)*C(7)*C(4) + RB(33) = RB(33)*C(7)*C(6) + RB(34) = RB(34)*C(7)*C(19) + RB(35) = RB(35)*C(3)*C(5) + RB(36) = RB(36)*CTB(36)*C(1) + RB(37) = RB(37)*C(1)*C(1) + RB(38) = RB(38)*C(1)*C(6) + RB(39) = RB(39)*C(1)*C(12) + RB(40) = RB(40)*CTB(40)*C(6) + RB(41) = RB(41)*C(3)*C(6) + RB(42) = RB(42)*C(4)*C(1) + RB(43) = RB(43)*C(5)*C(5) + RB(44) = RB(44)*C(7)*C(1) + RB(45) = RB(45)*C(5)*C(6) + RB(46) = RB(46)*C(1) + RB(47) = RB(47)*C(9) + RB(48) = RB(48)*C(1) + RB(49) = RB(49)*C(10) + RB(50) = RB(50)*C(9)*C(1) + RB(51) = RB(51)*C(13) + RB(52) = RB(52)*C(1)*C(11) + RB(55) = RB(55)*C(1) + RB(56) = RB(56)*C(14) + RB(57) = RB(57)*C(1)*C(13) + RB(58) = RB(58)*C(5)*C(9) + RB(59) = RB(59)*C(6) + RB(60) = RB(60)*C(14) + RB(61) = RB(61)*C(2) + RB(62) = RB(62)*C(1)*C(13) + RB(63) = RB(63)*C(5)*C(9) + RB(64) = RB(64)*C(6) + RB(65) = RB(65)*C(1) + RB(66) = RB(66)*C(1) + RB(68) = RB(68)*C(16) + RB(69) = RB(69)*C(1)*C(15) + RB(71) = RB(71)*C(1) + RB(72) = RB(72)*C(17) + RB(73) = RB(73)*C(1)*C(16) + RB(74) = RB(74)*C(1) + RB(75) = RB(75)*C(11) + RB(76) = RB(76)*C(1) + RB(77) = RB(77)*C(9)*C(11) + RB(78) = RB(78)*C(13) + RB(79) = RB(79)*C(2)*C(6) + RB(80) = RB(80)*C(8) + RB(81) = RB(81)*C(3)*C(6) + RB(82) = RB(82)*C(4)*C(6) + RB(83) = RB(83)*C(7)*C(6) + RB(84) = RB(84)*C(7)*C(6) + RB(85) = RB(85)*C(2)*C(11) + RB(86) = RB(86)*C(2) + RB(87) = RB(87)*C(2)*C(13) + RB(88) = RB(88)*C(6) + RB(89) = RB(89)*C(2)*C(13) + RB(90) = RB(90)*C(14) + RB(91) = RB(91)*C(6) + RB(92) = RB(92)*C(6) + RB(93) = RB(93)*C(9)*C(6) + RB(94) = RB(94)*C(2)*C(12) + RB(95) = RB(95)*C(6)*C(11) + RB(96) = RB(96)*C(6) + RB(97) = RB(97)*C(6)*C(13) + RB(98) = RB(98)*C(6)*C(13) + RB(99) = RB(99)*C(6) + RB(100) = RB(100)*C(6) + RB(101) = RB(101)*C(2)*C(18) + RB(102) = RB(102)*C(9)*C(11) + RB(103) = RB(103)*C(6)*C(15) + RB(104) = RB(104)*C(6) + RB(105) = RB(105)*C(6) + RB(106) = RB(106)*C(6) + RB(107) = RB(107)*C(4)*C(8) + RB(108) = RB(108)*C(4)*C(8) + RB(109) = RB(109)*C(5)*C(13) + RB(110) = RB(110)*C(4)*C(10) + RB(111) = RB(111)*C(5) + RB(112) = RB(112)*C(5)*C(12) + RB(113) = RB(113)*C(8) + RB(114) = RB(114)*C(3)*C(11) + RB(115) = RB(115)*C(2)*C(15) + RB(116) = RB(116)*C(3) + RB(117) = RB(117)*C(2) + RB(118) = RB(118)*C(2)*C(13) + RB(119) = RB(119)*C(2)*C(15) + RB(120) = RB(120)*C(2) + RB(121) = RB(121)*C(2)*C(16) + RB(123) = RB(123)*C(11) + RB(124) = RB(124)*C(2)*C(18) + RB(125) = RB(125)*C(11)*C(15) + RB(127) = RB(127)*C(2)*C(9) + RB(128) = RB(128)*C(1)*C(15) + RB(129) = RB(129)*C(2)*C(16) + RB(130) = RB(130)*C(9)*C(9) + RB(131) = RB(131)*C(18) + RB(132) = RB(132)*C(11) + RB(133) = RB(133)*C(19) + RB(134) = RB(134)*C(2)*C(5)*C(11) + RB(135) = RB(135)*C(11)*C(6) + RB(136) = RB(136)*C(9)*C(2) + RB(137) = RB(137)*C(14) + RB(138) = RB(138)*C(6) + RB(139) = RB(139)*C(2)*C(16) + RB(140) = RB(140)*C(9)*C(9) + RB(141) = RB(141)*C(11) + RB(142) = RB(142)*C(12) + RB(143) = RB(143)*C(11)*C(13) + RB(144) = RB(144)*C(9) + RB(145) = RB(145)*C(3) + RB(146) = RB(146)*C(5)*C(13) + RB(147) = RB(147)*C(7)*C(10) + RB(148) = RB(148)*C(17) + RB(149) = RB(149)*C(2) + RB(150) = RB(150)*C(10)*C(11) + RB(151) = RB(151)*C(10) + RB(152) = RB(152)*C(10) + RB(153) = RB(153)*C(10) + RB(154) = RB(154)*C(10) + RB(155) = RB(155)*C(10) + RB(156) = RB(156)*C(2)*C(11)*C(6) + RB(157) = RB(157)*CTB(157)*C(2)*C(11) + RB(158) = RB(158)*C(7)*C(11) + RB(159) = RB(159)*C(7)*C(13) + RB(160) = RB(160)*C(7)*C(13) + RB(161) = RB(161)*C(13) + RB(162) = RB(162)*C(1)*C(15) + RB(163) = RB(163)*C(7)*C(16) + RB(164) = RB(164)*C(5)*C(11)*C(11) + RB(165) = RB(165)*C(11)*C(11)*C(15) + RB(167) = RB(167)*C(2) + RB(168) = RB(168)*C(4)*C(6) + RB(170) = RB(170)*C(9) + RB(172) = RB(172)*C(3)*C(13) + RB(175) = RB(175)*C(3) + RB(176) = RB(176)*C(7)*C(15) + RB(181) = RB(181)*C(9) + RB(182) = RB(182)*C(18)*C(1) + RB(183) = RB(183)*C(6)*C(18) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! solving QSS species concentration +! ------------------------------------------- +! +! SUBROUTINE QSSA(RF, RB, XQ) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! PARAMETER (SMALL = 1.D-200) +! DIMENSION RF(*), RB(*), XQ(*) +! + RF(119) = 0.D0 + RF(125) = 0.D0 + RF(128) = 0.D0 + RF(132) = 0.D0 + RF(165) = 0.D0 + RF(173) = 0.D0 + RB(180) = 0.D0 + RB(184) = 0.D0 + +! C + DEN = +RF( 85) +RF(114) +RF(115) +RB( 46) + A1_0 = ( +RB( 85) +RB(114) +RB(115) )/MAX(DEN, SMALL) + A1_2 = ( +RF( 46) )/MAX(DEN, SMALL) +! CH + DEN = +RF( 6) +RF( 46) +RF( 86) +RF(116) +RF(117) & + +RF(118) +RF(120) +RF(121) +RF(122) +RF(123) +RF(124) & + +RF(170) +RB( 48) +RB( 88) + A2_0 = ( +RB( 6) +RB(118) +RB(119) +RB(121) +RB(124) & + +RB(125) +RB(170) )/MAX(DEN, SMALL) + A2_1 = ( +RB( 46) )/MAX(DEN, SMALL) + A2_3 = ( +RF( 88) +RB(117) )/MAX(DEN, SMALL) + A2_4 = ( +RF( 48) )/MAX(DEN, SMALL) + A2_5 = ( +RB( 86) +RB(116) +RB(123) )/MAX(DEN, SMALL) + A2_8 = ( +RB(120) )/MAX(DEN, SMALL) + + A2_10 = ( +RB(122) )/MAX(DEN, SMALL) +! CH2 + DEN = +RF( 7) +RF( 47) +RF( 87) +RF( 88) +RF(109) & + +RF(126) +RF(127) +RF(129) +RF(130) +RF(131) +RF(171) & + +RF(172) +RB( 21) +RB( 28) +RB( 91) +RB(117) +RB(133) & + +RB(138) +RB(141) +RB(142) +RB(178) + A3_0 = ( +RF( 21) +RF( 28) +RB( 47) +RB( 87) +RF( 91) & + +RB(109) +RB(119) +RB(126) +RB(127) +RB(128) +RB(128) & + +RB(129) +RB(130) +RB(131) +RB(171) +RB(172) +RB(173) & + +RB(173) )/MAX(DEN, SMALL) + A3_2 = ( +RB( 88) +RF(117) )/MAX(DEN, SMALL) + A3_4 = ( +RF(133) +RF(138) +RF(141) +RF(142) )/MAX(DEN, SMALL) + A3_5 = ( +RB( 7) )/MAX(DEN, SMALL) + A3_8 = ( +RB(132) )/MAX(DEN, SMALL) + A3_11 = ( +RF(178) )/MAX(DEN, SMALL) +! CH2(S) + DEN = +RF( 8) +RF( 9) +RF( 48) +RF( 89) +RF(133) & + +RF(134) +RF(135) +RF(136) +RF(137) +RF(138) +RF(139) & + +RF(140) +RF(141) +RF(142) +RF(143) +RF(144) +RF(174) & + +RB( 59) +RB( 64) +RB( 75) +RB( 92) + A4_0 = ( +RB( 8) +RB( 89) +RF( 92) +RB(134) +RB(135) & + +RB(136) +RB(137) +RB(139) +RB(140) +RB(143) +RB(174) )& + /MAX(DEN, SMALL) + A4_2 = ( +RB( 48) )/MAX(DEN, SMALL) + A4_3 = ( +RB(133) +RB(138) +RB(141) +RB(142) )/MAX(DEN, SMALL) + A4_5 = ( +RB( 9) )/MAX(DEN, SMALL) + A4_6 = ( +RF( 59) )/MAX(DEN, SMALL) + A4_7 = ( +RF( 64) )/MAX(DEN, SMALL) + A4_9 = ( +RB(144) )/MAX(DEN, SMALL) + A4_10 = ( +RF( 75) )/MAX(DEN, SMALL) +! HCO + DEN = +RF( 13) +RF( 14) +RF( 51) +RF( 52) +RF( 95) & + +RF(150) +RF(156) +RF(157) +RF(158) +RB( 7) +RB( 9) & + +RB( 15) +RB( 23) +RB( 30) +RB( 55) +RB( 86) +RB( 96) & + +RB(113) +RB(116) +RB(123) +RB(151) +RB(161) +RB(181) + A5_0 = ( +RB( 13) +RB( 14) +RF( 15) +RF( 23) +RF( 30) & + +RB( 51) +RB( 52) +RF( 55) +RB( 95) +RF( 96) +RF(113) & + +RB(150) +RF(151) +RB(156) +RB(157) +RB(158) )/MAX(DEN, SMALL) + A5_2 = ( +RF( 86) +RF(116) +RF(123) )/MAX(DEN, SMALL) + A5_3 = ( +RF( 7) )/MAX(DEN, SMALL) + A5_4 = ( +RF( 9) )/MAX(DEN, SMALL) + A5_8 = ( +RF(161) )/MAX(DEN, SMALL) + A5_11 = ( +RF(180) +RF(180) +RF(181) +RF(184) )/MAX(DEN, SMALL) +! CH2OH + DEN = +RF( 16) +RF( 56) +RF( 57) +RF( 58) +RF( 59) & + +RF( 97) +RF(159) +RB( 18) +RB( 53) +RB( 61) +RB( 65) & + +RB( 99) +RB(152) + A6_0 = ( +RB( 16) +RF( 18) +RF( 53) +RB( 56) +RB( 57) & + +RB( 58) +RF( 65) +RB( 97) +RF( 99) +RF(152) +RB(159) )& + /MAX(DEN, SMALL) + A6_4 = ( +RB( 59) )/MAX(DEN, SMALL) + A6_7 = ( +RF( 61) )/MAX(DEN, SMALL) + A6_11 = ( +RF(184) )/MAX(DEN, SMALL) +! CH3O + DEN = +RF( 17) +RF( 60) +RF( 61) +RF( 62) +RF( 63) & + +RF( 64) +RF( 98) +RF(160) +RB( 19) +RB( 54) +RB( 66) & + +RB(100) +RB(111) +RB(145) +RB(153) + A7_0 = ( +RB( 17) +RF( 19) +RF( 54) +RB( 60) +RB( 62) & + +RB( 63) +RF( 66) +RB( 98) +RF(100) +RF(111) +RF(145) & + +RF(153) +RB(160) )/MAX(DEN, SMALL) + A7_4 = ( +RB( 64) )/MAX(DEN, SMALL) + A7_6 = ( +RB( 61) )/MAX(DEN, SMALL) +! C2H3 + DEN = +RF( 22) +RF( 68) +RF( 69) +RF(103) +RF(161) & + +RF(175) +RF(176) +RB( 67) +RB( 71) +RB(104) +RB(120) & + +RB(132) +RB(154) + A8_0 = ( +RB( 22) +RF( 67) +RB( 68) +RB( 69) +RF( 71) & + +RB(103) +RF(104) +RF(154) +RB(176) )/MAX(DEN, SMALL) + A8_2 = ( +RF(120) )/MAX(DEN, SMALL) + A8_5 = ( +RB(161) )/MAX(DEN, SMALL) + A8_11 = ( +RB(175) )/MAX(DEN, SMALL) +! C2H5 + DEN = +RF( 24) +RF( 72) +RF( 73) +RF(163) +RB( 25) & + +RB( 70) +RB( 74) +RB(105) +RB(144) +RB(149) +RB(155) + A9_0 = ( +RB( 24) +RF( 25) +RF( 70) +RB( 72) +RB( 73) & + +RF( 74) +RF(105) +RF(149) +RF(155) +RB(163) )/MAX(DEN, SMALL) + A9_4 = ( +RF(144) )/MAX(DEN, SMALL) +! HCCO + DEN = +RF( 26) +RF( 75) +RF(164) +RB( 20) +RB( 27) & + +RB( 76) +RB(106) +RB(122) + A10_0 = ( +RF( 20) +RB( 26) +RF( 27) +RF( 76) +RF(106) & + +RB(125) +RB(164) +RB(165) +RB(165) )/MAX(DEN, SMALL) + A10_2 = ( +RF(122) )/MAX(DEN, SMALL) + A10_4 = ( +RB( 75) )/MAX(DEN, SMALL) + A10_8 = ( +RB(132) )/MAX(DEN, SMALL) +! CH2CHO + DEN = +RF(178) +RF(179) +RF(180) +RF(181) +RF(182) & + +RF(183) +RF(184) +RB(167) +RB(175) +RB(177) + A11_0 = ( +RF(167) +RF(177) +RB(179) +RB(182) +RB(183) )& + /MAX(DEN, SMALL) + A11_5 = ( +RB(181) )/MAX(DEN, SMALL) + A11_8 = ( +RF(175) )/MAX(DEN, SMALL) +! + A2_0 = A2_0 + A2_1*A1_0 + DEN = 1 -A2_1*A1_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A2_10 = A2_10/MAX(DEN, SMALL) + A2_8 = A2_8/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_9*A9_0 + DEN = 1 -A4_9*A9_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A4_10 = A4_10/MAX(DEN, SMALL) + A4_7 = A4_7/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_11*A11_0 + A5_8 = A5_8 + A5_11*A11_8 + DEN = 1 -A5_11*A11_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A5_3 = A5_3/MAX(DEN, SMALL) + A5_8 = A5_8/MAX(DEN, SMALL) + A3_0 = A3_0 + A3_11*A11_0 + A3_5 = A3_5 + A3_11*A11_5 + A3_8 = A3_8 + A3_11*A11_8 + A6_0 = A6_0 + A6_11*A11_0 + A6_5 = A6_11*A11_5 + A6_8 = A6_11*A11_8 + A8_0 = A8_0 + A8_11*A11_0 + A8_5 = A8_5 + A8_11*A11_5 + DEN = 1 -A8_11*A11_8 + A8_0 = A8_0/MAX(DEN, SMALL) + A8_2 = A8_2/MAX(DEN, SMALL) + A8_5 = A8_5/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_8*A8_0 + A2_5 = A2_5 + A2_8*A8_5 + DEN = 1 -A2_8*A8_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A2_10 = A2_10/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_8*A8_0 + A5_2 = A5_2 + A5_8*A8_2 + DEN = 1 -A5_8*A8_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A5_3 = A5_3/MAX(DEN, SMALL) + A3_0 = A3_0 + A3_8*A8_0 + A3_2 = A3_2 + A3_8*A8_2 + A3_5 = A3_5 + A3_8*A8_5 + A6_0 = A6_0 + A6_8*A8_0 + A6_2 = A6_8*A8_2 + A6_5 = A6_5 + A6_8*A8_5 + A10_0 = A10_0 + A10_8*A8_0 + A10_2 = A10_2 + A10_8*A8_2 + A10_5 = A10_8*A8_5 + A4_0 = A4_0 + A4_7*A7_0 + A4_6 = A4_6 + A4_7*A7_6 + DEN = 1 -A4_7*A7_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A4_10 = A4_10/MAX(DEN, SMALL) + A6_0 = A6_0 + A6_7*A7_0 + A6_4 = A6_4 + A6_7*A7_4 + DEN = 1 -A6_7*A7_6 + A6_0 = A6_0/MAX(DEN, SMALL) + A6_4 = A6_4/MAX(DEN, SMALL) + A6_2 = A6_2/MAX(DEN, SMALL) + A6_5 = A6_5/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_10*A10_0 + A4_2 = A4_2 + A4_10*A10_2 + A4_5 = A4_5 + A4_10*A10_5 + DEN = 1 -A4_10*A10_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_10*A10_0 + A2_4 = A2_4 + A2_10*A10_4 + A2_5 = A2_5 + A2_10*A10_5 + DEN = 1 -A2_10*A10_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_6*A6_0 + A4_2 = A4_2 + A4_6*A6_2 + A4_5 = A4_5 + A4_6*A6_5 + DEN = 1 -A4_6*A6_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_3*A3_0 + A4_2 = A4_2 + A4_3*A3_2 + A4_5 = A4_5 + A4_3*A3_5 + DEN = 1 -A4_3*A3_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_3*A3_0 + A2_4 = A2_4 + A2_3*A3_4 + A2_5 = A2_5 + A2_3*A3_5 + DEN = 1 -A2_3*A3_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_3*A3_0 + A5_4 = A5_4 + A5_3*A3_4 + A5_2 = A5_2 + A5_3*A3_2 + DEN = 1 -A5_3*A3_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_5*A5_0 + A4_2 = A4_2 + A4_5*A5_2 + DEN = 1 -A4_5*A5_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_5*A5_0 + A2_4 = A2_4 + A2_5*A5_4 + DEN = 1 -A2_5*A5_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_2*A2_0 + DEN = 1 -A4_2*A2_4 + A4_0 = A4_0/MAX(DEN, SMALL) + XQ(4) = A4_0 + XQ(2) = A2_0 +A2_4*XQ(4) + XQ(5) = A5_0 +A5_4*XQ(4) +A5_2*XQ(2) + XQ(3) = A3_0 +A3_4*XQ(4) +A3_2*XQ(2) +A3_5*XQ(5) + XQ(6) = A6_0 +A6_4*XQ(4) +A6_2*XQ(2) +A6_5*XQ(5) + XQ(10) = A10_0 +A10_4*XQ(4) +A10_2*XQ(2) +A10_5*XQ(5) + XQ(7) = A7_0 +A7_4*XQ(4) +A7_6*XQ(6) + XQ(8) = A8_0 +A8_2*XQ(2) +A8_5*XQ(5) + XQ(11) = A11_0 +A11_5*XQ(5) +A11_8*XQ(8) + XQ(9) = A9_0 +A9_4*XQ(4) + XQ(1) = A1_0 +A1_2*XQ(2) +! +! +! --------------------------------------------- +! +! update rates of reactions involving QSS species +! + RF( 6) = RF( 6)*XQ( 2) + RF( 7) = RF( 7)*XQ( 3) + RB( 7) = RB( 7)*XQ( 5) + RF( 8) = RF( 8)*XQ( 4) + RF( 9) = RF( 9)*XQ( 4) + RB( 9) = RB( 9)*XQ( 5) + RF( 13) = RF( 13)*XQ( 5) + RF( 14) = RF( 14)*XQ( 5) + RB( 15) = RB( 15)*XQ( 5) + RF( 16) = RF( 16)*XQ( 6) + RF( 17) = RF( 17)*XQ( 7) + RB( 18) = RB( 18)*XQ( 6) + RB( 19) = RB( 19)*XQ( 7) + RB( 20) = RB( 20)*XQ(10) + RB( 21) = RB( 21)*XQ( 3) + RF( 22) = RF( 22)*XQ( 8) + RB( 23) = RB( 23)*XQ( 5) + RF( 24) = RF( 24)*XQ( 9) + RB( 25) = RB( 25)*XQ( 9) + RF( 26) = RF( 26)*XQ(10) + RB( 27) = RB( 27)*XQ(10) + RB( 28) = RB( 28)*XQ( 3) + RB( 30) = RB( 30)*XQ( 5) + RF( 46) = RF( 46)*XQ( 2) + RB( 46) = RB( 46)*XQ( 1) + RF( 47) = RF( 47)*XQ( 3) + RF( 48) = RF( 48)*XQ( 4) + RB( 48) = RB( 48)*XQ( 2) + RF( 51) = RF( 51)*XQ( 5) + RF( 52) = RF( 52)*XQ( 5) + RB( 53) = RB( 53)*XQ( 6) + RB( 54) = RB( 54)*XQ( 7) + RB( 55) = RB( 55)*XQ( 5) + RF( 56) = RF( 56)*XQ( 6) + RF( 57) = RF( 57)*XQ( 6) + RF( 58) = RF( 58)*XQ( 6) + RF( 59) = RF( 59)*XQ( 6) + RB( 59) = RB( 59)*XQ( 4) + RF( 60) = RF( 60)*XQ( 7) + RF( 61) = RF( 61)*XQ( 7) + RB( 61) = RB( 61)*XQ( 6) + RF( 62) = RF( 62)*XQ( 7) + RF( 63) = RF( 63)*XQ( 7) + RF( 64) = RF( 64)*XQ( 7) + RB( 64) = RB( 64)*XQ( 4) + RB( 65) = RB( 65)*XQ( 6) + RB( 66) = RB( 66)*XQ( 7) + RB( 67) = RB( 67)*XQ( 8) + RF( 68) = RF( 68)*XQ( 8) + RF( 69) = RF( 69)*XQ( 8) + RB( 70) = RB( 70)*XQ( 9) + RB( 71) = RB( 71)*XQ( 8) + RF( 72) = RF( 72)*XQ( 9) + RF( 73) = RF( 73)*XQ( 9) + RB( 74) = RB( 74)*XQ( 9) + RF( 75) = RF( 75)*XQ(10) + RB( 75) = RB( 75)*XQ( 4) + RB( 76) = RB( 76)*XQ(10) + RF( 85) = RF( 85)*XQ( 1) + RF( 86) = RF( 86)*XQ( 2) + RB( 86) = RB( 86)*XQ( 5) + RF( 87) = RF( 87)*XQ( 3) + RF( 88) = RF( 88)*XQ( 3) + RB( 88) = RB( 88)*XQ( 2) + RF( 89) = RF( 89)*XQ( 4) + RB( 91) = RB( 91)*XQ( 3) + RB( 92) = RB( 92)*XQ( 4) + RF( 95) = RF( 95)*XQ( 5) + RB( 96) = RB( 96)*XQ( 5) + RF( 97) = RF( 97)*XQ( 6) + RF( 98) = RF( 98)*XQ( 7) + RB( 99) = RB( 99)*XQ( 6) + RB(100) = RB(100)*XQ( 7) + RF(103) = RF(103)*XQ( 8) + RB(104) = RB(104)*XQ( 8) + RB(105) = RB(105)*XQ( 9) + RB(106) = RB(106)*XQ(10) + RF(109) = RF(109)*XQ( 3) + RB(111) = RB(111)*XQ( 7) + RB(113) = RB(113)*XQ( 5) + RF(114) = RF(114)*XQ( 1) + RF(115) = RF(115)*XQ( 1) + RF(116) = RF(116)*XQ( 2) + RB(116) = RB(116)*XQ( 5) + RF(117) = RF(117)*XQ( 2) + RB(117) = RB(117)*XQ( 3) + RF(118) = RF(118)*XQ( 2) + RF(120) = RF(120)*XQ( 2) + RB(120) = RB(120)*XQ( 8) + RF(121) = RF(121)*XQ( 2) + RF(122) = RF(122)*XQ( 2) + RB(122) = RB(122)*XQ(10) + RF(123) = RF(123)*XQ( 2) + RB(123) = RB(123)*XQ( 5) + RF(124) = RF(124)*XQ( 2) + RF(126) = RF(126)*XQ( 3) + RF(127) = RF(127)*XQ( 3) + RF(129) = RF(129)*XQ( 3) + RF(130) = RF(130)*XQ( 3) + RF(131) = RF(131)*XQ( 3) + RB(132) = RB(132)*XQ( 8) + RF(133) = RF(133)*XQ( 4) + RB(133) = RB(133)*XQ( 3) + RF(134) = RF(134)*XQ( 4) + RF(135) = RF(135)*XQ( 4) + RF(136) = RF(136)*XQ( 4) + RF(137) = RF(137)*XQ( 4) + RF(138) = RF(138)*XQ( 4) + RB(138) = RB(138)*XQ( 3) + RF(139) = RF(139)*XQ( 4) + RF(140) = RF(140)*XQ( 4) + RF(141) = RF(141)*XQ( 4) + RB(141) = RB(141)*XQ( 3) + RF(142) = RF(142)*XQ( 4) + RB(142) = RB(142)*XQ( 3) + RF(143) = RF(143)*XQ( 4) + RF(144) = RF(144)*XQ( 4) + RB(144) = RB(144)*XQ( 9) + RB(145) = RB(145)*XQ( 7) + RB(149) = RB(149)*XQ( 9) + RF(150) = RF(150)*XQ( 5) + RB(151) = RB(151)*XQ( 5) + RB(152) = RB(152)*XQ( 6) + RB(153) = RB(153)*XQ( 7) + RB(154) = RB(154)*XQ( 8) + RB(155) = RB(155)*XQ( 9) + RF(156) = RF(156)*XQ( 5) + RF(157) = RF(157)*XQ( 5) + RF(158) = RF(158)*XQ( 5) + RF(159) = RF(159)*XQ( 6) + RF(160) = RF(160)*XQ( 7) + RF(161) = RF(161)*XQ( 8) + RB(161) = RB(161)*XQ( 5) + RF(163) = RF(163)*XQ( 9) + RF(164) = RF(164)*XQ(10) + RB(167) = RB(167)*XQ(11) + RF(170) = RF(170)*XQ( 2) + RF(171) = RF(171)*XQ( 3) + RF(172) = RF(172)*XQ( 3) + RF(174) = RF(174)*XQ( 4) + RF(175) = RF(175)*XQ( 8) + RB(175) = RB(175)*XQ(11) + RF(176) = RF(176)*XQ( 8) + RB(177) = RB(177)*XQ(11) + RF(178) = RF(178)*XQ(11) + RB(178) = RB(178)*XQ( 3) + RF(179) = RF(179)*XQ(11) + RF(180) = RF(180)*XQ(11) + RF(181) = RF(181)*XQ(11) + RB(181) = RB(181)*XQ( 5) + RF(182) = RF(182)*XQ(11) + RF(183) = RF(183)*XQ(11) + RF(184) = RF(184)*XQ(11) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! ! ompute WDOT +! +! SUBROUTINE RDOT(RF, RB, WDOT) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION RF(*), RB(*), WDOT(*), ROP(184) +! + DO I = 1, 184 + ROP(I) = RF(I) - RB(I) + ENDDO +! +! H2 + WDOT( 1) = -ROP( 3) +ROP( 8) +ROP( 36) +ROP( 37) & + +ROP( 38) +ROP( 39) +ROP( 42) +ROP( 44) & + +ROP( 46) +ROP( 48) +ROP( 50) +ROP( 52) & + +ROP( 55) +ROP( 57) +ROP( 62) +ROP( 65) & + +ROP( 66) +ROP( 69) +ROP( 71) +ROP( 73) & + +ROP( 74) +ROP( 76) -ROP( 78) -ROP( 79) & + -ROP(117) -ROP(127) +ROP(128) -ROP(136) & + +ROP(162) +ROP(166) +ROP(169) -ROP(170) & + +ROP(174) +ROP(182) +! H + WDOT( 2) = -ROP( 2) +ROP( 3) +ROP( 6) -ROP( 7) & + -2*ROP( 8) -ROP( 9) +ROP( 10) +ROP( 14) & + -ROP( 17) +ROP( 19) +ROP( 20) +2*ROP( 21) & + -ROP( 24) +ROP( 25) +ROP( 26) +2*ROP( 28) & + -ROP( 31) -ROP( 32) -ROP( 33) -ROP( 34) & + -ROP( 35) -2*ROP( 36) -2*ROP( 37) -2*ROP( 38) & + -2*ROP( 39) -ROP( 40) -ROP( 41) -ROP( 42) & + -ROP( 43) -ROP( 44) -ROP( 45) -ROP( 46) & + -3*ROP( 47) -3*ROP( 48) -ROP( 49) -ROP( 50) & + -ROP( 51) -ROP( 52) -ROP( 53) -ROP( 55) & + -ROP( 56) -ROP( 57) -ROP( 58) +ROP( 59) & + -2*ROP( 60) -ROP( 61) -2*ROP( 62) -2*ROP( 63) & + -ROP( 65) -2*ROP( 68) -2*ROP( 69) -2*ROP( 72) & + -2*ROP( 73) +ROP( 75) -ROP( 76) -ROP( 77) & + +ROP( 79) +ROP( 85) +ROP( 86) -ROP( 87) & + -2*ROP( 88) -ROP( 89) +2*ROP( 91) +2*ROP( 92) & + +ROP( 94) -ROP( 98) +ROP(100) +ROP(101) & + -ROP(103) +ROP(104) +ROP(105) -2*ROP(109) & + +ROP(111) +ROP(115) +3*ROP(117) +ROP(118) & + -ROP(119) +2*ROP(120) +ROP(121) +ROP(124) & + -ROP(126) -ROP(127) -4*ROP(128) -ROP(129) & + -2*ROP(130) -2*ROP(131) -ROP(132) -ROP(134) & + -2*ROP(135) -ROP(136) -2*ROP(137) -ROP(139) & + -2*ROP(140) -2*ROP(143) -ROP(144) +ROP(145) & + +2*ROP(149) +ROP(153) +ROP(154) +ROP(155) & + +ROP(156) +ROP(157) -ROP(160) -ROP(161) & + -ROP(163) +ROP(166) +2*ROP(167) -2*ROP(172) & + -2*ROP(173) -2*ROP(174) -ROP(176) +2*ROP(178) & + -ROP(179) -ROP(180) -2*ROP(181) -2*ROP(182) & + -ROP(183) -ROP(184) +! O + WDOT( 3) = -2*ROP( 1) -ROP( 2) -ROP( 3) -ROP( 4) & + -ROP( 5) -2*ROP( 6) -ROP( 7) -ROP( 8) & + -ROP( 9) -ROP( 10) -ROP( 11) -ROP( 12) & + -ROP( 13) -ROP( 14) -ROP( 15) -ROP( 16) & + -ROP( 17) -ROP( 18) -ROP( 19) -ROP( 20) & + -ROP( 21) -2*ROP( 22) -ROP( 23) -ROP( 24) & + -ROP( 25) -ROP( 26) -ROP( 27) -ROP( 28) & + +ROP( 29) +ROP( 35) +ROP( 41) +ROP( 48) & + +ROP( 67) -ROP( 68) -ROP( 69) +ROP( 71) & + +ROP( 81) -ROP( 85) -ROP( 86) +ROP( 88) & + -ROP(103) +ROP(104) -ROP(115) -ROP(117) & + -ROP(118) -ROP(119) -ROP(121) -ROP(122) & + -ROP(123) -ROP(124) -ROP(125) +ROP(132) & + +ROP(145) +ROP(154) -ROP(161) -ROP(166) & + -ROP(167) -ROP(170) +ROP(172) -ROP(176) & + -ROP(178) +! O2 + WDOT( 4) = +ROP( 1) +ROP( 4) +2*ROP( 6) +ROP( 8) & + +ROP( 13) +ROP( 14) -ROP( 15) +ROP( 16) & + -ROP( 18) -ROP( 20) -ROP( 21) +ROP( 22) & + -ROP( 23) +ROP( 26) -ROP( 27) -ROP( 28) & + -ROP( 29) -2*ROP( 30) -ROP( 31) -ROP( 32) & + -ROP( 33) -ROP( 34) -ROP( 35) +ROP( 42) & + +ROP( 46) +ROP( 47) -ROP( 48) +ROP( 51) & + +ROP( 52) -ROP( 53) -ROP( 55) +ROP( 56) & + +ROP( 57) +ROP( 58) -ROP( 61) -ROP( 64) & + -ROP( 65) -ROP( 67) +ROP( 68) +ROP( 69) & + -ROP( 71) -ROP( 76) +ROP( 82) +ROP( 85) & + +ROP( 86) +ROP( 87) -ROP( 88) +ROP( 89) & + -ROP( 91) -ROP( 92) +ROP( 95) -ROP( 96) & + +ROP( 97) -ROP( 99) +ROP(103) -ROP(104) & + -ROP(106) +ROP(107) +ROP(108) +ROP(109) & + +ROP(110) -ROP(113) +ROP(115) +ROP(117) & + +2*ROP(118) +3*ROP(119) +ROP(120) +2*ROP(121) & + +ROP(122) +ROP(123) +2*ROP(124) +3*ROP(125) & + +ROP(127) +2*ROP(128) +ROP(129) +ROP(130) & + +ROP(131) +ROP(132) +ROP(136) +ROP(137) & + +ROP(139) +ROP(140) +ROP(143) +ROP(144) & + -ROP(145) -ROP(146) +ROP(150) -ROP(151) & + -ROP(152) -ROP(154) +ROP(156) +ROP(157) & + -ROP(160) -ROP(161) -ROP(163) +2*ROP(165) & + +ROP(168) +2*ROP(170) +2*ROP(173) +ROP(174) & + -ROP(178) -ROP(179) -3*ROP(180) -ROP(181) & + -2*ROP(184) +! OH + WDOT( 5) = +ROP( 2) +ROP( 3) +ROP( 4) +ROP( 5) & + +ROP( 11) +ROP( 13) +ROP( 15) +ROP( 16) & + +ROP( 17) +ROP( 18) +ROP( 19) +ROP( 20) & + +ROP( 25) -ROP( 26) +2*ROP( 27) +ROP( 35) & + -ROP( 40) +2*ROP( 43) +ROP( 45) +ROP( 58) & + +ROP( 63) -ROP( 75) +ROP( 76) -ROP( 79) & + -2*ROP( 80) -2*ROP( 81) -ROP( 82) -ROP( 83) & + -ROP( 84) -ROP( 85) -ROP( 86) -ROP( 87) & + -ROP( 88) -ROP( 89) -ROP( 90) -ROP( 91) & + -ROP( 92) -ROP( 93) -ROP( 94) -ROP( 95) & + -ROP( 96) -ROP( 97) -ROP( 98) -ROP( 99) & + -ROP(100) -ROP(101) -ROP(102) -ROP(103) & + -ROP(104) -ROP(105) +ROP(109) +ROP(111) & + +ROP(112) +ROP(122) -ROP(125) +ROP(126) & + -ROP(132) +ROP(134) +ROP(146) -2*ROP(165) & + -ROP(168) -ROP(169) +ROP(179) +ROP(180) & + -ROP(183) -ROP(184) +! H2O + WDOT( 6) = +ROP( 40) +ROP( 41) +ROP( 45) +ROP( 59) & + +ROP( 64) +ROP( 79) +ROP( 81) +ROP( 82) & + +ROP( 83) +ROP( 84) +ROP( 88) +ROP( 91) & + +ROP( 92) +ROP( 93) +ROP( 95) +ROP( 96) & + +ROP( 97) +ROP( 98) +ROP( 99) +ROP(100) & + +ROP(103) +ROP(104) +ROP(105) +ROP(106) & + -ROP(118) +ROP(135) -ROP(137) +ROP(168) & + -ROP(174) +ROP(183) +! HO2 + WDOT( 7) = -ROP( 4) +ROP( 5) -ROP( 6) +ROP( 7) & + +ROP( 9) -ROP( 13) -ROP( 14) +ROP( 15) & + -ROP( 16) +ROP( 18) +ROP( 23) +2*ROP( 30) & + +ROP( 31) +ROP( 32) +ROP( 33) +ROP( 34) & + -ROP( 41) -ROP( 42) -ROP( 43) +ROP( 44) & + -ROP( 46) +ROP( 48) -ROP( 51) -ROP( 52) & + +ROP( 53) +ROP( 55) -ROP( 56) -ROP( 57) & + -ROP( 58) -ROP( 59) +ROP( 61) +ROP( 65) & + -ROP( 82) +ROP( 83) +ROP( 84) +ROP( 88) & + -ROP( 95) +ROP( 96) -ROP( 97) +ROP( 99) & + -2*ROP(107) -2*ROP(108) -ROP(109) -ROP(110) & + -ROP(111) -ROP(112) -ROP(117) -ROP(118) & + -ROP(119) -ROP(120) -ROP(121) -ROP(122) & + -ROP(124) -ROP(125) +ROP(147) -ROP(150) & + +ROP(151) +ROP(152) -ROP(156) -ROP(157) & + +ROP(160) +ROP(161) +ROP(163) -ROP(168) & + -ROP(170) +ROP(176) +2*ROP(180) +ROP(181) & + +2*ROP(184) +! H2O2 + WDOT( 8) = -ROP( 5) -ROP( 44) -ROP( 45) +ROP( 80) & + -ROP( 83) -ROP( 84) +ROP(107) +ROP(108) & + +ROP(113) -ROP(147) +! CH3 + WDOT( 9) = -ROP( 10) +ROP( 11) +ROP( 23) +ROP( 24) & + +ROP( 47) -ROP( 49) +ROP( 50) +ROP( 58) & + +ROP( 63) +ROP( 77) -ROP( 90) -ROP( 91) & + -ROP( 92) +ROP( 93) +ROP(102) -ROP(110) & + -ROP(111) -ROP(115) -ROP(120) +ROP(127) & + -ROP(129) +2*ROP(130) +ROP(136) -ROP(139) & + +2*ROP(140) +ROP(144) -ROP(145) -ROP(146) & + -ROP(147) -2*ROP(148) -2*ROP(149) -ROP(150) & + -ROP(151) -ROP(152) -ROP(153) -ROP(154) & + -ROP(155) -ROP(166) -ROP(169) +ROP(170) & + +ROP(181) +! CH4 + WDOT(10) = -ROP( 11) +ROP( 49) -ROP( 50) -ROP( 93) & + +ROP(110) -ROP(121) -ROP(130) -ROP(140) & + +ROP(147) +ROP(150) +ROP(151) +ROP(152) & + +ROP(153) +ROP(154) +ROP(155) +! CO + WDOT(11) = +ROP( 7) +ROP( 8) +ROP( 9) -ROP( 12) & + -ROP( 14) +ROP( 15) +2*ROP( 20) +ROP( 21) & + +ROP( 23) +2*ROP( 27) -ROP( 29) +ROP( 30) & + +ROP( 48) -ROP( 51) +ROP( 55) -ROP( 75) & + +2*ROP( 76) +ROP( 77) -ROP( 78) +ROP( 88) & + -ROP( 94) +ROP( 96) +ROP(102) +2*ROP(106) & + -ROP(112) +ROP(113) -ROP(115) -ROP(117) & + -ROP(118) -ROP(119) -ROP(120) -ROP(121) & + +ROP(123) -ROP(124) -2*ROP(125) +ROP(126) & + -ROP(131) -ROP(132) +ROP(134) +ROP(135) & + +ROP(143) +ROP(151) +ROP(161) -2*ROP(165) & + +ROP(166) -ROP(170) +ROP(179) +2*ROP(180) & + +ROP(181) +ROP(184) +! CO2 + WDOT(12) = -ROP( 7) -ROP( 8) -ROP( 9) +ROP( 12) & + +ROP( 14) +ROP( 21) +2*ROP( 28) +ROP( 29) & + -ROP( 47) -ROP( 48) +ROP( 59) +ROP( 64) & + +ROP( 75) -ROP( 87) -ROP( 88) -ROP( 89) & + +ROP( 91) +ROP( 92) +ROP( 94) -ROP(109) & + +ROP(112) +ROP(117) -ROP(119) -ROP(123) & + -ROP(126) -ROP(127) -2*ROP(128) -ROP(129) & + -ROP(130) -ROP(131) -ROP(132) -ROP(134) & + -ROP(135) -ROP(136) -ROP(137) -ROP(139) & + -ROP(140) -2*ROP(143) -ROP(144) -ROP(172) & + -2*ROP(173) -ROP(174) +2*ROP(178) +! CH2O + WDOT(13) = +ROP( 10) -ROP( 15) +ROP( 18) +ROP( 19) & + +ROP( 24) -ROP( 30) +ROP( 51) -ROP( 55) & + -ROP( 56) -ROP( 58) -ROP( 59) -ROP( 60) & + -ROP( 63) -ROP( 64) +ROP( 65) +ROP( 66) & + +ROP( 78) +ROP( 87) +ROP( 89) -ROP( 96) & + +ROP( 99) +ROP(100) +ROP(109) +ROP(111) & + -ROP(113) +ROP(118) -ROP(124) +ROP(143) & + +ROP(145) +ROP(146) -ROP(151) +ROP(152) & + +ROP(153) +ROP(161) +ROP(169) +ROP(172) & + +ROP(174) +ROP(179) +ROP(184) +! CH3OH + WDOT(14) = -ROP( 18) -ROP( 19) +ROP( 56) +ROP( 60) & + -ROP( 65) -ROP( 66) +ROP( 90) -ROP( 99) & + -ROP(100) +ROP(137) -ROP(152) -ROP(153) +! C2H2 + WDOT(15) = -ROP( 20) -ROP( 21) -ROP( 67) +ROP( 69) & + -ROP(101) -ROP(102) +ROP(103) +ROP(115) & + +ROP(119) +ROP(125) +ROP(128) +ROP(162) & + +ROP(165) +ROP(173) +ROP(176) +! C2H4 + WDOT(16) = -ROP( 23) -ROP( 24) +ROP( 25) +ROP( 68) & + -ROP( 71) -ROP( 72) +ROP( 74) -ROP(104) & + +ROP(105) +ROP(121) +ROP(129) +ROP(139) & + +ROP(144) +ROP(149) -ROP(154) +ROP(155) & + -ROP(162) -ROP(167) +! C2H6 + WDOT(17) = -ROP( 25) +ROP( 72) -ROP( 74) -ROP(105) & + -ROP(144) +ROP(148) -ROP(155) +! CH2CO + WDOT(18) = -ROP( 27) -ROP( 28) +ROP( 67) -ROP( 68) & + -ROP( 69) +ROP( 71) -ROP( 76) -ROP( 77) & + +ROP(101) -ROP(103) +ROP(104) -ROP(106) & + +ROP(120) +ROP(124) +ROP(131) +ROP(132) & + +ROP(154) -ROP(161) +ROP(167) -ROP(176) & + -ROP(178) -ROP(179) -ROP(180) -ROP(181) & + -ROP(184) +! N2 + WDOT(19) = 0.0 + + ! Correction for unit compatibility in Cantera + WDOT(1:19) = WDOT(1:19)*1D6 + + RETURN + END \ No newline at end of file diff --git a/samples/python/AVBP/mixture_database.dat b/samples/python/AVBP/mixture_database.dat new file mode 100755 index 00000000000..17db30799c2 --- /dev/null +++ b/samples/python/AVBP/mixture_database.dat @@ -0,0 +1,102 @@ +$MIXTURE + +!--------------------------------------------------------------------------------------------------------------------- +! Reactive mixture CH4/AIR. Reduced chemistry with PEA formalism, 2S-BFER scheme. +!--------------------------------------------------------------------------------------------------------------------- + mixture_name = BFER_nopea + validity_info = 300-700K/1-12atm + transport = computed + combustion_chemistry = reduced_pea + species_name = CH4 CO2 CO O2 H2O N2 + species_Schmidt_number = 0.7d0 0.7d0 0.7d0 0.7d0 0.7d0 0.7d0 + viscosity_law = power + mu_ref = 1.8405d-5 + T_ref = 300.d0 + viscosity_law_coeff = 0.6759d0 + prandtl_number = 0.7d0 + atom_for_z_calculation = C + fuel_tank_composition = 1.d0 0.d0 0.d0 0.d0 0.d0 0.d0 + oxydizer_tank_composition = 0.d0 0.d0 0.d0 0.233d0 0.d0 0.767d0 + + ! 2S-BFER Reaction #1 : CH4 + 1.5 O2 => CO + 2 H2O + !----------------------------------------- + reac_name = CH4-AIR-2S-BFER-1 + reac_species_number = 4 + reac_species_name = CH4 O2 CO H2O + reac_stoich_coeff = -1.d0 -1.5d0 1.d0 2.d0 + reac_Arrh_fwd_coeff = 0.5d0 0.65d0 0.d0 0.d0 + reac_Arrh_bwd_coeff = 0.d0 0.d0 0.d0 0.d0 + reac_preexp = 4.9d9 + reac_act_energ = 35500.0d0 + reac_temp_exp = 0.d0 + reac_third_body_number = 0 + reac_third_body_name = no + reac_third_body_eff = 0.d0 + + ! 2S-BFER Reaction #2 : CO + 0.5 O2 <=> CO2 + !---------------------------------- + reac_name = CH4-AIR-2S-BFER-2 + reac_species_number = 3 + reac_species_name = CO O2 CO2 + reac_stoich_coeff = -1.d0 -0.5d0 1.d0 + reac_Arrh_fwd_coeff = 1.d0 0.5d0 0.d0 + reac_Arrh_bwd_coeff = 0.d0 0.d0 1.d0 + reac_preexp = -2.0d8 + reac_act_energ = 12000.0d0 + reac_temp_exp = 0.7d0 + reac_third_body_number = 0 + reac_third_body_name = no + reac_third_body_eff = 0.d0 + +!--------------------------------------------------------------------------------------------------------------------- +! Reactive mixture CH4/AIR. Reduced chemistry with PEA formalism, 2S-BFER scheme. +!--------------------------------------------------------------------------------------------------------------------- + mixture_name = BFER_pea + validity_info = 300-700K/1-12atm + transport = computed + combustion_chemistry = reduced_pea + species_name = CH4 CO2 CO O2 H2O N2 + species_Schmidt_number = 0.7d0 0.7d0 0.7d0 0.7d0 0.7d0 0.7d0 + viscosity_law = power + mu_ref = 1.8405d-5 + T_ref = 300.d0 + viscosity_law_coeff = 0.6759d0 + prandtl_number = 0.7d0 + pea_method = pea2 + pea_coeff = 1.10d0 0.09d0 0.37d0 1.13d0 0.03d0 6.7d0 1.6d0 0.22d0 + pea_coeff = 0.95d0 0.08d0 2.5d-5 1.3d0 0.04d0 0.0087d0 1.2d0 0.04d0 1.2d0 0.05d0 + atom_for_z_calculation = C + fuel_tank_composition = 1.d0 0.d0 0.d0 0.d0 0.d0 0.d0 + oxydizer_tank_composition = 0.d0 0.d0 0.d0 0.233d0 0.d0 0.767d0 + + ! 2S-BFER Reaction #1 : CH4 + 1.5 O2 => CO + 2 H2O + !----------------------------------------- + reac_name = CH4-AIR-2S-BFER-1 + reac_species_number = 4 + reac_species_name = CH4 O2 CO H2O + reac_stoich_coeff = -1.d0 -1.5d0 1.d0 2.d0 + reac_Arrh_fwd_coeff = 0.5d0 0.65d0 0.d0 0.d0 + reac_Arrh_bwd_coeff = 0.d0 0.d0 0.d0 0.d0 + reac_preexp = 4.9d9 + reac_act_energ = 35500.0d0 + reac_temp_exp = 0.d0 + reac_third_body_number = 0 + reac_third_body_name = no + reac_third_body_eff = 0.d0 + + ! 2S-BFER Reaction #2 : CO + 0.5 O2 <=> CO2 + !---------------------------------- + reac_name = CH4-AIR-2S-BFER-2 + reac_species_number = 3 + reac_species_name = CO O2 CO2 + reac_stoich_coeff = -1.d0 -0.5d0 1.d0 + reac_Arrh_fwd_coeff = 1.d0 0.5d0 0.d0 + reac_Arrh_bwd_coeff = 0.d0 0.d0 1.d0 + reac_preexp = -2.0d8 + reac_act_energ = 12000.0d0 + reac_temp_exp = 0.7d0 + reac_third_body_number = 0 + reac_third_body_name = no + reac_third_body_eff = 0.d0 + +$end_MIXTURE \ No newline at end of file diff --git a/samples/python/AVBP/postproc.py b/samples/python/AVBP/postproc.py new file mode 100644 index 00000000000..6bea2f1c5e9 --- /dev/null +++ b/samples/python/AVBP/postproc.py @@ -0,0 +1,79 @@ +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Parameters of the solver +loglevel = 1 +refine_grid = 'refine' + +# Setting up the gas object (operating conditions) +if ct.__version__ >= '2.5.0': + gas = ct.Solution('gri30.yaml') +else: + gas = ct.Solution('gri30.cti') + +p = 1e5 +tin = 300.0 +phi = 1.0 +fuel = {'CH4':1} +oxidizer = {'O2': 1, 'N2': 3.76} +gas.TP = tin, p +gas.set_equivalence_ratio(phi, fuel, oxidizer) + +# Setting up the flame object +f = ct.FreeFlame(gas, width=0.02) +f.inlet.X = gas.X +f.inlet.T = gas.T + +f.energy_enabled = True +f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05, prune=0.01) +f.set_max_jac_age(10, 10) +f.set_time_step(1e-8, [10, 20, 40, 80, 100, 100, 150]) +f.max_time_step_count = 500 + +f.solve(loglevel, refine_grid) + +# Compute thermal flame thickness +z = f.flame.grid +T = f.T +grad = np.gradient(T,z) +thickness = (max(T) -min(T)) / max(grad) +print(' ') +print('laminar thermal flame thickness (delta_T) = ', thickness) +print(' ') + +# Compute HRR flame thickness +# Remark : slight difference when using np.gradient (5% in relative) +# Therefore manual computation of gradient is used +HRR = f.heat_release_rate +gradHRR = (HRR[2:]-HRR[0:-2])/(z[2:]-z[0:-2]) +HRR = HRR[1:-1] +x = z[1:-1] +gradHRR2 = (gradHRR[2:]-gradHRR[0:-2])/(x[2:]-x[0:-2]) +x = x[1:-1] +gradHRR = gradHRR[1:-1] +HRR = HRR[1:-1] +delta_HRR = -2.0*(-2.0*HRR*gradHRR2)**0.5/gradHRR2 +where = np.where(HRR > 1e3) +delta_HRR = np.nanmin(delta_HRR[where]) + +print(' ') +print('laminar HRR flame thickness (delta_HRR) = ', delta_HRR) +print(' ') +print('delta_T / delta_HRR = ', thickness / delta_HRR) +print(' ') + +# Compute schmidt numbers +print('SCHMIDT NUMBERS (in burnt gases):') +f.set_gas_state(f.flame.n_points-1) +list_species = f.gas.species_names +for species in list_species: + print (species,gas.viscosity/gas.mix_diff_coeffs[gas.species_index(species)]/gas.density) +print(' ') + +print('PRANDTL NUMBER (in fresh gases):') +f.set_gas_state(f.flame.n_points-f.flame.n_points) +Pr = gas.cp_mass * gas.viscosity / gas.thermal_conductivity +print('Prandtl = '+str(Pr)) \ No newline at end of file diff --git a/samples/python/AVBP/write_csv.py b/samples/python/AVBP/write_csv.py new file mode 100644 index 00000000000..e41ae5bac68 --- /dev/null +++ b/samples/python/AVBP/write_csv.py @@ -0,0 +1,37 @@ +import cantera as ct +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Parameters of the solver +loglevel = 1 +refine_grid = 'refine' + +# Setting up the gas object (operating conditions) +if ct.__version__ >= '2.5.0': + gas = ct.Solution('gri30.yaml') +else: + gas = ct.Solution('gri30.cti') +p = 1e5 +tin = 300.0 +phi = 1.0 +fuel = {'CH4':1} +oxidizer = {'O2': 1, 'N2': 3.76} +gas.TP = tin, p +gas.set_equivalence_ratio(phi, fuel, oxidizer) + +# Setting up the flame object +f = ct.FreeFlame(gas, width=0.02) +f.inlet.X = gas.X +f.inlet.T = gas.T + +f.energy_enabled = True +f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05, prune=0.01) +f.set_max_jac_age(10, 10) +f.set_time_step(1e-8, [10, 20, 40, 80, 100, 100, 150]) +f.max_time_step_count = 500 + +f.solve(loglevel, refine_grid) + +# Write AVBP solution for can2av +f.write_AVBP("./RESULTS/AVBP-Solution.csv") \ No newline at end of file diff --git a/samples/python/README.rst b/samples/python/README.rst new file mode 100644 index 00000000000..182e35f70dc --- /dev/null +++ b/samples/python/README.rst @@ -0,0 +1,7 @@ +Python Examples +=============== + +.. seealso:: + + To find examples covering a specific topic, see the + :ref:`index of example tags `. diff --git a/samples/python/kinetics/README.rst b/samples/python/kinetics/README.rst new file mode 100644 index 00000000000..6a46991bd09 --- /dev/null +++ b/samples/python/kinetics/README.rst @@ -0,0 +1,2 @@ +Kinetics +-------- diff --git a/samples/python/multiphase/README.rst b/samples/python/multiphase/README.rst new file mode 100644 index 00000000000..b6b2d91eff3 --- /dev/null +++ b/samples/python/multiphase/README.rst @@ -0,0 +1,2 @@ +Multiphase +---------- diff --git a/samples/python/onedim/README.rst b/samples/python/onedim/README.rst new file mode 100644 index 00000000000..1694c69de2b --- /dev/null +++ b/samples/python/onedim/README.rst @@ -0,0 +1,2 @@ +1D reacting flows +----------------- diff --git a/samples/python/onedim/adiabatic_flame.csv b/samples/python/onedim/adiabatic_flame.csv new file mode 100644 index 00000000000..42bb921593b --- /dev/null +++ b/samples/python/onedim/adiabatic_flame.csv @@ -0,0 +1,141 @@ +grid,velocity,T,D,X_H2,X_H,X_O,X_O2,X_OH,X_H2O,X_HO2,X_H2O2,X_AR,X_N2 +0,0.726900879,300,1.33861236,0.154929577,4.93387039e-16,-4.84126673e-16,0.14084507,3.97637309e-16,1.79757153e-18,-3.87453949e-16,-3.03668592e-17,0.704225352,-1.50725451e-19 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temperature: 698.1678485027371 + basis: mass + components: [grid, velocity, T, D, H2, H, O, O2, OH, H2O, HO2, H2O2, AR, N2] + products: + size: 0 + type: outlet + points: 1 diff --git a/samples/python/reactors/README.rst b/samples/python/reactors/README.rst new file mode 100644 index 00000000000..4c8863778a6 --- /dev/null +++ b/samples/python/reactors/README.rst @@ -0,0 +1,2 @@ +Reactor networks +---------------- diff --git a/samples/python/surface_chemistry/README.rst b/samples/python/surface_chemistry/README.rst new file mode 100644 index 00000000000..baaa67d5443 --- /dev/null +++ b/samples/python/surface_chemistry/README.rst @@ -0,0 +1,2 @@ +Surface chemistry +----------------- diff --git a/samples/python/thermo/README.rst b/samples/python/thermo/README.rst new file mode 100644 index 00000000000..4b7a803f88e --- /dev/null +++ b/samples/python/thermo/README.rst @@ -0,0 +1,2 @@ +Thermodynamics +-------------- diff --git a/samples/python/transport/README.rst b/samples/python/transport/README.rst new file mode 100644 index 00000000000..ce84aae8342 --- /dev/null +++ b/samples/python/transport/README.rst @@ -0,0 +1,2 @@ +Transport +--------- From 68a09c47ee4e1b8b840ad28af745ce6b42b8c1cc Mon Sep 17 00:00:00 2001 From: pestre Date: Thu, 30 Jan 2025 12:05:19 +0100 Subject: [PATCH 06/98] Merge differences in src directory Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: new file: src/base/Parser.cpp modified: src/base/application.h modified: src/clib/ctonedim.cpp modified: src/extensions/pythonShim.cpp new file: src/kinetics/CustomKinetics.cpp modified: src/kinetics/Kinetics.cpp modified: src/kinetics/KineticsFactory.cpp modified: src/oneD/Boundary1D.cpp modified: src/oneD/Domain1D.cpp modified: src/oneD/DomainFactory.cpp new file: src/oneD/Flamelet.cpp modified: src/oneD/IonFlow.cpp modified: src/oneD/Sim1D.cpp modified: src/oneD/StFlow.cpp modified: src/oneD/refine.cpp new file: src/transport/AVBPTransport.cpp modified: src/transport/TransportFactory.cpp Conflicts: src/extensions/pythonShim.cpp Author: pestre Date: Thu Jan 30 12:05:19 2025 +0100 On branch WIP/merge_CERFACS_devs You are currently cherry-picking commit 22c89db5c. Changes to be committed: new file: src/base/Parser.cpp modified: src/clib/ctonedim.cpp modified: src/extensions/pythonShim.cpp new file: src/kinetics/CustomKinetics.cpp modified: src/kinetics/Kinetics.cpp modified: src/kinetics/KineticsFactory.cpp modified: src/oneD/Boundary1D.cpp modified: src/oneD/Domain1D.cpp modified: src/oneD/DomainFactory.cpp new file: src/oneD/Flamelet.cpp modified: src/oneD/IonFlow.cpp modified: src/oneD/Sim1D.cpp modified: src/oneD/StFlow.cpp modified: src/oneD/refine.cpp new file: src/transport/AVBPTransport.cpp modified: src/transport/TransportFactory.cpp --- src/base/Parser.cpp | 275 ++++++ src/clib/ctonedim.cpp | 5 +- src/extensions/pythonShim.cpp | 1 + src/kinetics/CustomKinetics.cpp | 58 ++ src/kinetics/Kinetics.cpp | 2 + src/kinetics/KineticsFactory.cpp | 2 + src/oneD/Boundary1D.cpp | 183 ++-- src/oneD/Domain1D.cpp | 4 +- src/oneD/DomainFactory.cpp | 43 +- src/oneD/Flamelet.cpp | 471 ++++++++++ src/oneD/IonFlow.cpp | 2 +- src/oneD/Sim1D.cpp | 324 ++++++- src/oneD/StFlow.cpp | 1274 +++++++++++++++++++++++++++- src/oneD/refine.cpp | 417 +++++++++ src/transport/AVBPTransport.cpp | 278 ++++++ src/transport/TransportFactory.cpp | 7 + 16 files changed, 3241 insertions(+), 105 deletions(-) create mode 100644 src/base/Parser.cpp create mode 100644 src/kinetics/CustomKinetics.cpp create mode 100644 src/oneD/Flamelet.cpp create mode 100644 src/transport/AVBPTransport.cpp diff --git a/src/base/Parser.cpp b/src/base/Parser.cpp new file mode 100644 index 00000000000..bbee10b6160 --- /dev/null +++ b/src/base/Parser.cpp @@ -0,0 +1,275 @@ +#include "cantera/base/Parser.h" + +#include +#include +#include +#include +#include + +void Param::print() { + cout << m_name; + for (int i = 0; i < m_args.size(); ++i) + cout << " " << m_args[i]; + cout << endl; +} + +double Param::readDouble(const int i) { + double value; + std::string value_str; + if ( i >= m_args.size() ) { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: no argument " << i << " of param " << m_name << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } else { + //std::stringstream stream(m_args[i]); + value_str = Param::readString(i); + std::replace( value_str.begin(), value_str.end(), 'd', 'e'); + std::stringstream stream(value_str); + if ( stream >> value ) { + return(value); + } else { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: argument " << i << " of param " << m_name << " in not a double" << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } + } +} + +int Param::readInteger(const int i) { + int value; + if ( i >= m_args.size() ) { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: no argument " << i << " of param " << m_name << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } else { + std::stringstream stream(m_args[i]); + if ( stream >> value ) { + return(value); + } else { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: argument " << i << " of param " << m_name << " in not an integer" << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } + } +} + +string Param::readString(const int i) { + if ( i >= m_args.size() ) { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: no argument " << i << " of param " << m_name << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } else { + return(m_args[i]); + } +} + +bool Param::readBool(const int i) { + if ( i >= m_args.size() ) { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: no argument " << i << " of param " << m_name << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } else { + if ((m_args[i]=="true")||(m_args[i]=="TRUE")) + return(true); + else if ((m_args[i]=="false")||(m_args[i]=="FALSE")) + return(false); + else { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: argument " << i << " of param " << m_name << " in not a boolean" << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } + } +} + +Param * Parser::getParam(const string& name) { + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if ( p->Name() == name ) { + p->incrCount(); + return(&(*p)); + } + } + cout << " Param " << name << " is required ! " << endl; + exit(1); +} + +Param * Parser::getParam(const string& name, const size_t n) { + size_t count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if (p->Name() == name) { + if (count == n ) { + p->incrCount(); + return(&(*p)); + } else { + ++count; + } + } + } + cout << n <<"th param " << name << " does not exist ! " << endl; + exit(1); +} + +Param * Parser::getParam(const string& name, const size_t n, const size_t m) { + size_t global_count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if (p->Name() == name && global_count >= n && global_count <= m) { + p->incrCount(); + return(&(*p)); + } + global_count = global_count + 1; + } + cout << " param " << name << " does not exist for selected mixture ! " << endl; + exit(1); +} + +// Non-existing method in cantera version +Param * Parser::getParam(const string& name, const size_t n, const size_t m, const size_t l) { + size_t global_count = 0; + size_t count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if (p->Name() == name && global_count >=n && global_count <=m) { + if (count == l ) { + p->incrCount(); + return(&(*p)); + } else { + ++count; + } + } + global_count = global_count + 1; + } + cout << n <<"th param " << name << " does not exist ! " << endl; + exit(1); +} + + +size_t Parser::getParamNumber(const string& name, const size_t n) { + size_t global_count = 0; + size_t param_count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if (p->Name() == name) { + if (param_count == n) { + return(global_count); + } + param_count = param_count + 1; + } + global_count = global_count + 1; + } + return(string::npos); +} + +bool Parser::checkParam(const string& name) { + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if ( p->Name() == name ) { + p->incrCount(); + return(true); + } + } + return(false); +} + +// Non-existing method in cantera version +bool Parser::checkParam(const string& name, const size_t n, const size_t m) { + size_t global_count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if ( p->Name() == name && global_count >= n && global_count <= m) { + p->incrCount(); + return(true); + } + global_count = global_count + 1; + } + return(false); +} + + +size_t Parser::nbParamOccurence(const string& name) { + size_t count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if ( p->Name() == name ) { + ++count; + } + } + return(count); +} + +void Parser::parseFile(const string& file) { + +// Disclaimer + //cout << "--------------------------------------------" << endl; + //cout << " Parsing input file "+ file<< endl; + //cout << "--------------------------------------------" << endl; + +// File exist ? + ifstream inputfile(file); + if (!inputfile.good()) { + cout << "------------------------------------------------------" << endl; + cout << " Parser error: input file "+file+" does not exist !" << endl; + cout << "------------------------------------------------------" << endl; + exit(1); + } + +// Loop on lines + bool goodParam; + while (inputfile.good()) { + string line; + Param buffer_param; + goodParam = false; + getline(inputfile,line); + if (addParamFromLine(buffer_param,line)) { + m_params.push_back(buffer_param); + m_count += 1; + //i_count.push_back(m_count); + } + } + +// Print params +// for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) +// p->print(); + +} + +bool Parser::addParamFromLine(Param& param,const string& line) { + // look for a hash (Comment operator) and trim + size_t hashPos = line.find_first_of("!",0); + string trimmed_line = line.substr(0,hashPos); + + // look for first character /= of "=" + string delimiters = " \t="; + size_t beg = trimmed_line.find_first_not_of(delimiters,0); + + // Empty line + if (beg == string::npos) return(false); + + // look for "=" and store Param name + size_t delpos = trimmed_line.find_first_of(delimiters,beg); + param.setName(trimmed_line.substr(beg,delpos-beg)); + + // look for parameter arguments, separated by space + trimmed_line = trimmed_line.substr(delpos+2,trimmed_line.size()); + + // Remove initial spaces + beg = trimmed_line.find_first_not_of(" ",0); + size_t end = trimmed_line.find_last_not_of(" \t"); + trimmed_line = trimmed_line.substr(beg,end); + + // Loop on arguments + while (!(beg == string::npos)) { + beg = trimmed_line.find_first_of(" ",0); + if (!(beg == string::npos)) { + param.addArgs(trimmed_line.substr(0,beg)); + trimmed_line = trimmed_line.substr(beg,trimmed_line.size()); + size_t space = trimmed_line.find_first_not_of(" ",0); + if (!(space == string::npos)) { + trimmed_line = trimmed_line.substr(space,trimmed_line.size()); + } + } else { + param.addArgs(trimmed_line.substr(0,trimmed_line.size())); + } + } + return(true); +} diff --git a/src/clib/ctonedim.cpp b/src/clib/ctonedim.cpp index 6b5855a0396..90411c25c6e 100644 --- a/src/clib/ctonedim.cpp +++ b/src/clib/ctonedim.cpp @@ -618,10 +618,11 @@ extern "C" { } } - int sim1D_solve(int i, int loglevel, int refine_grid) + int sim1D_solve(int i, int loglevel, const char* refine_grid) { try { - bool r = (refine_grid == 0 ? false : true); + // bool r = (refine_grid == 0 ? false : true); + string r = (std::strcmp(refine_grid, "remesh") ? "disabled" : "refine"); SimCabinet::item(i).solve(loglevel, r); return 0; } catch (...) { diff --git a/src/extensions/pythonShim.cpp b/src/extensions/pythonShim.cpp index 15a71b09b6a..181e356ca71 100644 --- a/src/extensions/pythonShim.cpp +++ b/src/extensions/pythonShim.cpp @@ -73,6 +73,7 @@ void loadCanteraPython() const char* venv_path = getenv("VIRTUAL_ENV"); if (venv_path != nullptr) { PyConfig pyconf; + // pyconf.buffered_stdio = 0; PyConfig_InitPythonConfig(&pyconf); #ifdef _WIN32 diff --git a/src/kinetics/CustomKinetics.cpp b/src/kinetics/CustomKinetics.cpp new file mode 100644 index 00000000000..cc4b08c6449 --- /dev/null +++ b/src/kinetics/CustomKinetics.cpp @@ -0,0 +1,58 @@ +/** + * @file CustomKinetics.cpp + * + * @ingroup chemkinetics + */ + +// +// Author: Q. Cazeres, A. Felden, P. Pepiot +// +// +#include "cantera/kinetics/CustomKinetics.h" +// #include "cantera/kinetics/Kinetics.h" +#include "cantera/thermo/ThermoPhase.h" + +#include +#include + +using namespace std; + +namespace Cantera +{ + CustomKinetics::CustomKinetics() : GasKinetics() + { + printf("WARNING: Using customized kinetics from f90 file.\n"); + handle = dlopen("customkinetics.so", RTLD_LAZY); + + // load symbol + ck = (ck_t) dlsym(handle, "customkinetics_"); + + } + + void CustomKinetics::get_wdot_reduced(double* wdot) + { + + double P = thermo().pressure(); + double T = thermo().temperature(); + // New yarc2 format + //double rho = thermo().density(); + const double* m_y = thermo().massFractions(); + + ck(&P,&T,&m_y[0],&wdot[0]); + + // New yarc2 format + //ck(&P,&T,&rho,&m_y[0],&wdot[0]); + + // Old yarc format + //mol/kmol conversion cantera is in kmol + for (size_t i=0;i @@ -40,6 +41,7 @@ KineticsFactory::KineticsFactory() { addDeprecatedAlias("surface", "surf"); reg("edge", []() { return new EdgeKinetics(); }); addDeprecatedAlias("edge", "Edge"); + reg("custom", []() { return new CustomKinetics(); }); } KineticsFactory* KineticsFactory::factory() { diff --git a/src/oneD/Boundary1D.cpp b/src/oneD/Boundary1D.cpp index 919ae93c12e..41d60814024 100644 --- a/src/oneD/Boundary1D.cpp +++ b/src/oneD/Boundary1D.cpp @@ -36,11 +36,21 @@ void Boundary1D::_init(size_t n) Domain1D& r = container().domain(m_index-1); if (!r.isConnector()) { // multi-point domain m_left_nv = r.nComponents(); - if (m_left_nv > c_offset_Y) { - m_left_nsp = m_left_nv - c_offset_Y; - } else { - m_left_nsp = 0; + + if (m_type == cFlameletFlow) { + if (m_left_nv > c_offset_Yflamelet) { + m_left_nsp = m_left_nv - c_offset_Yflamelet; + } else { + m_left_nsp = 0; + } + }else{ + if (m_left_nv > c_offset_Y) { + m_left_nsp = m_left_nv - c_offset_Y; + } else { + m_left_nsp = 0; + } } + m_left_loc = container().start(m_index-1); m_left_points = r.nPoints(); m_flow_left = dynamic_cast(&r); @@ -59,10 +69,19 @@ void Boundary1D::_init(size_t n) Domain1D& r = container().domain(m_index+1); if (!r.isConnector()) { // multi-point domain m_right_nv = r.nComponents(); - if (m_right_nv > c_offset_Y) { - m_right_nsp = m_right_nv - c_offset_Y; - } else { - m_right_nsp = 0; + + if (m_type == cFlameletFlow) { + if (m_right_nv > c_offset_Yflamelet) { + m_right_nsp = m_right_nv - c_offset_Yflamelet; + } else { + m_right_nsp = 0; + } + }else{ + if (m_right_nv > c_offset_Y) { + m_right_nsp = m_right_nv - c_offset_Y; + } else { + m_right_nsp = 0; + } } m_right_loc = container().start(m_index+1); m_flow_right = dynamic_cast(&r); @@ -140,6 +159,25 @@ void Inlet1D::setMoleFractions(const double* xin) } } +void Inlet1D::setMassFractions(const std::string& xin) +{ + m_xstr = xin; + if (m_flow) { + m_flow->phase().setMassFractionsByName(xin); + m_flow->phase().getMassFractions(m_yin.data()); + needJacUpdate(); + } +} + +void Inlet1D::setMassFractions(const double* xin) +{ + if (m_flow) { + m_flow->phase().setMassFractions(xin); + m_flow->phase().getMassFractions(m_yin.data()); + needJacUpdate(); + } +} + void Inlet1D::init() { _init(0); @@ -184,57 +222,88 @@ void Inlet1D::eval(size_t jg, double* xg, double* rg, double* xb = xg + m_flow->loc(); double* rb = rg + m_flow->loc(); - // The first flow residual is for u. This, however, is not modified by - // the inlet, since this is set within the flow domain from the - // continuity equation. - - if (m_flow->doEnergy(0)) { - // The third flow residual is for T, where it is set to T(0). Subtract - // the local temperature to hold the flow T to the inlet T. - rb[c_offset_T] -= m_temp; - } else { - rb[c_offset_T] -= m_flow->T_fixed(0); - } + if ( m_flow->nEq() == 1 ) { // Solving in mixture fraction space + if (m_flow->doEnergy(0)) { + // The third flow residual is for T, where it is set to T(0). Subtract + // the local temperature to hold the flow T to the inlet T. + rb[c_offset_Tflamelet] -= m_temp; + } else { + rb[c_offset_Tflamelet] -= m_flow->T_fixed(0); + } + for (size_t k = 0; k < m_nsp; k++) { + if (k != m_flow_right->leftExcessSpecies()) { + rb[c_offset_Yflamelet+k] -= m_yin[k]; + } + } + } else { // Phisical space + // The first flow residual is for u. This, however, is not modified by + // the inlet, since this is set within the flow domain from the + // continuity equation. + + if (m_flow->doEnergy(0)) { + // The third flow residual is for T, where it is set to T(0). Subtract + // the local temperature to hold the flow T to the inlet T. + rb[c_offset_T] -= m_temp; + } else { + rb[c_offset_T] -= m_flow->T_fixed(0); + } - if (m_flow->isFree()) { - // if the flow is a freely-propagating flame, mdot is not specified. - // Set mdot equal to rho*u, and also set lambda to zero. - m_mdot = m_flow->density(0) * xb[c_offset_U]; - rb[c_offset_L] = xb[c_offset_L]; - } else if (m_flow->isStrained()) { - // The flow domain sets this to -rho*u. Add mdot to specify the mass - // flow rate - rb[c_offset_L] += m_mdot; - - // spreading rate. The flow domain sets this to V(0), - // so for finite spreading rate subtract m_V0. - rb[c_offset_V] -= m_V0; - } else { - rb[c_offset_U] = m_flow->density(0) * xb[c_offset_U] - m_mdot; - rb[c_offset_L] = xb[c_offset_L]; - } + if (m_flow->isFree()) { + // if the flow is a freely-propagating flame, mdot is not specified. + // Set mdot equal to rho*u, and also set lambda to zero. + m_mdot = m_flow->density(0) * xb[c_offset_U]; + rb[c_offset_L] = xb[c_offset_L]; + } else if (m_flow->isStrained()) { + // The flow domain sets this to -rho*u. Add mdot to specify the mass + // flow rate + rb[c_offset_L] += m_mdot; + + // spreading rate. The flow domain sets this to V(0), + // so for finite spreading rate subtract m_V0. + rb[c_offset_V] -= m_V0; + } else { + rb[c_offset_U] = m_flow->density(0) * xb[c_offset_U] - m_mdot; + rb[c_offset_L] = xb[c_offset_L]; + } - // add the convective term to the species residual equations - for (size_t k = 0; k < m_nsp; k++) { - if (k != m_flow_right->leftExcessSpecies()) { - rb[c_offset_Y+k] += m_mdot*m_yin[k]; + // add the convective term to the species residual equations + for (size_t k = 0; k < m_nsp; k++) { + if (k != m_flow_right->leftExcessSpecies()) { + rb[c_offset_Y+k] += m_mdot*m_yin[k]; + } } } } else { // right inlet (should only be used for counter-flow flames) // Array elements corresponding to the last point in the flow domain + double* rb = rg + loc() - m_flow->nComponents(); - rb[c_offset_V] -= m_V0; - if (m_flow->doEnergy(m_flow->nPoints() - 1)) { - rb[c_offset_T] -= m_temp; // T - } else { - rb[c_offset_T] -= m_flow->T_fixed(m_flow->nPoints() - 1); - } - rb[c_offset_U] += m_mdot; // u - for (size_t k = 0; k < m_nsp; k++) { - if (k != m_flow_left->rightExcessSpecies()) { - rb[c_offset_Y+k] += m_mdot * m_yin[k]; + + if (m_flow->nEq() == 1 ) { // mixture fraction space + if (m_flow->doEnergy(m_flow->nPoints() - 1)) { + rb[c_offset_Tflamelet] -= m_temp; // T + } else { + rb[c_offset_Tflamelet] -= m_flow->T_fixed(m_flow->nPoints() - 1); + } + for (size_t k = 0; k < m_nsp; k++) { + if (k != m_flow_left->rightExcessSpecies()) { + rb[c_offset_Yflamelet+k] -= m_yin[k]; + } + } + } else { // physical space + + rb[c_offset_V] -= m_V0; + if (m_flow->doEnergy(m_flow->nPoints() - 1)) { + rb[c_offset_T] -= m_temp; // T + } else { + rb[c_offset_T] -= m_flow->T_fixed(m_flow->nPoints() - 1); + } + rb[c_offset_U] += m_mdot; // u + for (size_t k = 0; k < m_nsp; k++) { + if (k != m_flow_left->rightExcessSpecies()) { + rb[c_offset_Y+k] += m_mdot * m_yin[k]; + } } } } @@ -392,10 +461,18 @@ void Outlet1D::eval(size_t jg, double* xg, double* rg, integer* diagg, int* db = diag - nc; size_t last = m_flow_left->nPoints() - 1; - if (m_flow_left->doEnergy(last)) { - rb[c_offset_T] = xb[c_offset_T] - xb[c_offset_T - nc]; // zero T gradient + if (m_flow_left->nEq() == 1) { // mixture fraction space + if (m_flow_left->doEnergy(last)) { + rb[c_offset_Tflamelet] = xb[c_offset_Tflamelet] - xb[c_offset_Tflamelet - nc]; // zero T gradient + } else { + rb[c_offset_Tflamelet] = xb[c_offset_Tflamelet] - m_flow_left->T_fixed(last); + } } else { - rb[c_offset_T] = xb[c_offset_T] - m_flow_left->T_fixed(last); + if (m_flow_left->doEnergy(last)) { + rb[c_offset_T] = xb[c_offset_T] - xb[c_offset_T - nc]; // zero T gradient + } else { + rb[c_offset_T] = xb[c_offset_T] - m_flow_left->T_fixed(last); + } } size_t kSkip = c_offset_Y + m_flow_left->rightExcessSpecies(); for (size_t k = c_offset_Y; k < nc; k++) { diff --git a/src/oneD/Domain1D.cpp b/src/oneD/Domain1D.cpp index f1ff73b96ca..73e740476bb 100644 --- a/src/oneD/Domain1D.cpp +++ b/src/oneD/Domain1D.cpp @@ -14,9 +14,9 @@ namespace Cantera { -Domain1D::Domain1D(size_t nv, size_t points, double time) +Domain1D::Domain1D(size_t nv, size_t points, double time, size_t nsoot, size_t neq) { - resize(nv, points); + resize(nv+nsoot+neq, points); } Domain1D::~Domain1D() diff --git a/src/oneD/DomainFactory.cpp b/src/oneD/DomainFactory.cpp index e11957e2259..4b3995df647 100644 --- a/src/oneD/DomainFactory.cpp +++ b/src/oneD/DomainFactory.cpp @@ -6,6 +6,7 @@ #include "cantera/oneD/DomainFactory.h" #include "cantera/oneD/Boundary1D.h" #include "cantera/oneD/StFlow.h" +#include "cantera/oneD/Flamelet.h" #include "cantera/oneD/IonFlow.h" #include "cantera/transport/Transport.h" @@ -17,63 +18,73 @@ std::mutex DomainFactory::domain_mutex; DomainFactory::DomainFactory() { - reg("inlet", [](shared_ptr solution, const string& id) { + reg("inlet", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Inlet1D(solution, id); }); - reg("empty", [](shared_ptr solution, const string& id) { + reg("empty", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Empty1D(solution, id); }); - reg("symmetry-plane", [](shared_ptr solution, const string& id) { + reg("symmetry-plane", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Symm1D(solution, id); }); - reg("outlet", [](shared_ptr solution, const string& id) { + reg("outlet", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Outlet1D(solution, id); }); - reg("outlet-reservoir", [](shared_ptr solution, const string& id) { + reg("outlet-reservoir", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new OutletRes1D(solution, id); }); - reg("surface", [](shared_ptr solution, const string& id) { + reg("surface", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Surf1D(solution, id); }); - reg("reacting-surface", [](shared_ptr solution, const string& id) { + reg("reacting-surface", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new ReactingSurf1D(solution, id); }); - reg("gas-flow", [](shared_ptr solution, const string& id) { - return new StFlow(solution, id); + reg("gas-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + return new StFlow(solution, id, sections); }); - reg("ion-flow", [](shared_ptr solution, const string& id) { + reg("ion-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new IonFlow(solution, id); }); - reg("free-flow", [](shared_ptr solution, const string& id) { + reg("free-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { StFlow* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new StFlow(solution, id); + ret = new StFlow(solution, id, sections); } ret->setFreeFlow(); return ret; }); - reg("axisymmetric-flow", [](shared_ptr solution, const string& id) { + reg("axisymmetric-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { StFlow* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new StFlow(solution, id); + ret = new StFlow(solution, id, sections); } ret->setAxisymmetricFlow(); return ret; }); - reg("unstrained-flow", [](shared_ptr solution, const string& id) { + reg("unstrained-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { StFlow* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new StFlow(solution, id); + ret = new StFlow(solution, id, sections); } ret->setUnstrainedFlow(); return ret; }); + reg("flamelet-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + StFlow* ret; + if (solution->transport()->transportModel() == "ionized-gas") { + ret = new IonFlow(solution, id); + } else { + ret = new Flamelet(solution, id, sections); // neq = 1 for flamelet + } + ret->setFlameletFlow(); + return ret; + }); } DomainFactory* DomainFactory::factory() diff --git a/src/oneD/Flamelet.cpp b/src/oneD/Flamelet.cpp new file mode 100644 index 00000000000..96efc38633d --- /dev/null +++ b/src/oneD/Flamelet.cpp @@ -0,0 +1,471 @@ +// ! Flamelet definitions +// + +#include "cantera/transport/TransportBase.h" +#include "cantera/numerics/funcs.h" + + +#include "cantera/base/SolutionArray.h" +#include "cantera/oneD/StFlow.h" +#include "cantera/oneD/refine.h" +#include "cantera/transport/Transport.h" +#include "cantera/transport/TransportFactory.h" +#include "cantera/numerics/funcs.h" +#include "cantera/base/global.h" +#include "cantera/base/Parser.h" + +#include + +#include "cantera/oneD/Flamelet.h" +// import erf function +using namespace std; + +namespace Cantera +{ + +Flamelet::Flamelet(IdealGasPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : + StFlow(ph, nsp, nsoot, neq, points) { + m_dovisc = true; + m_updateChi = true; + m_do_unityLewisNumber = true; + } + +Flamelet::Flamelet(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) + : StFlow(th.get(), nsp, nsoot, neq, points) { + m_solution = Solution::create(); + m_solution->setThermo(th); + } + +Flamelet::Flamelet(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) + : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) { + m_solution = sol; + m_id = id; + m_kin = m_solution->kinetics().get(); + m_trans = m_solution->transport().get(); + + m_solution->registerChangedCallback(this, [this]() { + setKinetics(m_solution->kinetics()); + setTransport(m_solution->transport()); + }); + + if (m_trans->transportModel() == "none") { + // @deprecated + warn_deprecated("StFlow", + "An appropriate transport model\nshould be set when instantiating the " + "Solution ('gas') object.\nImplicit setting of the transport model " + "is deprecated and\nwill be removed after Cantera 3.0."); + setTransportModel("mixture-averaged"); + } + } + +Flamelet::~Flamelet() {} + +void Flamelet::resize(size_t ncomponents, size_t points) +{ + Domain1D::resize(ncomponents, points); + m_rho.resize(m_points, 0.0); + m_wtm.resize(m_points, 0.0); + m_cp.resize(m_points, 0.0); + m_hr.resize(m_points, 0.0); + m_h.resize(m_points, 0.0); + m_tcon.resize(m_points, 0.0); + m_visc.resize(m_points, 0.0); + h_RT.resize(m_nsp, 0.0); + cp_R.resize(m_nsp, 0.0); + m_hk.resize(m_nsp, m_points, 0.0); + m_Lek.resize(m_nsp*m_points); + + m_diff.resize(m_nsp*m_points); + if (m_do_multicomponent) { + m_multidiff.resize(m_nsp*m_nsp*m_points); + m_dthermal.resize(m_nsp, m_points, 0.0); + } + + m_wdot.resize(m_nsp,m_points, 0.0); + m_do_energy.resize(m_points,false); + m_qdotRadiation.resize(m_points, 0.0); + m_fixedtemp.resize(m_points); + + m_dz.resize(m_points-1); + m_z.resize(m_points); + m_chi.resize(m_points); + m_updateChi = true; +} + +void Flamelet::eval(size_t jg, double* xg, + double* rg, integer* diagg, double rdt) +{ + // if evaluating a Jacobian, and the global point is outside + // the domain of influence for this domain, then skip + // evaluating the residual + if (jg != npos && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) { + return; + } + + // if evaluating a Jacobian, compute the steady-state residual + if (jg != npos) { + rdt = 0.0; + } + + // start of local part of global arrays + double* x = xg + loc(); + double* rsd = rg + loc(); + integer* diag = diagg + loc(); + + size_t jmin, jmax; + + if (jg == npos) { // evaluate all points + jmin = 0; + jmax = m_points - 1; + } else { // evaluate points for Jacobian + size_t jpt = (jg == 0) ? 0 : jg - firstPoint(); + jmin = std::max(jpt, 1) - 1; + jmax = std::min(jpt+1,m_points-1); + } + + // properties are computed for grid points from j0 to j1 + size_t j0 = std::max(jmin, 1) - 1; + size_t j1 = std::min(jmax+1,m_points-1); + + //----------------------------------------------------- + // update properties + //----------------------------------------------------- + // update thermodynamic properties + updateThermo(x, j0, j1); + + // update transport properties + if (jg == npos) { + updateTransport(x, j0, j1); + } + + //--------------------------------------------------- + // evaluate the chi profile + //--------------------------------------------------- + if ( m_updateChi ) setChi(); + + //---------------------------------------------------- + // evaluate the residual equations at all required + // grid points + //---------------------------------------------------- + + for (size_t j = jmin; j <= jmax; j++) { + //---------------------------------------------- + // left boundary + //---------------------------------------------- + + if (j == 0) { + + // these may be modified by a boundary object + rsd[index(c_offset_Tflamelet, j)] = T(x,j); + + // The default boundary condition for species is zero + // flux. However, the boundary object may modify this. + double sum = 0.0; + for ( size_t k = 0; k < m_nsp; k++) { + sum += Y(x,k,0); + rsd[index(c_offset_Yflamelet + k, j)] = Y(x,k,j); + } + rsd[index(c_offset_Yflamelet + leftExcessSpecies(), 0)] = 1.0 - sum; + } + + //---------------------------------------------- + // right boundary + //---------------------------------------------- + + else if (j == m_points - 1) { + + // the boundary object connected to the right of this + // one may modify or replace these equations. The + // default boundary conditions are zero u, V, and T, + // and zero diffusive flux for all species. + rsd[index(c_offset_Tflamelet,j)] = T(x,j); + + double sum = 0.0; + for (size_t k = 0; k < m_nsp; k++) { + sum += Y(x,k,j); + rsd[index(c_offset_Yflamelet + k ,j)] = Y(x,k,j); + } + rsd[index(c_offset_Yflamelet + rightExcessSpecies(), j)] = 1.0 - sum; + diag[index(c_offset_Yflamelet + rightExcessSpecies(), j)] = 0; + } + + //------------------------------------------ + // interior points + //------------------------------------------ + + else { + + //------------------------------------------------- + // Species equations + // + // rho * dY/dt = 1/2 * 1/Le_k * \rho * \chi * d^2Y/dz^2 + // + 1/4 * (1/Le_k - 1 ) * ( d\rho\chi/dz + \rho * \chi * Cp * 1/\lambda * d(\lambda * 1/Cp)/dz ) + // + M_k * \omega_k + // + // Temperature equation + // + // rho * dT/dt = 1/2 * \rho * \chi * d^2T/dz^2 + 1/2 * \rho * \chi 1/Cp * dCp/dz * dT/dz + HR + // + 1/2 * \rho * \chi 1/Cp * dT/dz * ∑_k Cp_k dYk/dz + //------------------------------------------------- + getWdot(x,j); + + double drhoChidZ = (m_rho[j+1]*chi(j+1) - m_rho[j-1]*chi(j-1))/(z(j+1) - z(j-1)); + double dlambdaoverCpdZ = (m_tcon[j+1]/m_cp[j+1] - m_tcon[j-1]/m_cp[j-1])/(z(j+1) - z(j-1)); + + for (size_t k = 0; k < m_nsp; k++) { + rsd[index(c_offset_Yflamelet + k, j)] = + m_wt[k]*wdot(k,j)/m_rho[j] + + 0.5*chi(j)/Lek(k,j)*d2Ydz2(x,k,j) + + 0.25 / m_rho[j] * (1.0/Lek(k,j) - 1.0) + * ( drhoChidZ + m_rho[j] * chi(j) * m_cp[j] / m_tcon[j] * dlambdaoverCpdZ ) + * cdif1(x,c_offset_Yflamelet+k,j) + - rdt*(Y(x,k,j) - Y_prev(k,j)); + diag[index(c_offset_Yflamelet + k, j)] = 1; + } + + // heat release term + setGas(x,j); + + m_thermo->getEnthalpy_RT_ref(&h_RT[0]); + m_thermo->getCp_R_ref(&cp_R[0]); + + double dCpdZ; + double sum = 0.0; + double sum2 = 0.0; + for (size_t k = 0; k < m_nsp; k++) { + sum += wdot(k,j) * h_RT[k]; + sum2 += cp_R[k] / m_wt[k] * GasConstant / Lek(k,j) + * cdif1(x,c_offset_Yflamelet+k,j); + } + sum *= -T(x,j) * GasConstant / m_cp[j]; // consistent units + m_hr[j] = sum*m_cp[j]; + dCpdZ = (m_cp[j+1] - m_cp[j-1])/(z(j+1) - z(j-1)); + + rsd[index(c_offset_Tflamelet, j)] = + sum/m_rho[j] + + 0.5*chi(j)*d2Tdz2(x,j) + + 0.5*chi(j)/m_cp[j]*dCpdZ*cdif1(x,c_offset_Tflamelet,j) + + 0.5*chi(j)/m_cp[j]*sum2*cdif1(x,c_offset_Tflamelet,j) + - rdt*(T(x,j) - T_prev(j)); + diag[index(c_offset_Tflamelet, j)] = 1; + } + } +} + +string Flamelet::componentName(size_t n) const +{ + switch (n) { + case c_offset_Tflamelet: + return "T"; + default: + if (n >= c_offset_Yflamelet && n < (c_offset_Yflamelet + m_nsp)) { + return m_thermo->speciesName(n - c_offset_Yflamelet); + } else { + return ""; + } + } +} + +size_t Flamelet::componentIndex(const string &name) const +{ + if (name=="T") { + return c_offset_Tflamelet; + } else { + for (size_t n=m_neq; nsetTemperature(T(x,j)); + const double* yy = x + m_nv*j + c_offset_Yflamelet; + m_thermo->setMassFractions_NoNorm(yy); + m_thermo->setPressure(m_press); +} + +void Flamelet::resetBadValues(double* xg) +{ + double* x = xg + loc(); + for (size_t j = 0; j < m_points; j++) { + double* Y = x + m_nv*j + c_offset_Yflamelet; + m_thermo->setMassFractions(Y); + m_thermo->getMassFractions(Y); + } +} + +vector Flamelet::dCpdT(const Array2D sol) +{ + vector dCpdT; + double delta_T = 1.0; + double cp_l, cp_u; + double * yspec = new double[m_nsp]; + m_thermo->setPressure(m_press); + for (size_t n = 0; n < m_points; n++) { + for (size_t k = 0; k < m_nsp; k++) { + yspec[k] = sol(k+1,n); + } + m_thermo->setMassFractions_NoNorm(yspec); + m_thermo->setTemperature(sol(0,n)-delta_T); + cp_l = m_thermo->cp_mass(); + m_thermo->setTemperature(sol(0,n)+delta_T); + cp_u = m_thermo->cp_mass(); + dCpdT.push_back( ( cp_u - cp_l ) / ( 2.0 * delta_T )); + } + return dCpdT; + delete[] yspec; +} + +vector Flamelet::d2CpdT2(const Array2D sol) +{ + vector d2CpdT2; + double delta_T = 1.0; + double cp_l, cp_c, cp_u; + double * yspec = new double[m_nsp]; + m_thermo->setPressure(m_press); + for (size_t n = 0; n < m_points; n++) { + for (size_t k = 0; k < m_nsp; k++) { + yspec[k] = sol(k+1,n); + } + m_thermo->setMassFractions_NoNorm(yspec); + m_thermo->setTemperature(sol(0,n)); + cp_c = m_thermo->cp_mass(); + m_thermo->setTemperature(sol(0,n)-2.0*delta_T); + cp_l = m_thermo->cp_mass(); + m_thermo->setTemperature(sol(0,n)+2.0*delta_T); + cp_u = m_thermo->cp_mass(); + d2CpdT2.push_back( ( cp_u + cp_l - 2.0*cp_c ) / ( 4.0 * std::pow(delta_T,2.0) )); + } + return d2CpdT2; + delete[] yspec; +} + +/** + * Set the gas state to be consistent with the solution at the + * midpoint between j and j + 1. + */ +void Flamelet::setGasAtMidpoint(const double* x, size_t j) +{ + m_thermo->setTemperature(0.5*(T(x,j)+T(x,j+1))); + const double* yyj = x + m_nv*j + c_offset_Yflamelet; + const double* yyjp = x + m_nv*(j+1) + c_offset_Yflamelet; + for (size_t k = 0; k < m_nsp; k++) { + m_ybar[k] = 0.5*(yyj[k] + yyjp[k]); + } + + m_thermo->setMassFractions_NoNorm(m_ybar.data()); + m_thermo->setPressure(m_press); +} + +void Flamelet::updateTransport(double* x, size_t j0, size_t j1) +{ + for (size_t j = j0; j < j1; j++) { + setGasAtMidpoint(x,j); + m_visc[j] = m_trans->viscosity(); + m_tcon[j] = m_trans->thermalConductivity(); + m_trans->getMixDiffCoeffs(&m_diff[j*m_nsp]); + for (size_t k = 0; k < m_nsp; k++) { + if ( m_do_unityLewisNumber ) { + m_Lek[m_nsp*j+k] = 1.0; + } else { + m_Lek[m_nsp*j+k] = m_tcon[j] / ( m_rho[j] * m_cp[j] * m_diff[j*m_nsp+k] ); + } + } + } +} + +void Flamelet::setChi() +{ + m_chi[0]=0.0; + m_chi[m_points-1]=0.0; + for (size_t j = 1; j < m_points-1; j++) { + m_chi[j] = m_chiSt * exactChi(z(j)) / exactChi(m_zSt); + } + m_updateChi = false; +} + +double Flamelet::exactChi(double zz) +{ + double p1 = fabs(2.0*zz - 1.0); + double q1 = 1.0 - p1; + return exp(-2.0 * erfinv(p1,q1) * erfinv(p1,q1)); +} + +double Flamelet::erfinv(double p1,double q1) +{ + double X,S,T,LNQ,F; + T = 0.0; + S = 0.0; + const double C = 0.5625; + const double C1 = 0.87890625; + const double C2 =-0.2302585092994045684017991454684364e3; + const double R = 0.8862269254527580136490837416705726; + const double A[7] = {0.841467547194693616e-01,0.160499904248262200e1,0.809451641478547505e1,0.164273396973002581e2,0.154297507839223692e2,0.669584134660994039e1,0.108455979679682472e1}; + const double B[7] = {.352281538790042405e-2,0.293409069065309557,0.326709873508963100e1,0.123611641257633210e2,0.207984023857547070e2,0.170791197367677668e2,0.669253523595376683e1}; + const double A1[7] = {0.552755110179178015e2,0.657347545992519152e3,0.124276851197202733e4,0.818859792456464820e3,0.234425632359410093e3,0.299942187305427917e2,0.140496035731853946e1}; + const double B1[6] = {0.179209835890172156e3,0.991315839349539886e3,0.138271033653003487e4,0.764020340925985926e3,0.194354053300991923e3,0.228139510050586581e2}; + + const double A2[7] ={0.500926197430588206e1,0.111349802614499199e3,0.353872732756132161e3,0.356000407341490731e3,0.143264457509959760e3,0.240823237485307567e2,0.140496035273226366e1}; + const double B2[6]= {0.209004294324106981e2,0.198607335199741185e3,0.439311287748524270e3,0.355415991280861051e3,0.123303672628828521e3,0.186060775181898848e2}; + const double A3[11]={0.237121026548776092e4,0.732899958728969905e6,0.182063754893444775e7,0.269191299062422172e7,0.304817224671614253e7,0.130643103351072345e7,0.296799076241952125e6,0.457006532030955554e5,0.373449801680687213e4,0.118062255483596543e3,0.100000329157954960e1}; + const double B3[10]={0.851911109952055378e6,0.194746720192729966e7,0.373640079258593694e7,0.397271370110424145e7,0.339457682064283712e7,0.136888294898155938e7,0.303357770911491406e6,0.459721480357533823e5,0.373762573565814355e4,0.118064334590001264e3}; + const double A4[9]={0.154269429680540807e12,0.430207405012067454e12,0.182623446525965017e12,0.248740194409838713e11,0.133506080294978121e10,0.302446226073105850e08,0.285909602878724425e6,0.101789226017835707e04,0.100000004821118676e1}; + const double B4[9]={0.220533001293836387e12,0.347822938010402687e12,0.468373326975152250e12,0.185251723580351631e12,0.249464490520921771e11,0.133587491840784926e10,0.302480682561295591e08,0.285913799407861384e6,0.101789250893050230e04}; + + if (p1 <= 0.0 || q1 <= 0.0) { + return 0.0; + } + if (p1 <= 0.75) { + X = C - p1*p1; + S = (((((A[0]*X + A[1])*X + A[2])*X + A[3])*X + A[4])*X + A[5])*X + A[6]; + T = ((((((B[0]*X + B[1])*X + B[2])*X + B[3])*X + B[4])*X + B[5])*X + B[6])*X+1.0; + X=p1*(S/T); + F=erf(X)-p1; + return X-R*exp(X*X)*F; + } + // p = [0,0.75] + else if (p1 >0.75 && p1 <= 0.9375) { + X = C1 - p1*p1; + if (X < 0.1) { + S = ((((((A1[0]*X + A1[1])*X + A1[2])*X + A1[3])*X+ A1[4])*X + A1[5])*X + A1[6]); + T = ((((((B1[0]*X + B1[1])*X + B1[2])*X + B1[3])*X+ B1[4])*X + B1[5])*X +1.0); + } + else if (X>0.1) { + S = ((((((A2[0]*X + A2[1])*X + A2[2])*X + A2[3])*X+ A2[4])*X + A2[5])*X + A2[6]); + T = ((((((B2[0]*X + B2[1])*X + B2[2])*X + B2[3])*X+ B2[4])*X + B2[5])*X + 1.0); + } + X = p1*(S/T); + T = exp(X*X)*erfc(X)-exp(X*X)*q1; + return X + R*T; + } + else if (p1 > 0.9375) { + LNQ = log(q1); + X= 1.0 / pow(-LNQ,0.5); + if (LNQ > C2) { + S = (((((((((A3[0]*X + A3[1])*X + A3[2])*X + A3[3])*X + A3[4])*X+ A3[5])*X + A3[6])*X + A3[7])*X + A3[8])*X+ A3[9])*X + A3[10]; + T = (((((((((B3[0]*X + B3[1])*X + B3[2])*X + B3[3])*X + B3[4])*X+ B3[5])*X + B3[6])*X + B3[7])*X + B3[8])*X + B3[9])*X + 1.0; + } + else if (LNQ < C2) { + S = (((((((A4[0]*X + A4[1])*X + A4[2])*X + A4[3])*X + A4[4])*X+ A4[5])*X + A4[6])*X + A4[7])*X + A4[8]; + T = ((((((((B4[0]*X + B4[1])*X + B4[2])*X + B4[3])*X + B4[4])*X+ B4[5])*X + B4[6])*X + B4[7])*X + B4[8])*X + 1.0; + } + X=S/(X*T); + T = exp(X*X)*erfc(X); + F = log(T) - LNQ - X*X; + return X + R*T*F; + } + else { + return -2.0; + } + +} + +} \ No newline at end of file diff --git a/src/oneD/IonFlow.cpp b/src/oneD/IonFlow.cpp index 8eb6b3c649c..77c8fa8f6f3 100644 --- a/src/oneD/IonFlow.cpp +++ b/src/oneD/IonFlow.cpp @@ -16,7 +16,7 @@ namespace Cantera { IonFlow::IonFlow(ThermoPhase* ph, size_t nsp, size_t points) : - StFlow(ph, nsp, points) + StFlow(ph, nsp, 0, c_offset_Y, points) { // make a local copy of species charge for (size_t k = 0; k < m_nsp; k++) { diff --git a/src/oneD/Sim1D.cpp b/src/oneD/Sim1D.cpp index 39782ae57d3..c658c3a3efd 100644 --- a/src/oneD/Sim1D.cpp +++ b/src/oneD/Sim1D.cpp @@ -471,13 +471,31 @@ int Sim1D::newtonSolve(int loglevel) } } -void Sim1D::solve(int loglevel, bool refine_grid) +void Sim1D::solve(int loglevel, const string& refine_grid) { int new_points = 1; double dt = m_tstep; m_nsteps = 0; finalize(); + double domain_size = 0.0; + for (size_t n = 0; n < nDomains(); n++) + { + Domain1D& d = domain(n); + size_t length = d.grid().size(); + + domain_size += d.grid(length-1); + } + domain_size = domain_size/2.0; + + const double& criterion=1.0e-4; + + double mesh_distance; + // maximum number of remeshes (problem sometimes encountered, eternal loop) + int MAX_REMESHES = 20; + int n_remeshes = 0; + + while (new_points > 0) { size_t istep = 0; int nsteps = m_steps[istep]; @@ -560,8 +578,54 @@ void Sim1D::solve(int loglevel, bool refine_grid) if (loglevel > 2) { show(); } +/////////////////////////////////////////////////// + + //if (std::strcmp(refine_grid, "remesh") == 0) + if (refine_grid == "remesh") + { + // print new line + if (loglevel>=0) + { + cout<=0) + { + cout<<"old mesh = ["< znew, xnew; + std::vector dsize; + + double distance=0.0; + for (size_t n = 0; n < nDomains(); n++) + { + Domain1D& d = domain(n); + Refiner& r = d.refiner(); + + // proceed with the remeshing + // double this_distance = r.remeshFromSolution( d.grid().size(), + // d.grid().data(), &m_state[start(n)], + // dist_min, domain_size ); + double this_distance = r.remeshFromSolution( d.grid().size(), + d.grid().data(), m_state->data() + start(n), + dist_min, domain_size ); + distance += this_distance; + + // interpolate the solution on the new grid points + int np_old = d.nPoints(); // old domain grid points + int np_new = r.z_new_size(); // new domain grid points + // loop over points in the new grid + for (size_t m = 0; m < np_new; m++) + { + // new position + double znew_curr = r.z_new(m); + // add it to the global array + znew.push_back(znew_curr); + // interpolation + if (np_new>1) + { + int m_old = r.indxtp(np_old,znew_curr,d.grid().data()); + double z0_old = d.grid(m_old ); + double z1_old = d.grid(m_old+1); + for (size_t i = 0; i < d.nComponents(); i++) + { + double x0_old = value(n,i,m_old ); + double x1_old = value(n,i,m_old+1); + double slope = (x1_old-x0_old)/(z1_old-z0_old); + double val = x0_old + slope * (znew_curr-z0_old); + xnew.push_back(val); + } + } + else + { + for (size_t i = 0; i < d.nComponents(); i++) + { + xnew.push_back(value(n,i,0)); + } + } + } + dsize.push_back(np_new); + } + + // At this point, the new grid znew and the new solution + // vector xnew have been constructed, but the domains + // themselves have not yet been modified. Now update each + // domain with the new grid. + + size_t gridstart = 0, gridsize; + for (size_t n = 0; n < nDomains(); n++) { + Domain1D& d = domain(n); + gridsize = dsize[n]; + d.setupGrid(gridsize, &znew[gridstart]); + gridstart += gridsize; + } + + // Replace the current solution vector with the new one + *m_state = xnew; + resize(); + finalize(); + return distance; +} + + +void Sim1D::getRatio() //from MUTAGEN +{ + for (size_t n = 0; n < nDomains(); n++) + { + Domain1D& d = domain(n); + Refiner& r = d.refiner(); + // r.getRatio(d.grid().size(), d.grid().data(), &m_state[start(n)]); + r.getRatio(d.grid().size(), d.grid().data(), m_state->data() + start(n)); + } +} + +/** +* Add a point in a domain +*/ +void Sim1D::addPoint(size_t ndomain, double zpoint, vector xpoint, int loglevel, bool newjac) //from MUTAGEN +{ + vector znew, xnew; + vector dsize; + + // check the domain number + if ((ndomain<0)||(ndomain>=nDomains())) + { + cout<<"wrong ndomain"<(xpoint.size())!=ncomp) + { + cout<<"wrong number of components in xpoint"<0) + { + if (zpoint(xnew.begin(), xnew.end())); + + // resize the work array + m_xnew.resize(xnew.size()); + // copy(xnew.begin(), xnew.end(), m_xnew.begin()); + + resize(); + finalize(); +} int Sim1D::setFixedTemperature(double t) { diff --git a/src/oneD/StFlow.cpp b/src/oneD/StFlow.cpp index ee7130a414f..fe8bccbb11a 100644 --- a/src/oneD/StFlow.cpp +++ b/src/oneD/StFlow.cpp @@ -10,15 +10,19 @@ #include "cantera/transport/TransportFactory.h" #include "cantera/numerics/funcs.h" #include "cantera/base/global.h" +#include "cantera/base/Parser.h" +#include using namespace std; namespace Cantera { -StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t points) : - Domain1D(nsp+c_offset_Y, points), - m_nsp(nsp) +StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : + Domain1D(nsp, points, 0.0, nsoot, neq), + m_nsp(nsp), + m_neq(neq), + m_nsoot(nsoot) { m_type = cFlowType; m_points = points; @@ -29,9 +33,15 @@ StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t points) : m_thermo = ph; size_t nsp2 = m_thermo->nSpecies(); - if (nsp2 != m_nsp) { + // the species mass fractions are the last components in the solution + // vector, so the total number of components is the number of species + // plus the offset of the first mass fraction. + + + m_nv = m_neq + m_nsp + m_nsoot; + if (nsp2 + m_nsoot != m_nsp) { m_nsp = nsp2; - Domain1D::resize(m_nsp+c_offset_Y, points); + Domain1D::resize(m_nv, points); } // make a local copy of the species molecular weight vector @@ -43,7 +53,7 @@ StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t points) : // the species mass fractions are the last components in the solution // vector, so the total number of components is the number of species // plus the offset of the first mass fraction. - m_nv = c_offset_Y + m_nsp; + // m_nv = c_offset_Y + m_nsp; // enable all species equations by default m_do_species.resize(m_nsp, true); @@ -61,22 +71,29 @@ StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t points) : m_qdotRadiation.resize(m_points, 0.0); //-------------- default solution bounds -------------------- - setBounds(c_offset_U, -1e20, 1e20); // no bounds on u - setBounds(c_offset_V, -1e20, 1e20); // V - setBounds(c_offset_T, 200.0, 2*m_thermo->maxTemp()); // temperature bounds - setBounds(c_offset_L, -1e20, 1e20); // lambda should be negative - setBounds(c_offset_E, -1e20, 1e20); // no bounds for inactive component - + if (m_neq == 1) { + setBounds(c_offset_Tflamelet, 200.0, 2*m_thermo->maxTemp()); // temperature bounds + } else { + setBounds(c_offset_U, -1e20, 1e20); // no bounds on u + setBounds(c_offset_V, -1e20, 1e20); // V + setBounds(c_offset_T, 200.0, 2*m_thermo->maxTemp()); // temperature bounds + setBounds(c_offset_L, -1e20, 1e20); // lambda should be negative + setBounds(c_offset_E, -1e20, 1e20); // no bounds for inactive component + } // mass fraction bounds for (size_t k = 0; k < m_nsp; k++) { - setBounds(c_offset_Y+k, -1.0e-7, 1.0e5); + setBounds(m_neq+k, -1.0e-7, 1.0e5); } //-------------------- grid refinement ------------------------- - m_refiner->setActive(c_offset_U, false); - m_refiner->setActive(c_offset_V, false); - m_refiner->setActive(c_offset_T, false); - m_refiner->setActive(c_offset_L, false); + if (m_neq == 1) { + m_refiner->setActive(c_offset_Tflamelet, false); + } else { + m_refiner->setActive(c_offset_U, false); + m_refiner->setActive(c_offset_V, false); + m_refiner->setActive(c_offset_T, false); + m_refiner->setActive(c_offset_L, false); + } vector gr; for (size_t ng = 0; ng < m_points; ng++) { @@ -88,17 +105,31 @@ StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t points) : m_kRadiating.resize(2, npos); m_kRadiating[0] = m_thermo->speciesIndex("CO2"); m_kRadiating[1] = m_thermo->speciesIndex("H2O"); + + // P. Wolf + //---------------------AVBP PEA initialization------------------- + AVBPReadInputPea(); + + // B. Franzelli + //---------------------AVBP thickening initialisation------------ + AVBPReadInputChem(); + + // E. Lameloise + //---------------------Soot computation initialisation----------- + if (m_nsoot > 0){ + initSoot(); + } } -StFlow::StFlow(shared_ptr th, size_t nsp, size_t points) - : StFlow(th.get(), nsp, points) +StFlow::StFlow(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) + : StFlow(th.get(), nsp, nsoot, neq, points) { m_solution = Solution::create(); m_solution->setThermo(th); } -StFlow::StFlow(shared_ptr sol, const string& id, size_t points) - : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), points) +StFlow::StFlow(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) + : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) { m_solution = sol; m_id = id; @@ -189,8 +220,11 @@ void StFlow::resize(size_t ncomponents, size_t points) m_rho.resize(m_points, 0.0); m_wtm.resize(m_points, 0.0); m_cp.resize(m_points, 0.0); + m_h.resize(m_points, 0.0); + m_hr.resize(m_points, 0.0); m_visc.resize(m_points, 0.0); m_tcon.resize(m_points, 0.0); + avbp_thick.resize(m_points,0.0); m_diff.resize(m_nsp*m_points); if (m_do_multicomponent) { @@ -207,6 +241,20 @@ void StFlow::resize(size_t ncomponents, size_t points) m_dz.resize(m_points-1); m_z.resize(m_points); + + // P. Wolf + m_zmixfrac.resize(m_points); + // Soot + if (m_nsoot > 0){ + sootConsumption.resize(m_nsp, 0.0); + m_soot_diff.resize(m_nsoot, m_points, 0.0); + m_soot_soret.resize(m_nsoot, m_points, 0.0); + m_qdotNucleation.resize(m_points, 0.0); + m_qdotCondensation.resize(m_nsoot, m_points, 0.0); + m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); + m_qdotSg.resize(m_nsoot, m_points, 0.0); + m_qdotOxidation.resize(m_nsoot, m_points, 0.0); + } } void StFlow::setupGrid(size_t n, const double* z) @@ -224,6 +272,17 @@ void StFlow::setupGrid(size_t n, const double* z) } } +void StFlow::setupGrid(size_t n) +{ + resize(m_nv, n); + + m_z[0] = 0.0; + for (size_t j = 1; j < m_points; j++) { + m_z[j] = (double) j / ( (double) (n-1) ); + m_dz[j-1] = m_z[j] - m_z[j-1]; + } +} + void StFlow::resetBadValues(double* xg) { double* x = xg + loc(); @@ -283,6 +342,10 @@ void StFlow::setGas(const double* x, size_t j) const double* yy = x + m_nv*j + c_offset_Y; m_thermo->setMassFractions_NoNorm(yy); m_thermo->setPressure(m_press); + // P. Wolf + if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ + calcMixFrac(x,j); + } } void StFlow::setGasAtMidpoint(const double* x, size_t j) @@ -295,6 +358,34 @@ void StFlow::setGasAtMidpoint(const double* x, size_t j) } m_thermo->setMassFractions_NoNorm(m_ybar.data()); m_thermo->setPressure(m_press); + // P. Wolf + if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ + calcMixFrac(x,j); + } +} + + /// Calculates and updates the mixture fraction at point j + /// WARNING: Only correct if no Carbon atoms in the oxidizer line + /// and pure fuel in the fuel line + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + +void StFlow::calcMixFrac(const double* x, size_t j) { + size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom + size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel + double Z_C = 0.0; // passive scalar for C atom + double Z_C_F; // value of the passive scalar in fuel line + double W_C = this->m_thermo->atomicWeight(id_C); // Molecular weight of C atom + double W_fuel = this->m_thermo->molecularWeight(id_fuel); + double n_C; // Number of C atoms in each species + + for (size_t k=0; km_nsp; k++) { + n_C = this->m_thermo->nAtoms(k,id_C); + Z_C += n_C*x[index(c_offset_Y + k, j)]/this->m_thermo->molecularWeight(k); + } + Z_C = Z_C*W_C; + Z_C_F = W_C*this->m_thermo->nAtoms(id_fuel,id_C)/W_fuel; + m_zmixfrac[j] = Z_C/Z_C_F; // ie Z_C=0 in oxidizer line } bool StFlow::fixed_mdot() { @@ -399,6 +490,9 @@ void StFlow::updateProperties(size_t jg, double* x, size_t jmin, size_t jmax) // update the species diffusive mass fluxes whether or not a // Jacobian is being evaluated updateDiffFluxes(x, j0, j1); + if (m_nsoot > 0){ + updateSootDiffFluxes(x, j0, j1); + } } void StFlow::evalResidual(double* x, double* rsd, int* diag, @@ -450,6 +544,12 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, k_P_CO2 /= k_P_ref; k_P += m_press * X(x, m_kRadiating[0], j) * k_P_CO2; } + // absorption coefficient for soot + if (m_nsoot != 0 && m_do_soot_radiation) { + double k_P_soot = 0.0; + k_P_soot = 3.83 * CRad0 * fv(x,j) * T(x,j) / CRad2; + k_P += k_P_soot; + } // calculation of the radiative heat loss term radiative_heat_loss = 2 * k_P *(2 * StefanBoltz * pow(T(x, j), 4) @@ -464,6 +564,12 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, //---------------------------------------------- // left boundary //---------------------------------------------- + if (m_nsoot > 0){ + getDistributionOrdre0(x,j); + } + //avbp_thick.resize(m_points,avbp_fthick); ///////////////////////////// NEW to handle pytest + AVBPcompute_local_thick(x,j); + double thick_j = avbp_thick[j]; if (j == 0) { // these may be modified by a boundary object @@ -494,9 +600,16 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, for (size_t k = 0; k < m_nsp; k++) { sum += Y(x,k,0); rsd[index(c_offset_Y + k, 0)] = - -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); +// no thick -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); + -(m_flux(k,0) * thick_j + rho_u(x,0)* Y(x,k,0)); } rsd[index(c_offset_Y + leftExcessSpecies(), 0)] = 1.0 - sum; + if (m_nsoot > 0){ + for (size_t k = 0; k < m_nsoot; k++){ + rsd[index(c_offset_S + k, 0)] = - (m_soot_diff(k,0) + + rho_u(x,0)* Ys(x,k,0)); + } + } // set residual of poisson's equ to zero rsd[index(c_offset_E, 0)] = x[index(c_offset_E, j)]; @@ -513,6 +626,11 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, // \rho dV/dt + \rho u dV/dz + \rho V^2 // = d(\mu dV/dz)/dz - lambda //------------------------------------------------- + AVBPcompute_local_thick(x,j); + double thick_j = avbp_thick[j]; + double inv_thick = 1.0 / thick_j; + double thick_prev = avbp_thick[j-1]; + if (m_usesLambda) { rsd[index(c_offset_V,j)] = (shear(x, j) - lambda(x, j) - rho_u(x, j) * dVdz(x, j) @@ -524,6 +642,42 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, diag[index(c_offset_V, j)] = 0; } + //------------------------------------------------- + // Soot equation + // + // \rho u dYs/dz + d(-0.554 \mu 1/T dT/dx Ys)/dz + // = d(\rho Ds dYs/dz)/dz + \rhos \rho qdots + // + // convection - Thermophoresis = Diffusion + Source + //------------------------------------------------- + if (m_nsoot > 0) { + sootSource(x,j); + for (size_t k = 0; k < m_nsoot; k++){ + // Convection + double soot_convec = rho_u(x,j)*dYsdz(x,k,j); + // Diffusion + double soot_diffus = 2.0 * (m_soot_diff(k,j) - m_soot_diff(k,j-1)) + / (z(j+1) - z(j-1)); + // Thermophoresis + double soot_soret = 2.0 * (m_soot_soret(k,j) - m_soot_soret(k,j-1)) + / (z(j+1) - z(j-1)); + // Source terms [m3/kg/s] + double soot_source = 0; + soot_source += (k == 0 ? m_qdotNucleation[j] : 0.0); + soot_source += (m_do_condensation ? m_qdotCondensation(k,j) : 0.0); + soot_source += (m_do_coagulation ? m_qdotCoagulation(k,j) : 0.0); + soot_source += (m_do_sg ? m_qdotSg(k,j) : 0.0); + soot_source += (m_do_oxidation ? m_qdotOxidation(k,j) : 0.0); + // kg/s/m^3 + soot_source *= (rho_soot * m_rho[j]); + if(k == m_nsoot - 1 && m_trash_section){soot_source = 0.0;} + // Residual + rsd[index(c_offset_S + k, j)] = + (soot_source - soot_convec + soot_diffus + soot_soret) / m_rho[j] + - rdt * (Ys(x,k,j) - Ys_prev(k,j)); + diag[index(c_offset_S + k, j)] = 1; + } + } //------------------------------------------------- // Species equations // @@ -531,12 +685,20 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, // = M_k\omega_k //------------------------------------------------- getWdot(x,j); + if (m_nsoot > 0 && m_do_retroaction){ + for (size_t k=0; k < m_nsp; k++){ + // (kmol.m^(-3).s^(-1)) + m_wdot(k,j) -= sootConsumption[k]; + } + } for (size_t k = 0; k < m_nsp; k++) { double convec = rho_u(x,j)*dYdz(x,k,j); - double diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) +// no thick double diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) + double diffus = 2.0*(m_flux(k,j)*thick_j - m_flux(k,j-1)*thick_prev) / (z(j+1) - z(j-1)); rsd[index(c_offset_Y + k, j)] - = (m_wt[k]*(wdot(k,j)) + = (m_wt[k]*(wdot(k,j)*inv_thick) +// no thick = (m_wt[k]*(wdot(k,j)) - convec - diffus)/m_rho[j] - rdt*(Y(x,k,j) - Y_prev(k,j)); diag[index(c_offset_Y + k, j)] = 1; @@ -555,16 +717,20 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, setGas(x,j); double dtdzj = dTdz(x,j); double sum = 0.0; + double sum2 = 0.0; grad_hk(x, j); for (size_t k = 0; k < m_nsp; k++) { - double flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); +// no thick double flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); + double flxk = 0.5*(m_flux(k,j-1)*thick_prev + m_flux(k,j)*thick_j); sum += wdot(k,j)*m_hk(k,j); - sum += flxk * m_dhk_dz(k,j) / m_wt[k]; + sum2 += flxk * m_dhk_dz(k,j) / m_wt[k]; } rsd[index(c_offset_T, j)] = - m_cp[j]*rho_u(x,j)*dtdzj - - divHeatFlux(x,j) - sum; +// no thick //- divHeatFlux(x,j) - sum; + - AVBPdivHeatFlux(x,j) - sum*inv_thick - sum2; + rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); rsd[index(c_offset_T, j)] -= rdt*(T(x,j) - T_prev(j)); rsd[index(c_offset_T, j)] -= (m_qdotRadiation[j] / (m_rho[j] * m_cp[j])); @@ -690,6 +856,8 @@ string StFlow::componentName(size_t n) const default: if (n >= c_offset_Y && n < (c_offset_Y + m_nsp)) { return m_thermo->speciesName(n - c_offset_Y); + } else if (n >= c_offset_S && n < (c_offset_S + m_nsoot)) { + return sectionName(n-c_offset_S); } else { return ""; } @@ -708,6 +876,8 @@ size_t StFlow::componentIndex(const string& name) const return c_offset_L; } else if (name == "eField") { return c_offset_E; + } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()) { + return stoi(name.substr(2))+c_offset_S; // offset not required in previous version, why? } else { for (size_t n=c_offset_Y; npressure(); + vector did_section(m_nsoot,false); + bool wrote_header = false; const auto grid = arr.getComponent("grid").as>(); setupGrid(nPoints(), &grid[0]); @@ -833,15 +1005,41 @@ void StFlow::fromArray(SolutionArray& arr, double* soln) string name = componentName(i); if (arr.hasComponent(name)) { const vector data = arr.getComponent(name).as>(); + if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ + size_t n = stoi(name.substr(2)); + did_section[n]=true; + writelog("Adding soot section to soln "+name+"\n"); + } for (size_t j = 0; j < nPoints(); j++) { soln[index(i,j)] = data[j]; } + } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ + size_t n = stoi(name.substr(2)); + did_section[n]=true; + writelog("Creating soot section in soln "+name+"\n"); + for (size_t j = 0; j < nPoints(); j++) { + soln[index(n+c_offset_S,j)] = 0.0; + } } else { warn_user("StFlow::fromArray", "Saved state does not contain values for " "component '{}' in domain '{}'.", name, id()); } } + if (soot_loglevel >= 1 && m_nsoot != 0) { + wrote_header = false; + for (size_t ks = 0; ks < m_nsoot; ks++) { + if (did_section[ks] == false) { + if (!wrote_header) { + writelog("\n\n"); + writelog("Missing data for soot sections:\n"); + wrote_header = true; + } + writelog(m_section_name[ks]+" "); + } + } + } + updateProperties(npos, soln + loc(), 0, m_points - 1); setMeta(arr.meta()); } @@ -853,6 +1051,8 @@ string StFlow::flowType() const { return "Free Flame"; } else if (m_type == cAxisymmetricStagnationFlow) { return "Axisymmetric Stagnation"; + } else if (m_type == cFlameletFlow){ + return "Flamelet"; } else { throw CanteraError("StFlow::flowType", "Unknown value for 'm_type'"); } @@ -1005,10 +1205,1020 @@ void StFlow::fixTemperature(size_t j) needJacUpdate(); } } +/* ------------------------------------------------------------------------ + Reads the mixture_database.dat file and sets accordingly the PEA function(s) + P. Wolf modif by J. Wirtz +--------------------------------------------------------------------------*/ +void StFlow::AVBPReadInputPea() { + Parser parser; + Param* param; + + ifstream avbp_mixturedb("mixture_database.dat"); + if (avbp_mixturedb.good()){ + parser.parseFile("mixture_database.dat"); + // In case of pea, the name of the gas should be the same than the one in the mixture_database. + // Get number of mixtures in database + size_t n_mixtures = parser.nbParamOccurence("mixture_name"); + size_t idx_beg = std::string::npos; + size_t idx_end = std::string::npos; + // Loop through all occurences of keyword "mixture name" + for (size_t i=0; i< n_mixtures; ++i) { + param = parser.getParam("mixture_name",i); + std::string current_str = param->readString(0); + // Check if mixture_name is the one requested in the cti file + if ( current_str == m_thermo->name() ) { + // Store bounding idx to get important info + idx_beg = parser.getParamNumber("mixture_name",i); + idx_end = parser.getParamNumber("mixture_name",i+1); + + // Get the fuel of the 2-step chemistry + param = parser.getParam("species_name", idx_beg, idx_end); + for (size_t i=0; ireadString(i); + if (avbp_species.find('C')!=string::npos && avbp_species.find('H')!=string::npos){ + avbp_fuel = avbp_species; + } + if (avbp_species == "H2"){ + avbp_fuel = avbp_species; + } + + } + + // Check if PEA method and search for the coefficient + if (parser.checkParam("pea_method", idx_beg, idx_end) == true){ + param = parser.getParam("pea_method", idx_beg, idx_end); + std::string avbp_pea = param->readString(0); + if (avbp_pea == "pea1"){ + avbp_ipea = 1; + cout<<"ipea set to 1, PEA_1 will be applied"<readDouble(i); + } + } + else if (avbp_pea == "pea2") { + avbp_ipea = 2; + cout<<"ipea set to 2, PEA_2 will be applied"<readDouble(i); + } + param = parser.getParam("pea_coeff", idx_beg, idx_end, 1); + for (size_t i=0; i<10; i++) { + avbp_pea_coeffs[i+8] = param->readDouble(i); + } + + } + else{ + throw CanteraError("readAvbpInputPEA","ipea is set to a weird value"); + } + } + else { + avbp_ipea = 0; + } + } + else { + // pea not considered as mixture_name (mixture_database.dat) does not correspond to gas name (cti) + avbp_ipea = 0; + } + + // calculate the global equivalence ratio phi_cst + if ((avbp_ipea==1)||(avbp_ipea==2)){ + size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom + size_t id_H = this->m_thermo->elementIndex("H"); // Index of H atom + size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel + size_t id_ox = this->m_thermo->speciesIndex("O2"); // Index of O2 + size_t n_C = this->m_thermo->nAtoms(id_fuel,id_C); + size_t n_H = this->m_thermo->nAtoms(id_fuel,id_H); + //Calculate in mass units phi = s_m*Yf/Yo + phi_cst = (n_C + n_H/4)*this->m_thermo->molecularWeight(id_ox)/this->m_thermo->molecularWeight(id_fuel); + phi_cst = phi_cst*1./0.2333; // WARNING: valid only for Fuel/AIR mixture + } + + if (avbp_ipea!=0){ + break; + } + + } + } + else { + avbp_ipea = 0; + } +} +/********** + Reading the AVBP input_chem.dat + B. Franzelli +*************/ +void StFlow::AVBPReadInputChem() { + avbp_fthick = m_thick; + if (avbp_fthick > 1.0) { + cout << "INFO: Thickening applied with constant value." << endl; + } + else { + avbp_fthick = 1.0; + } +} +void StFlow::AVBPcompute_local_thick(double* x,size_t j){ + avbp_thick[j] = avbp_fthick; +} + +//----------------------// +// SOOT RELATED MTEHODS // +//----------------------// +void StFlow::initSoot(){ + //---------------------------------------------------- + // Initializes soot computation + //---------------------------------------------------- + + // Sets offset of soot sections in solution array + // Resizes necessay arrays + // Sets sections names "YsXX", disables refinement on soot and sets clipping + + // Offset definition + c_offset_S = c_offset_Y + m_nsp; + // Array allocation + m_section_name.resize(m_nsoot); + sootConsumption.resize(m_nsp, 0.0); + q.resize(m_nsoot,0.0); + vSectMin.resize(m_nsoot, 0.0); + vSectMax.resize(m_nsoot, 0.0); + vSectMean.resize(m_nsoot, 0.0); + sSectMean.resize(m_nsoot, 0.0); + dSectMean.resize(m_nsoot, 0.0); + dSectCol.resize(m_nsoot, 0.0); + kfractal.resize(m_nsoot, 1.0); + Dfractal.resize(m_nsoot, 3); + nNucMean.resize(m_nsoot, 0.0); + rNucMean.resize(m_nsoot, 0.0); + rSectCol.resize(m_nsoot, 0.0); + aSectCol.resize(m_nsoot, 0.0); + theta_surf.resize(m_nsoot,2.0); + m_soot_diff.resize(m_nsoot, m_points, 0.0); + m_soot_soret.resize(m_nsoot, m_points, 0.0); + m_qdotNucleation.resize(m_points, 0.0); + m_qdotCondensation.resize(m_nsoot, m_points, 0.0); + m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); + collision_mat.resize(m_nsoot, m_nsoot, 0.0); + m_qdotSg.resize(m_nsoot, m_points, 0.0); + m_qdotOxidation.resize(m_nsoot, m_points, 0.0); + // Sections setup + for (size_t k = 0; k < m_nsoot; k++) { + std::string string_k = std::to_string(k); + m_section_name[k] = "Ys" + string_k; + m_refiner->setActive(c_offset_S+k, false); + setBounds(c_offset_S + k, -1.0e-5, 1e5); + } + +} + +void StFlow::setPrecursors(vector id_precursors){ + //---------------------------------------------------- + // Recovers precursor data for further computation + //---------------------------------------------------- + + if (m_nsoot <= 0){ + writelog("\n--> CANTERA SOOT : no sections :(\n"); + return; + } + size_t id_C = m_thermo->elementIndex("C"); + W_C = m_thermo->atomicWeight(id_C); + n_PAH = id_precursors.size(); + m_precursors.resize(n_PAH); + W_PAH.resize(n_PAH,0.0); + n_C.resize(n_PAH,0.0); + for (size_t k = 0; k != n_PAH; k++){ + m_precursors[k] = id_precursors[k] - c_offset_Y; + W_PAH[k] = m_thermo->molecularWeight(m_precursors[k]); + n_C[k] = m_thermo->nAtoms(m_precursors[k],id_C); + } +} + +void StFlow::finalizeSoot(){ + //---------------------------------------------------- + // Soot setup finalization + //---------------------------------------------------- + // Creates soot volumes + sootCreationVol(); + // Computes collision matrix + sootCollisionInverse(); + // Load surface reactions + if (m_do_sg || m_do_oxidation){ + loadHaca(m_haca_model); + loadSurface();} + + if (soot_loglevel >= 1){showSootInfo();} + if (soot_loglevel >= 2){showSootSections();} +} + +void StFlow::sootCreationVol(){ + // Sections creations + // PAH list boundaries + size_t n_C_min = *min_element(n_C.begin(),n_C.end()); + size_t n_C_max = *max_element(n_C.begin(),n_C.end()); + // First section lower boundary : smallest possible dimer + vSectMin[0] = 2.0 * (double)n_C_min * V_C2; + // First section upper boundary : biggest possible dimer + vSectMax[0] = V_C2 * max(2.0 * n_C_min + n_C_max, 2.0 * n_C_max); + // Following sections : geometrical progression + vSectMin[1] = vSectMax[0]; + if (m_trash_section){ + double vTrashLowLim = Pi * pow(dTrashLowLim,3.0) / 6; + for (size_t k = 1; k < m_nsoot - 2; k++){ + double exponent = double(k) / double(m_nsoot-2); + vSectMax[k] = vSectMin[1] * pow(vTrashLowLim / vSectMin[1],exponent); + vSectMin[k+1] = vSectMax[k]; + } + vSectMax[m_nsoot - 2] = vTrashLowLim; + vSectMin[m_nsoot - 1] = vTrashLowLim; + }else{ + for (size_t k = 1; k < m_nsoot - 1; k++){ + double exponent = double(k) / double(m_nsoot-1); + vSectMax[k] = vSectMin[1] * pow(bigSoot / vSectMin[1],exponent); + vSectMin[k+1] = vSectMax[k]; + } + } + + vSectMax[m_nsoot-1] = bigSoot; + // Building mean values + for (size_t k = 0; k < m_nsoot; k++){ + vSectMean[k] = (vSectMax[k] + vSectMin[k]) / 2.0 ; //(vSectMax[k] - vSectMin[k]) / log (vSectMax[k] / vSectMin[k]); + dSectMean[k] = pow(6 / Pi * vSectMean[k], 1.0 / 3.0); + } + + // Sections morphology + for (size_t k = 0; k < m_nsoot; k++){ + if (vSectMean[k] >= vlim1){ + // Fractal dimension + Dfractal[k] = Df; + // Fractal prefactor + kfractal[k] = 4.46 * pow(Dfractal[k], -2.08); + } + } + + if (m_soot_morphology == "sphere" || m_soot_morphology == "rodrigues"){ + // Soot morphological properties as defined by P. Rodrigues (PhD Thesis, 2018) + // For spheres, theta = 2.0 + for (size_t k = 0; k < m_nsoot; k++){ + if (m_soot_morphology == "rodrigues" && vSectMin[k] >= vlim1){ + theta_surf[k] = (3.0 * (log(vSectMean[k] / vlim1)) + + 2.0 * (log(vlim1 / V_C2))) + / (log(vSectMean[k] / V_C2)); + if (k == m_nsoot-1 && m_trash_section){theta_surf[k] = theta_surf[k-1];} + } + // Collision diameter + dSectCol[k] = 6 / pow(36 * Pi, 1.0 /Dfractal[k]) + * pow(vSectMean[k], (Dfractal[k]-2.0) / Dfractal[k]) + * pow(S_C2 * + pow(vSectMean[k]/V_C2,theta_surf[k] / 3.0),(3.0-Dfractal[k]) / Dfractal[k]); + // Collision radius + rSectCol[k] = dSectCol[k] / 2.0; + // Collision cross-section + aSectCol[k] = Pi * pow(rSectCol[k], 2.0); + // Surface area + sSectMean[k] = S_C2 * pow(vSectMean[k] / V_C2, theta_surf[k] / 3.0); + // Nuclei number + nNucMean[k] = pow(sSectMean[k], 2) / (36. * Pi * pow(vSectMean[k], 2.)); + // Nuclei radius[m] + rNucMean[k] = 3. * vSectMean[k] / sSectMean[k]; + } + // // From P. Rodrigues, trick to help numerical stability (not tested its impact) + // dSectCol[m_nsoot-1] = dSectMean[m_nsoot-1]; + // rSectCol[m_nsoot-1] = dSectCol[m_nsoot-1] / 2.0; + // aSectCol[m_nsoot-1] = Pi * pow(rSectCol[m_nsoot-1], 2.0); + }else if (m_soot_morphology == "thajudeen"){ + // Soot morphological properties as defined by Thajudeen (2012) + for (size_t k = 0; k < m_nsoot; k++){ + // Nuclei number + nNucMean[k] = max(1., vSectMean[k] / vlim1); + // Nuclei radius + rNucMean[k] = min(pow(3.0 * vSectMean[k] / (4.0 * Pi), 1./3.), pow(3.0 * vlim1 / (4.0 * Pi), 1.0/3.0)); + if (vSectMean[k] >= vlim1){ + // Collision radius (Smoluchowski radius) + double alpha1 = 0.253 * pow(Dfractal[k], 2.0) - 1.209 * Dfractal[k] + 1.433; + double alpha2 = -0.218 * pow(Dfractal[k], 2.0) + 0.964 * Dfractal[k] - 0.180; + double phi_r = 1 / (alpha1 * log(nNucMean[k]) + alpha2); + rSectCol[k] = rNucMean[k] * phi_r * pow(nNucMean[k] / kfractal[k], 1/Dfractal[k]); + // Collision cross-section (Projected Area) + double alpha3 = 0.439 * pow(Dfractal[k], 2.0) - 2.221 * Dfractal[k] + 2.787; + double alpha4 = -0.232 * pow(Dfractal[k], 3.0) + 1.273 * pow(Dfractal[k], 2.0) - 2.183 * Dfractal[k] + 1.906; + double phi_p = pow(nNucMean[k], -alpha3) / alpha4; + aSectCol[k] = Pi * pow(rNucMean[k], 2.) * phi_p * pow(nNucMean[k] / kfractal[k], 2.0/Dfractal[k]); + }else{ + rSectCol[k] = dSectMean[k] / 2.; + aSectCol[k] = Pi * pow(rSectCol[k], 2.); + } + //Collision diameter ("Smoluchowski diameter") + dSectCol[k] = 2. * rSectCol[k]; + // Surface area (computed from smoluchowski radius, close to Rodrigues definition) + sSectMean[k] = Pi * pow(dSectCol[k], 2.); + // theta parameter (needed for surface reactions) + theta_surf[k] = 3. * log(sSectMean[k]/S_C2) / log(vSectMean[k]/V_C2); + } + } +} + +void StFlow::sootCollisionInverse(){ + //---------------------------------------------------- + // Computes colision matrix (coagulation) + //---------------------------------------------------- + + for (size_t k = 0; k < m_nsoot; k++){ + for (size_t l = k; l < m_nsoot; l++){ + for (size_t m = l; m < m_nsoot; m++){ + double vol_min = vSectMin[l] + vSectMin[k]; + if(vol_min <= vSectMax[m] && vol_min >= vSectMin[m]){ + collision_mat(k,l) = m; + } + } + } + } +} + +void StFlow::loadSurface(){ + //---------------------------------------------------- + // Resizes and compute surface reactions arrays + //---------------------------------------------------- + + kpower.resize(m_nsoot,0.0); + mpower.resize(m_nsoot,0.0); + vc2power.resize(m_nsoot,0.0); + vc2powerm.resize(m_nsoot,0.0); + vmax_kpower.resize(m_nsoot,0.0); + vmin_kpower.resize(m_nsoot,0.0); + vmax_mpower.resize(m_nsoot,0.0); + vmin_mpower.resize(m_nsoot,0.0); + vmaxmc2_kpower.resize(m_nsoot,0.0); + vminpc2_kpower.resize(m_nsoot,0.0); + vmaxmc2_mpower.resize(m_nsoot,0.0); + vminpc2_mpower.resize(m_nsoot,0.0); + vc2powervect.resize(m_nsoot,0.0); + vc2powermvect.resize(m_nsoot,0.0); + for (size_t k = 0; k < m_nsoot; k++){ + kpower[k] = (theta_surf[k] + 3.0)/3.0; + mpower[k] = theta_surf[k]/3.0; + vc2power[k] = (3.0 - theta_surf[k] )/3.0; + vc2powerm[k] = - mpower[k]; + vmax_kpower[k] = pow(vSectMax[k],kpower[k]); + vmin_kpower[k] = pow(vSectMin[k],kpower[k]); + vmax_mpower[k] = pow(vSectMax[k],mpower[k]); + vmin_mpower[k] = pow(vSectMin[k],mpower[k]); + vmaxmc2_kpower[k] = pow(vSectMax[k] - V_C2,kpower[k]); + vminpc2_kpower[k] = pow(vSectMin[k] + V_C2,kpower[k]); + vmaxmc2_mpower[k] = pow(vSectMax[k] - V_C2,mpower[k]); + vminpc2_mpower[k] = pow(vSectMin[k] + V_C2,mpower[k]); + vc2powervect[k] = pow(V_C2,vc2power[k]); + vc2powermvect[k] = pow(V_C2,vc2powerm[k]); + } +} + +void StFlow::showSootInfo(){ + writelog("\n{:=^47}{:9}{:=^47}", "", "SOOT INFO", ""); + writelog("\n{:21}{:2}{}", "NUMBER OF SECTIONS", ":", m_nsoot); + writelog("\n{:21}{:1}","PRECURSORS", ":"); + for (size_t k = 0; k != n_PAH; k++){ + writelog(" {}", m_thermo->speciesName(m_precursors[k])); + } + if (dTrashLowLim > 0){writelog("\n{:21}{:2}{} m", "MAX DIAMETER", ":", dTrashLowLim);} + writelog("\n{:21}{:2}{}", "AGGREGATES MORPHOLOGY", ":", m_soot_morphology); + writelog("\n{:21}{:2}{}", "RETROACTION", ":", m_do_retroaction); + writelog("\n{:21}{:2}{}", "CONDENSATION", ":", m_do_condensation); + writelog("\n{:21}{:2}{}", "COAGULATION", ":", m_do_coagulation); + writelog("\n{:21}{:2}{}", "SURFACE GROWTH", ":", m_do_sg); + writelog("\n{:21}{:2}{}", "OXIDATION", ":", m_do_oxidation); + if (m_do_sg || m_do_oxidation){ + writelog("\n{:21}{:2}", "HACA MODEL", ":"); + if (m_haca_model == 1){ + writelog("Mauss"); + }else if (m_haca_model == 2){ + writelog("Blanquart"); + }else if (m_haca_model == 3){ + writelog("Kazakov"); + writelog("\n{:21}{:2}{}{:2}", "-> Flame temperature", ":", kazakovTad, " K"); + } + } + writelog("\n{:21}{:2}{}", "RADIATIVE HEAT LOSSES", ":", m_do_soot_radiation); + writelog("\n{:21}{:2}{}", "SORET EFFECT", ":", m_do_soot_soret); + writeline('=', 103, false, true); + writelog("\n"); +} +void StFlow::showSootSections(){ + //---------------------------------------------------- + // Displays section informations + //---------------------------------------------------- + + if (m_nsoot <= 0){ + writelog ("\nSOOT INFO : no sections to show :("); + return; + } + writelog("\n{:=^36}{:30}{:=^37}", "", "SOOT SECTIONS INFO (SI UNITS)", ""); + writelog("\n Section Vol. min. Vol. mean Vol. max. Diam. mean Diam. coll"); + writeline('-', 103, false, true); + for (size_t k = 0; k < m_nsoot; k++) { + writelog("\n {:10d} {:10.4g} {:10.4g} {:10.4g} {:10.4g} {:10.4g}", + k,vSectMin[k],vSectMean[k],vSectMax[k],dSectMean[k],dSectCol[k]); + } + writeline('=', 103, false, true); + writelog("\n"); +} + +void StFlow::sootSource(const double* x, size_t j) { + //---------------------------------------------------- + // Computes soot source terms + //---------------------------------------------------- + // Dimerization + sootDimerization(x,j); + // Nucleation + sootNucleation(x,j); + // Condensation + if (m_do_condensation){sootCondensation(x,j);} + // Coagulation + if (m_do_coagulation){sootCoagulation(x,j);} + // Surface chemistry + if (m_do_sg || m_do_oxidation){sootSurface(x,j);} +} + +void StFlow::sootDimerization(const double* x, size_t j){ + //---------------------------------------------------- + // Computes dimerization source term + //---------------------------------------------------- + double omega = 0, c_dimer = 0; + double V_k, d2_k, omega_k, C_k, gamma_k, k_k; + for (size_t k = 0; k < n_PAH; k++){ + // PAH volume [m3] + V_k = n_C[k] * V_C2 / 2.0; + // Squared PAH diameter [m2] + d2_k = pow(6.0 * V_k / Pi, 2.0/3.0); + // PAH concentraiton [kmol/m3] + C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; + // PAH sticking coefficient [-] + gamma_k = Cn_cst * pow(W_PAH[k], 4.0); + // Reaction rate constant [m3/kmol/s] + k_k = sqrt(4.0 * Pi * Boltzmann * T(x,j) / (W_C * n_C[k] / Avogadro)) * d2_k * Avogadro; + // PAH dimerization reaction rate [kmol/m3/s] + omega_k = gamma_k * k_k * pow(C_k, 2.0); + // PAH consumption [kmol/m3/s] (x2 because 2 mol PAH -> 1 mol dimer) + sootConsumption[m_precursors[k]] = 2 * omega_k; + // Adds PAH contribution to overall local dimerization rate + omega += omega_k; + // Adds PAH contribution to overall dimer carbon atoms + c_dimer += omega_k * n_C[k]; + + } + // Overall dimerization rate [1/kg/s] + r_dimer = omega * Avogadro / m_rho[j]; + // Overall dimer volume [m3] + V_dimer = c_dimer * V_C2 / omega; + + // double K00 = 0, cdimer = 0; + // double V_k, d_k, kdimfwd_k, K00_k, C_k; + // for (size_t k = 0; k < n_PAH; k++){ + // // PAH volume [m3] + // V_k = n_C[k] * V_C2 / 2.0; + // // PAH diameter [m] + // d_k = pow(6.0 * V_k / Pi, 1.0/3.0); + // // PAH concentraiton [mol/m3] + // C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; + // // m6/s/kg/mol2 + // kdimfwd_k = Cn_cst * pow(W_PAH[k], 4.0) / m_rho[j] + // * sqrt((4.0 * Pi * Boltzmann * T(x,j)) / ((W_C / Avogadro) * n_C[k])) + // * pow(d_k, 2.0) * pow(Avogadro, 2.0) ; + // // (mol.g^(-1).s^(-1)) + // K00_k = pow(C_k, 2.0) * kdimfwd_k / Avogadro; + // // (mol.g^(-1).s^(-1)) + // K00 += K00_k; + // cdimer += K00_k * n_C[k]; + // // Precursor consumption (mol/m3/s) + // // (x2 because 2 mol PAH -> 1 mol dimer) + // sootConsumption[m_precursors[k]] = 2 * K00_k * m_rho[j]; + // } + // // Dimerization rate [1/kg/s] + // r_dimer = K00 * Avogadro; + // // Equivalent dimer volume [m3] + // V_dimer = cdimer * V_C2 / K00; +} + +void StFlow::sootNucleation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute nucleation source terms + //---------------------------------------------------- + // [m(11/2)/s/kg] + beta_fm = sqrt(Pi * Boltzmann * T(x,j) + / (rho_soot * 2.0)) / m_rho[j]; + // Dimer collision frequency [m6/s/kg] + beta_dimer = eps_nucl * beta_fm * sqrt(2.0 / V_dimer) + * pow (2.0 * pow(6.0 * V_dimer / Pi, 1.0 / 3.0), 2.0); + // // Dimer particle density [1/m3] + // N_dimer = sqrt((r_dimer / beta_dimer)); + // // Source term for nucleation [m3/kg/s] + // m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer, 2.0); + + // Dimer diameter [m] + double d_dimer = 2.0 * pow(3.0 * V_dimer / (4.0 * Pi), 1.0/3.0); + // Dimer mass [kg] + double m_dimer = V_dimer * rho_soot; + // Reaction rate constant [m3/kmol/s] + // k_nuc = beta_dimer * m_rho[j] * Avogadro / 2 + double k_nuc = eps_nucl * Avogadro * pow(d_dimer, 2.0) + * sqrt(4.0 * Pi * Boltzmann * T(x, j) / m_dimer); + // Dimer concentration (QSS Assumption) [kmol/m3] + double C_dimer = sqrt((r_dimer / Avogadro * m_rho[j]) / (2.0 * k_nuc)); + // Dimer number concentration [1/m3] + N_dimer = C_dimer * Avogadro; + // Nucleation reaction rate [kmol/m3/s] + double omega_nuc = k_nuc * pow(C_dimer, 2.0); + // Nucleation rate [m3/kg/s] + m_qdotNucleation[j] = omega_nuc * Avogadro * V_dimer / m_rho[j] * 2.0; + +} + +void StFlow::sootCondensation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute condensation source term and corrects + // nucleation source term + //---------------------------------------------------- + + double kCond = 0; + double interval, vmoy, term1, term2, term3; + vector beta_cond(m_nsoot,0.0); + for (size_t k = 0; k < m_nsoot; k++){ + // Condensation collision kernel[m6/s/kg] + beta_cond[k] = eps_cond * beta_fm * sqrt(1.0/vSectMean[k]+1.0/V_dimer) + * pow(dSectCol[k] + pow(6.0 / Pi * V_dimer, 1.0/3.0), 2.0); + // Collisional frequency between a dimer and any soot particle [m3/s/kg] + kCond += beta_cond[k] * (q[k] * (vSectMax[k] - vSectMin[k]) / (vSectMean[k])); + } + // Correction of dimer density and nucleation source term + N_dimer = - (kCond / (2.0 * beta_dimer)) + + sqrt((r_dimer / beta_dimer) + + pow(kCond / (2.0 * beta_dimer),2.0)); + // Nucleation source term [m3/kg/1] + m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer,2.0); + + // Condensation source terms + for (size_t k = 0; k < m_nsoot; k++){ + interval = (vSectMax[k] - V_dimer) - vSectMin[k]; + vmoy = ((vSectMax[k] - V_dimer) + vSectMin[k]) / 2; + term1 = N_dimer * beta_cond[k] * q[k] / vmoy * V_dimer * interval; + if ( k==0 ){ + term2 = 0.0; + term3 = 0.0; + }else{ + interval = vSectMax[k-1] - (vSectMax[k-1] - V_dimer); + vmoy = (vSectMax[k-1] + (vSectMax[k-1] - V_dimer)) / 2; + term2 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * V_dimer * interval; + term3 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * vmoy * interval; + } + m_qdotCondensation(k,j) = term1 + term2 + term3; + if ( k>0 ){ + m_qdotCondensation(k-1,j) -= term3; + } + } +} + + +void StFlow::sootCoagulation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute coagulation source terms + //---------------------------------------------------- + + for (size_t k = 0; k < m_nsoot; k++){ + m_qdotCoagulation(k,j) = 0.0; + } + // Viscosity (Cantera) [Pa.s-1] [CLEAN BUT SLOW] + // setGas(x,j); + // double visc = m_trans->viscosity(); + // Viscosity (Sutherland, air) [Pa.s-1] [TRASH BUT QUICK] + double visc = Csut1 * pow(T(x,j),1.5) / (T(x,j) + Csut2); + // Mean free path [m] + double mfp_rod = Boltzmann * T(x,j) / (sqrt(2.0) * Pi * pow(d_gaz,2.0) * m_press); + double mfp_tha = 66.4e-7 * (101325. / m_press) * (T(x,j) / 293.) * (1. + 110./293.) / (1 + 110. / T(x,j)); + double beta_coag_lk = 0.0; + for (size_t k = 0; k < m_nsoot; k++){ + for (size_t l = k; l < m_nsoot; l++){ + if (m_collision_model == "rodrigues" || m_collision_model == "sphere"){ + //Cunnningham numbers [-] + double Cu_k = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[k]; + double Cu_l = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[l]; + // Coagulation rate in continuous regime [m^6.kg^(-1).s-(-1)] + double beta_cont_lk = (2.0 * Boltzmann * T(x,j)) / (3.0 * visc) + * (dSectCol[l] + dSectCol[k]) + * (Cu_l / dSectCol[l] + Cu_k / dSectCol[k]) + / m_rho[j]; + // Coagulation rate in free molecular regime [m^6.kg^(-1).s-(-1)] + double beta_fm_lk = eps_coag * beta_fm + * sqrt(1 / vSectMean[k] + 1 / vSectMean[l]) + * pow(dSectCol[k] + dSectCol[l], 2.0); + // Overall coagulation rate [m^6.kg^(-1).s-(-1)] + beta_coag_lk = (beta_fm_lk * beta_cont_lk) + / (beta_fm_lk + beta_cont_lk); + }else if (m_collision_model == "thajudeen"){ + double reduced_mass = rho_soot * vSectMean[k] * vSectMean[l] / (vSectMean[k] + vSectMean[l]); + double smoluchowski_radius = rNucMean[k] * (1.203 - (0.4315*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])) * pow(rSectCol[k]/rNucMean[k] + rSectCol[l]/rNucMean[k], 0.8806 + (0.3497*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])); + double kn_diff_k = mfp_tha * Pi * rSectCol[k] / aSectCol[k]; + double kn_diff_l = mfp_tha * Pi * rSectCol[l] / aSectCol[l]; + double f_k = (6.0 * Pi * rSectCol[k] * visc) / (1 + kn_diff_k * (1.257 + 0.4 * exp(-1.1/kn_diff_k))); + double f_l = (6.0 * Pi * rSectCol[l] * visc) / (1 + kn_diff_l * (1.257 + 0.4 * exp(-1.1/kn_diff_l))); + double friction_coefficient = f_k * f_l / (f_k + f_l); + double projected_area = pow(smoluchowski_radius, 2.0) * Pi; + double kn_diff = (sqrt(Boltzmann * T(x,j) * reduced_mass) * Pi * smoluchowski_radius) / (friction_coefficient * projected_area); + double H = (4.0 * Pi * pow(kn_diff, 2.0) + 25.836 * pow(kn_diff, 3.0) + eps_coag * sqrt(8.0 * Pi) * 11.211 * pow(kn_diff, 4.0)) / (1 + 3.502 * kn_diff + 7.211 * pow(kn_diff, 2.0) + 11.211 * pow(kn_diff, 3.0)); + beta_coag_lk = (H * friction_coefficient * pow(projected_area, 2.0)) / (reduced_mass * pow(Pi, 2.0) * smoluchowski_radius) / m_rho[j]; + } + // Section of the particle corresponding to the coagulation of (l,k)y + size_t m = collision_mat(k,l); + // Loss of mass in section l due to coagulation with k + double terml = beta_coag_lk * q[l] * q[k] / vSectMean[k] + * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); + // Loss of mass in section k due to coagulation with l + double termk = beta_coag_lk * q[l] * q[k] / vSectMean[l] + * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); + double termm, termmplus; + // Gain in mass in m and m+1 thanks to coagulation of (l,k) + if (vSectMax[l] + vSectMax[k] <= vSectMax[m]){ + termm = terml + termk; + termmplus = 0.0; + }else{ + termm = (terml + termk) + * (vSectMax[m] - (vSectMin[k] + vSectMin[l])) + / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); + termmplus = (terml + termk) + * (vSectMax[k]+vSectMax[l]-vSectMax[m]) + / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); + } + if (m < m_nsoot-1){ + m_qdotCoagulation(m+1,j) += termmplus; + }else{ + termm = terml + termk; + } + m_qdotCoagulation(m,j) += termm; + m_qdotCoagulation(l,j) -= terml; + m_qdotCoagulation(k,j) -= termk; + } + } +} + +void StFlow::updateSootDiffFluxes(const double* x, size_t j0, size_t j1) +{ + //---------------------------------------------------- + // Computes soot molecular and thermal diffusion fluxes + //---------------------------------------------------- + for (size_t j = j0; j < j1; j++) { + // Evaluate gas at midpoints : j->j+1/2 + double Tmid = 0.5 * (T(x,j)+T(x,j+1)); + // [CLEAN BUT SLOW] + // setGasAtMidpoint(x,j); + // double wtm = m_thermo->meanMolecularWeight(); + // double rho = m_thermo->density(); + // double visco = m_trans->viscosity(); + // [TRASH BUT QUICK] + double wtm = 0.5*(m_wtm[j]+m_wtm[j+1]); + double rho = 0.5*(m_rho[j]+m_rho[j+1]); + double visco = Csut1 * pow(Tmid,1.5) / (Tmid + Csut2); + // Evaluate centered differencies at j+1/2 + double dT = T(x,j+1)-T(x,j); + double dz = z(j+1) - z(j); + // Evaluate viscosity + for (size_t k = 0; k < m_nsoot; k++){ + // Evaluate soot mass fraction at j+1/2 + + double Ysmid = 0.5 * (Ys(x,k,j)+Ys(x,k,j+1)); + // Evaluate centered differencies at j+1/2 + double dYs = Ys(x,k,j+1) - Ys(x,k,j); + //Evaluate diffusion coefficient at j+1/2 + double Ds = 3 / (2 * rho_soot * pow(dSectMean[k], 2.0) + * (1 + alphaT * Pi / 8)) + * sqrt ((wtm*Boltzmann*Tmid)/(2*Pi*Avogadro)); + // Evaluate soot mass diffusion flux at j+1/2 + m_soot_diff(k,j) = rho * Ds * dYs/dz; + // Evaluate soot mass soret flux at j+1/2 + if (m_do_soot_soret){ + m_soot_soret(k,j) = C_soot_soret * visco * Ysmid * dT/dz / Tmid; + } + } + } +} + +void StFlow::sootSurface(const double* x, size_t j){ + //---------------------------------------------------- + // Compute surface chemistry source terms + //---------------------------------------------------- + + // Computes reaction rates + sootSurfaceInitialization(x,j); + double term1, term2, term3; + //--------------- + // SURFACE GROWTH + //--------------- + if (m_do_sg){ + for (size_t k = 0; k < m_nsoot; k++){ + term1 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] + * (vmaxmc2_mpower[k] - vmin_mpower[k]); + if (k==0){ + term2 = 0.0; + term3 = 0.0; + }else{ + term2 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k-1] / mpower[k-1] * q[k-1] + * (vmax_mpower[k-1] - vmaxmc2_mpower[k-1]); + term3 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powermvect[k-1] / kpower[k-1] * q[k-1] + * (vmax_kpower[k-1] - vmaxmc2_kpower[k-1]); + } + // Surface growth source term [m3/kg/s] + m_qdotSg(k,j) = term1 + term2 + term3; + if (k > 0){m_qdotSg(k-1,j) -= term3;} + } + } + //---------- + // OXYDATION + //---------- + if (m_do_oxidation){ + for (size_t k=m_nsoot; k --> 0;){ + term1 = alpha_surf * kox / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] + * (vmax_mpower[k] - vminpc2_mpower[k]); + if (k==m_nsoot-1){ + term2 = 0.0; + term3 = 0.0; + }else if (k==m_nsoot-2 && m_trash_section) { + term2 = 0.0; + term3 = 0.0; + }else{ + term2 = alpha_surf * kox / m_rho[j] * vc2powervect[k+1] / mpower[k+1] * q[k+1] + * (vminpc2_mpower[k+1] - vmin_mpower[k+1]); + term3 = alpha_surf * kox / m_rho[j] * vc2powermvect[k+1] / kpower[k+1] * q[k+1] + * (vminpc2_kpower[k+1] - vmin_kpower[k+1]); + } + // Oxidation source term [m3/kg/s] + m_qdotOxidation(k,j) = - (term1 + term2 - term3); + if (k < m_nsoot - 1){ + m_qdotOxidation(k+1,j) -= term3; + } + } + } +} + +void StFlow::sootSurfaceInitialization(const double* x, size_t j){ + // Recover species concentrations [kmol/m3] + double conc_H = 0, conc_H2 = 0, conc_OH = 0, conc_H2O = 0, conc_C2H2 = 0, conc_O2 = 0; + double k01f = 0, k01b = 0, k02f = 0, k02b = 0, k03f = 0, k03b = 0, k04f = 0, k04b = 0; + double k05f = 0, k05b = 0, k06f = 0, k06bisf = 0; + double r01f = 0, r01b = 0, r02f = 0, r02b = 0, r03f = 0, r03b = 0, r04f = 0, r04b = 0; + double r05f = 0, r05b = 0, r06f = 0, r06bisf = 0, r07f = 0; + double ko2, koh, kd, krev, chi, chip, chic, alpha_kazakov; + size_t k; + // Recover molar concentrations + k = m_thermo->speciesIndex("H"); + if (k != npos){conc_H = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("H2"); + if (k != npos){conc_H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){conc_H2O = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){conc_C2H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("O2"); + if (k != npos){conc_O2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("OH"); + if (k != npos){conc_OH = Y(x,k,j) * m_rho[j] / m_wt[k];} + // SI units + double slt = 1.0e3 / GasConstant / T(x,j); // 1e3 because GasConstant in J/kmol/K + double T_log=log(T(x,j)); + if (m_haca_model == 1 || m_haca_model == 11){ //Mauss + // Arrhenius constants + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); // [m3/kmol/s] + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); // [m3/kmol/s] + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); // [m3/kmol/s] + k02b = ak02b * exp(nk02b*T_log - ek02b*slt); // [m3/kmol/s] + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [m3/kmol/s] + k03b = ak03b * exp(nk03b*T_log - ek03b*slt); // [1/s] + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); // [m3/kmol/s] + k04b = ak04b * exp(nk04b*T_log - ek04b*slt); // [1/s] + k05f = ak05f * exp(nk05f*T_log - ek05f*slt); // [1/s] + k05b = ak05b * exp(nk05b*T_log - ek05b*slt); // [m3/kmol/s] + k06f = ak06f * exp(nk06f*T_log - ek06f*slt); // [m3/kmol/s] + k06bisf = k06f; + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_OH; + r02b = k02b * conc_H2O; + r03f = k03f * conc_H; + r03b = k03b; + r04f = k04f * conc_C2H2; + r04b = k04b; + r05f = k05f; + r05b = k05b * conc_H; + r06f = k06f * conc_O2; + r06bisf = k06bisf * conc_O2; + r07f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + double fk10 = r05f / (r04b+r06bisf+r05f); + double A_QSS = (r01f + r02f + r03b + r07f + r05b * (1.0 - fk10)) / (r01b + r02b + r03f + r04f * fk10); + double B_QSS = r04f / ( r04b + r06bisf + r05f); + double D_QSS = r05b / (r04b + r06f + r05f); + + chi = 1.0; + chip = chi * A_QSS; + chic = chi * (A_QSS*B_QSS + D_QSS); + // Partial reaction rates[1/s] + koh = r07f * chi; + kd = r04f * chip; + ko2 = r06f * (chip + chic); + krev = r04b * chic; + // Partial surface growth and oxidation rates [1/s] + ksg = kd - krev; + kox = ko2 + koh; + } else if (m_haca_model == 2){ //Blanquart + // Arrhenius constants [m3/kmol/s] + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); + k02b = ak02b * exp(nk02b*T_log - ek02b*slt); + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [1/s] + k03b = ak03b * exp(nk03b*T_log - ek03b*slt); + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); + k05f = ak05f * exp(nk05f*T_log - ek05f*slt); + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_OH; + r02b = k02b * conc_H2O; + r03f = k03f; + r03b = k03b * conc_H; + r04f = k04f * conc_C2H2; + r05f = k05f * conc_O2; + r06f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + chi = (r01f + r02f + r03f) / (r01b + r02b + r03b + r04f + r05f); // * 1.7e15; + // Oxidation O2 [must be 1/s] + ko2 = chi * r05f; + // Oxidation OH [1/s] + koh = r06f * chi; + // Oxidation + kox = ko2 + koh; + // Surface growth [1/s] + ksg = chi * r04f; + } else if (m_haca_model == 3){ //Kazakov + // Fraction of sites available at the surface of the particle for reaction [-] + alpha_kazakov = (1.0 + tanh(8.168e3/kazakovTad - 4.57)) / 2.0; + // Arrhenius constants [m3/kmol/s] + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_H; + r03f = k03f * conc_C2H2; + r04f = k04f * conc_O2; + r05f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + chi = r01f / (r01b + r02f + r03f + r04f); // * 2.3e14 + // Oxidation O2 [1/s] + ko2 = alpha_kazakov * chi * r04f; + // Oxidation OH [1/s] + koh = r05f * chi; + //Oxidation [1/s] + kox = ko2 + koh; + // Surface growth [1/s] + ksg = alpha_kazakov * chi * r03f; + } + //------------------------- + // RETROACTION ON GAS PHASE + //------------------------- + if (m_do_retroaction){ + double deltaQ = 0.0, soot_surface = 0.0; + for (size_t k = 0; k < m_nsoot; k++){ + deltaQ += vc2powervect[k] / mpower[k] * q[k] * (vmax_mpower[k]-vmin_mpower[k]); + } + //Overall active sites concentration [kmol/m3] + soot_surface = alpha_surf * n_sites * deltaQ / (V_C2 * Avogadro); // n_sites added here + // Surface chemistry reaction rates [kmol/s/m3] + double w01f = 0, w01b = 0, w02f = 0, w02b = 0, w03f = 0, w03b = 0; + double w04f = 0, w04b = 0, w05f = 0, w05b = 0, w06f = 0, w06bisf = 0; + double w07f = 0; + if (m_do_sg || m_do_oxidation){ + // Reaction rates for reactions occuring on both oxidation & surface growth + if (m_haca_model == 1){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chip; + w02f = r02f * soot_surface * chi; + w02b = r02b * soot_surface * chip; + w03f = r03f * soot_surface * chip; + w03b = r03b * soot_surface * chi; + w05f = r05f * soot_surface * chic; + w05b = r05b * soot_surface * chi; + w06bisf = r06bisf * soot_surface * chic; + }else if (m_haca_model == 2){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chi; + w02f = r02f * soot_surface * chi; + w02b = r02b * soot_surface * chi; + w03f = r03f * soot_surface * chi; + w03b = r03b * soot_surface * chi; + }else if (m_haca_model == 3){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chi; + w02f = r02f * soot_surface * chi; + } + } + // Reaction rates for reactions occuring on surfacce growth only + if (m_do_sg){ + if (m_haca_model == 1){ + w04f = r04f * soot_surface * chip; + w04b = r04b * soot_surface * chic; + }else if (m_haca_model == 2){ + w04f = r04f * soot_surface * chi; + }else if (m_haca_model == 3){ + w03f = r03f * soot_surface * chi; + } + } + // Reaction rates for reactions occuring on oxidation only + if (m_do_oxidation){ + if (m_haca_model == 1){ + // Reaction rates [kmol/m3/s] + w06f = r06f * soot_surface * chip; + w07f = r07f * soot_surface * chi; + }else if (m_haca_model == 2){ + w05f = r05f * soot_surface * chi; + w06f = r06f * soot_surface * chi; + }else if (m_haca_model == 3){ + w04f = r04f * soot_surface * chi; + w05f = r05f * soot_surface * chi; + } + } + + // Gaseous species consumption [kmol/s/m3] + if (m_haca_model == 1){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption[k] = - (w01f - w01b) - (w03f - w03b) + (w05f - w05b);} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption[k] = (w04f - w04b);} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption[k] = (w01f - w01b);} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption[k] = - w06f - w06bisf;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption[k] = 2.0 * w06f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption[k] = - (w02f - w02b) - w07f;} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){sootConsumption[k] = + (w02f - w02b);} + k = m_thermo->speciesIndex("HCO"); + if (k != npos){sootConsumption[k] = 2.0 * w06bisf + w07f;} + k = m_thermo->speciesIndex("CH"); + if (k != npos){sootConsumption[k] = w07f;} + }else if (m_haca_model == 2){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption[k] = -(w01f-w01b) + (w03f-w03b) + w04f;} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption[k] = -w04f;} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption[k] = (w01f-w01b) + w05f + w06f;} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption[k] = -w05f;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption[k] = 2.0 * w05f + w06f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption[k] = -(w02f-w02b) - w06f;} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){sootConsumption[k] = (w02f-w02b);} + }else if (m_haca_model == 3){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption[k] = -(w01f-w01b) - w02f + w03f;} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption[k] = -w03f;} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption[k] = (w01f-w01b) + w05f;} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption[k] = -w04f;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption[k] = 2.0 * w04f + w05f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption[k] = - w05f;} + } + } +} + +void StFlow::getDistributionOrdre0(const double* x, size_t j){ + for (size_t k = 0; k < m_nsoot; k++){ + // Soot volume fraction density [1/m3] + q[k] = m_rho[j] * Ys(x,k,j) / (rho_soot * (vSectMax[k] - vSectMin[k])); + } +} +//-----------------------------// +// END OF SOOT RELATED METHODS // +//-----------------------------// void StFlow::evalRightBoundary(double* x, double* rsd, int* diag, double rdt) { size_t j = m_points - 1; + AVBPcompute_local_thick(x,j); + double thick_prev = avbp_thick[j-1]; // the boundary object connected to the right of this one may modify or // replace these equations. The default boundary conditions are zero u, V, @@ -1019,9 +2229,17 @@ void StFlow::evalRightBoundary(double* x, double* rsd, int* diag, double rdt) double sum = 0.0; // set residual of poisson's equ to zero rsd[index(c_offset_E, j)] = x[index(c_offset_E, j)]; + if (m_nsoot > 0){ + for (size_t k = 0; k < m_nsoot; k++){ + if (m_do_retroaction){sum += Ys(x,k,j);} + rsd[index(c_offset_S + k, j)] = + m_soot_diff(k,j-1) + rho_u(x,j)*Ys(x,k,j); + } + } for (size_t k = 0; k < m_nsp; k++) { sum += Y(x,k,j); - rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); + rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1)*thick_prev + rho_u(x,j)*Y(x,k,j); +// no thick rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); } rsd[index(c_offset_Y + rightExcessSpecies(), j)] = 1.0 - sum; diag[index(c_offset_Y + rightExcessSpecies(), j)] = 0; diff --git a/src/oneD/refine.cpp b/src/oneD/refine.cpp index 9d1fe555c67..f830115f2a4 100644 --- a/src/oneD/refine.cpp +++ b/src/oneD/refine.cpp @@ -248,4 +248,421 @@ int Refiner::getNewGrid(int n, const double* z, int nn, double* zn) zn[jn] = z[n-1]; return 0; } + + +double Refiner::remeshFromSolution(int np, const doublereal* z, const doublereal* x, const double dist_min, const double domain_size) //from MUTAGEN +// int np; : number of points in the old mesh +// double* z : array of the old mesh points +// double* x : array of variables on the old mesh +{ + + double distance; + + if (m_domain->nPoints() == 1) + { + m_z_new.clear(); + m_z_new.push_back(z[0]); + distance=0.0; + return distance; + } + + if (m_domain->nPoints() <= 0) + { + distance=0.0; + return distance; + } + + // a few defintions + double z_start = z[0]; + double z_end = z[np-1]; + + // compute w_old + // [w_old] = [m^-1] + vector w_old(np-1); + for (int i=0;iz[i+1]-z[i]) + { + dz_min = z[i+1]-z[i]; + z_center = z[i]; + } + } + + // init w1 with a very small (but non-zero) value + // [w1] = [m^-1] + vector w1(np-1); + for (int i=0;i vn(np); + vector gn(np); + vector gc(np-1); + vector cc(np-1); + // loop over active components + for (int icomp=0;icomp m_min_range*vv) + { + // compute w1 for gradient + for (int i=0;i m_min_range*gg) + { + // compute w1 for curvature + for (int i=0;i w2(np-1); + // first, copy w1 in w2 + copy(w1.begin(),w1.end(),w2.begin()); + // parameters + double bndr = m_ratio; + double bndq = 2.0*log10(bndr); + for (int i=0;i w3(np-1); + double rwidth = 5.0; // parameter for the gaussian width + double alpha = 2.5; // the integration interval is [-alpha.sigma;+alpha.sigma] + int nint = 100; // half the number of integration intervals + double w2_max = *max_element(w2.begin(), w2.end()); // max value of w2 + double sigma = rwidth/w2_max; // width of the gaussian [m] + double gintg = sigma*sqrt(Pi); // integral of the gaussian [m] + double dz_int = alpha*sigma/static_cast(nint); // integration step size [m] + for (int i=0;i(j)+0.5)*dz_int; + double zc = 0.5*(z[i+1]+z[i ]); + double zint = zc+c; + double f; + // value at zc+c + if (zint<=z_start) + { + f = 0.0; + } + else if (zint>=z_end) + { + f = 0.0; + } + else + { + int i1=indxtp(np,zint,z); + f = w2[i1]; + } + // convolution product + f = f * exp(-c*c/(sigma*sigma)); + // integration and normalization + w3[i] = w3[i] + f*dz_int/gintg; + } + } + + // compute distance between the two meshes + distance=0.0; + for (int i=0;i w4(np); + w4[0] = 0.0; + for (int i=0;i(1.0+w4_last + 0.5); + + // final remeshing + m_z_new.clear(); + for (int i_new=0;i_new(i_new); + int i = indxtp(np,w,&w4[0]); + double slope = (z[i+1] -z[i])/(w4[i+1]-w4[i]); + double dz = slope*(w-w4[i]); + double z_add = z[i] + dz; + if (z_add<=z_center+domain_size) + { + m_z_new.push_back(z_add); + } + } + + // New size + np_new = m_z_new.size(); + + // Add points if necessary + bool done=false; + if (m_z_new[np_new-1]>=z_center+domain_size) + { + done = true; + } + while(!done) + { + double ratio_last = (m_z_new[np_new-1] - m_z_new[np_new-2])/(m_z_new[np_new-2] - m_z_new[np_new-3]); + double z_add = m_z_new[np_new-1] + ratio_last*(m_z_new[np_new-1] - m_z_new[np_new-2]); + m_z_new.push_back(z_add); + np_new++; + if (m_z_new[np_new-1]>=z_center+domain_size) + { + done = true; + } + } + +/* DO NOTHING... + m_z_new.clear(); + for (int i=0;inPoints() == 1) + { + return; + } + + if (m_domain->nPoints() <= 0) + { + return; + } + + // get gradient and curvature criterions in w1 + vector vn(np); + vector gn(np); + vector gc(np-1); + vector cc(np-1); + vector grad_max(np-1); + vector curve_max(np-1); + // loop over active components + for (int icomp=0;icomp m_min_range*vv) + { + // compute w1 for gradient + for (int i=0;i m_min_range*gg) + { + // compute w1 for curvature + for (int i=0;i +bool has_key(const M& m, int j) { + if (m.find(j) != m.end()) return true; + return false; +} + +static void r_drawline() { + string s(78,'#'); + s += '\n'; + writelog(s.c_str()); +} + +/** + * Return the square root of machine precision. + */ +static doublereal eps() { + doublereal e = 1.0; + while (1.0 + e != 1.0) e *= 0.5; + return sqrt(e); +} + } diff --git a/src/transport/AVBPTransport.cpp b/src/transport/AVBPTransport.cpp new file mode 100644 index 00000000000..509345c859c --- /dev/null +++ b/src/transport/AVBPTransport.cpp @@ -0,0 +1,278 @@ +/** + * @file AVBPTransport.cpp + * Simplified AVBP transport properties for ideal gas mixtures. + */ + +/* $Author: B. Franzelli (v. 1.7) $ + * $Revision: A. Felden (v 2.1-2.3) $ + * $Date: 01/2018 $ + */ + +#include "cantera/transport/AVBPTransport.h" +#include "cantera/thermo/ThermoPhase.h" +#include "cantera/base/stringUtils.h" +#include "cantera/base/utilities.h" +#include "cantera/base/Parser.h" + +#include +#include +#include +#include +#include +#include + +using namespace std; + +namespace Cantera +{ + +// AVBPTransport::AVBPTransport() : +// m_lambda(0.0) +// { +// } + +void AVBPTransport::init(ThermoPhase* thermo, int mode, int log_level) +{ + + GasTransport::init(thermo, mode, log_level); + + ifstream avbp_mixturedb("mixture_database.dat"); + + if (avbp_mixturedb.good()){ + //cout << thermo->name() << thermo->id() << endl; + //std::string mixture_id; + //mixture_id = thermo->name(); + //cout<<"INFO: using simplified transport data for "<< m_thermo->name()<<" from the 'mixture_database.dat' file."<0){ +// cout<<"-Exponent for Second Sutherland Constant: "<cp_mass(); + m_density = m_thermo->density(); + if(avbp_beta<0){ + double avbp_absbeta; + avbp_absbeta = - avbp_beta; + m_viscmix = avbp_mu0 * pow(m_temp/avbp_T0,avbp_absbeta); + } + else if(avbp_beta>0){ + double coeff; + coeff= (avbp_T0 + avbp_beta) / pow(avbp_T0,1.5); + m_viscmix = avbp_mu0 * coeff * pow(m_temp, 1.5) / (m_temp + avbp_beta); + } + else{ + m_viscmix = avbp_mu0; + } + m_lambda = m_viscmix * m_cp / avbp_Prandtl; +} + + +double AVBPTransport::viscosity() +{ + update_T(); + update_C(); + + double vismix = 0.0; + + // AVBP Transport Properties + if(avbp_beta<0){ + double avbp_absbeta; + avbp_absbeta = - avbp_beta; + vismix = avbp_mu0 * pow(m_temp/avbp_T0,avbp_absbeta); + } + else if(avbp_beta>0){ + double coeff; + coeff= (avbp_T0 + avbp_beta) / pow(avbp_T0,1.5); + vismix = avbp_mu0 * coeff * pow(m_temp, 1.5) / (m_temp + avbp_beta); + } + else{ + vismix = avbp_mu0; + } + + m_viscmix = vismix; + return m_viscmix; +} + + +double AVBPTransport::thermalConductivity() +{ + update_T(); + update_C(); + + double m_cp = 0.0; + double m_vismix = 0.0; + m_cp = m_thermo->cp_mass(); + + if(avbp_beta<0){ + double avbp_absbeta; + avbp_absbeta = - avbp_beta; + m_vismix = avbp_mu0 * pow(m_temp/avbp_T0,avbp_absbeta); + }else if(avbp_beta>0){ + double coeff; + coeff = (avbp_T0 + avbp_beta) / pow(avbp_T0,1.5); + m_vismix = avbp_mu0 * coeff * pow (m_temp, 1.5) / (m_temp + avbp_beta); + }else{ + m_vismix = avbp_mu0; + } + + m_lambda = m_vismix * m_cp / avbp_Prandtl; + return m_lambda; +} + + +void AVBPTransport::getMixDiffCoeffs(double* const d) +{ + update_T(); + update_C(); + + double m_cp = 0.0; + double m_density = 0.0; + m_cp = m_thermo->cp_mass(); + m_density = m_thermo->density(); + + double m_vismix = 0.0; + if(avbp_beta<0){ + double avbp_absbeta; + avbp_absbeta = - avbp_beta; + m_vismix = avbp_mu0 * pow(m_temp/avbp_T0,avbp_absbeta); + }else if(avbp_beta>0){ + double coeff; + coeff = (avbp_T0 + avbp_beta) / pow(avbp_T0,1.5); + m_vismix = avbp_mu0 * coeff * pow(m_temp,1.5)/ (m_temp + avbp_beta); + }else{ + m_vismix = avbp_mu0; + } + + for (size_t k=0; ktemperature(); + if (t == m_temp && m_nsp == m_thermo->nSpecies()) { + return; + } + if (t <= 0.0) { + throw CanteraError("AVBPTransport::update_T", + "negative temperature {}", t); + } + + GasTransport::update_T(); + +} + +void AVBPTransport::update_C() +{ + // signal that concentration-dependent quantities will need to + // be recomputed before use, and update the local mole + // fractions. + + m_thermo->getMoleFractions(m_molefracs.data()); + + // add an offset to avoid a pure species condition + for (size_t k = 0; k < m_nsp; k++) { + m_molefracs[k] = std::max(Tiny, m_molefracs[k]); + } +} + + +/** + * Parse the specific mixture_param.dat input file of + * AVBP v7 ++. Use the Parser.cpp located in ../base + */ +void AVBPTransport::read_mixture(std::string inputfile) +{ + Parser parser; + Param* param; + + parser.parseFile(inputfile); + // Get number of mixtures in database + size_t n_mixtures = parser.nbParamOccurence("mixture_name"); + size_t idx_beg = std::string::npos; + size_t idx_end = std::string::npos; + // Loop through all occurences of keyword "mixture name" + for (size_t i=0; i< n_mixtures; ++i) { + param = parser.getParam("mixture_name",i); + std::string current_str = param->readString(0); + // Check if mixture_name is the one requested in the cti file + if ( current_str == m_thermo->name() ) { + // Store bounding idx to get important info + idx_beg = parser.getParamNumber("mixture_name",i); + idx_end = parser.getParamNumber("mixture_name",i+1); + } + } + // Get an error if requested mixture does not match any entry in database + if (idx_beg == idx_end) { + cout<<"FATAL ERROR: cannot find the requested mixture in the 'mixture_database.dat' file.\n \ + Make sure that the name of your gas instance in the Cantera mechanism (.cti/.xml) file matches that provided in the 'mixture_database.dat'."<readDouble(0); + // SCH LE + param = parser.getParam("species_Schmidt_number", idx_beg, idx_end); + avbp_Le.resize(m_nsp); + avbp_Sch.resize(m_nsp); + for (size_t i=0; ireadDouble(i); + avbp_Le[i]= avbp_Sch[i] / avbp_Prandtl; + } + // VISCO + param = parser.getParam("mu_ref", idx_beg, idx_end); + avbp_mu0 = param->readDouble(0); + param = parser.getParam("T_ref", idx_beg, idx_end); + avbp_T0 = param->readDouble(0); + param = parser.getParam("viscosity_law_coeff", idx_beg, idx_end); + avbp_beta = param->readDouble(0); + param = parser.getParam("viscosity_law", idx_beg, idx_end); + avbp_law = param->readString(0); + if (avbp_law == "power") { + avbp_beta = - avbp_beta; + } +} + +double AVBPTransport::pressure_ig() +{ + return (m_thermo->molarDensity() * GasConstant * + m_thermo->temperature()); + +} + +} \ No newline at end of file diff --git a/src/transport/TransportFactory.cpp b/src/transport/TransportFactory.cpp index 70183c71c77..ca28ef10025 100644 --- a/src/transport/TransportFactory.cpp +++ b/src/transport/TransportFactory.cpp @@ -4,6 +4,7 @@ // at https://cantera.org/license.txt for license and copyright information. // known transport models +#include "cantera/transport/AVBPTransport.h" #include "cantera/transport/MultiTransport.h" #include "cantera/transport/MixTransport.h" #include "cantera/transport/UnityLewisTransport.h" @@ -36,6 +37,11 @@ TransportFactory::TransportFactory() addDeprecatedAlias("mixture-averaged", "Mix"); reg("mixture-averaged-CK", []() { return new MixTransport(); }); addDeprecatedAlias("mixture-averaged-CK", "CK_Mix"); + + reg("AVBP", []() { return new AVBPTransport(); }); + reg("AVBP-CK", []() { return new AVBPTransport(); }); + addDeprecatedAlias("AVBP", "CK_AVBP"); + reg("multicomponent", []() { return new MultiTransport(); }); addDeprecatedAlias("multicomponent", "Multi"); reg("multicomponent-CK", []() { return new MultiTransport(); }); @@ -48,6 +54,7 @@ TransportFactory::TransportFactory() addDeprecatedAlias("high-pressure", "HighP"); m_CK_mode["CK_Mix"] = m_CK_mode["mixture-averaged-CK"] = true; m_CK_mode["CK_Multi"] = m_CK_mode["multicomponent-CK"] = true; + m_CK_mode["CK_AVBP"] = m_CK_mode["AVBP-CK"] = true; } TransportFactory* TransportFactory::factory() { From f298a7d4eed0dbd037c6c62d142a6363664f9673 Mon Sep 17 00:00:00 2001 From: pestre Date: Wed, 5 Mar 2025 23:38:58 +0100 Subject: [PATCH 07/98] Merge differences in test directory Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: modified: test/clib/test_ctonedim.cpp new file: test/data/surface2-gas.inp new file: test/data/surface2-thermo.dat new file: test/data/surface2.inp modified: test/oneD/test_oneD.cpp --- test/clib/test_ctonedim.cpp | 2 +- test/data/surface2-gas.inp | 5 +++ test/data/surface2-thermo.dat | 59 +++++++++++++++++++++++++++++++++++ test/data/surface2.inp | 32 +++++++++++++++++++ test/oneD/test_oneD.cpp | 2 +- 5 files changed, 98 insertions(+), 2 deletions(-) create mode 100644 test/data/surface2-gas.inp create mode 100644 test/data/surface2-thermo.dat create mode 100644 test/data/surface2.inp diff --git a/test/clib/test_ctonedim.cpp b/test/clib/test_ctonedim.cpp index 7da241b7ed0..c8dcb7c1e9f 100644 --- a/test/clib/test_ctonedim.cpp +++ b/test/clib/test_ctonedim.cpp @@ -233,7 +233,7 @@ TEST(ctonedim, freeflame_from_parts) // solve and save stflow_solveEnergyEqn(flow, 1); - bool refine_grid = false; + const char* refine_grid = "disabled"; int loglevel = 0; sim1D_solve(flame, loglevel, refine_grid); ret = sim1D_save(flame, "gtest-freeflame.yaml", "clib", diff --git a/test/data/surface2-gas.inp b/test/data/surface2-gas.inp new file mode 100644 index 00000000000..0769550dab8 --- /dev/null +++ b/test/data/surface2-gas.inp @@ -0,0 +1,5 @@ +ELEMENTS H O PT END + +SPECIES + H H2 H2O H2O2 HO2 O O2 OH +END diff --git a/test/data/surface2-thermo.dat b/test/data/surface2-thermo.dat new file mode 100644 index 00000000000..74280083617 --- /dev/null +++ b/test/data/surface2-thermo.dat @@ -0,0 +1,59 @@ +THERMO + 300.0 1000.0 3000.0 +H 120186H 1 G 0300.00 5000.00 1000.00 1 + 0.02500000E+02 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2 + 0.02547162E+06-0.04601176E+01 0.02500000E+02 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00 0.02547162E+06-0.04601176E+01 4 +H2 121286H 2 G 0300.00 5000.00 1000.00 1 + 0.02991423E+02 0.07000644E-02-0.05633828E-06-0.09231578E-10 0.15827519E-14 2 +-0.08350340E+04-0.13551101E+01 0.03298124E+02 0.08249441E-02-0.08143015E-05 3 +-0.09475434E-09 0.04134872E-11-0.10125209E+04-0.03294094E+02 4 +H2O 20387H 2O 1 G 0300.00 5000.00 1000.00 1 + 0.02672145E+02 0.03056293E-01-0.08730260E-05 0.12009964E-09-0.06391618E-13 2 +-0.02989921E+06 0.06862817E+02 0.03386842E+02 0.03474982E-01-0.06354696E-04 3 + 0.06968581E-07-0.02506588E-10-0.03020811E+06 0.02590232E+02 4 +H2O2 120186H 2O 2 G 0300.00 5000.00 1000.00 1 + 0.04573167E+02 0.04336136E-01-0.14746888E-05 0.02348903E-08-0.14316536E-13 2 +-0.01800696E+06 0.05011369E+01 0.03388753E+02 0.06569226E-01-0.14850125E-06 3 +-0.04625805E-07 0.02471514E-10-0.01766314E+06 0.06785363E+02 4 +HO2 20387H 1O 2 G 0300.00 5000.00 1000.00 1 + 0.04072191E+02 0.02131296E-01-0.05308145E-05 0.06112269E-09-0.02841164E-13 2 +-0.15797270E+03 0.03476029E+02 0.02979963E+02 0.04996697E-01-0.03790997E-04 3 + 0.02354192E-07-0.08089024E-11 0.01762273E+04 0.09222724E+02 4 +O 120186O 1 G 0300.00 5000.00 1000.00 1 + 0.02542059E+02-0.02755061E-03-0.03102803E-07 0.04551067E-10-0.04368051E-14 2 + 0.02923080E+06 0.04920308E+02 0.02946428E+02-0.16381665E-02 0.02421031E-04 3 +-0.16028431E-08 0.03890696E-11 0.02914764E+06 0.02963995E+02 4 +O2 121386O 2 G 0300.00 5000.00 1000.00 1 + 0.03697578E+02 0.06135197E-02-0.12588420E-06 0.01775281E-09-0.11364354E-14 2 +-0.12339301E+04 0.03189165E+02 0.03212936E+02 0.11274864E-02-0.05756150E-05 3 + 0.13138773E-08-0.08768554E-11-0.10052490E+04 0.06034737E+02 4 +OH 121286O 1H 1 G 0300.00 5000.00 1000.00 1 + 0.02882730E+02 0.10139743E-02-0.02276877E-05 0.02174683E-09-0.05126305E-14 2 + 0.03886888E+05 0.05595712E+02 0.03637266E+02 0.01850910E-02-0.16761646E-05 3 + 0.02387202E-07-0.08431442E-11 0.03606781E+05 0.13588605E+01 4 +O_Pt 92491O 1PT 1 I 300.00 3000.00 1000.00 1 + 0.19454180E+01 0.91761647E-03-0.11226719E-06-0.99099624E-10 0.24307699E-13 2 +-0.14005187E+05-0.11531663E+02-0.94986904E+00 0.74042305E-02-0.10451424E-05 3 +-0.61120420E-08 0.33787992E-11-0.13209912E+05 0.36137905E+01 4 +O2_Pt 92491O 2PT 3 I 300.00 3000.00 1000.00 1 + 0.19454180E+01 0.91761647E-03-0.11226719E-06-0.99099624E-10 0.24307699E-13 2 +-0.14005187E+05-0.11531663E+02-0.94986904E+00 0.74042305E-02-0.10451424E-05 3 +-0.61120420E-08 0.33787992E-11-0.13209912E+05 0.36137905E+01 4 +H_Pt 92491H 1PT 1 I 300.00 3000.00 1000.00 1 + 0.10696996E+01 0.15432230E-02-0.15500922E-06-0.16573165E-09 0.38359347E-13 2 +-0.50546128E+04-0.71555238E+01-0.13029877E+01 0.54173199E-02 0.31277972E-06 3 +-0.32328533E-08 0.11362820E-11-0.42277075E+04 0.58743238E+01 4 +H2O_Pt 92491O 1H 2PT 1 I 300.00 3000.00 1000.00 1 + 0.25803051E+01 0.49570827E-02-0.46894056E-06-0.52633137E-09 0.11998322E-12 2 +-0.38302234E+05-0.17406322E+02-0.27651553E+01 0.13315115E-01 0.10127695E-05 3 +-0.71820083E-08 0.22813776E-11-0.36398055E+05 0.12098145E+02 4 +OH_Pt 92491O 1H 1PT 1 I 300.00 3000.00 1000.00 1 + 0.18249973E+01 0.32501565E-02-0.31197541E-06-0.34603206E-09 0.79171472E-13 2 +-0.26685492E+05-0.12280891E+02-0.20340881E+01 0.93662683E-02 0.66275214E-06 3 +-0.52074887E-08 0.17088735E-11-0.25319949E+05 0.89863186E+01 4 +_Pt_ PT 1 S 300.0 3000.0 1000.0 1 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 2 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 3 + 0.00000000E+00 0.00000000E+00 0.00000000E+00 0.00000000E+00 4 +END diff --git a/test/data/surface2.inp b/test/data/surface2.inp new file mode 100644 index 00000000000..706f24a97a3 --- /dev/null +++ b/test/data/surface2.inp @@ -0,0 +1,32 @@ +SITE/PT_SURFACE/ SDEN/2.72E-9/ +_Pt_ H_Pt O2_Pt/3/ H2O_Pt OH_Pt O_Pt +END + + REACTIONS JOULES/MOLE MWON + H2 + 2_Pt_ => 2H_Pt 4.4579E+10 0.5 0.0 + FORD/_Pt_ 1/ + 2H_Pt => H2 + 2_Pt_ 3.70E+21 0.00 67400.0 + COV/H_Pt 0.0 0.0 -6000.0/ + COV/OH_Pt 0.0 1.0 -3000.0/ + H + _Pt_ => H_Pt 1.00 0.0 0.0 + STICK + O2 + 2_Pt_ => 2O_Pt 1.80E+21 -0.5 0.0 + DUPLICATE + O2 + 2_Pt_ => 2O_Pt 0.023 0.00 0.00 + DUPLICATE STICK MWOFF + 2O_Pt => O2 + 2_Pt_ 3.70E+21 0.00 213200.0 + COV/O_Pt 0.0 0.0 -60000.0/ + O + _Pt_ => O_Pt 1.00 0.0 0.0 + STICK + MWON + H2O + _Pt_ => H2O_Pt 0.75 0.0 0.0 + STICK + H2O_Pt => H2O + _Pt_ 1.0E+13 0.00 40300.0 + OH + _Pt_ => OH_Pt 1.00 0.0 0.0 + STICK + OH_Pt => OH + _Pt_ 1.0E+13 0.00 192800.0 + H_Pt + O_Pt = OH_Pt + _Pt_ 3.70E+21 0.00 11500.0 + H_Pt + OH_Pt = H2O_Pt + _Pt_ 3.70E+21 0.00 17400.0 + OH_Pt + OH_Pt = H2O_Pt + O_Pt 3.70E+21 0.00 48200.0 + O2_Pt = O2 + 3 _Pt_ 3.70E+21 0.00 11500.0 +END diff --git a/test/oneD/test_oneD.cpp b/test/oneD/test_oneD.cpp index 502cefe683b..d3898c7db9e 100644 --- a/test/oneD/test_oneD.cpp +++ b/test/oneD/test_oneD.cpp @@ -84,7 +84,7 @@ TEST(onedim, freeflame) // solve flow->solveEnergyEqn(); - bool refine_grid = false; + string refine_grid = "disabled"; int loglevel = 0; flame.solve(loglevel, refine_grid); flame.save("gtest-freeflame.yaml", "cpp", "Solution from C++ interface", true); From e118cf6c4f1e1e8521689d7ed54d6212611c1a89 Mon Sep 17 00:00:00 2001 From: Antoine Date: Thu, 6 Mar 2025 00:05:33 +0100 Subject: [PATCH 08/98] Merge differences for other files On branch WIP/Merge_cantera-avbp Changes to be committed: modified: .gitignore modified: README.rst modified: SConstruct new file: install_cantera.py new file: main.yaml new file: run_compil new file: run_compil_kraken --- .gitignore | 3 + README.rst | 114 +++++++++++++++++++++++++++++---- install_cantera.py | 154 +++++++++++++++++++++++++++++++++++++++++++++ main.yaml | 66 +++++++++++++++++++ run_compil | 5 ++ run_compil_kraken | 9 +++ 6 files changed, 339 insertions(+), 12 deletions(-) create mode 100644 install_cantera.py create mode 100644 main.yaml create mode 100755 run_compil create mode 100755 run_compil_kraken diff --git a/.gitignore b/.gitignore index 33b3bd9bc41..05cd53db369 100644 --- a/.gitignore +++ b/.gitignore @@ -53,3 +53,6 @@ coverage.info .coverage doc/sphinx/matlab/*.rst !doc/sphinx/matlab/index.rst +reduced.yaml +INSTALL_DIR/ +*.code-workspace \ No newline at end of file diff --git a/README.rst b/README.rst index 8de8170cc89..b0af3713729 100644 --- a/README.rst +++ b/README.rst @@ -33,23 +33,113 @@ using the following MyBinder link: Installation ============ -|pip| |anaconda| |conda-forge| +To ensure a smooth installation, we highly recommend setting up Cantera within a virtual environment. +Follow the steps below for a **local** installation: -`Installation instructions for the current release of Cantera -`_ are available from the main `Cantera -documentation site `_. +0. Clone the Cantera repository:: -- The Python module can also be installed using pip on Windows, macOS, and Linux. + cd /Users/$USER/Documents + git clone https://nitrox.cerfacs.fr/cantera/cantera-avbp.git -- Conda packages containing the Cantera Python and Matlab modules are also available - for Windows, macOS, and Linux. +1. Create a virtual environment in your home directory:: -- Additional installation packages are provided for Windows, macOS, Ubuntu, Fedora, - RHEL, Gentoo, and FreeBSD. + cd $HOME + python3 -m venv env_cantera + source ~/env_cantera/bin/activate + +2. (optional) Create an alias to load ``env_cantera``:: + + echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.zshrc + source ~/.zshrc + +3. Navigate to the Cantera directory:: + + cd /Users/$USER/Documents/cantera-avbp + +4. Switch to the right branch and run the installation script:: + + git checkout 3.0 + python3 install_cantera.py + + +5. When prompted about NFS, answer ``no``. +6. Wait for the compilation and installation process to complete successfully. + +If everything goes well, you should see the following message:: + + ******************************************************************************** + To use this newly installed Cantera version, update your environment variables + by adding the following lines to your.bashrc (or equivalent): + + #cantera-avbp-3.0 + export PYTHONPATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH + export PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH + export PYTHON_CMD=/Users/$USER/canavbp3/bin/python3 + + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB=/Users/$USER/cantera-avbp/INSTALL_DIR/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + + #Required for MacOS: + export DYLD_LIBRARY_PATH=$CUSTOM_LIB + + DONT FORGET TO SOURCE YOUR .bashrc! + + ******************************************************************************** + + +Copy and paste the provided lines into your ``.zshrc`` or ``.bashrc`` file and **source it**. + +For **KRAKEN** users, use the following commands to install Cantera: + +1. Load the necessary modules:: + + module purge && module load python/3.9.5 + +2. Install ``ruamel.yaml`` package (not installed by default on KRAKEN):: + + pip3 install --user ruamel.yaml + +3. Create a virtual environment in your home folder and activate it:: + + cd $HOME + python3 -m venv --system-site-packages env_cantera + source ~/env_cantera/bin/activate + +4. (optional) Create an alias to load ``env_cantera``:: + + echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.bashrc + source ~/.bashrc + +5. Clone cantera-avbp repository (e.g. in your ``/scratch``), navigate to it and run the installation script:: + + git clone https://nitrox.cerfacs.fr/cantera/cantera-avbp.git /scratch/cfd/$USER + cd /scratch/cfd/$USER/cantera-avbp + git checkout 3.0 + python3 install_cantera.py + +When prompted about NFS, answer 'yes' and wait for the compilation and installation to finish. + +If everything goes well, you will see a similar message as above, but with an additional question:: + + + We suggest adding the alias 'load_cantera' to purge and load necessary modules in ~/.bashrc + Do you want to add the alias to ~/.bashrc? (yes/no) + + +Answer ``yes`` to this question, then copy and paste the environment variables you need into your ``.bashrc`` file and **source it**. + +Finally, load Cantera with the following command:: + + load_cantera + + +Test if everything works using a sample script, for example:: + + python3 samples/python/AVBP/ARC.py -- For other platforms, or for users wishing to install a development version of - Cantera, `compilation instructions `_ - are also available. Documentation ============= diff --git a/install_cantera.py b/install_cantera.py new file mode 100644 index 00000000000..4245b5d93a8 --- /dev/null +++ b/install_cantera.py @@ -0,0 +1,154 @@ +# Small python script for Cantera CERFACS installation + +import sys +import os +import subprocess + +# Asking about the environment +if sys.version_info[0] < 3: + quit('You should compile cantera with python 3 ! Use module load python/3.9.5') + string_argument = raw_input('Are you installing Cantera on NFS machine ? (yes/no) ') + python_version = 2 +else: + string_argument = input('Are you installing Cantera on NFS machine ? (yes/no) ') + python_version = 3 + +if string_argument in ['yes', 'y']: + argument = 'NFS' +elif string_argument in ['no', 'n']: + argument = 'local' +else: + quit('Invalid answer ! \n Really ?! How could you fail a yes or no question ?') + +dir_path = os.path.dirname(os.path.realpath(__file__)) + +install_dir_path = os.path.dirname(os.path.realpath(__file__)) + "/INSTALL_DIR" + +if not os.path.isdir(install_dir_path): + os.mkdir(install_dir_path) + +#create mech_lib folder in INSTALL_DIR +if not os.path.isdir(install_dir_path + "/mech_lib"): + os.mkdir(install_dir_path + "/mech_lib") + +file_path = dir_path + "/cantera.conf" + +def fill_cantera_conf(file_path, install_dir_path): + f = open(file_path, 'w') + + text = """\ +prefix = '{0}' +""" + + f.write(text.format(install_dir_path)) + + if argument == 'local': + text = """\ +boost_inc_dir = '/opt/homebrew/Cellar/boost/{0}/include' +verbose_tests = True +""" + # use the output of ls /opt/homebrew/Cellar/boost/ to get the version number + f.write(text.format(subprocess.check_output('ls /opt/homebrew/Cellar/boost/', shell=True).decode('utf-8').split('\n')[0])) + else : + text = """\ +boost_inc_dir = '/softs/local/boost/1.78.0_gcc112/include' +""" + f.write(text) + + f.close() + +def execute_with_live_display(command): + process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True) + + while True: + # Read a line from the output + line = process.stdout.readline() + + # Break the loop if there are no more lines + if not line and process.poll() is not None: + break + + # Display the line in real-time + print(line.strip()) + + # Wait for the process to complete + process.wait() + + # Return the exit code of the process + return process.returncode + + +if argument == 'local': + print("""To run cantera, the installation of: \n + - python, boost and gcc with brew command. \n + - numpy, cython, scons, wheel and ruamel.yaml with pip3 command. \n + are required.""") + update_argument = input('Do you want to install/update those libraries ? (yes/no) ') + + if update_argument in ['yes', 'y']: + if subprocess.call('which brew', shell=True) == 1: + subprocess.call('/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"', shell=True) + subprocess.call('brew install boost', shell=True) + subprocess.call('brew install gcc', shell=True) + subprocess.call('pip3 install numpy --no-use-pep517', shell=True) + subprocess.call('pip3 install cython', shell=True) + subprocess.call('pip3 install scons==3.1.2', shell=True) + subprocess.call('pip3 install wheel', shell=True) + subprocess.call('pip3 install ruamel.yaml', shell=True) + elif update_argument in ['no', 'n']: + pass + else: + quit('Invalid answer ! \n Really ?! How could you fail a yes or no question ?') + + fill_cantera_conf(file_path, install_dir_path) + error = subprocess.call('scons build && scons install', shell=True) +else: + fill_cantera_conf(file_path, install_dir_path) + error = execute_with_live_display("./run_compil") + + +#only print the following if the installation was successful +if argument == 'NFS' and not error: + #add an alias to load necessary modules + print("We suggest to add the alias 'load_cantera_mod' to purge and load necessary modules in ~/.bashrc") + #ask user if he wants to add the alias to ~/.bashrc + add_alias = input('Do you want to add the alias to ~/.bashrc ? (yes/no) ') + if add_alias in ['yes', 'y']: + err = subprocess.call("echo 'alias load_cantera_mod=\"module purge && module load compiler/gcc/11.2.0\"' >> ~/.bashrc", shell=True) + if not err : + print("Alias load_cantera_mod added to ~/.bashrc") + else : + print("FAILED to add alias load_cantera_mod to ~/.bashrc, you can do it manually :\ + alias load_cantera_mod='module purge && module load compiler/gcc/11.2.0'") + else : + print("Alias load_cantera_mod NOT added to ~/.bashrc") + +if not error: + print("*" * 80) + print() + print("To use this brandnew Cantera installation, you must update some of your environment variables.") + print("To do so, you can add the following lines to your .bashrc (or equivalent):") + text="""\ +#cantera-avbp-3.0 +export PYTHONPATH={0}/lib/python{1}.{2}/site-packages:$PYTHONPATH +export PKG_CONFIG_PATH={0}/lib/pkgconfig:$PKG_CONFIG_PATH +export LD_LIBRARY_PATH={0}/lib:$LD_LIBRARY_PATH +export PATH={0}/bin:$PATH +export PYTHON_CMD={3} + +#Only if you dont already have a custom lib folder: +export CUSTOM_LIB={0}/mech_lib +export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + +#Required for MacOS: +export DYLD_LIBRARY_PATH=$CUSTOM_LIB + """ + #get the output of which python to get the path to the python executable + pythonpath = subprocess.check_output('which python3', shell=True).decode('utf-8').split('\n')[0] + print() + print(text.format(install_dir_path,str(python_version), str(sys.version_info[1]),pythonpath)) + print() + print("DONT FORGET TO SOURCE YOUR .bashrc !") + print() + print("*" * 80) + diff --git a/main.yaml b/main.yaml new file mode 100644 index 00000000000..603fff34ed1 --- /dev/null +++ b/main.yaml @@ -0,0 +1,66 @@ +name: Tests + +on: + push: + branches: + - '**' + +jobs: + ubuntu-multiple-pythons: + name: ${{ matrix.os }} with Python ${{ matrix.python-version }} + runs-on: ${{ matrix.os }} + timeout-minutes: 60 + strategy: + matrix: + python-version: ['3.9'] + os: ['self-hosted'] + fail-fast: false + env: + HDF5_LIBDIR: /usr/lib/x86_64-linux-gnu/hdf5/serial + HDF5_INCLUDEDIR: /usr/include/hdf5/serial + steps: + - uses: actions/checkout@v3 + name: Checkout the repository + with: + submodules: recursive + - name: Setup Python + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + architecture: x64 + - name: Install Apt dependencies + run: | + sudo apt -y update + sudo apt -y install libboost-dev gfortran libopenmpi-dev libpython3-dev \ + libblas-dev liblapack-dev libhdf5-dev libfmt-dev + gcc --version + - name: Upgrade pip + run: python3 -m pip install -U pip setuptools wheel + - name: Install Python dependencies + # h5py is optional; some versions don't have binaries (yet) + run: | + python3 -m pip install ruamel.yaml scons==3.1.2 numpy cython pandas pytest \ + pytest-github-actions-annotate-failures pint + python3 -m pip install h5py + - name: Build Cantera + run: | + python3 `which scons` build env_vars=all -j2 debug=n --debug=time \ + system_fmt=y hdf_libdir=$HDF5_LIBDIR hdf_include=$HDF5_INCLUDEDIR \ + cc_flags=-D_GLIBCXX_ASSERTIONS + - name: Upload shared library + uses: actions/upload-artifact@v3 + if: matrix.python-version == '3.10' + with: + path: build/lib/libcantera_shared.so + name: libcantera_shared-${{ matrix.os }}.so + retention-days: 2 + - name: Test Cantera + run: + python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time + - name: Save the wheel file to install Cantera + uses: actions/upload-artifact@v3 + with: + path: build/python/dist/Cantera*.whl + retention-days: 2 + name: cantera-wheel-${{ matrix.python-version }}-${{ matrix.os }} + if-no-files-found: error \ No newline at end of file diff --git a/run_compil b/run_compil new file mode 100755 index 00000000000..64c909a8246 --- /dev/null +++ b/run_compil @@ -0,0 +1,5 @@ +module purge +module load python/3.9.5 +module load compiler/gcc/11.2.0 +module list +scons build && scons install diff --git a/run_compil_kraken b/run_compil_kraken new file mode 100755 index 00000000000..2d82c92a262 --- /dev/null +++ b/run_compil_kraken @@ -0,0 +1,9 @@ +#!/bin/bash +module purge +module load python/3.9.5 +module load compiler/gcc/11.2.0 +#require the installation of ruamel.yaml +scons build python2_package=n prefix=/softs/local/cantera-avbp/3.0 blas_lapack_libs=lapack,atlas debug_linker_flags='-L/usr/lib64/atlas' +mv /softs/local/cantera-avbp/3.0 /softs/local/cantera-avbp/3.0-`date +%d%b%Y` +scons install + From b0f7cbc5ee18dde72b6b660293d8c2f9c46d87f0 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 4 Apr 2025 21:22:16 +0200 Subject: [PATCH 09/98] Add missing part needed for compile_fortran import On branch WIP/Merge_cantera-avbp Your branch is up to date with 'origin/WIP/Merge_cantera-avbp'. Changes to be committed: modified: ../../../interfaces/cython/cantera/composite.py --- interfaces/cython/cantera/composite.py | 160 +++++++++++++++++++++++++ 1 file changed, 160 insertions(+) diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py index fa879ece2fe..ca58c2000db 100644 --- a/interfaces/cython/cantera/composite.py +++ b/interfaces/cython/cantera/composite.py @@ -411,6 +411,166 @@ class _WeakrefProxy: pass +def compile_fortran(f90_filename, force=False, fortran_format='f90', + mechanism_lib=None, output=False, remote_install=True): + """ Creates dynamic library to compute chemistry source terms for Cantera + + Compile a f90 file (potentially generated through create_mech_f90) containing + all routines necessary to return wdot to Cantera during runs. The output is a + dynamic library, used in Cantera via the custom kinetics keyword. + + :param f90_filename: name of the f90 file to compile + :param force: if True, compiles fortran even if it hasn't been changed + :param fortran_format: string specifying if it's for example in f77 format + :param mechanism_lib: path to the directory where dynamic libraries are to be compiled + :param output: if True displays the output of the make + :param remote_install: if False the compilation will be done automatically in the sources + :return: None + """ + + ## Test to know if subroutine has the right name to do the compiling + line_custom = None + f = open(f90_filename,'r') + for lines in f.readlines(): + if 'subroutine' in lines.lower() and '(p,t,y,wdot)' in lines.replace(" ","").lower(): + line_custom = lines + break + f.close() + + if line_custom == None: + print("The main subroutine of the f90 file should be written : 'subroutine customkinetics (P, T, y, wdot)' to work") + sys.exit() + else: + if 'customkinetics' not in line_custom.lower(): + print("The main subroutine of the f90 file should be written : 'subroutine customkinetics (P, T, y, wdot)' to work") + sys.exit() + + # Check installation path + if not remote_install: + # Finds the path to the cantera module and then copies the f90 file in the correct directory + path_to_init = os.path.realpath(__file__) + + terminator = path_to_init.rfind('/lib') + path = (path_to_init[:terminator]) + + lib_name = '/lib' + + path_to_dir = path + lib_name + + if not os.path.isdir(path_to_dir) and os.path.isdir(path_to_dir + '64'): + lib_name = '/lib64' + path_to_dir = path + lib_name + + elif not os.path.isdir(path_to_dir) and not os.path.isdir(path_to_dir + '64'): + print('There is a problem with your installation, ' + path_to_dir + ' does not exist') + sys.exit() + + elif not os.environ.get('CUSTOM_LIB'): + if mechanism_lib: + path_to_dir = mechanism_lib + else: + # path_to_file = os.path.realpath(__file__) + # terminator = path_to_file.rfind('/') + # path = (path_to_file[:terminator]) + # lib_name = '/mech_lib' + + path_to_dir = './mech_lib' + + path_to_dir = os.path.abspath(path_to_dir) + + if not os.path.isdir(path_to_dir): + try: + os.mkdir(path_to_dir) + except PermissionError: + print("Please specify a mech_lib directory to write in that is accessible " + "with the argument mechanism_lib=the_path_you_want") + quit() + else: + print('The directory ' + path_to_dir + ' has been created') + print('The necessary files for the compilation and customised kinetics run will be stored there') + print("If this location does not suit you, please specify a path as mechanism_lib argument") + + else: + path_to_dir = os.environ['CUSTOM_LIB'] + + # Correct path definitions + + path_to_ext = path_to_dir + '/customkinetics.f90' + path_to_makefile = path_to_dir + '/Makefile' + + make_call = 'make -C ' + path_to_dir + if not output: + make_call += ' &> compilation_output.txt' + + # Copying f90 file to the right place + + if not f90_filename.endswith('.f90'): + f90_filename = f90_filename + '.f90' + + if not os.path.isfile(path_to_ext) or not filecmp.cmp(f90_filename, path_to_ext) or force: + + shutil.copy(f90_filename, path_to_ext) + + # Checks if the Makefile exists, if not creates it + if not os.path.isfile(path_to_makefile): + + f = open(path_to_makefile, 'w') + text = """\ +customkinetics.so: customkinetics.f90 +\tgfortran -ffixed-line-length-0 -c customkinetics.f90 -g -fPIC -o customkinetics.o +\tgfortran -shared -o customkinetics.so customkinetics.o + """ + if fortran_format == 'f77': + text = """\ +customkinetics.so: customkinetics.f90 +\tgfortran -ffixed-line-length-0 -ffixed-form -c customkinetics.f90 -g -fPIC -o customkinetics.o +\tgfortran -shared -o customkinetics.so customkinetics.o + """ + f.write(text) + f.close() + print('The Makefile was missing or wrongly named') + print('The correct Makefile has been created (' + path_to_makefile + ')') + + # In remote installation, sets the correct LD_LIBRARY_PATH for the dynamic library + if not os.environ.get('CUSTOM_LIB'): + custom_env_set = 'export CUSTOM_LIB=' + path_to_dir + environment_set = 'export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH' + + if mechanism_lib: + dir_status = 'you chose' + else: + dir_status = 'automatically created' + + text = ("""\ + +This part is not automated as it would require sneaky modifications of your bashrc and that is privacy violation ! + +Please copy those commands in your bashrc (or execute them in your shell): +{0} +{1} + +It will add the directory {2} to the dynamic library path blab bla bla, informatics stuff ... + +I advise you stick to only one directory for the compilation for 2 reasons: +- 1: it will be boring to add the path again. +- 2: it's absolutely useless to have several.""") + + print(text.format(custom_env_set, environment_set, dir_status)) + sys.exit() + + process = subprocess.call(make_call, shell=True) + + if process != 0: + print('The compilation of the f90 file failed ! There is something wrong ...') + if not output: + print('Check compilation_output.txt for intel') + exit() + else: + + print('Compilation of the f90 successful') + subprocess.call('rm -f compilation_output.txt', shell=True) + time.sleep(0.05) # Necessary for python to understand there was a change + class SolutionArray(SolutionArrayBase): """ A class providing a convenient interface for representing many thermodynamic From 8058ffb5bb58f9d01e2d8b735e5f4f9e5a25e1b1 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 22 Apr 2025 14:30:28 +0200 Subject: [PATCH 10/98] Add test files to the gitignore On branch WIP/merge_CERFACS_devs Changes to be committed: modified: .gitignore --- .gitignore | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 05cd53db369..58f78274f12 100644 --- a/.gitignore +++ b/.gitignore @@ -55,4 +55,6 @@ doc/sphinx/matlab/*.rst !doc/sphinx/matlab/index.rst reduced.yaml INSTALL_DIR/ -*.code-workspace \ No newline at end of file +*.code-workspace +samples/python/AVBP/RESULTS/ +test_problems/cxx_samples/flamespeed.yaml \ No newline at end of file From 1c91e26e17794966b99c2e1ca32176c50a17e644 Mon Sep 17 00:00:00 2001 From: joebarteam11 <85874120+joebarteam11@users.noreply.github.com> Date: Fri, 29 Dec 2023 23:39:56 +0100 Subject: [PATCH 11/98] [Bugfix] Segfault if no transport specified in the YAML file call "registerChangedCallback" before transport setting if transportModel() is "none" --- src/oneD/StFlow.cpp | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/src/oneD/StFlow.cpp b/src/oneD/StFlow.cpp index fe8bccbb11a..e71b0f8244d 100644 --- a/src/oneD/StFlow.cpp +++ b/src/oneD/StFlow.cpp @@ -135,6 +135,12 @@ StFlow::StFlow(shared_ptr sol, const string& id, size_t nsoot, size_t m_id = id; m_kin = m_solution->kinetics().get(); m_trans = m_solution->transport().get(); + + m_solution->registerChangedCallback(this, [this]() { + setKinetics(m_solution->kinetics()); + setTransport(m_solution->transport()); + }); + if (m_trans->transportModel() == "none") { // @deprecated warn_deprecated("StFlow", @@ -143,10 +149,7 @@ StFlow::StFlow(shared_ptr sol, const string& id, size_t nsoot, size_t "is deprecated and\nwill be removed after Cantera 3.0."); setTransportModel("mixture-averaged"); } - m_solution->registerChangedCallback(this, [this]() { - setKinetics(m_solution->kinetics()); - setTransport(m_solution->transport()); - }); + } StFlow::~StFlow() From 5a9cde018103c5c4325fe9aa461dba8baf54eb22 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 22 Apr 2025 16:08:43 +0200 Subject: [PATCH 12/98] Bugfix : set the transport model in the file Lu_ARC.yaml On branch WIP/merge_CERFACS_devs Changes to be committed: modified: ARC.py modified: inputs/Lu_ARC.yaml --- samples/python/AVBP/ARC.py | 1 - samples/python/AVBP/inputs/Lu_ARC.yaml | 1 + 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/samples/python/AVBP/ARC.py b/samples/python/AVBP/ARC.py index edc2a530c53..10609e6425e 100644 --- a/samples/python/AVBP/ARC.py +++ b/samples/python/AVBP/ARC.py @@ -18,7 +18,6 @@ gas.TP = tin, p gas.set_equivalence_ratio(phi, fuel, oxidizer) -# gas.transport_model = 'UnityLewis' loglevel = 1 refine_grid = 'refine' diff --git a/samples/python/AVBP/inputs/Lu_ARC.yaml b/samples/python/AVBP/inputs/Lu_ARC.yaml index 91213b6c00c..b759a9f8c64 100644 --- a/samples/python/AVBP/inputs/Lu_ARC.yaml +++ b/samples/python/AVBP/inputs/Lu_ARC.yaml @@ -1649,6 +1649,7 @@ phases: state: T: 300.0 P: 1.01325e+05 + transport: unity-Lewis-number species: - name: H2 composition: From a73dda24c2b42c2eb08207f063dd02c5454cdd36 Mon Sep 17 00:00:00 2001 From: AntoinePestre <101113311+AntoinePestre@users.noreply.github.com> Date: Tue, 29 Apr 2025 11:01:59 +0200 Subject: [PATCH 13/98] Update README.rst for cantera installation --- README.rst | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/README.rst b/README.rst index b0af3713729..4fc9524aaee 100644 --- a/README.rst +++ b/README.rst @@ -39,7 +39,7 @@ Follow the steps below for a **local** installation: 0. Clone the Cantera repository:: cd /Users/$USER/Documents - git clone https://nitrox.cerfacs.fr/cantera/cantera-avbp.git + git clone git@github.com:cerfacs/cantera.git 1. Create a virtual environment in your home directory:: @@ -47,23 +47,28 @@ Follow the steps below for a **local** installation: python3 -m venv env_cantera source ~/env_cantera/bin/activate -2. (optional) Create an alias to load ``env_cantera``:: +2. Install specific python packages:: + + pip install numpy==1.26.4 + pip install scipy==1.13 + +3. (optional) Create an alias to load ``env_cantera``:: echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.zshrc source ~/.zshrc -3. Navigate to the Cantera directory:: +4. Navigate to the Cantera directory:: - cd /Users/$USER/Documents/cantera-avbp + cd /Users/$USER/Documents/cantera -4. Switch to the right branch and run the installation script:: +5. Switch to the right branch and run the installation script:: - git checkout 3.0 + git checkout dev_cantera-avbp python3 install_cantera.py -5. When prompted about NFS, answer ``no``. -6. Wait for the compilation and installation process to complete successfully. +6. When prompted about NFS, answer ``no``. +7. Wait for the compilation and installation process to complete successfully. If everything goes well, you should see the following message:: From fc6c3ac3b6bfccdc4d8ae590522332095f3337e3 Mon Sep 17 00:00:00 2001 From: AntoinePestre <101113311+AntoinePestre@users.noreply.github.com> Date: Tue, 29 Apr 2025 11:06:08 +0200 Subject: [PATCH 14/98] Change repository name --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 4fc9524aaee..aafcdcf899d 100644 --- a/README.rst +++ b/README.rst @@ -59,7 +59,7 @@ Follow the steps below for a **local** installation: 4. Navigate to the Cantera directory:: - cd /Users/$USER/Documents/cantera + cd /Users/$USER/Documents/cantera-avbp 5. Switch to the right branch and run the installation script:: From 9591ec37ffa408e3183cf43a68ebd5a4a0056b78 Mon Sep 17 00:00:00 2001 From: AntoinePestre <101113311+AntoinePestre@users.noreply.github.com> Date: Wed, 30 Apr 2025 10:32:08 +0200 Subject: [PATCH 15/98] Correction of git clone link --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index aafcdcf899d..3271a1d7fb0 100644 --- a/README.rst +++ b/README.rst @@ -39,7 +39,7 @@ Follow the steps below for a **local** installation: 0. Clone the Cantera repository:: cd /Users/$USER/Documents - git clone git@github.com:cerfacs/cantera.git + git clone git@github.com:cerfacs/cantera-avbp.git 1. Create a virtual environment in your home directory:: From 683ddb84bfd3128d34b45f499552bee81b2b485d Mon Sep 17 00:00:00 2001 From: pestre Date: Wed, 8 Jan 2025 11:11:57 +0100 Subject: [PATCH 16/98] Rebase dev_cantera-avbp onto v3.1.0a4 Committer: pestre Changes to be committed from rebase conflict: new file: doc/doxygen/cantera-doxygen.css new file: doc/sphinx/develop/compiling/compilation-reqs.md new file: doc/sphinx/develop/compiling/config-options.rst new file: doc/sphinx/develop/compiling/configure-build.md new file: doc/sphinx/develop/compiling/dependencies.md new file: doc/sphinx/develop/compiling/source-code.md new file: doc/sphinx/develop/compiling/special-cases.md new file: doc/sphinx/develop/index.md new file: doc/sphinx/examples/index.md new file: doc/sphinx/favicon.png new file: doc/sphinx/index.md new file: doc/sphinx/install/conda.md new file: doc/sphinx/install/index.md new file: doc/sphinx/install/pip.md new file: doc/sphinx/python/ck_conversion.rst new file: doc/sphinx/python/constants.rst new file: doc/sphinx/python/cti_conversion.rst new file: doc/sphinx/python/ctml_conversion.rst new file: doc/sphinx/python/importing.rst new file: doc/sphinx/python/index.rst new file: doc/sphinx/python/kinetics.rst new file: doc/sphinx/python/onedim.rst new file: doc/sphinx/python/scripts.rst new file: doc/sphinx/python/thermo.rst new file: doc/sphinx/python/transport.rst new file: doc/sphinx/python/units.rst new file: doc/sphinx/python/utilities.rst new file: doc/sphinx/python/yaml_conversion.rst new file: doc/sphinx/python/zerodim.rst new file: doc/sphinx/reference/bibliography.md new file: doc/sphinx/reference/glossary.md new file: doc/sphinx/reference/index.md new file: doc/sphinx/reference/releasenotes/index.md new file: doc/sphinx/reference/science/reactors/controlreactor.md new file: doc/sphinx/reference/science/reactors/index.md new file: doc/sphinx/userguide/ck2yaml-tutorial.md new file: doc/sphinx/userguide/creating-mechanisms.md new file: doc/sphinx/userguide/faq.md new file: doc/sphinx/userguide/index.md new file: doc/sphinx/userguide/input-errors.md new file: doc/sphinx/userguide/input-tutorial.md new file: doc/sphinx/userguide/legacy2yaml-tutorial.md new file: doc/sphinx/userguide/python-tutorial.md new file: doc/sphinx/userguide/thermobuild.md You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. 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It +corresponds to an extensive thermodynamic control volume $V$, in which all state +variables are homogeneously distributed. The system is generally unsteady -- that is, +all states are functions of time. In particular, transient state changes due to chemical +reactions are possible. However, thermodynamic (but not chemical) equilibrium is assumed +to be present throughout the reactor at all instants of time. + +Reactors can interact with the surrounding environment in multiple ways: + +- Expansion/compression work: By moving the walls of the reactor, its volume can be + changed and expansion or compression work can be done by or on the reactor. + +- Heat transfer: An arbitrary heat transfer rate can be defined to cross the boundaries + of the reactor. + +- Mass transfer: The reactor can have multiple inlets and outlets. For the inlets, + arbitrary states can be defined. Fluid with the current state of the reactor exits the + reactor at the outlets. + +- Surface interaction: One or multiple walls can influence the chemical reactions in the + reactor. This is not just restricted to catalytic reactions, but mass transfer between + the surface and the fluid can also be modeled. + +All of these interactions do not have to be constant, but can vary as a function of time +or state. For example, heat transfer can be described as a function of the temperature +difference between the reactor and the environment, or the wall movement can be modeled +depending on the pressure difference. Interactions of the reactor with the environment +are defined on one or more walls, inlets, and outlets. + +In addition to single reactors, Cantera is also able to interconnect reactors into a +*reactor network*. Each reactor in a network may be connected so that the contents of one +reactor flow into another. Reactors may also be in contact with one another or the +environment via walls that conduct heat or move to do work. + +## Reactor Types and Governing Equations + +All reactor types are modelled using combinations of Cantera's governing equations of +state. The specific governing equations defining Cantera's supported reactor models are +derived and described below. + + +````{grid} 2 +:gutter: 3 + +```{grid-item-card} Control Volume Reactor +:link: controlreactor +:link-type: doc + +A reactor where the volume is prescribed by the motion of the reactor's walls. The state variables are the volume, mass, total internal energy, and species mass fractions. +``` + +```` + +```{toctree} +:hidden: + +controlreactor +``` \ No newline at end of file From cd7e6a7c302bd3aa8cc0322fe5c4838027015e07 Mon Sep 17 00:00:00 2001 From: pestre Date: Mon, 13 Jan 2025 19:21:29 +0100 Subject: [PATCH 17/98] Add missing files in include directory from cantera-avbp and merge differences Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: new file: doc/sphinx/_static/images/favicon.png new file: include/cantera/base/Parser.h modified: include/cantera/base/ct_defs.h new file: include/cantera/kinetics/CustomKinetics.h modified: include/cantera/kinetics/Kinetics.h modified: include/cantera/oneD/Boundary1D.h modified: include/cantera/oneD/Domain1D.h modified: include/cantera/oneD/DomainFactory.h new file: include/cantera/oneD/Flamelet.h modified: include/cantera/oneD/OneDim.h modified: include/cantera/oneD/Sim1D.h modified: include/cantera/oneD/StFlow.h modified: include/cantera/oneD/refine.h new file: include/cantera/transport/AVBPTransport.h interactive rebase in progress; onto 7aec821a8 Last commands done (2 commands done): pick 43b14705c Add doc files from cantera-avbp pick dbacaadf6 Add missing files in include directory from cantera-avbp and merge differences Next commands to do (12 remaining commands): pick 08696f03b Change refine_grid param type to string pick 20ede9daf Merge differences in interfaces directory You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. Changes to be committed: new file: include/cantera/base/Parser.h modified: include/cantera/base/ct_defs.h new file: include/cantera/kinetics/CustomKinetics.h modified: include/cantera/kinetics/Kinetics.h modified: include/cantera/oneD/Boundary1D.h modified: include/cantera/oneD/Domain1D.h modified: include/cantera/oneD/DomainFactory.h new file: include/cantera/oneD/Flamelet.h modified: include/cantera/oneD/OneDim.h modified: include/cantera/oneD/Sim1D.h modified: include/cantera/oneD/StFlow.h modified: include/cantera/oneD/refine.h new file: include/cantera/transport/AVBPTransport.h --- include/cantera/base/Parser.h | 66 ++ include/cantera/base/ct_defs.h | 38 + include/cantera/kinetics/CustomKinetics.h | 49 + include/cantera/kinetics/Kinetics.h | 2 + include/cantera/oneD/Boundary1D.h | 13 + include/cantera/oneD/Domain1D.h | 2 +- include/cantera/oneD/DomainFactory.h | 6 +- include/cantera/oneD/Flamelet.h | 180 ++++ include/cantera/oneD/OneDim.h | 2 +- include/cantera/oneD/Sim1D.h | 5 + include/cantera/oneD/StFlow.h | 1177 ++++++++++++++++++++- include/cantera/oneD/refine.h | 32 + include/cantera/transport/AVBPTransport.h | 120 +++ 13 files changed, 1681 insertions(+), 11 deletions(-) create mode 100644 include/cantera/base/Parser.h create mode 100644 include/cantera/kinetics/CustomKinetics.h create mode 100644 include/cantera/oneD/Flamelet.h create mode 100644 include/cantera/transport/AVBPTransport.h diff --git a/include/cantera/base/Parser.h b/include/cantera/base/Parser.h new file mode 100644 index 00000000000..3b879187de4 --- /dev/null +++ b/include/cantera/base/Parser.h @@ -0,0 +1,66 @@ +// Small parser for driving CANTERA C++ program +#include +#include +#include +using std::cout; +using std::endl; +using std::string; +#include +using std::ifstream; +#include + +class Param { +private: + size_t m_count; + string m_name; + std::vector m_args; +public: + Param() { + m_count = 0; + } + Param(const string& name) { + m_count = 0; + setName(name); + } + void setName(const string& name) { + m_name = name; + } + string Name() { + return m_name; + } + void print(); + void addArgs(const string& arg) { + m_args.push_back(arg); + } + size_t nbArgs() { + return(m_args.size()); + } + void incrCount() { + ++m_count; + } + double readDouble(const int i); + int readInteger(const int i); + bool readBool(const int i); + string readString(const int i); +}; + +class Parser { +private: + std::list m_params; + //std::list i_count; + size_t m_count; +public: + Parser() { + m_count = 0; + } + void parseFile(const string& file); + bool addParamFromLine(Param& param,const string& line); + Param * getParam(const string& name); + Param * getParam(const string& name, const size_t n); + Param * getParam(const string& name, const size_t n, const size_t m); + Param * getParam(const string& name, const size_t n, const size_t m, const size_t l); + size_t getParamNumber(const string& name, const size_t n); + bool checkParam(const string& name); + bool checkParam(const string& name, const size_t n, const size_t m); + size_t nbParamOccurence(const string& name); +}; diff --git a/include/cantera/base/ct_defs.h b/include/cantera/base/ct_defs.h index bf3e0e32744..3cccfa4ef2f 100644 --- a/include/cantera/base/ct_defs.h +++ b/include/cantera/base/ct_defs.h @@ -179,6 +179,44 @@ typedef map Composition; //! index returned by functions to indicate "no position" const size_t npos = static_cast(-1); +//! Soot +// Thermal accomodation factor +const double alphaT = 0.9; +// Active sites : Blanquart and Pitsch (2017) [kmol4/kg4] +const double Cn_cst = 7.5e-12; +// Soot particle density [kg/m3] +const double rho_soot = 1.86e3; +//C2 molecule volume : 2*Wc/rho_soot/Avogadro [m3] +const double V_C2 = 2. * 12. / rho_soot / Avogadro; +// C2 molecule surface area [m2] +const double S_C2 = Pi * pow(6.0 * V_C2 / Pi, 2.0/3.0); +// Soot particle fractal dimension +const double Df = 1.80; +// Amplification factors +const double eps_nucl = 2.5; +const double eps_cond = 1.3; +const double eps_coag = 2.2; +// Biggest soot [m-3] +const double bigSoot = 1.0e-15; +//Condensation +const double alphaV = 1.0 - 2.0 / Df; +const double alphaS = 3.0 / Df - 1.0; +const double vlim1 = 3.98 * 1.0e-25; // [m3] +//Coagulation +const double d_gaz = 2.0e-10; // [m] +const double Csut1 = 1.4558e-6; // [Pa/s] +const double Csut2 = 110.4; +//Surface +const double alpha_surf = 1.0; // Proportion of active sites at soot surface +// Radiative +const double aRadSoot = 1.57; +const double bRadSoot = 0.56; +const double CRad0 = 36 * Pi * aRadSoot * bRadSoot / (pow(pow(aRadSoot,2.0) - pow(bRadSoot,2.0) + + 2, 2.0) + pow(2 * aRadSoot * bRadSoot, 2.0)); +const double CRad2 = Planck * lightSpeed / Boltzmann; +// Soot soret +const double C_soot_soret = 0.554; + } // namespace #endif diff --git a/include/cantera/kinetics/CustomKinetics.h b/include/cantera/kinetics/CustomKinetics.h new file mode 100644 index 00000000000..4c720b33800 --- /dev/null +++ b/include/cantera/kinetics/CustomKinetics.h @@ -0,0 +1,49 @@ +/** + * @file CustomKinetics.h + * + * @ingroup chemkinetics + */ + +// Author: Q. Cazeres, A. Felden, P. Pepiot + +#include "GasKinetics.h" + +namespace Cantera +{ + /** + * Kinetics manager implementing reaction mechanism GRI-Mech 3.0 + * @deprecated + */ + class CustomKinetics : public GasKinetics + { + public: + /// Default constructor. + CustomKinetics(); + + // virtual int type() const { + // return cCustomKinetics; + // } + + void getNetProductionRates(double* net) { + get_wdot_reduced(net); + } + + string kineticsType() const override { + return "custom"; + } + + void closeDynamicLib() { + close_dl(); + } + + void* handle; + +private: + typedef void (*ck_t)(double*,double*,const double*, double*); + // New yarc2 format + //typedef void (*ck_t)(const double*,const double*,const double*,const double*,double*); + ck_t ck; + void get_wdot_reduced(double* wdot); + void close_dl(); + }; +} diff --git a/include/cantera/kinetics/Kinetics.h b/include/cantera/kinetics/Kinetics.h index 7d81acb3426..97584aedd34 100644 --- a/include/cantera/kinetics/Kinetics.h +++ b/include/cantera/kinetics/Kinetics.h @@ -132,6 +132,8 @@ class Kinetics virtual ~Kinetics() = default; + virtual void closeDynamicLib(); + //! Kinetics objects are not copyable or assignable Kinetics(const Kinetics&) = delete; Kinetics& operator=(const Kinetics&)= delete; diff --git a/include/cantera/oneD/Boundary1D.h b/include/cantera/oneD/Boundary1D.h index 55bf729af45..351d82de6aa 100644 --- a/include/cantera/oneD/Boundary1D.h +++ b/include/cantera/oneD/Boundary1D.h @@ -80,6 +80,16 @@ class Boundary1D : public Domain1D throw NotImplementedError("Boundary1D::setMoleFractions"); } + //! Set the mass fractions by specifying a string. + virtual void setMassFractions(const std::string& xin) { + throw NotImplementedError("Boundary1D::setMassFractions"); + } + + //! Set the mass fractions by specifying an array. + virtual void setMassFractions(const double* xin) { + throw NotImplementedError("Boundary1D::setMassFractions"); + } + //! Mass fraction of species k. virtual double massFraction(size_t k) { throw NotImplementedError("Boundary1D::massFraction"); @@ -168,6 +178,9 @@ class Inlet1D : public Boundary1D void setMoleFractions(const string& xin) override; void setMoleFractions(const double* xin) override; + void setMassFractions(const std::string& xin) override; + void setMassFractions(const double* xin) override; + double massFraction(size_t k) override { return m_yin[k]; } diff --git a/include/cantera/oneD/Domain1D.h b/include/cantera/oneD/Domain1D.h index 5a2082be9d7..42d7b442689 100644 --- a/include/cantera/oneD/Domain1D.h +++ b/include/cantera/oneD/Domain1D.h @@ -33,7 +33,7 @@ class Domain1D * @param points Number of grid points. * @param time (unused) */ - Domain1D(size_t nv=1, size_t points=1, double time=0.0); + Domain1D(size_t nv=1, size_t points=1, double time=0.0, size_t nsoot=0, size_t neq=0); virtual ~Domain1D(); Domain1D(const Domain1D&) = delete; diff --git a/include/cantera/oneD/DomainFactory.h b/include/cantera/oneD/DomainFactory.h index 747c2f7a713..0b5211979cf 100644 --- a/include/cantera/oneD/DomainFactory.h +++ b/include/cantera/oneD/DomainFactory.h @@ -19,7 +19,7 @@ namespace Cantera //! ```cpp //! shared_ptr d1 = newDomain("Inlet", sol, "reactants"); //! ``` -class DomainFactory : public Factory, const string&> +class DomainFactory : public Factory, const string&, const size_t&> { public: /** @@ -51,7 +51,7 @@ class DomainFactory : public Factory, const strin //! @ingroup onedGroup template shared_ptr newDomain( - const string& domainType, shared_ptr solution, const string& id="") + const string& domainType, shared_ptr solution, const string& id="", const size_t& sections=0) { string id_ = id; if (id_ == "") { @@ -59,7 +59,7 @@ shared_ptr newDomain( } auto ret = std::dynamic_pointer_cast( shared_ptr( - DomainFactory::factory()->create(domainType, solution, id_))); + DomainFactory::factory()->create(domainType, solution, id_, sections))); if (!ret) { throw CanteraError("newDomain", "Invalid cast: unable to access 'Domain1D' as '{}'.", demangle(typeid(T))); diff --git a/include/cantera/oneD/Flamelet.h b/include/cantera/oneD/Flamelet.h new file mode 100644 index 00000000000..a76dfc09edd --- /dev/null +++ b/include/cantera/oneD/Flamelet.h @@ -0,0 +1,180 @@ +#ifndef CT_FLAMELET_H +#define CT_FLAMELET_H + +// #include "Domain1D.h" +#include "cantera/base/Array.h" +#include "cantera/oneD/StFlow.h" +#include "cantera/kinetics/Kinetics.h" +#include "cantera/thermo/IdealGasPhase.h" +#include "cantera/thermo/ThermoPhase.h" + + + +#include +/** + * A class for counter-flow diffusion flames in mixture fraction space + * @ingroup onedim + * L. Esclapez - 01/2018 + */ + +namespace Cantera +{ + +class Flamelet : public StFlow +{ +public: + Flamelet(IdealGasPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); + + //! Delegating constructor + Flamelet(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); + + //! Create a new flow domain. + //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and + //! transport properties + //! @param id name of flow domain + //! @param points initial number of grid points + Flamelet(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points=1); + + virtual ~Flamelet(); + + virtual void eval(size_t j, double* x, double* r, integer* mask, double rdt) override; + + virtual string type() const override{ + return "flamelet-flow"; + } + + virtual string flowType() const override{ + return "Flamelet"; + } + + virtual void resize(size_t components, size_t points) override; + + virtual string componentName(size_t n) const override; + + virtual size_t componentIndex(const string& name) const override; + + vector dCpdT(const Array2D sol); + + vector d2CpdT2(const Array2D sol); + + virtual void setGas(const double* x, size_t j) override; + + virtual void setGasAtMidpoint(const double* x, size_t j) override; + + virtual void resetBadValues(double* xg) override; + + virtual void setChiSt(double chiSt) { + m_chiSt = chiSt; + m_updateChi = true; + } + + virtual void setzSt(double zSt) { + m_zSt = zSt; + m_updateChi = true; + } + + virtual double chiSt() const { + return m_chiSt; + } + + virtual double zSt() const { + return m_zSt; + } + + void setChi(); + + void setUnityLewisNumber(bool doLewisNumber) { + m_do_unityLewisNumber = doLewisNumber; + } + + virtual void updateTransport(double* x, size_t j0, size_t j1) override; + + virtual void _getInitialSoln(double* x) override{ + for (size_t j = 0; j < m_points; j++) { + T(x,j) = m_thermo->temperature(); + m_thermo->getMassFractions(&Y(x, 0, j)); + } + } + + void showChiProfile() { + std::cout << "Chi profile " << std::endl; + for (size_t i = 0; i < m_points; i++) { + std::cout << z(i) << " " << m_chi[i] << std::endl; + } + } + + double chi(size_t j) const { + return m_chi[j]; + } + + size_t indexSt() const + { + auto low = std::lower_bound(m_z.begin(), m_z.end(), m_zSt); + return (low - m_z.begin()); + } + + virtual double T(const double* x, size_t j) const override { + return x[index(c_offset_Tflamelet, j)]; + } + virtual double& T(double* x, size_t j) override { + return x[index(c_offset_Tflamelet, j)]; + } + virtual double T_prev(size_t j) const override { + return prevSoln(c_offset_Tflamelet, j); + } + + virtual double Y(const double* x, size_t k, size_t j) const override { + return x[index(c_offset_Yflamelet + k, j)]; + } + + virtual double& Y(double* x, size_t k, size_t j) override { + return x[index(c_offset_Yflamelet + k, j)]; + } + + virtual double Y_prev(size_t k, size_t j) const override { + return prevSoln(c_offset_Yflamelet + k, j); + } + + double d2Ydz2(const double* x, size_t k, size_t j) const { + double c1 = (Y(x,k,j) - Y(x,k,j-1)); + double c2 = (Y(x,k,j+1) - Y(x,k,j)); + return 2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + + double d2Tdz2(const double* x, size_t j) const { + double c1 = (T(x,j) - T(x,j-1)); + double c2 = (T(x,j+1) - T(x,j)); + return 2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + + double Lek(size_t k, size_t j) { + return m_Lek[j*m_nsp+k]; + } + + double exactChi(double zz); + + double erfinv(double p1, double q1); + + // Lewis number stuff + bool m_do_unityLewisNumber = true; + vector m_Lek; + + // Thermo stuff + vector h_RT; + vector cp_R; + + + // Scalar dissipation rate stuff + vector m_chi; + vector m_exactchi; + double m_chiSt = 0.0; + double m_zSt = 0.0; + bool m_updateChi = true; + +// private: + // vector m_ybar; +}; + +} + +#endif \ No newline at end of file diff --git a/include/cantera/oneD/OneDim.h b/include/cantera/oneD/OneDim.h index c1dd6b58271..1003d91cb76 100644 --- a/include/cantera/oneD/OneDim.h +++ b/include/cantera/oneD/OneDim.h @@ -376,7 +376,7 @@ class OneDim int m_nsteps = 0; //! Maximum number of timesteps allowed per call to solve() - int m_nsteps_max = 500; + int m_nsteps_max = 5000; private: // statistics diff --git a/include/cantera/oneD/Sim1D.h b/include/cantera/oneD/Sim1D.h index f9cd9a0ca79..ef31a29a1b3 100644 --- a/include/cantera/oneD/Sim1D.h +++ b/include/cantera/oneD/Sim1D.h @@ -217,6 +217,11 @@ class Sim1D : public OneDim //! Refine the grid in all domains. int refine(int loglevel=0); + /// Remesh the grid in all domains. + double remesh(int loglevel, const double dist_min=1e9, const double domain_size=50.0); //from MUTAGEN + void addPoint(size_t ndomain, double zpoint, vector xpoint, int loglevel, bool newjac=true); //from MUTAGEN + void getRatio(); //from MUTAGEN + //! Add node for fixed temperature point of freely propagating flame int setFixedTemperature(double t); diff --git a/include/cantera/oneD/StFlow.h b/include/cantera/oneD/StFlow.h index 268f1428bbc..2ddbeb4ebf1 100644 --- a/include/cantera/oneD/StFlow.h +++ b/include/cantera/oneD/StFlow.h @@ -2,6 +2,7 @@ // This file is part of Cantera. See License.txt in the top-level directory or // at https://cantera.org/license.txt for license and copyright information. +// CERFACS : This file is no more used in CANTERA. CERFACS devs done in this file should be moved somewhere else (Flow1D or in a specific cantera-avbp file) #ifndef CT_STFLOW_H #define CT_STFLOW_H @@ -11,6 +12,35 @@ namespace Cantera { +//------------------------------------------ +// constants +//------------------------------------------ + +//! Offsets of solution components in the 1D solution array. +enum offset +{ + c_offset_U //! axial velocity + , c_offset_V //! strain rate + , c_offset_T //! temperature + , c_offset_L //! (1/r)dP/dr + , c_offset_E //! electric poisson's equation + , c_offset_Y //! mass fractions +}; + +//! Offsets of solution components in the 1D solution array for mixture fraction space +enum offset_z +{ + c_offset_Tflamelet, //! Temperature + c_offset_Yflamelet, //! Species mass fractions + // c_offset_Chi not used +}; + +class Transport; + +//! @defgroup flowGroup Flow Domains +//! One-dimensional flow domains. +//! @ingroup onedGroup + /** * This class represents 1D flow domains that satisfy the one-dimensional * similarity solution for chemically-reacting, axisymmetric flows. @@ -26,18 +56,684 @@ class StFlow : public Flow1D //! to evaluate all thermodynamic, kinetic, and transport properties. //! @param nsp Number of species. //! @param points Initial number of grid points - StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t points = 1); + //! @param n_eq Number of non-species equations (default = 4 for spatial resolution) + + //StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t points = 1); + StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); //! Delegating constructor - StFlow(shared_ptr th, size_t nsp = 1, size_t points = 1); + StFlow(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); //! Create a new flow domain. //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and //! transport properties //! @param id name of flow domain //! @param points initial number of grid points - StFlow(shared_ptr sol, const string& id="", size_t points=1); + StFlow(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Y, size_t points=1); + + virtual ~StFlow(); // virtual kw required for derived class destructors (flamelet) + + virtual string type() const override; + + //! @name Problem Specification + //! @{ + + void setupGrid(size_t n, const double* z) override; + void setupGrid(size_t n); + + virtual void resetBadValues(double* xg) override; + + ThermoPhase& phase() { + return *m_thermo; + } + + Kinetics& kinetics() { + return *m_kin; + } + + /** + * Set the thermo manager. + * + * @deprecated To be removed after %Cantera 3.0 (unused) + */ + void setThermo(ThermoPhase& th); + + void setKinetics(shared_ptr kin) override; + + //! Set the kinetics manager. + //! @deprecated To be removed after %Cantera 3.0; + //! replaced by Domain1D::setKinetics() + void setKinetics(Kinetics& kin); + + void setTransport(shared_ptr trans) override; + + //! Set transport model to existing instance + //! @deprecated To be removed after %Cantera 3.0; + //! replaced by Domain1D::setKinetics() + void setTransport(Transport& trans); + + //! Set the transport model + //! @since New in %Cantera 3.0. + void setTransportModel(const string& trans); + + //! Retrieve transport model + //! @since New in %Cantera 3.0. + string transportModel() const; + + //! Enable thermal diffusion, also known as Soret diffusion. + //! Requires that multicomponent transport properties be + //! enabled to carry out calculations. + void enableSoret(bool withSoret) { + m_do_soret = withSoret; + } + bool withSoret() const { + return m_do_soret; + } + + //! Set the pressure. Since the flow equations are for the limit of small + //! Mach number, the pressure is very nearly constant throughout the flow. + void setPressure(double p) { + m_press = p; + } + + //! The current pressure [Pa]. + double pressure() const { + return m_press; + } + + //! Set the number of non-species equations + void setNequation(size_t neq){ + m_neq = neq; + } + + //! The current number of non-species equations + size_t nEq(){ + return m_neq; + } + + //! Write the initial solution estimate into array x. + void _getInitialSoln(double* x) override; + + void _finalize(const double* x) override; + + //! Sometimes it is desired to carry out the simulation using a specified + //! temperature profile, rather than computing it by solving the energy + //! equation. This method specifies this profile. + void setFixedTempProfile(vector& zfixed, vector& tfixed) { + m_zfix = zfixed; + m_tfix = tfixed; + } + + /** + * Set the temperature fixed point at grid point j, and disable the energy + * equation so that the solution will be held to this value. + */ + void setTemperature(size_t j, double t) { + m_fixedtemp[j] = t; + m_do_energy[j] = false; + } + + //! The fixed temperature value at point j. + double T_fixed(size_t j) const { + return m_fixedtemp[j]; + } + + /// Returns the mixture fraction at point j + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + double getMixFrac(size_t j) { + return m_zmixfrac[j]; + } + + /// Updates the mixture fraction at point j + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + void calcMixFrac(const double* x,size_t j); + + //! @} + + string componentName(size_t n) const override; + + size_t componentIndex(const string& name) const override; + + //! Returns true if the specified component is an active part of the solver state + virtual bool componentActive(size_t n) const; + + //! Print the solution. + void show(const double* x) override; + + shared_ptr asArray(const double* soln) const override; + void fromArray(SolutionArray& arr, double* soln) override; + + //! Set flow configuration for freely-propagating flames, using an internal point + //! with a fixed temperature as the condition to determine the inlet mass flux. + void setFreeFlow() { + // m_type = cFreeFlow; // AP : test to remove the domain type (not used in Flow1D.h) + m_dovisc = false; + m_isFree = true; + m_usesLambda = false; + } + + //! Set flow configuration for axisymmetric counterflow flames, using specified + //! inlet mass fluxes. + void setAxisymmetricFlow() { + // m_type = cAxisymmetricStagnationFlow; // AP : test to remove the domain type (not used in Flow1D.h) + m_dovisc = true; + m_isFree = false; + m_usesLambda = true; + } + + //! Set flow configuration for burner-stabilized flames, using specified inlet mass + //! fluxes. + void setUnstrainedFlow() { + // m_type = cAxisymmetricStagnationFlow; // AP : test to remove the domain type (not used in Flow1D.h) + m_dovisc = false; + m_isFree = false; + m_usesLambda = false; + } + + void setFlameletFlow() { + // m_type = cFlameletFlow; // AP : test to remove the domain type (not used in Flow1D.h) + m_dovisc = true; + m_isFree = false; + m_usesLambda = true; + } + + //! Return the type of flow domain being represented, either "Free Flame" or + //! "Axisymmetric Stagnation". + //! @see setFreeFlow setAxisymmetricFlow + //! @deprecated To be removed after %Cantera 3.0; replaced by type(). + virtual string flowType() const; + + virtual void setFuelSpecies(const std::string fuel) { + m_fuel = fuel; + } + + void solveEnergyEqn(size_t j=npos); + + //! Get the solving stage (used by IonFlow specialization) + //! @since New in %Cantera 3.0 + virtual size_t getSolvingStage() const; + + //! Solving stage mode for handling ionized species (used by IonFlow specialization) + //! - @c stage=1: the fluxes of charged species are set to zero + //! - @c stage=2: the electric field equation is solved, and the drift flux for + //! ionized species is evaluated + virtual void setSolvingStage(const size_t stage); + + //! Set to solve electric field in a point (used by IonFlow specialization) + virtual void solveElectricField(size_t j=npos); + + //! Set to fix voltage in a point (used by IonFlow specialization) + virtual void fixElectricField(size_t j=npos); + + //! Retrieve flag indicating whether electric field is solved or not (used by + //! IonFlow specialization) + virtual bool doElectricField(size_t j) const; + + //! Turn radiation on / off. + /*! + * The simple radiation model used was established by Liu and Rogg + * @cite liu1991. This model considers the radiation of CO2 and H2O. + * + * This model uses the optically thin limit and the gray-gas approximation to + * simply calculate a volume specified heat flux out of the Planck absorption + * coefficients, the boundary emissivities and the temperature. Polynomial lines + * calculate the species Planck coefficients for H2O and CO2. The data for the + * lines are taken from the RADCAL program @cite RADCAL. + * The coefficients for the polynomials are taken from + * [TNF Workshop](https://tnfworkshop.org/radiation/) material. + */ + void enableRadiation(bool doRadiation) { + m_do_radiation = doRadiation; + } + + //! Returns `true` if the radiation term in the energy equation is enabled + bool radiationEnabled() const { + return m_do_radiation; + } + + //! Return radiative heat loss at grid point j + double radiativeHeatLoss(size_t j) const { + return m_qdotRadiation[j]; + } + + //! Set the emissivities for the boundary values + /*! + * Reads the emissivities for the left and right boundary values in the + * radiative term and writes them into the variables, which are used for the + * calculation. + */ + void setBoundaryEmissivities(double e_left, double e_right); + + // Turn soot formation on / off. + // setSections + const size_t getSections() const{ + return m_nsoot; + } + + void setSections(size_t nSec) { + m_nsoot = nSec; + } + + void setPrecursors(std::vector id_precursors); + + void setSootLoglevel(size_t loglevel){ + soot_loglevel = loglevel; + } + + size_t getSootLoglevel(){ + return soot_loglevel; + } + + void enableCondensation(bool doCondensation) { + m_do_condensation = doCondensation; + } + bool condensationEnabled(){ + return m_do_condensation; + } + + void enableCoagulation(bool doCoagulation) { + m_do_coagulation = doCoagulation; + } + bool coagulationEnabled(){ + return m_do_coagulation; + } + + void setCollisionModel(std::string collisionModel){ + m_collision_model = collisionModel; + } + + std::string getCollisionModel(){ + return m_collision_model; + } + + void setSootMorphology(std::string morphologyModel){ + m_soot_morphology = morphologyModel; + } + + std::string getSootMorphology(){ + return m_soot_morphology; + } + + void enableRetroaction(bool doRetroaction){ + m_do_retroaction = doRetroaction; + } + bool retroactionEnabled(){ + return m_do_retroaction; + } + + void enableSootRadiation(bool do_soot_radiation){ + m_do_soot_radiation = do_soot_radiation; + } + + bool sootRadiationEnabled(){ + return m_do_soot_radiation; + } + + void enableSootSoret(bool do_soot_soret){ + m_do_soot_soret = do_soot_soret; + } + + bool sootSoretEnabled(){ + return m_do_soot_soret; + } + + void enableSurfaceGrowth(bool do_sg){ + m_do_sg = do_sg; + } + bool surfaceGrowthEnabled(){ + return m_do_sg; + } + + void enableOxidation(bool do_oxidation){ + m_do_oxidation = do_oxidation; + } + bool oxidationEnabled(){ + return m_do_oxidation; + } + + void enableTrashSection(double trash_section){ + if (trash_section > 0){ + m_trash_section = true; + dTrashLowLim = trash_section; + }else{ + m_trash_section = false; + dTrashLowLim = 0.0; + } + } + + bool trashSectionEnabled(){ + return m_trash_section; + } + + void setHaca(size_t haca_model){ + m_haca_model = haca_model; + } + + size_t getHaca(){ + return m_haca_model; + } + + double getKazakovTad(){ + return kazakovTad; + } + void setKazakovTad(double kazakov_tad){ + kazakovTad = kazakov_tad; + } + + void loadHaca(size_t m_haca_model){ + if (m_haca_model == 1){ //Mauss + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.0 / S_C2; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Mauss HACA-RC model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; + ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; + // S-H + OH <-> S* + H2O + ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; + ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; + // S* + H <-> S-H + ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; + ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; + // S* + C2H2 <-> S-H + ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; + ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; + // S* <-> S-H + H + ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; + ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; + // S* + O2 -> S-H + 2CO + ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 8.4000e03; + // S* + O2 -> S-H + 2HCO + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + }else if (m_haca_model == 11){ //Mauss tuned (Guo 2016) + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.0 / S_C2; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Mauss HACA-RC model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; + ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; + // S-H + OH <-> S* + H2O + ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; + ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; + // S* + H <-> S-H + ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; + ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; + // S* + C2H2 <-> S-H + ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; + ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; + // S* <-> S-H + H + ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; + ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; + // S* + O2 -> S-H + 2CO + ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 190.000e03; + // S* + O2 -> S-H + 2HCO + // S-H + OH -> S-H + CO + gamma_oh = 0.10; + }else if (m_haca_model == 2){ //Blanquart + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.7e19; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Blanquart HACA model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.0e8 * 1e-3; nk01f = 1.8; ek01f = 68420.0; + ak01b = 8.68e4 * 1e-3; nk01b = 2.36; ek01b = 25460.0; + // S-H + OH <-> S* + H2O + ak02f = 6.72e1 * 1e-3; nk02f = 3.33; ek02f = 6090.0; + ak02b = 6.44e-1 * 1e-3; nk02b = 3.79; ek02b = 27960.0; + // S-H <-> S* + H + ak03f = 1.13e16; nk03f = -0.06; ek03f = 476050.0; + ak03b = 4.17e13 * 1e-3; nk03b = 0.15; ek03b = 0.0; + // S* + C2H2 -> S-H + ak04f = 2.52e9 * 1e-3; nk04f = 1.77; ek04f = 13540.0; + // S* + O2 -> S + 2CO + ak05f = 2.2e12 * 1e-3; nk05f = 0.0; ek05f = 31380.0; + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + }else if (m_haca_model == 3){ + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [m-2] + double lambda = 2.3e19; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Kazakov HACA model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/mol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 2.5e14 * 1e-3; nk01f = 0.0; ek01f = 66900.0; + ak01b = 3.9e12 * 1e-3; nk01b = 0.0; ek01b = 39000.0; + // S* + H -> S-H + ak02f = 1.0e14 * 1e-3; nk02f = 0.0; ek02f = 0.0; + // S* + C2H2 -> S-H + H + ak03f = 8.4e11 * 1e-3; nk03f = 0.4; ek03f = 35100.0; + // S* + O2 -> S + 2CO + ak04f = 2.2e12 * 1e-3; nk04f = 0.0; ek04f = 31300.0; + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + } + } + + void finalizeSoot(); + void loadSurface(); + //Initialize soot + void initSoot(); + void showSootInfo(); + // Sections generation and display + void sootCreationVol(); + void showSootSections(); + void sootCollisionModel(); + void getDistributionOrdre0(const double* x, size_t j); + // Soot source terms + void sootSource(const double* x, size_t j); + void sootDimerization(const double* x, size_t j); + void sootNucleation(const double* x, size_t j); + void sootCondensation(const double* x, size_t j); + void sootCoagulation(const double* x, size_t j); + void sootSurface(const double* x, size_t j); + void sootSurfaceInitialization(const double* x, size_t j); + void sootCollisionInverse(); + // Returns section name + std::string sectionName(size_t n) const { + return m_section_name[n]; + } + + const vector& vMin() const { + return vSectMin; + } + + const vector& vMax() const { + return vSectMax; + } + + const vector& vMean() const { + return vSectMean; + } + + const vector& dMean() const { + return dSectMean; + } + + const vector& dCol() const { + return dSectCol; + } + + const vector& aCol() const { + return aSectCol; + } + + const vector& sMean() const { + return sSectMean; + } + + const vector& thetaSoot() const { + return theta_surf; + } + + const vector& fractalPrefactor() const { + return kfractal; + } + const vector& fractalDimension() const { + return Dfractal; + } + + const double rhoSoot() const { + return rho_soot; + } + + const double getSootInception(size_t j) const { + return m_qdotNucleation[j] * m_rho[j]; + } + + const double getSootCondensation(size_t k, size_t j) const { + return m_qdotCondensation(k,j) * m_rho[j]; + } + + const double getSootCoagulation(size_t k, size_t j) const { + return m_qdotCoagulation(k,j) * m_rho[j]; + } + + const double getSootSg(size_t k, size_t j) const { + return m_qdotSg(k,j) * m_rho[j]; + } + + const double getSootOxidation(size_t k, size_t j) const { + return m_qdotOxidation(k,j) * m_rho[j]; + } + + const double fv(const double* x, size_t j){ + double val = 0.0; + for (size_t k=0; k < m_nsoot; k++){ + val += Ys(x,k,j); + } + val *= m_rho[j] / rho_soot; + return val; + } + + const double sootPrimaryDiam(size_t k) const { + return 2.0 * rNucMean[k]; + } + + const double sootPrimaryPart(size_t k) const { + return nNucMean[k]; + } + + void setThick(double thickness){ + m_thick = thickness; + AVBPReadInputChem(); + } + + double getThick() const { + return m_thick; + } + + //! Return emissivity at left boundary + double leftEmissivity() const { return m_epsilon_left; } + + //! Return emissivity at right boundary + double rightEmissivity() const { return m_epsilon_right; } + + void fixTemperature(size_t j=npos); + + bool doEnergy(size_t j) { + return m_do_energy[j]; + } + + //! Change the grid size. Called after grid refinement. + void resize(size_t components, size_t points) override; + + //! Set the gas object state to be consistent with the solution at point j. + virtual void setGas(const double* x, size_t j); + + //! Set the gas state to be consistent with the solution at the midpoint + //! between j and j + 1. + virtual void setGasAtMidpoint(const double* x, size_t j); + + double density(size_t j) const { + return m_rho[j]; + } + + //! seems unused + double cpBar(size_t j) const { + return m_cpm[j]; + } + + double enthalpy(size_t j) const { + return m_h[j]; + } + + double thCond(size_t j) const { + return m_tcon[j]; + } + + double HR(size_t j) const { + return m_hr[j]; + } + + //! @deprecated To be removed after %Cantera 3.0. Superseded by isFree() + virtual bool fixed_mdot(); + + /** + * Retrieve flag indicating whether flow is freely propagating. + * The flow is unstrained and the axial mass flow rate is not specified. + * For free flame propagation, the axial velocity is determined by the solver. + * @since New in %Cantera 3.0 + */ + bool isFree() const { + return m_isFree; + } + + /** + * Retrieve flag indicating whether flow uses radial momentum. + * If `true`, radial momentum equation for @f$ V @f$ as well as + * @f$ d\Lambda/dz = 0 @f$ are solved; if `false`, @f$ \Lambda(z) = 0 @f$ and + * @f$ V(z) = 0 @f$ by definition. + * @since New in %Cantera 3.0 + */ + bool isStrained() const { + return m_usesLambda; + } + + void setViscosityFlag(bool dovisc) { + m_dovisc = dovisc; + } + + + // P. Wolf + void AVBPReadInputPea(); + + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + // B. Franzelli modifications to perform thickening + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + void AVBPReadInputChem(); + void AVBPcompute_local_thick(double* x,size_t j); + + double AVBPthick(size_t j) const { + return avbp_thick[j]; + } + + /** + * Evaluate the residual function for axisymmetric stagnation flow. If + * j == npos, the residual function is evaluated at all grid points. + * Otherwise, the residual function is only evaluated at grid points + * j-1, j, and j+1. This option is used to efficiently evaluate the + * Jacobian numerically. + */ void eval(size_t j, double* x, double* r, integer* mask, double rdt) override; //! Evaluate all residual components at the right boundary. @@ -51,15 +747,484 @@ class StFlow : public Flow1D } //! Write the net production rates at point `j` into array `m_wdot` - void getWdot(double* x, size_t j) { - setGas(x,j); - m_kin->getNetProductionRates(&m_wdot(0,j)); + // void getWdot(double* x, size_t j) { + // setGas(x,j); + // m_kin->getNetProductionRates(&m_wdot(0,j)); + // } +/// write the net production rates at point j into array m_wdot +/// Modified by P. Wolf March 2010 - Thanks to Alireza N. +/// when PEA activated: production rates depends on mixture fraction at point j +/// WARNING: the following is valid only for fuel/AIR right now + void getWdot(double *x, size_t j) + { + double zloc; + double phi; + setGas(x, j); // We'll need to set the gas before retrieving + // std::cout << "after setGas" << std::endl; + zloc = getMixFrac(j); // the Mixture Fraction and calculating wdot + phi = zloc / (1. - zloc) * phi_cst; + + switch (avbp_ipea) + { + case 0: + m_kin->getNetProductionRates(&m_wdot(0, j)); + break; + // ipea = 1, apply the PEA on fuel oxydation reaction only + case 1: + double pea_f; // pea correction function + // Now set the PEA correction function + pea_f = 0.5 * (1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) + + avbp_pea_coeffs[2] / 4. * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) + * (1. + tanh((avbp_pea_coeffs[5] - phi) / avbp_pea_coeffs[6])); + + // Multiply reaction rate of reaction 1 by the pea coeff + m_kin->setMultiplier(1, pea_f); + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + // Restore the original reaction rates (not necessary) + m_kin->setMultiplier(1, 1.0 / pea_f); + break; + // ipea = 2, apply PEA on both reactions + case 2: + // TEST 081014: differencie bien les cas + double pea2_f[2]; // pea correction function + // Now set the PEA correction function + pea2_f[0] = 2. / ((1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) + + avbp_pea_coeffs[2] * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) + + avbp_pea_coeffs[5] * (1. + tanh((phi - avbp_pea_coeffs[6]) / avbp_pea_coeffs[7]))); + + pea2_f[1] = 0.5 * ((1. + tanh((avbp_pea_coeffs[8] - phi) / avbp_pea_coeffs[9])) + + avbp_pea_coeffs[10] * (1. + tanh((phi - avbp_pea_coeffs[11]) / avbp_pea_coeffs[12])) + + avbp_pea_coeffs[13] * (1. + tanh((phi - avbp_pea_coeffs[14]) / avbp_pea_coeffs[15])) + * (1. + tanh((avbp_pea_coeffs[16] - phi) / avbp_pea_coeffs[17]))); + // Multiply reaction rates by the pea coeff + if (m_kin->nReactions() == 2) + { + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, pea2_f[n]); + } + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + // Restore the original reaction rates (not necessary) + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, 1.0 / pea2_f[n]); + } + } + else + { + throw CanteraError("getWdot", "ipea = 2 but there ain't 2 reactions"); + } + break; + // ipea = 3, apply PEA on both reactions (for CM2 only) + case 3: + double pea3_f[2]; // pea correction function + + // Now set the PEA correction function + if (phi > 1.0) + { + // pea3_f[0] = max(avbp_pea_coeffs[0]*phi*phi + avbp_pea_coeffs[1]*phi + avbp_pea_coeffs[2],0.0); + pea3_f[0] = avbp_pea_coeffs[0] * phi * phi + avbp_pea_coeffs[1] * phi + avbp_pea_coeffs[2]; + } + else + { + pea3_f[0] = 1; + } + pea3_f[1] = pea3_f[0]; + + // Multiply reaction rates by the pea coeff + if (m_kin->nReactions() == 2) + { + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, pea2_f[n]); + } + + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + + // Restore the original reaction rates (not necessary) + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, 1.0 / pea2_f[n]); + } + } + else + { + throw CanteraError("getWdot", "ipea = 3 but there ain't 2 reactions"); + } + + break; + + default: + throw CanteraError("getWdot", "ipea is set to a weird value"); + break; + } } //! Evaluate the residual function. This function is called in eval //! after updateProperties is called. virtual void evalResidual(double* x, double* rsd, int* diag, double rdt, size_t jmin, size_t jmax); + + /** + * Update the thermodynamic properties from point j0 to point j1 + * (inclusive), based on solution x. + */ + virtual void updateThermo(const double* x, size_t j0, size_t j1) { + for (size_t j = j0; j <= j1; j++) { + setGas(x,j); + m_rho[j] = m_thermo->density(); + m_wtm[j] = m_thermo->meanMolecularWeight(); + m_cp[j] = m_thermo->cp_mass(); + m_thermo->getPartialMolarEnthalpies(&m_hk(0, j)); + } + } + + //-------------------------------- + // central-differenced derivatives + //-------------------------------- + double cdif1(const double*x, size_t n, size_t j) const { + double c1 = (x[index(n,j+1)] - x[index(n,j-1)]); + return c1/(z(j+1) - z(j-1)); + } + + //! seems unused + double cdif2(const double* x, size_t n, size_t j, + const double* f) const { + double c1 = (f[j] + f[j-1])*(x[index(n,j)] - x[index(n,j-1)]); + double c2 = (f[j+1] + f[j])*(x[index(n,j+1)] - x[index(n,j)]); + return (c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + + //! @name Solution components + //! @{ + + virtual double T(const double* x, size_t j) const { + return x[index(c_offset_T, j)]; + } + virtual double& T(double* x, size_t j) { + return x[index(c_offset_T, j)]; + } + virtual double T_prev(size_t j) const { + return prevSoln(c_offset_T, j); + } + + double rho_u(const double* x, size_t j) const { + return m_rho[j]*x[index(c_offset_U, j)]; + } + + double u(const double* x, size_t j) const { + return x[index(c_offset_U, j)]; + } + + double V(const double* x, size_t j) const { + return x[index(c_offset_V, j)]; + } + double V_prev(size_t j) const { + return prevSoln(c_offset_V, j); + } + + double lambda(const double* x, size_t j) const { + return x[index(c_offset_L, j)]; + } + + virtual double Y(const double* x, size_t k, size_t j) const { + return x[index(c_offset_Y + k, j)]; + } + + virtual double& Y(double* x, size_t k, size_t j) { + return x[index(c_offset_Y + k, j)]; + } + + virtual double Y_prev(size_t k, size_t j) const { + return prevSoln(c_offset_Y + k, j); + } + + //Soot + double Ys(const double* x, size_t k, size_t j) const { + return x[index(c_offset_S+k, j)]; + } + + double& Ys(double* x, size_t k, size_t j) { + return x[index(c_offset_S+k, j)]; + } + + double Ys_prev(size_t k, size_t j) const { + return prevSoln(c_offset_S + k, j); + } + //---- + + double X(const double* x, size_t k, size_t j) const { + return m_wtm[j]*Y(x,k,j)/m_wt[k]; + } + + double flux(size_t k, size_t j) const { + return m_flux(k, j); + } + //! @} + + //! @name convective spatial derivatives. + //! + //! These use upwind differencing, assuming u(z) is negative + //! @{ + double dVdz(const double* x, size_t j) const { + size_t jloc = (u(x,j) > 0.0 ? j : j + 1); + return (V(x,jloc) - V(x,jloc-1))/m_dz[jloc-1]; + } + + double dYdz(const double* x, size_t k, size_t j) const { + size_t jloc = (u(x,j) > 0.0 ? j : j + 1); + return (Y(x,k,jloc) - Y(x,k,jloc-1))/m_dz[jloc-1]; + } + + // Soot + double dYsdz(const double* x, size_t k, size_t j) const { + size_t jloc = (u(x,j) > 0.0 ? j : j + 1); + return (Ys(x,k,jloc) - Ys(x,k,jloc-1))/m_dz[jloc-1]; + } + + double dTdz(const double* x, size_t j) const { + size_t jloc = (u(x,j) > 0.0 ? j : j + 1); + return (T(x,jloc) - T(x,jloc-1))/m_dz[jloc-1]; + } + //! @} + + double shear(const double* x, size_t j) const { + double c1 = m_visc[j-1]*(V(x,j) - V(x,j-1)); + double c2 = m_visc[j]*(V(x,j+1) - V(x,j)); + return 2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + + double divHeatFlux(const double* x, size_t j) const { + double c1 = m_tcon[j-1]*(T(x,j) - T(x,j-1)); + double c2 = m_tcon[j]*(T(x,j+1) - T(x,j)); + return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + + double AVBPdivHeatFlux(const double* x, size_t j) const { + double c1 = avbp_thick[j-1]*m_tcon[j-1]*(T(x,j) - T(x,j-1)); + double c2 = avbp_thick[j]*m_tcon[j]*(T(x,j+1) - T(x,j)); + return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + + size_t mindex(size_t k, size_t j, size_t m) { + return m*m_nsp*m_nsp + m_nsp*j + k; + } + + //! Update the diffusive mass fluxes. + virtual void updateDiffFluxes(const double* x, size_t j0, size_t j1); + virtual void updateSootDiffFluxes(const double* x, size_t j0, size_t j1); + + //! Get the gradient of species specific molar enthalpies + virtual void grad_hk(const double* x, size_t j); + + //--------------------------------------------------------- + // member data + //--------------------------------------------------------- + + double m_press = -1.0; // pressure + + // grid parameters + vector m_dz; + + // mixture thermo properties + vector m_rho; + vector m_wtm; + + // P. Wolf + vector m_zmixfrac; + + vector m_cpm; + vector m_h; + + // species thermo properties + vector m_wt; + vector m_cp; + + // transport properties + vector m_ybar; + vector m_visc; + vector m_tcon; + vector m_diff; + vector m_multidiff; + Array2D m_dthermal; + Array2D m_flux; + + //! Array of size #m_nsp by #m_points for saving molar enthalpies + Array2D m_hk; + + //! Array of size #m_nsp by #m_points-1 for saving enthalpy fluxes + Array2D m_dhk_dz; + + // production rates + vector m_hr; + Array2D m_wdot; + + size_t m_nsp; //!< Number of species in the mechanism + size_t m_neq; //!< Number of non-species equations + size_t m_nsoot; + std::string m_fuel; + + ThermoPhase* m_thermo = nullptr; + Kinetics* m_kin = nullptr; + Transport* m_trans = nullptr; + + MultiJac* m_jac = nullptr; + + // boundary emissivities for the radiation calculations + double m_epsilon_left = 0.0; + double m_epsilon_right = 0.0; + + //! Indices within the ThermoPhase of the radiating species. First index is + //! for CO2, second is for H2O. + vector m_kRadiating; + + // Pierre WOLF: added parameters for input_pea.dat + size_t avbp_ipea = 0; + std::string avbp_fuel; + vector avbp_pea_coeffs; + double phi_cst; + + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + // B. Franzelli modifications to perform thickening + // input_chem parameters + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + double avbp_fthick; + vector avbp_thick; + double m_thick = 1.0; + + // flags + vector m_do_energy; + bool m_do_soret = false; + vector m_do_species; + bool m_do_multicomponent = false; + + //! flag for the radiative heat loss + bool m_do_radiation = false; + + //! radiative heat loss vector + vector m_qdotRadiation; + + // ---------------------- + // SOOT RELATED VARIABLES + // ---------------------- + bool m_do_soot_soret = true; + bool m_do_condensation = false; + bool m_do_soot_radiation = false; + bool m_do_coagulation = false; + std::string m_soot_morphology; + bool m_do_retroaction = false; + bool m_do_sg = false; + bool m_do_oxidation = false; + bool m_trash_section = false; + std::string m_collision_model = "rodrigues"; + size_t soot_loglevel=1; + size_t c_offset_S = 6; + size_t n_PAH = 0; + size_t m_haca_model; + double Y_PAH; + double C_PAH; + double dTrashLowLim; + vector W_PAH; + double W_C; + vector n_C; + double N_dimer; + double beta_dimer; + double r_dimer; + double V_dimer; + double beta_fm; + double n_sites; + double kazakovTad; + double ksg; + double kox; + vector sootConsumption; + vector vSectMin; + vector vSectMax; + vector dSectMean; + vector dSectCol; + vector rSectCol; + vector aSectCol; + vector vSectMean; + vector sSectMean; + vector Dfractal; + vector kfractal; + vector nNucMean; + vector rNucMean; + vector rSmolMean; + vector PAMean; + vector m_qdotNucleation; + Array2D m_qdotCondensation; + Array2D m_qdotCoagulation; + Array2D m_qdotSg; + Array2D m_qdotOxidation; + vector q; + vector theta_surf; + vector jpower; + vector kpower; + vector mpower; + vector vc2power; + vector vc2powerm; + vector vmax_kpower; + vector vmin_kpower; + vector vmax_jpower; + vector vmin_jpower; + vector vmax_mpower; + vector vmin_mpower; + vector vmaxmc2_kpower; + vector vminpc2_kpower; + vector vmaxmc2_jpower; + vector vminpc2_jpower; + vector vmaxmc2_mpower; + vector vminpc2_mpower; + vector vc2powervect; + vector vc2powermvect; + vector m_section_name; + vector m_precursors; + Array2D m_soot_diff ; + Array2D m_soot_soret ; + Array2D collision_mat; + //Surface reactions + double ak00f, nk00f, ek00f, ak01f, nk01f, ek01f, ak02f, nk02f, ek02f, + ak03f, nk03f, ek03f, ak04f, nk04f, ek04f, ak05f, nk05f, ek05f, + ak06f, nk06f, ek06f, ak07f, nk07f, ek07f; + double ak00b, nk00b, ek00b, ak01b, nk01b, ek01b, ak02b, nk02b, ek02b, + ak03b, nk03b, ek03b, ak04b, nk04b, ek04b, ak05b, nk05b, ek05b, + ak06b, nk06b, ek06b, ak07b, nk07b, ek07b; + double gamma_oh; + // ----------------------------- + // END OF SOOT RELATED VARIABLES + // ----------------------------- + + // fixed T and Y values + vector m_fixedtemp; + vector m_zfix; + vector m_tfix; + + //! Index of species with a large mass fraction at each boundary, for which + //! the mass fraction may be calculated as 1 minus the sum of the other mass + //! fractions + size_t m_kExcessLeft = 0; + size_t m_kExcessRight = 0; + + bool m_dovisc; + bool m_isFree; + bool m_usesLambda; + + //! Update the transport properties at grid points in the range from `j0` + //! to `j1`, based on solution `x`. + virtual void updateTransport(double* x, size_t j0, size_t j1); + +public: + //! Location of the point where temperature is fixed + double m_zfixed = Undef; + + //! Temperature at the point used to fix the flame location + double m_tfixed = -1.0; + +// private: +// vector m_ybar; }; } diff --git a/include/cantera/oneD/refine.h b/include/cantera/oneD/refine.h index 59261f10041..19fb85807ff 100644 --- a/include/cantera/oneD/refine.h +++ b/include/cantera/oneD/refine.h @@ -71,6 +71,13 @@ class Domain1D; int analyze(size_t n, const double* z, const double* x); int getNewGrid(int n, const double* z, int nn, double* znew); + + double remeshFromSolution(int np, const double* z, const double* x, const double dist_min=1e9, const double domain_size=50.0); //from MUTAGEN + + int indxtp(int np,double val,const double* array); //from MUTAGEN + + void getRatio(int np, const double* z, double* x); //from MUTAGEN + int nNewPoints() { return static_cast(m_loc.size()); } @@ -81,6 +88,29 @@ class Domain1D; bool keepPoint(size_t j) { return (m_keep[j] != -1); } + + + double z_new(const int m) //from MUTAGEN + { + return m_z_new[m]; + } + + int z_new_size() //from MUTAGEN + { + return m_z_new.size(); + } + + double grad_max() //from MUTAGEN + { + return m_grad_max; + } + + double curve_max() //from MUTAGEN + { + return m_curve_max; + } + + double value(const double* x, size_t i, size_t j); double maxRatio() { @@ -111,6 +141,8 @@ class Domain1D; Domain1D* m_domain; size_t m_nv; size_t m_npmax = 1000; + vector m_z_new; //from MUTAGEN + double m_grad_max, m_curve_max; //from MUTAGEN double m_thresh = std::sqrt(std::numeric_limits::epsilon()); double m_gridmin = 1e-10; //!< minimum grid spacing [m] }; diff --git a/include/cantera/transport/AVBPTransport.h b/include/cantera/transport/AVBPTransport.h new file mode 100644 index 00000000000..f6680b4b2ed --- /dev/null +++ b/include/cantera/transport/AVBPTransport.h @@ -0,0 +1,120 @@ +/** + * + * @file AVBPTransport.h + * Header file defining class AVBPTransport which implements + * the simplified transport model used in the solver AVBP + */ + +/* $Author: B. Franzelli (v. 1.7) $ + * $Revision: A. Felden (v 2.1-2.3) $ + * $Date: 01/2018 $ + */ + + +#ifndef CT_AVBPTRAN_H +#define CT_AVBPTRAN_H + +#include "GasTransport.h" +#include "cantera/numerics/DenseMatrix.h" + +// STL includes +#include +#include +#include +#include +#include + +namespace Cantera +{ + +// class GasTransportParams; + +/** + * Class AVBPTransport + * Constant Sch for each species, Pr, and simplified viscosity + */ +class AVBPTransport : public GasTransport +{ + +public: + //! Default constructor. + AVBPTransport() = default; + + //! Return the model id for transport + /*! + * @return cAVBPAverage + */ + // virtual int model() const { + // warn_deprecated("AVBPTransport::model", + // "To be removed after Cantera 2.3."); + // return cAVBPTransport; + // } + string transportModel() const override { + return (m_mode == CK_Mode) ? "AVBP-CK" : "AVBP"; + } + // virtual std::string transportType() const { + // return "AVBP"; + // } + + //! Return the thermal diffusion coefficients + //virtual void getThermalDiffCoeffs(double* const dt); + + //! Returns the mixture thermal conductivity + double thermalConductivity() override; + + //! Get the Electrical mobilities (m^2/V/s). + //virtual void getMobilities(double* const mobil); + + //! Update the internal parameters whenever the temperature has changed + void update_T() override; + + //! Update the internal parameters whenever the concentrations have changed + void update_C() override; + + //virtual void getSpeciesFluxes(size_t ndim, + // const double* const grad_T, + // size_t ldx, + // const double* const grad_X, + // size_t ldf, double* const fluxes); + + //! Initialize the transport object + //virtual bool initGas(GasTransportParams& tr); + void init(ThermoPhase* thermo, int mode=0, int log_level=0) override; + + //! Viscosity of the mixture + virtual double viscosity(); + + virtual void getSpeciesViscosities(double* const visc) { + update_T(); + updateViscosity_T(); + std::copy(m_visc.begin(), m_visc.end(), visc); + } + + //! Mixture diffusion coefficients [m^2/s]. + virtual void getMixDiffCoeffs(double* const d); + + virtual void read_mixture(std::string s); + + size_t avbp_ipea; + vector avbp_pea_coeffs; + +protected: + + //! Calculate the pressure from the ideal gas law + double pressure_ig(); + + double m_lambda; + //bool m_debug; + + // AVBP variables + vector avbp_Sch; + vector avbp_Le; + double avbp_Prandtl; + double avbp_mu0; + double avbp_T0; + double avbp_beta; + std::string avbp_fuel; + +}; +} +#endif From e3787efeb9681902f68f141871056b0b559cfaa4 Mon Sep 17 00:00:00 2001 From: pestre Date: Fri, 17 Jan 2025 12:43:31 +0100 Subject: [PATCH 18/98] Change refine_grid param type to string Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: modified: include/cantera/clib/ctonedim.h modified: include/cantera/oneD/Sim1D.h --- include/cantera/clib/ctonedim.h | 2 +- include/cantera/oneD/Sim1D.h | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/include/cantera/clib/ctonedim.h b/include/cantera/clib/ctonedim.h index 7b21c382858..f8db2287abe 100644 --- a/include/cantera/clib/ctonedim.h +++ b/include/cantera/clib/ctonedim.h @@ -89,7 +89,7 @@ extern "C" { CANTERA_CAPI int sim1D_show(int i, const char* fname); CANTERA_CAPI int sim1D_setTimeStep(int i, double stepsize, size_t ns, const int* nsteps); CANTERA_CAPI int sim1D_getInitialSoln(int i); - CANTERA_CAPI int sim1D_solve(int i, int loglevel, int refine_grid); + CANTERA_CAPI int sim1D_solve(int i, int loglevel, const char* refine_grid); CANTERA_CAPI int sim1D_refine(int i, int loglevel); CANTERA_CAPI int sim1D_setRefineCriteria(int i, int dom, double ratio, double slope, double curve, double prune); diff --git a/include/cantera/oneD/Sim1D.h b/include/cantera/oneD/Sim1D.h index ef31a29a1b3..3e7494c51f5 100644 --- a/include/cantera/oneD/Sim1D.h +++ b/include/cantera/oneD/Sim1D.h @@ -203,7 +203,7 @@ class Sim1D : public OneDim void setTimeStep(double stepsize, size_t n, const int* tsteps); - void solve(int loglevel = 0, bool refine_grid = true); + void solve(int loglevel = 0, const string& refine_grid = "refine"); void eval(double rdt=-1.0, int count = 1) { OneDim::eval(npos, m_state->data(), m_xnew.data(), rdt, count); From a42110afde06b9095751c1baf8f70a77e69477ef Mon Sep 17 00:00:00 2001 From: pestre Date: Fri, 17 Jan 2025 13:35:01 +0100 Subject: [PATCH 19/98] Merge differences in interfaces directory Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: modified: interfaces/cython/cantera/_onedim.pxd modified: interfaces/cython/cantera/_onedim.pyx modified: interfaces/cython/cantera/composite.py modified: interfaces/cython/cantera/cti2yaml.py modified: interfaces/cython/cantera/kinetics.pxd modified: interfaces/cython/cantera/kinetics.pyx modified: interfaces/cython/cantera/onedim.py modified: interfaces/cython/setup.cfg.in modified: interfaces/python_minimal/setup.cfg.in modified: interfaces/python_sdist/SConscript modified: interfaces/python_sdist/pyproject.toml modified: interfaces/python_sdist/setup.cfg.in modified: interfaces/python_sdist/setup.py modified: interfaces/sourcegen/sourcegen/_orchestrate.py Author: pestre interactive rebase in progress; onto 7aec821a8 Last commands done (4 commands done): pick 08696f03b Change refine_grid param type to string pick 20ede9daf Merge differences in interfaces directory Next commands to do (10 remaining commands): pick 925ed423a Merge differences in samples directory pick 68a09c47e Merge differences in src directory You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. Changes to be committed: modified: interfaces/cython/cantera/_onedim.pxd modified: interfaces/cython/cantera/_onedim.pyx modified: interfaces/cython/cantera/composite.py modified: interfaces/cython/cantera/cti2yaml.py modified: interfaces/cython/cantera/kinetics.pxd modified: interfaces/cython/cantera/kinetics.pyx modified: interfaces/cython/cantera/onedim.py --- interfaces/cython/cantera/_onedim.pxd | 73 +- interfaces/cython/cantera/_onedim.pyx | 648 ++++++++++++++- interfaces/cython/cantera/composite.py | 5 + interfaces/cython/cantera/cti2yaml.py | 7 +- interfaces/cython/cantera/kinetics.pxd | 2 + interfaces/cython/cantera/kinetics.pyx | 7 + interfaces/cython/cantera/onedim.py | 1018 +++++++++++++++++++++++- 7 files changed, 1718 insertions(+), 42 deletions(-) diff --git a/interfaces/cython/cantera/_onedim.pxd b/interfaces/cython/cantera/_onedim.pxd index 3863e088096..8e77fe12f20 100644 --- a/interfaces/cython/cantera/_onedim.pxd +++ b/interfaces/cython/cantera/_onedim.pxd @@ -13,7 +13,7 @@ from .thermo cimport * cdef extern from "cantera/oneD/DomainFactory.h" namespace "Cantera": cdef shared_ptr[CxxDomain1D] CxxNewDomain1D "newDomain" ( - string, shared_ptr[CxxSolution], string) except +translate_exception + string, shared_ptr[CxxSolution], string, size_t) except +translate_exception cdef extern from "cantera/oneD/Domain1D.h": @@ -38,6 +38,7 @@ cdef extern from "cantera/oneD/Domain1D.h": double transient_atol(size_t) double grid(size_t) void setupGrid(size_t, double*) except +translate_exception + void setupGrid(size_t) except +translate_exception void setID(string) string& id() string domainType "type"() @@ -83,6 +84,8 @@ cdef extern from "cantera/oneD/Flow1D.h": void setBoundaryEmissivities(double, double) double leftEmissivity() double rightEmissivity() + void setThick(double) + double getThick() void solveEnergyEqn() void fixTemperature() cbool doEnergy(size_t) @@ -100,7 +103,61 @@ cdef extern from "cantera/oneD/Flow1D.h": double rightControlPointTemperature() except +translate_exception double rightControlPointCoordinate() except +translate_exception void setRightControlPointTemperature(double) except +translate_exception - + void setSections(size_t) + size_t getSections() + void setFlameletFlow() + string flowType() + + + void setPrecursors(vector[size_t]&) + void showSootSections() + void setSootSoret(cbool) + void enableCondensation(cbool) + cbool condensationEnabled() + void enableCoagulation(cbool) + cbool coagulationEnabled() + void setCollisionModel(string) + string getCollisionModel() + void enableRetroaction(cbool) + cbool retroactionEnabled() + void setSootMorphology(string) + cbool getSootMorphology() + void enableSurfaceGrowth(cbool) + cbool surfaceGrowthEnabled() + void enableOxidation(cbool) + cbool oxidationEnabled() + void enableSootRadiation(cbool) + cbool sootRadiationEnabled() + void enableSootSoret(cbool) + cbool sootSoretEnabled() + void enableTrashSection(double) + cbool trashSectionEnabled() + void finalizeSoot() + size_t getHaca() + void setHaca(size_t) + double getKazakovTad() + void setKazakovTad(double) + size_t getSootLoglevel() + void setSootLoglevel(size_t) + + vector[double]& vMin() + vector[double]& vMax() + vector[double]& vMean() + vector[double]& dMean() + vector[double]& sMean() + vector[double]& dCol() + vector[double]& aCol() + vector[double]& thetaSoot() + vector[double]& fractalPrefactor() + vector[double]& fractalDimension() + double sootPrimaryPart(size_t) + double sootPrimaryDiam(size_t) + double rhoSoot() + double getSootInception(size_t) + double getSootCondensation(size_t, size_t) + double getSootCoagulation(size_t, size_t) + double getSootSg(size_t, size_t) + double getSootOxidation(size_t, size_t) cdef extern from "cantera/oneD/Sim1D.h": cdef cppclass CxxSim1D "Cantera::Sim1D": @@ -115,7 +172,7 @@ cdef extern from "cantera/oneD/Sim1D.h": void setMaxTimeStepCount(int) int maxTimeStepCount() void getInitialSoln() except +translate_exception - void solve(int, cbool) except +translate_exception + void solve(int, string&) except +translate_exception void refine(int) except +translate_exception void setRefineCriteria(size_t, double, double, double, double) except +translate_exception vector[double] getRefineCriteria(int) except +translate_exception @@ -158,6 +215,13 @@ cdef extern from "cantera/oneD/Sim1D.h": cdef extern from "cantera/thermo/IdealGasPhase.h": cdef cppclass CxxIdealGasPhase "Cantera::IdealGasPhase" +cdef extern from "cantera/oneD/Flamelet.h": + cdef cppclass CxxFlamelet "Cantera::Flamelet" (CxxStFlow): + CxxFlamelet(CxxStFlow*) + double chiSt() #except +translate_exception + double zSt() #except +translate_exception + void setChiSt(double) #except +translate_exception + void setzSt(double) #except +translate_exception cdef class Domain1D: cdef shared_ptr[CxxDomain1D] _domain @@ -175,6 +239,9 @@ cdef class ReactingSurface1D(Boundary1D): cdef class FlowBase(Domain1D): cdef CxxFlow1D* flow +cdef class FlameletFlow(_FlowBase): + cdef CxxFlamelet* flamelet + cdef class Sim1D: cdef CxxSim1D* sim cdef readonly object domains diff --git a/interfaces/cython/cantera/_onedim.pyx b/interfaces/cython/cantera/_onedim.pyx index e7335ab0a1a..4cc2ecdc033 100644 --- a/interfaces/cython/cantera/_onedim.pyx +++ b/interfaces/cython/cantera/_onedim.pyx @@ -306,11 +306,14 @@ cdef class Boundary1D(Domain1D): self.boundary = NULL else: self._domain = CxxNewDomain1D( - stringify(self._domain_type), phase._base, stringify(name)) + stringify(self._domain_type), phase._base, stringify(name), + #add kwargs if kwargs provided + kwargs['sections'] if 'sections' in kwargs else 0, + ) self.domain = self._domain.get() self.boundary = self.domain - def __init__(self, phase, name=None): + def __init__(self, phase, name=None, **kwargs): if self.boundary is NULL: raise TypeError("Can't instantiate abstract class Boundary1D.") Domain1D.__init__(self, phase, name=name) @@ -415,6 +418,21 @@ cdef class ReactingSurface1D(Boundary1D): gas phase. """ _domain_type = "reacting-surface" + def __cinit__(self, _SolutionBase phase, *args, name="", **kwargs): + # once legacy path is removed, the parent __cinit__ is sufficient + self.legacy = phase.phase_of_matter == "gas" + if self.legacy: + # legacy pathway - deprecation is handled in __init__ + self.surf = new CxxReactingSurf1D() + self.domain = (self.surf) + else: + self._domain = CxxNewDomain1D(stringify(self._domain_type), phase._base, stringify(name), + #add kwargs if kwargs provided + kwargs['sections'] if 'sections' in kwargs else 0, + ) + self.domain = self._domain.get() + self.surf = self.domain + self.boundary = (self.surf) def __init__(self, _SolutionBase phase, name=None): gas = None @@ -447,7 +465,10 @@ cdef class FlowBase(Domain1D): """ Base class for 1D flow domains """ def __cinit__(self, _SolutionBase phase, *args, name="", **kwargs): self._domain = CxxNewDomain1D( - stringify(self._domain_type), phase._base, stringify(name)) + stringify(self._domain_type), phase._base, stringify(name), + #add kwargs if kwargs provided + kwargs['sections'] if 'sections' in kwargs else 0, + ) self.domain = self._domain.get() self.flow = self.domain @@ -591,6 +612,543 @@ cdef class FlowBase(Domain1D): data[j] = self.flow.radiativeHeatLoss(j) return data + # BEGIN of soot API + + property soot_loglevel: + """ + Outputs soot sections informations. + + :param None + + :return None + """ + def __set__(self, loglevel): + self.flow.setSootLoglevel(loglevel) + def __get__(self): + return self.flow.getSootLoglevel() + + property soot_sections: + """ + Returns number of soot sections. + + :param None + + :return int : + Number of sections + """ + def __set__(self, nSec): + #self.flow.setSections(nSec) + raise KeyError ('/!\ SOOT ERROR : You cannot set sections number this way !') + def __get__(self): + return self.flow.getSections() + + property soot_precursors: + """ + Sets soot precursors. + + : param precrursors = list[str] : + precursors names (in mechanism nomenclature) + + : return None + """ + def __set__(self, precursors): + cdef vector[size_t] id_precursors + if isinstance(precursors, str): + precursors = [precursors] + av_precursors = [precursor for precursor in precursors if precursor in self.gas.species_names] + id_precursors = [self.component_index(precursor) for precursor in av_precursors] + if len(id_precursors) == 0: + raise KeyError('/!\ SOOT ERROR : No acceptable precursors !') + else: + self.flow.setPrecursors(id_precursors) + def __get__(self): + raise NotImplementedError('Getter not implemented yet.') + + property soot_trash_section: + """ + Gets / sets trash section size (<0 if disabled). + + : param trash_section = float : + trash section size [m] + + : return bool : + trash section enabled + """ + def __set__(self, trash_section): + self.flow.enableTrashSection(trash_section) + def __get__(self): + return self.flow.trashSectionEnabled() + + property soot_do_retroaction: + """ + Gets / sets whether retroaction on gas phase is activated or not. + + : param do_retroaction = bool : + reatroaction enabled + + : return bool : + retroaction enabled + """ + def __set__(self, do_retroaction): + self.flow.enableRetroaction(do_retroaction) + def __get__(self): + return self.flow.retroactionEnabled() + + property soot_do_condensation: + """ + Gets / sets whether dimer condensation on soot particles is activated or not. + + : param do_condensation = bool : + condensation enabled + + : return bool : + condensation enabled + """ + def __set__(self, do_condensation): + self.flow.enableCondensation(do_condensation) + def __get__(self): + return self.flow.condensationEnabled() + + property soot_do_coagulation: + """ + Gets / sets whether coagulation between soot particles is activated or not. + + : param do_coagulation = bool : + coagulation enabled + + : return bool : + coagulation enabled + """ + def __set__(self, do_coagulation): + self.flow.enableCoagulation(do_coagulation) + def __get__(self): + return self.flow.coagulationEnabled() + + property soot_morphology: + """ + """ + def __set__(self, morphology_model): + self.flow.setSootMorphology(stringify(morphology_model)) + def __get__(self): + self.flow.getSootMorphology() + + property soot_collision_model: + """ + Gets / sets whether coagulation between soot particles is activated or not. + + : return str : + coagulation enabled + """ + def __set__(self, collision_model): + self.flow.setCollisionModel(stringify(collision_model)) + def __get__(self): + return self.flow.getCollisionModel() + + property soot_haca: + """ + Gets / sets haca model. + : param haca_model = str or int : + "mauss" : 1 + "blanquart" : 2 + "kazakov" : 3 + "mauss tuned" : 11 + : return int : + haca model + """ + def __set__(self, haca_model): + haca = 0 + if haca_model in [1, 'mauss']: + haca = 1 + if haca_model in [11, 'mauss tuned']: + haca = 11 + elif haca_model in [2, 'blanquart']: + haca = 2 + elif haca_model in [3, 'kazakov']: + haca = 3 + if haca not in [1,11,2,3]: + raise KeyError ('/!\ SOOT ERROR : haca_model must be mauss(1), mauss tuned(11), blanquart(2), or kazakov(3)') + self.flow.setHaca(haca) + def __get__(self): + return self.flow.getHaca() + + property soot_do_surface_growth: + """ + Gets / sets whether acetylene condensation on soot particles is activated or not. + + : param do_surface_growth = bool : + surface growth enabled + + : return bool : + surface growth enabled + """ + def __set__(self, do_surface_growth): + self.flow.enableSurfaceGrowth(do_surface_growth) + def __get__(self): + return self.flow.surfaceGrowthEnabled() + + property soot_do_oxidation: + """ + Gets / sets whether soot particles oxidation is activated or not. + + : param do_oxidation = bool : + oxidation enabled + + : return bool : + oxidation enabled + """ + def __set__(self, do_oxidation): + self.flow.enableOxidation(do_oxidation) + def __get__(self): + return self.flow.oxidationEnabled() + + property kazakov_flame_temperature : + """ + Gets / sets flame temperature used as reference for Kazakov's surface reactions model + + : param adiabatic_temperature = double : + adiabatic temperature (K) + + : return double : + adiabatic temperature (K) + """ + def __set__(self, tad): + self.flow.setKazakovTad(tad) + def __get__(self): + return self.flow.getKazakovTad() + + property soot_do_radiation: + """ + Gets / sets whether soot particles radiative heat losses are considered or not. + + : param do_soot_radiation = bool : + soot radiation enabled + + : return bool : + soot radiation enabled + """ + def __set__(self,do_soot_radiation): + if not self.energy_enabled and do_soot_radiation: + if self.soot_loglevel >= 1: + print(' ') + print('SOOT INFO : Energy equation is disabled') + print(" ==> RHL won't be computed") + self.radiation_enabled = False + if not self.radiation_enabled and do_soot_radiation: + if self.soot_loglevel >= 1: + print(' ') + print('SOOT INFO : RHL were disabled') + print(" ==> RHL now enabled") + self.radiation_enabled = True + self.flow.enableSootRadiation(do_soot_radiation) + def __get__(self): + return self.flow.sootRadiationEnabled() + + property soot_do_soret: + """ + Gets / sets whether soret effect is computed on soot particles. + + : param do_soot_soret = bool : + soot soret enabled + + : return bool : + soot soret enabled + """ + def __set__(self,do_soot_soret): + self.flow.enableSootSoret(do_soot_soret) + def __get__(self): + return self.flow.sootSoretEnabled() + + property soot_finalize: + """ + Generates sections, collision matrix and loads surface reactions constants if needed. + To be used after modifications on : collision model, precursors, oxidation or surface growth. + + : param None + + : return None + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return self.flow.finalizeSoot() + + + property sections_min_v: + """" + Gets soot sections minimal volumes. + + : param None + + : return (sections) numpy array : + minimal volume of each section [m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.vMin()) + + property sections_max_v: + """" + Gets soot sections maximal volumes. + + : param None + + : return (sections) numpy array : + maximal volume of each section [m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.vMax()) + + property sections_mean_v: + """" + Gets soot sections mean volumes. + + : param None + + : return (sections) numpy array : + mean volume of each section [m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.vMean()) + + property sections_mean_d: + """" + Gets soot sections mean diameters. + + : param None + + : return (sections) numpy array : + mean diameter of each section [m] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.dMean()) + + property sections_col_d: + """" + Gets soot sections colision diameters. + + : param None + + : return (sections) numpy array : + colision diameter of each section [m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.dCol()) + + property sections_col_a: + """" + Gets soot sections collisional cross-section + + : param None + + : return (sections) numpy array : + mean section of each section [m-2] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.aCol()) + + property sections_mean_s: + """" + Gets soot sections surface area + + : param None + + : return (sections) numpy array : + mean section of each section [m-2] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.sMean()) + + property sections_fractal_prefactor: + """ + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.fractalPrefactor()) + + property sections_fractal_dimension: + """ + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.fractalDimension()) + + property sections_theta: + """ + Gets soot sections theta value (fractality). + + : param None + + : return (sections) numpy array : + theta factor of each section + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return np.asarray(self.flow.thetaSoot()) + + property soot_density: + """" + Gets soot density. + + : param None + + : return float : + soot density [kg.m-3] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + return self.flow.rhoSoot() + + # property soot_dump_inception: + # """ + # Gets soot nucleation source terms. + + # : param None + + # : return (sections x points) numpy array : + # inception source terms [s-1] + # """ + # def __set__(self, dummy): + # raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + # def __get__(self): + # data = np.zeros((self.soot_sections, self.n_points)) + # for j in range(self.n_points): + # data[0,j] = self.flow.getSootInception(j) + # return data + + property soot_dump_condensation: + """ + Gets soot condensation source terms. + + : param None + + : return (sections x points) numpy array : + condensation source terms [s-1] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty((self.soot_sections, self.n_points)) + for k in range(self.soot_sections): + for j in range(self.n_points): + data[k,j] = self.flow.getSootCondensation(k,j) + return data + + property soot_dump_coagulation: + """ + Gets soot coagulation source terms. + + : param None + + : return (sections x points) numpy array : + coagulation source terms [s-1] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty((self.soot_sections, self.n_points)) + for k in range(self.soot_sections): + for j in range(self.n_points): + data[k,j] = self.flow.getSootCoagulation(k,j) + return data + + property soot_dump_surface_growth: + """ + Gets soot surface growth source terms. + + : param None + + : return (sections x points) numpy array : + surface growth source terms [s-1] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty((self.soot_sections, self.n_points)) + for k in range(self.soot_sections): + for j in range(self.n_points): + data[k,j] = self.flow.getSootSg(k,j) + return data + + property soot_dump_oxidation: + """ + Gets soot oxidation source terms. + + : param None + + : return (sections x points) numpy array : + oxidation source terms [s-1] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty((self.soot_sections, self.n_points)) + for k in range(self.soot_sections): + for j in range(self.n_points): + data[k,j] = self.flow.getSootOxidation(k,j) + return data + + property sections_np: + """ + Gets number of primary particles per aggregate. + + : param None + + : return (sections) numpy array : + number of primary particles per aggregate + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty(self.soot_sections) + for k in range(self.soot_sections): + data[k] = self.flow.sootPrimaryPart(k) + return data + + property sections_dp: + """ + Gets primary particles diameter. + + : param None + + : return (sections) numpy array : + primary particles diameter [m] + """ + def __set__(self, dummy): + raise KeyError ('/!\ SOOT ERROR : You cannot set such data !') + def __get__(self): + data = np.empty(self.soot_sections) + for k in range(self.soot_sections): + data[k] = self.flow.sootPrimaryDiam(k) + return data + + # END of soot API + + property thick: + """ + Thickening that will be applied [JW] + """ + def __set__(self, thickness): + self.flow.setThick(thickness) + def __get__(self): + return self.flow.getThick() + def set_free_flow(self): """ Set flow configuration for freely-propagating flames, using an internal @@ -606,6 +1164,25 @@ cdef class FlowBase(Domain1D): """ self.flow.setAxisymmetricFlow() + def set_flamelet_flow(self): + """ + Set flow configuration for flamelet solutions, using specified inlet + mass fluxes. + """ + self.flow.setFlameletFlow() + + property flow_type: + """ + Return the type of flow domain being represented, either "Free Flame" or + "Axisymmetric Stagnation". + + .. deprecated:: 3.0 + + Method to be removed after Cantera 3.0; superseded by `domain_type`. + """ + def __get__(self): + return pystr(self.flow.flowType()) + @property def type(self): """ @@ -695,6 +1272,37 @@ cdef class FreeFlow(FlowBase): _domain_type = "free-flow" +cdef class FlameletFlow(FlowBase): + """A flamelet flow domain. The equations solved are standard equations for + adiabatic one-dimensional flow in Z-space. The solution variables are: + + *T* + temperature + + *Y_k* + species mass fractions + + """ + _domain_type = "flamelet-flow" + + def __cinit__(self, _SolutionBase phase, *args, name="", **kwargs): + self.flamelet = self.flow + + property ChiSt: + """ ChiSt """ + def __get__(self): + return self.flamelet.chiSt() + def __set__(self, val): + self.flamelet.setChiSt(val) + + property ZSt: + """ ZSt """ + def __get__(self): + return self.flamelet.zSt() + def __set__(self, val): + self.flamelet.setzSt(val) + + cdef class UnstrainedFlow(FlowBase): r"""An unstrained flow domain. The equations solved are standard equations for adiabatic one-dimensional flow. The solution variables are: @@ -983,8 +1591,8 @@ cdef class Sim1D: def show(self): """ print the current solution. """ - if not self._initialized: - self.set_initial_guess() + # if not self._initialized: + # self.set_initial_guess() self.sim.show() def set_time_step(self, stepsize, n_steps): @@ -1036,7 +1644,7 @@ cdef class Sim1D: """ return False - def solve(self, loglevel=1, refine_grid=True, auto=False): + def solve(self, loglevel=1, refine_grid='refine', auto=False): """ Solve the problem. @@ -1044,7 +1652,8 @@ cdef class Sim1D: integer flag controlling the amount of diagnostic output. Zero suppresses all output, and 5 produces very verbose output. :param refine_grid: - if True, enable grid refinement. + if "refine", enable grid refinement, + if "remesh", remeshing of the grid. :param auto: if True, sequentially execute the different solution stages and attempt to automatically recover from errors. Attempts to first solve on the initial grid with energy enabled. If that does not @@ -1055,10 +1664,19 @@ cdef class Sim1D: will be calculated. """ + if type(refine_grid) == bool: + print("WARNING : Keyword status has been changed to string to enable the remesh feature") + print("True --> 'refine' or 'remesh'") + print("False --> 'disabled'") + if refine_grid: + refine_grid = 'refine' + else: + refine_grid = 'disabled' + if not auto: if not self._initialized: self.set_initial_guess() - self.sim.solve(loglevel, refine_grid) + self.sim.solve(loglevel, stringify(refine_grid)) return def set_transport(multi): @@ -1132,7 +1750,7 @@ cdef class Sim1D: log('Solving on {} point grid with energy equation enabled', N) self.energy_enabled = True try: - self.sim.solve(loglevel, False) + self.sim.solve(loglevel, stringify('disabled')) solved = True except CanteraError as e: log(str(e)) @@ -1154,7 +1772,7 @@ cdef class Sim1D: log('Initial solve failed; Retrying with energy equation disabled') self.energy_enabled = False try: - self.sim.solve(loglevel, False) + self.sim.solve(loglevel, stringify('disabled')) solved = True except CanteraError as e: log(str(e)) @@ -1170,7 +1788,7 @@ cdef class Sim1D: log('Solving on {} point grid with energy equation re-enabled', N) self.energy_enabled = True try: - self.sim.solve(loglevel, False) + self.sim.solve(loglevel, stringify('disabled')) solved = True except CanteraError as e: log(str(e)) @@ -1182,11 +1800,11 @@ cdef class Sim1D: restore_tolerances() raise e - if solved and not self.extinct() and refine_grid: + if solved and not self.extinct() and refine_grid != 'disabled': # Found a non-extinct solution on the fixed grid log('Solving with grid refinement enabled') try: - self.sim.solve(loglevel, True) + self.sim.solve(loglevel, stringify('refine')) solved = True except CanteraError as e: log(str(e)) @@ -1205,7 +1823,7 @@ cdef class Sim1D: if self.extinct(): log('Flame is extinct on {} point grid', N) - if not refine_grid: + if refine_grid == 'disabled': break if not solved: @@ -1225,7 +1843,7 @@ cdef class Sim1D: # Final call with expensive options enabled if have_user_tolerances or solve_multi or soret_doms: - self.sim.solve(loglevel, refine_grid) + self.sim.solve(loglevel, stringify('refine')) def refine(self, loglevel=1): """ diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py index bc6de6fb0f7..4b5fe32d4fc 100644 --- a/interfaces/cython/cantera/composite.py +++ b/interfaces/cython/cantera/composite.py @@ -7,6 +7,11 @@ import csv as _csv import importlib.metadata import warnings +import shutil +import filecmp +import subprocess +import time +import os _pandas = None diff --git a/interfaces/cython/cantera/cti2yaml.py b/interfaces/cython/cantera/cti2yaml.py index 9c7d3703d9c..b8a1847cdfb 100644 --- a/interfaces/cython/cantera/cti2yaml.py +++ b/interfaces/cython/cantera/cti2yaml.py @@ -110,12 +110,17 @@ def applyUnits(value): 'GasKinetics': 'gas', 'Interface': 'surface', 'Edge': 'edge', + 'AVBP': 'AVBP', 'Mix': 'mixture-averaged', + 'mixture-averaged': 'mixture-averaged', 'Multi': 'multicomponent', + 'multicomponent': 'multicomponent', 'Ion': 'ionized-gas', 'molar_volume': 'species-molar-volume', 'solvent_volume': 'solvent-molar-volume', - 'unity': 'unity' + 'unity': 'unity', + 'UnityLewis': 'unity', + 'custom': 'custom', } # constants that can be used in .cti files diff --git a/interfaces/cython/cantera/kinetics.pxd b/interfaces/cython/cantera/kinetics.pxd index e341f762ed1..426e379ee33 100644 --- a/interfaces/cython/cantera/kinetics.pxd +++ b/interfaces/cython/cantera/kinetics.pxd @@ -40,6 +40,8 @@ cdef extern from "cantera/kinetics/Kinetics.h" namespace "Cantera": void invalidateCache() except +translate_exception void resizeReactions() + void closeDynamicLib() except +translate_exception + shared_ptr[CxxReaction] reaction(size_t) except +translate_exception double reactantStoichCoeff(int, int) except +translate_exception double productStoichCoeff(int, int) except +translate_exception diff --git a/interfaces/cython/cantera/kinetics.pyx b/interfaces/cython/cantera/kinetics.pyx index 43168f365a1..3da95917668 100644 --- a/interfaces/cython/cantera/kinetics.pyx +++ b/interfaces/cython/cantera/kinetics.pyx @@ -137,6 +137,13 @@ cdef class Kinetics(_SolutionBase): if not 0 <= n < self.n_total_species: raise ValueError("Kinetics Species index ({0}) out of range".format(n)) + def reset_custom(self): + """ + Function calling the dlclose in CustomKinetics + in order to close the dynamic library (handle) + """ + self.kinetics.closeDynamicLib() + def kinetics_species_index(self, species, int phase=0): """ The index of species ``species`` of phase ``phase`` within arrays returned diff --git a/interfaces/cython/cantera/onedim.py b/interfaces/cython/cantera/onedim.py index e02af7c3b34..4bdd5cda10b 100644 --- a/interfaces/cython/cantera/onedim.py +++ b/interfaces/cython/cantera/onedim.py @@ -5,6 +5,8 @@ from pathlib import Path import warnings import numpy as np +import csv as _csv +import os from ._cantera import * from .composite import Solution, SolutionArray @@ -25,12 +27,48 @@ def __init__(self, domains, gas, grid=None): if grid is None: grid = np.linspace(0.0, 0.1, 6) self.flame.grid = grid + # self.flame.soot_sections = sections super().__init__(domains) #: The `Solution` object representing the species and reactions in the flame self.gas = gas self.flame.P = gas.P + def other_components(self, domain=None): + """ + The method returns simulation components that are specific to a class + derived from `FlameBase` or a specific ``domain`` within the `FlameBase` + simulation object. Entries may include: + + * ``grid``: grid point positions along the flame [m] + * ``velocity``: normal velocity [m/s] + * ``spread_rate``: tangential velocity gradient [1/s] + * ``lambda``: radial pressure gradient [N/m^4] + * ``eField``: electric field strength + + :param domain: + Index of a specific domain within the `Sim1D.domains` + list. The default is to return other columns of the `Sim1D` object. + + .. deprecated:: 3.0 + + Method to be removed after Cantera 3.0. After moving SolutionArray HDF + export to the C++ core, this method is unused. + """ + warnings.warn("FlameBase.other_components: Method to be removed after " + "Cantera 3.0 (unused).", DeprecationWarning, stacklevel=2) + if domain is None: + return self._other + + dom = self.domains[self.domain_index(domain)] + if isinstance(dom, Inlet1D): + return tuple([e for e in self._other + if e not in {'grid', 'lambda', 'eField'}]) + elif isinstance(dom, (FreeFlow, AxisymmetricFlow, IdealGasFlow, FlameletFlow)): + return self._other + else: + return () + def set_refine_criteria(self, ratio=10.0, slope=0.8, curve=0.8, prune=0.0): """ Set the criteria used for grid refinement. @@ -250,6 +288,476 @@ def boundary_emissivities(self, epsilon): if len(epsilon) != 2: raise ValueError("Boundary emissivities must both be set at the same time.") self.flame.boundary_emissivities = epsilon[0], epsilon[1] + + # BEGIN of soot API + + def soot_setup(self, precursors=["A2"], condensation=True, coagulation=True, morphology='rodrigues', collision_model='rodrigues', + retroaction=True, haca_model = 'mauss', kazakov_temperature = 0, + surface_growth=True, oxidation=True, radiation=True, trash_section=-1.0, + loglevel = 2): + """ + Sets soot computation up. + + : param precursors = list[str] : + list of precursors in mechanism nomenclature (default : ['A2']) + : param condensation = bool : + condensation enabled (default : True) + : param coagulation = bool : + coagulation enabled (default : True) + : param retroaction = bool : + retroaction on gas phase enabled (default : True) + : param collision_model = str : + Collision model :sphere, rodrigues or thajudeen (default : rodrigues) + : param haca_model = string or int : + haca_model to use (default : Mauss) + 1 : Mauss + 11 : Mauss (tuned as Guo 2016) + 2 : Blanquart + 3 : Kazakov + : param suface_growth = bool : + surface growth enabled (default : True) + : param oxidation = bool : + oxidation enabled (default : True) + : param kazakov = double : + adiabatic flame temperature, only for Kazakov's haca model (default : 0 (automatically computed)) + : param radiation = bool : + soot radiative heat losses enabled (default : True) + : param trash_section = float : + trash section size, <=0 if no trash section (default : -1.0) + : param show_sections = bool : + show sections informations (default : False) + + : return None + """ + if self.flame.soot_sections == 0: + raise CanteraError('/!\ SOOT ERROR : cannot set sections properties (no sections)') + self.flame.soot_loglevel = loglevel + # Impacts geomery, need to use "flame.soot_finalize" + self.flame.soot_precursors = precursors + self.flame.soot_trash_section = trash_section + self.flame.soot_morphology = morphology + self.flame.soot_collision_model = collision_model + # Processes, need to use "flame.soot_finalize" + self.flame.soot_haca = haca_model + if self.flame.soot_haca == 3 : + if kazakov_temperature > 0: + self.flame.kazakov_flame_temperature = kazakov_temperature + else: + self.flame.kazakov_flame_temperature = self.adiabatic_flame_temperature + self.flame.soot_do_surface_growth = surface_growth + self.flame.soot_do_oxidation = oxidation + # Processes, do not impact geometry + self.flame.soot_do_retroaction = retroaction + self.flame.soot_do_condensation = condensation + self.flame.soot_do_coagulation = coagulation + self.flame.soot_do_radiation = radiation + self.flame.soot_finalize + + @property + def soot_Y(self): + """ + Gets soot mass fraction. + + : param None + + : return (sections x points) numpy array : + soot mass fraction for each section at each point + """ + data = np.empty((self.flame.soot_sections, self.flame.n_points)) + ns = self.flame.soot_sections + for k in range(ns): + data[k,:] = self.profile(self.flame, 'Ys'+str(k)) + return data + + @property + def soot_Q(self): + """ + + """ + Ys = self.soot_Y + density = self.density + soot_density = self.flame.soot_density + + data = np.empty(np.shape(Ys)) + for section in range(self.flame.soot_sections): + data[section,:] = density / soot_density * Ys[section,:] + + return data + + @property + def soot_q(self): + """" + Gets the volume distribution of the soot volume fraction + + : param None + + : return (sections x points) numpy array : + volume distribution of the soot volume fraction for each section at each point [m-3] + """ + Q = self.soot_Q + vMin = self.flame.sections_min_v + vMax = self.flame.sections_max_v + + data = np.empty(np.shape(Q)) + for section in range(self.flame.soot_sections): + data[section, :] = Q[section,:] / (vMax[section] - vMin[section]) + + return data + + @property + def soot_N(self): + """" + Gets the particles number density relative to each section + + : param None + + : return (sections x points) numpy array : + particles number density for each section at each point [m-3] + """ + q = self.soot_q + vMin = self.flame.sections_min_v + vMax = self.flame.sections_max_v + + data = np.empty(np.shape(q)) + for section in range(self.flame.soot_sections): + data[section, :] = q[section, :] * np.log(vMax[section]/vMin[section]) + + return data + + def soot_fv(self, **kwargs): + """ + Gets the soot volume fraction. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + soot volume fraction at each point + """ + first, last = self.getSectionBounds(**kwargs) + + data = np.sum(self.soot_Q[first:last, :], axis=0) + + return data + + def soot_Np(self, **kwargs): + """ + Gets the soot particles number density. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + soot particles number density at each point [m-3] + """ + first, last = self.getSectionBounds(**kwargs) + + data = np.sum(self.soot_N[first:last,:], axis=0) + + return data + + def soot_psdf(self, HAB, out='dNp/dlogd'): + """ + Gets the particles size distribution function at specified HAB. + + : param HAB = float : + Height Above the Burner surface at which PSDF shall be taken [m] + : param out = str : + Output to be computed : 'Np', 'Q' or 'dNp/dlogd' (default) + + : return (sections) numpy array : + particle size distribution for each section at specified HAB [m-3] + """ + if out in ['Q', 'dNp/dlogd', 'dV/dlogd']: + vals = self.soot_q + elif (out == 'Np'): + vals = self.soot_N + else: + raise KeyError("PSDF type should be 'Np', 'Q' or 'dNp/dlogd', not " + out) + if out == 'dV/dlogd': + vals = np.multiply(vals, np.pi * self.soot_mean_d ** 3 / 6) + z = self.flame.grid + data = np.asarray([np.interp(HAB,z,vals[k,:]) for k in range(self.flame.soot_sections)]) + if out=='dNp/dlogd': + data *= 3/(3-self.flame.sections_theta) + + return data + + def soot_mean_d(self, **kwargs): + """" + Gets soot particles mean diameter. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + mean diameter of soot particles at each point [m] + """ + first, last = self.getSectionBounds(**kwargs) + Ys = self.soot_Y[first:last,:] + dMean = self.flame.sections_mean_d[first:last] + data = [sum(Ys[:,i]*dMean)/sum(Ys[:,i]) for i in range(self.flame.n_points)] + return np.asarray(data) + + def soot_mean_s(self, **kwargs): + """" + Gets soot particles mean sections. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + mean section of soot particles at each point [m] + """ + first, last = self.getSectionBounds(**kwargs) + Ys = self.soot_Y[first:last,:] + sMean = self.flame.sections_mean_s[first:last] + data = [sum(Ys[:,i]*sMean)/sum(Ys[:,i]) for i in range(self.flame.n_points)] + return np.asarray(data) + + def soot_mean_v(self, **kwargs): + """" + Gets soot particles mean volumes. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + mean volume of soot particles at each point [m^3] + """ + first, last = self.getSectionBounds(**kwargs) + Ys = self.soot_Y[first:last,:] + vMean = self.flame.sections_mean_v[first:last] + data = [sum(Ys[:,i]*vMean)/sum(Ys[:,i]) for i in range(self.flame.n_points)] + return np.asarray(data) + + def soot_np(self, **kwargs): + """ + Gets number of primary particles per aggregate. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + number of primary particles per aggregate + """ + first, last = self.getSectionBounds(**kwargs) + Ys = self.soot_Y[first:last,:] + npart = self.flame.sections_np[first:last] + data = [max(1, sum(Ys[:,i]*npart)/sum(Ys[:,i])) if sum(Ys[:,i])>0 else None for i in range(self.flame.n_points)] + + return np.asarray(data) + + def soot_dp(self, **kwargs): + """ + Gets primary particles diameter. + + : param first = int : + > 0 :index of first section to take into account (starting at 0) + : param last = int : + > 0 : index of last section to take into account (starting at 0) + < 0 : number of sections to remove, starting from the last one + : param min = float : + mean diameter of first section to take into account [m] + : param max = float : + mean diameter of last section to take into account [m] + + : return (points) numpy array : + mean primary particles diameter [m] + """ + first, last = self.getSectionBounds(**kwargs) + + dpart = self.flame.sections_dp[first:last] * 1e7 + Ys = self.soot_Y[first:last,:] + data = [max(dpart[0], sum(Ys[:,i]*dpart)/sum(Ys[:,i])) if sum(Ys[:,i])>0 else None for i in range(self.flame.n_points)] + + return np.asarray(data) + + @property + def soot_source(self): + """ + Gets soot source terms. + + : param None + + : return dictionnary of (sections x points) numpy arrays : + soot source terms [s-1] + keys : + ['inception', 'condensation', 'coagulation', 'surface_growth', 'oxidation'] + """ + soot_source = {} + soot_source['inception'] = self.flame.soot_dump_inception + soot_source['condensation'] = self.flame.soot_dump_condensation + soot_source['coagulation'] = self.flame.soot_dump_coagulation + soot_source['surface_growth'] = self.flame.soot_dump_surface_growth + soot_source['oxidation'] = self.flame.soot_dump_oxidation + + return soot_source + + def soot_mcac_input(self, output='CANTERA2MCAC.dat', d_min=5e-9, fv_min=1e-10, x_max=0, t_max=0): + """ + Generates inputs for flame coupling with MCAC + + : param output : Output file to write the MCAC input file on + : param min_diam : Diameter of the smallest particle considered in MCAC + : param min_fv : Minimal volume fraction to consider (remove flame foot) + : param max_x : Maximal HAB to consider (remove flame end) (starting from the end if max_x < 0) + : param max_t : Maximal residence time to consider (remove flame end) (starting from the end if max_t < 0) + + : return : Dict containing MCAC inputs + """ + + ########################## + # RECOVER LOWER BOUNDARY # + ########################## + # Soot particles with diameter < min_diam are not considered in MCAC + first_section = self.getSectionBounds(d_min=d_min)[0] + if first_section == None: + first_section = 0 + + ########################## + # RECOVER RESIDENCE TIME # + ########################## + velocity = np.where(self.u == 0, 1e-10, self.u) # To avoid integration errors + time = [np.trapz(1/velocity[:idx+1], self.grid[:idx+1]) for idx in range(self.flame.n_points)] + + ####################### + # RECOVER SOURCE TERM # + ####################### + # Get source term for each section at each point + soot_source = self.soot_source + source_terms = soot_source['inception'][first_section:,:] + soot_source['surface_growth'][first_section:,:] + soot_source['oxidation'][first_section:,:] + soot_source['condensation'][first_section:,:] + soot_source['coagulation'][first_section:,:] + source_term = np.sum(source_terms, axis=0) + + # Nucleation is the mass entering the first section + nucleation = np.clip(source_terms[0,:], 0., None) + # Surface reactions are the rest + surface_reactions = source_term - nucleation + + # Recover the expected overall sourceterm dfv/dt to correct (don't ) + fv = self.soot_fv(first=first_section) + target_source_term = np.gradient(fv, time) + correction_factor = np.divide(target_source_term, source_term, out=np.zeros(source_term.shape, dtype=float), where=source_term!=0.) + nucleation *= correction_factor * self.flame.soot_density + surface_reactions *= correction_factor * self.flame.soot_density + + #################### + # RECOVER THE REST # + #################### + temperature = self.T + mean_diameter = self.soot_mean_d(first=first_section) + + ############# + # CLIP DATA # + ############# + # Clip flame beggining (no soot) + first_point = next(idx for idx,val in enumerate(fv) if val >= fv_min) + # Clip flame end (long residence times possible) + if x_max <= 0: + x_max = self.grid[-1] + x_max + last_point_x = next(idx for idx,val in enumerate(self.grid) if val >= x_max) + if t_max <= 0: + t_max = time[-1] + t_max + last_point_t = next(idx for idx,val in enumerate(time) if val >= t_max) + last_point = min(last_point_x, last_point_t) + + #################### + # WRITE INPUT FILE # + #################### + if output is not None: + with open(output, 'w') as f: + for index in range(first_point, last_point+1): + f.write('%.4e %.4e %.4e %.4e 0. %.4e %.4e\n' % (time[index], temperature[index], fv[index], mean_diameter[index], surface_reactions[index], nucleation[index])) + + return {'time':time, 'temperature':temperature, 'fv':fv, 'mean_diameter':mean_diameter, 'surface_reactions':surface_reactions, 'nucleation':nucleation} + + + def getSectionBounds(self, **kwargs): + """ + Gets index of sections given their mean diameter + :param first: Index of the first section to consider + :param d_min: Mean diameter of the first section to consider [m] + :param v_min: Mean volume of the first section to consider [m^3] + :param last: Index of the first section to consider + :param d_max: Mean diameter of the last section to consider [m] + :param v_max: Mean volume of the last section to consider [m^3] + """ + first = None + last = None + + if 'first' in kwargs and 'min' in kwargs : + raise KeyError('Cannot specify both section indice and diameter') + elif 'first' in kwargs : + first = kwargs['first'] + elif 'd_min' in kwargs: + dMean = self.flame.sections_mean_d + if kwargs['d_min'] > dMean[0] and kwargs['d_min'] < dMean[-1]: + first = next(idx for idx,val in enumerate(dMean) if val >= kwargs['d_min']) + elif 'v_min' in kwargs: + vMean = self.flame.sections_mean_v + if kwargs['v_min'] > vMean[0] and kwargs['v_min'] < vMean[-1]: + first = next(idx for idx,val in enumerate(vMean) if val >= kwargs['v_min']) + + if 'last' in kwargs and 'max' in kwargs: + raise KeyError('Cannot specify both section indice and diameter') + elif 'last' in kwargs: + last = kwargs['last'] + if last > 0 : + last += 1 + elif 'd_max' in kwargs: + dMean = self.flame.sections_mean_d + if kwargs['d_max'] > dMean[0] and kwargs['d_max'] < dMean[-1]: + last = next(idx for idx,val in enumerate(dMean) if val > kwargs['d_max']) + elif 'v_max' in kwargs: + vMean = self.flame.sections_mean_v + if kwargs['v_max'] > vMean[0] and kwargs['v_max'] < vMean[-1]: + last = next(idx for idx,val in enumerate(vMean) if val > kwargs['v_max']) + + return first, last + + # END of soot API @property def grid(self): @@ -398,6 +906,115 @@ def set_gas_state(self, point): self.gas.set_unnormalized_mass_fractions(Y) self.gas.TP = self.value(self.flame, 'T', point), self.P + def write_csv(self, filename, species='X', quiet=True, normalize=True): + """ + Write the velocity, temperature, density, and species profiles + to a CSV file. + + :param filename: + Output file name + :param species: + Attribute to use obtaining species profiles, for example ``X`` for + mole fractions or ``Y`` for mass fractions. + :param normalize: + Boolean flag to indicate whether the mole/mass fractions should + be normalized. + + .. deprecated:: 3.0 + + Method to be removed after Cantera 3.0; superseded by `save`. + """ + warnings.warn("FlameBase.write_csv: Superseded by 'save'. To be removed " + "after Cantera 3.0.", DeprecationWarning, stacklevel=2) + + # save data + cols = ('extra', 'T', 'D', species) + self.to_array(normalize=normalize).write_csv(filename, cols=cols) + + if not quiet: + print("Solution saved to '{0}'.".format(filename)) + + def write_AVBP(self, filename, quiet=True): + """ + Instanciate a solution for can2av + to a CSV file. + + :param filename: + Output file name + """ + II = self.gas.n_reactions + KK = self.gas.n_species + JJ = self.flame.n_points + z = self.grid + T = self.T + u = self.velocity + Lreac = list(self.gas.forward_rates_of_progress) + for index, object in enumerate(Lreac): + Lreac[index] = "FwRate_" +str(index+1) + Lreac_r = list(self.gas.reverse_rates_of_progress) + for index, object in enumerate(Lreac_r): + Lreac_r[index] = "RvRate_" +str(index+1) + Wspec = list(self.gas.species_names) + for index, object in enumerate(Wspec): + Wspec[index] = "w_" +object + Lreac_n = list(self.gas.net_rates_of_progress) + for index, object in enumerate(Lreac_n): + Lreac_n[index] = "NetRate_" +str(index+1) + fcsv = open(filename,'w') + writer = _csv.writer(fcsv) + writer.writerow(['Grid Points: ', str(JJ),' Sl= ',u[0]]) + writer.writerow(['x_axis','u','Temperature','rho','Pressure'] + + self.gas.species_names + + Wspec + + Lreac + + Lreac_r + + Lreac_n + + ['Heat_release']) + for n in range(self.flame.n_points): + self.set_gas_state(n) + HR = 0.0 + for m in range(KK): + HR = HR - self.gas.standard_enthalpies_RT[m]*self.gas.net_production_rates[m] + HR = HR * 8313.608 * T[n] + writer.writerow([z[n], u[n], T[n], self.gas.density, self.flame.P] + + list(self.gas.Y/np.sum(self.gas.Y)) + + list(self.gas.molecular_weights) + + list(1000*self.gas.forward_rates_of_progress) + + list(1000*self.gas.reverse_rates_of_progress) + + list(1000*self.gas.net_rates_of_progress) + + list([HR])) + + fcsv.close() + if not quiet: + print("Solution saved to '{0}'.".format(filename)) + + def write_AVBP_energy(self, filename='AVBP_energy.csv', quiet = False): + """ + Dumps energy profile to be imposed in AVBP as : + Line 1 : number of grid points + Next lines : grid | Temperature | density | Cv mass + + : param filename: + Output file name + + : returns : + File with inputs + """ + f = open(filename,'w') + grid = self.grid + T = self.T + points = len(grid) + f.write("%d\n"%(points)) + for i in range(points): + self.set_gas_state(i) + density = self.gas.density + cv_mass = self.gas.cv_mass + f.write("%1.5e %1.5e %1.5e %1.5e \n"%(grid[i], T[i], density, cv_mass)) + f.close() + if not quiet: + print("\nAVBP energy inputs saved to '{0}'.".format(filename)) + + def to_array(self, domain=None, normalize=False): """ Retrieve domain data as a `SolutionArray` object. @@ -581,7 +1198,7 @@ class FreeFlame(FlameBase): """A freely-propagating flat flame.""" __slots__ = ('inlet', 'flame', 'outlet') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ A domain of type `FreeFlow` named 'flame' will be created to represent the flame. The three domains comprising the stack are stored as ``self.inlet``, @@ -597,15 +1214,15 @@ def __init__(self, gas, grid=None, width=None): """ #: `Inlet1D` at the left of the domain representing premixed reactants - self.inlet = Inlet1D(name='reactants', phase=gas) + self.inlet = Inlet1D(name='reactants', phase=gas, sections=sections) #: `Outlet1D` at the right of the domain representing the burned products - self.outlet = Outlet1D(name='products', phase=gas) + self.outlet = Outlet1D(name='products', phase=gas, sections=sections) if not hasattr(self, 'flame'): # Create flame domain if not already instantiated by a child class #: `FreeFlow` domain representing the flame - self.flame = FreeFlow(gas, name='flame') + self.flame = FreeFlow(gas, name='flame', sections=sections) if width is not None: if grid is not None: @@ -776,7 +1393,7 @@ class BurnerFlame(FlameBase): """A burner-stabilized flat flame.""" __slots__ = ('burner', 'flame', 'outlet') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -795,15 +1412,15 @@ def __init__(self, gas, grid=None, width=None): """ #: `Inlet1D` at the left of the domain representing the burner surface through #: which reactants flow - self.burner = Inlet1D(name='burner', phase=gas) + self.burner = Inlet1D(name='burner', phase=gas, sections=sections) #: `Outlet1D` at the right of the domain representing the burned gas - self.outlet = Outlet1D(name='outlet', phase=gas) + self.outlet = Outlet1D(name='outlet', phase=gas, sections=sections) if not hasattr(self, 'flame'): # Create flame domain if not already instantiated by a child class #: `UnstrainedFlow` domain representing the flame - self.flame = UnstrainedFlow(gas, name='flame') + self.flame = UnstrainedFlow(gas, name='flame', sections=sections) if width is not None: if grid is not None: @@ -914,7 +1531,7 @@ class CounterflowDiffusionFlame(FlameBase): """ A counterflow diffusion flame """ __slots__ = ('fuel_inlet', 'flame', 'oxidizer_inlet') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -933,15 +1550,15 @@ def __init__(self, gas, grid=None, width=None): """ #: `Inlet1D` at the left of the domain representing the fuel mixture - self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas) + self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas, sections=sections) self.fuel_inlet.T = gas.T #: `Inlet1D` at the right of the domain representing the oxidizer mixture - self.oxidizer_inlet = Inlet1D(name='oxidizer_inlet', phase=gas) + self.oxidizer_inlet = Inlet1D(name='oxidizer_inlet', phase=gas, sections=sections) self.oxidizer_inlet.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame') + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) if width is not None: if grid is not None: @@ -1233,7 +1850,7 @@ class ImpingingJet(FlameBase): """An axisymmetric flow impinging on a surface at normal incidence.""" __slots__ = ('inlet', 'flame', 'surface') - def __init__(self, gas, grid=None, width=None, surface=None): + def __init__(self, gas, grid=None, width=None, surface=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1254,10 +1871,10 @@ def __init__(self, gas, grid=None, width=None, surface=None): """ #: `Inlet1D` at the left of the domain representing the incoming reactants - self.inlet = Inlet1D(name='inlet', phase=gas) + self.inlet = Inlet1D(name='inlet', phase=gas, sections=sections) #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame') + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) self.flame.set_axisymmetric_flow() if width is not None: @@ -1323,7 +1940,7 @@ class CounterflowPremixedFlame(FlameBase): """ A premixed counterflow flame """ __slots__ = ('reactants', 'flame', 'products') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1341,15 +1958,15 @@ def __init__(self, gas, grid=None, width=None): """ #: `Inlet1D` at the left of the domain representing premixed reactants - self.reactants = Inlet1D(name='reactants', phase=gas) + self.reactants = Inlet1D(name='reactants', phase=gas, sections=sections) self.reactants.T = gas.T #: `Inlet1D` at the right of the domain representing burned products - self.products = Inlet1D(name='products', phase=gas) + self.products = Inlet1D(name='products', phase=gas, sections=sections) self.products.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame') + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) if width is not None: if grid is not None: @@ -1430,7 +2047,7 @@ class CounterflowTwinPremixedFlame(FlameBase): """ __slots__ = ('reactants', 'flame', 'products') - def __init__(self, gas, grid=None, width=None): + def __init__(self, gas, grid=None, width=None, sections=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1446,14 +2063,14 @@ def __init__(self, gas, grid=None, width=None): represent the flame. The three domains comprising the stack are stored as ``self.reactants``, ``self.flame``, and ``self.products``. """ - self.reactants = Inlet1D(name='reactants', phase=gas) + self.reactants = Inlet1D(name='reactants', phase=gas, sections=sections) self.reactants.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame') + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) #The right boundary is a symmetry plane - self.products = SymmetryPlane1D(name='products', phase=gas) + self.products = SymmetryPlane1D(name='products', phase=gas, sections=sections) if width is not None: if grid is not None: @@ -1505,3 +2122,358 @@ def set_initial_guess(self, data=None, group=None): self.set_profile('velocity', [0.0, 1.0], [uu, 0]) self.set_profile('spread_rate', [0.0, 1.0], [0.0, a]) self.set_profile("lambda", [0.0, 1.0], [L, L]) + + +class Flamelet(FlameBase): + """ A diffusion flamelet (Z-space) """ + __slots__ = ('oxidizer_inlet', 'flame', 'fuel_inlet') + _other = ('grid') + + def __init__(self, gas, grid=None,): + """ + :param gas: + `Solution` (using the IdealGas thermodynamic model) used to + evaluate all gas properties and reaction rates. + :param grid: + A list of points to be used as the initial grid. Not recommended + unless solving only on a fixed grid; Use the `width` parameter + instead. + + A domain of class `FlameletFlow` named ``flame`` will be created to + represent the flame. The three domains comprising the stack are stored as + ``self.oxidizer_inlet``, ``self.flame``, and ``self.fuel_inlet``. + """ + + #: `Inlet1D` at the left of the domain representing the fuel mixture + self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas) + self.fuel_inlet.T = gas.T + + #: `Inlet1D` at the right of the domain representing the oxidizer mixture + self.oxidizer_inlet = Inlet1D(name='oxidizer_inlet', phase=gas) + self.oxidizer_inlet.T = gas.T + + #: `FlameletFlow` domain representing the flame + self.flame = FlameletFlow(gas, name='flame') + + if grid is None: + grid = np.array([0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]) + # Note: flamelet initialisation is very sensitive to the number of grid points. + # Do not hesitate to try some: experience shows that between 10 and 20 is often a good guess + + grid = grid / max(grid) # Width of the grid must anyway be 1 because in Z-space + + super().__init__((self.oxidizer_inlet, self.flame, self.fuel_inlet), gas, grid) + + @property + def ChiSt(self): + return self.flame.ChiSt + + @ChiSt.setter + def ChiSt(self, val): + self.flame.ChiSt = val + + @property + def ZSt(self): + return self.flame.ZSt + + @ZSt.setter + def ZSt(self, val): + self.flame.ZSt = val + + def set_initial_guess(self, data=None, group=None): + """ + Set the initial guess for the solution. By default, the initial guess + is generated by assuming infinitely-fast chemistry. Alternatively, a + previously calculated result can be supplied as an initial guess via + 'data' and 'key' inputs (see `FlameBase.set_initial_guess`). + """ + super().set_initial_guess(data=data, group=group) + if data: + return + + moles = lambda el: (self.gas.elemental_mass_fraction(el) / + self.gas.atomic_weight(el)) + + # Compute stoichiometric mixture composition + Yin_f = self.fuel_inlet.Y + self.gas.TPY = self.fuel_inlet.T, self.P, Yin_f + + T0f = self.fuel_inlet.T + + sFuel = moles('O') + if 'C' in self.gas.element_names: + sFuel -= 2 * moles('C') + if 'H' in self.gas.element_names: + sFuel -= 0.5 * moles('H') + + Yin_o = self.oxidizer_inlet.Y + self.gas.TPY = self.oxidizer_inlet.T, self.P, Yin_o + + T0o = self.oxidizer_inlet.T + + sOx = moles('O') + if 'C' in self.gas.element_names: + sOx -= 2 * moles('C') + if 'H' in self.gas.element_names: + sOx -= 0.5 * moles('H') + + zst = 1.0 / (1 - sFuel / sOx) + Yst = zst * Yin_f + (1.0 - zst) * Yin_o + + self.flame.ZSt = zst + + # get adiabatic flame temperature and composition + Tbar = 0.5 * (T0f + T0o) + self.gas.TPY = Tbar, self.P, Yst + self.gas.equilibrate('HP') + Teq = self.gas.T + Yeq = self.gas.Y + + # estimate strain rate + zz = self.flame.grid + nz = len(zz) + + Y = np.zeros((nz, self.gas.n_species)) + T = np.zeros(nz) + for j, zmix in enumerate(zz): + if zmix > zst: + Y[j] = Yeq + (Yin_f - Yeq) * (zmix - zst) / (1.0 - zst) + T[j] = Teq + (T0f - Teq) * (zmix - zst) / (1.0 - zst) + else: + Y[j] = Yin_o + zmix * (Yeq - Yin_o) / zst + T[j] = T0o + (Teq - T0o) * zmix / zst + + T[0] = T0f + T[-1] = T0o + + self.set_profile('T', zz, T) + for k,spec in enumerate(self.gas.species_names): + self.set_profile(spec, zz, Y[:,k]) + + def extinct(self): + return max(self.T) - max(self.fuel_inlet.T, self.oxidizer_inlet.T) < 10 + + def solve(self, loglevel=1, refine_grid='refine', auto=False, stage=1): + """ + Solve the problem. + + :param loglevel: + integer flag controlling the amount of diagnostic output. Zero + suppresses all output, and 5 produces very verbose output. + :param refine_grid: + if True, enable grid refinement. + :param auto: if True, sequentially execute the different solution stages + and attempt to automatically recover from errors. Attempts to first + solve on the initial grid with energy enabled. If that does not + succeed, a fixed-temperature solution will be tried followed by + enabling the energy equation, and then with grid refinement enabled. + If non-default tolerances have been specified or multicomponent + transport is enabled, an additional solution using these options + will be calculated. + :param stage: solution stage; only used when transport model is ``ionized-gas``. + """ + if self.flame.transport_model == 'ionized-gas': + warnings.warn( + "The 'ionized-gas' transport model is untested for " + "'Flamelet' objects.", UserWarning) + self.flame.solving_stage = stage + + super().solve(loglevel, refine_grid, auto) + # Do some checks if loglevel is set + if loglevel > 0: + if self.extinct(): + print('WARNING: Flame is extinct.') + # else: + # # Check if the flame is very thick + # # crude width estimate based on temperature + # z_flame = self.grid[self.T > np.max(self.T) / 2] + # flame_width = z_flame[-1] - z_flame[0] + # domain_width = self.grid[-1] - self.grid[0] + # if flame_width / domain_width > 0.4: + # print('WARNING: The flame is thick compared to the domain ' + # 'size. The flame might be affected by the plug-flow ' + # 'boundary conditions. Consider increasing the inlet mass ' + # 'fluxes or using a larger domain.') + + # # Check if the temperature peak is close to a boundary + # z_center = (self.grid[np.argmax(self.T)] - self.grid[0]) / domain_width + # if z_center < 0.25: + # print('WARNING: The flame temperature peak is close to the ' + # 'fuel inlet. Consider increasing the ratio of the ' + # 'fuel inlet mass flux to the oxidizer inlet mass flux.') + # if z_center > 0.75: + # print('WARNING: The flame temperature peak is close to the ' + # 'oxidizer inlet. Consider increasing the ratio of the ' + # 'oxidizer inlet mass flux to the fuel inlet mass flux.') + + def write_csv(self, filename, species='X', quiet=True): + """ + Write the velocity, temperature, density, and species profiles + to a CSV file. + + :param filename: + Output file name + :param species: + Attribute to use obtaining species profiles, e.g. ``X`` for + mole fractions or ``Y`` for mass fractions. + """ + + z = self.grid + T = self.T + + csvfile = open(filename, 'w') + writer = _csv.writer(csvfile) + writer.writerow(['z (m)', + 'T (K)', 'rho (kg/m3)'] + self.gas.species_names) + for n in range(self.flame.n_points): + self.set_gas_state(n) + writer.writerow([z[n], T[n], self.gas.density] + + list(getattr(self.gas, species))) + csvfile.close() + if not quiet: + print("Solution saved to '{0}'.".format(filename)) + # def strain_rate(self, definition, fuel=None, oxidizer='O2', stoich=None): + # r""" + # Return the axial strain rate of the counterflow diffusion flame in 1/s. + + # :param definition: + # The definition of the strain rate to be calculated. Options are: + # ``mean``, ``max``, ``stoichiometric``, ``potential_flow_fuel``, and + # ``potential_flow_oxidizer``. + # :param fuel: The fuel species. Used only if ``definition`` is + # ``stoichiometric``. + # :param oxidizer: The oxidizer species, default ``O2``. Used only if + # ``definition`` is ``stoichiometric``. + # :param stoich: The molar stoichiometric oxidizer-to-fuel ratio. + # Can be omitted if the oxidizer is ``O2``. Used only if ``definition`` + # is ``stoichiometric``. + + # The parameter ``definition`` sets the method to compute the strain rate. + # Possible options are: + + # ``mean``: + # The mean axial velocity gradient in the entire domain + + # .. math:: a_{mean} = \left| \frac{\Delta u}{\Delta z} \right| + + # ``max``: + # The maximum axial velocity gradient + + # .. math:: a_{max} = \max \left( \left| \frac{du}{dz} \right| \right) + + # ``stoichiometric``: + # The axial velocity gradient at the stoichiometric surface. + + # .. math:: + + # a_{stoichiometric} = \left| \left. \frac{du}{dz} + # \right|_{\phi=1} \right| + + # This method uses the additional keyword arguments ``fuel``, + # ``oxidizer``, and ``stoich``. + + # >>> f.strain_rate('stoichiometric', fuel='H2', oxidizer='O2', + # stoich=0.5) + + # ``potential_flow_fuel``: + # The corresponding axial strain rate for a potential flow boundary + # condition at the fuel inlet. + + # .. math:: a_{f} = \sqrt{-\frac{\Lambda}{\rho_{f}}} + + # ``potential_flow_oxidizer``: + # The corresponding axial strain rate for a potential flow boundary + # condition at the oxidizer inlet. + + # .. math:: a_{o} = \sqrt{-\frac{\Lambda}{\rho_{o}}} + # """ + # if definition == 'mean': + # return - (self.velocity[-1] - self.velocity[0]) / self.grid[-1] + + # elif definition == 'max': + # return np.max(np.abs(np.gradient(self.velocity) / np.gradient(self.grid))) + + # elif definition == 'stoichiometric': + # if fuel is None: + # raise KeyError('Required argument "fuel" not defined') + # if oxidizer != 'O2' and stoich is None: + # raise KeyError('Required argument "stoich" not defined') + + # if stoich is None: + # # oxidizer is O2 + # stoich = - 0.5 * self.gas.n_atoms(fuel, 'O') + # if 'H' in self.gas.element_names: + # stoich += 0.25 * self.gas.n_atoms(fuel, 'H') + # if 'C' in self.gas.element_names: + # stoich += self.gas.n_atoms(fuel, 'C') + + # d_u_d_z = np.gradient(self.velocity) / np.gradient(self.grid) + # phi = (self.X[self.gas.species_index(fuel)] * stoich / + # np.maximum(self.X[self.gas.species_index(oxidizer)], 1e-20)) + # z_stoich = np.interp(-1., -phi, self.grid) + # return np.abs(np.interp(z_stoich, self.grid, d_u_d_z)) + + # elif definition == 'potential_flow_fuel': + # return np.sqrt(- self.L[0] / self.density[0]) + + # elif definition == 'potential_flow_oxidizer': + # return np.sqrt(- self.L[0] / self.density[-1]) + + # else: + # raise ValueError('Definition "' + definition + '" is not available') + + # def mixture_fraction(self, m): + # r""" + # Compute the mixture fraction based on element ``m`` or from the + # Bilger mixture fraction by setting ``m="Bilger"`` + + # The mixture fraction is computed from the elemental mass fraction of + # element ``m``, normalized by its values on the fuel and oxidizer + # inlets: + + # .. math:: Z = \frac{Z_{\mathrm{mass},m}(z) - + # Z_{\mathrm{mass},m}(z_\mathrm{oxidizer})} + # {Z_{\mathrm{mass},m}(z_\mathrm{fuel}) - + # Z_{\mathrm{mass},m}(z_\mathrm{oxidizer})} + + # or from the Bilger mixture fraction: + + # .. math:: Z = \frac{\beta-\beta_{\mathrm{oxidizer}}} + # {\beta_{\mathrm{fuel}}-\beta_{\mathrm{oxidizer}}} + + # with + + # .. math:: \beta = 2\frac{Z_C}{M_C}+2\frac{Z_S}{M_S} + # +\frac{1}{2}\frac{Z_H}{M_H}-\frac{Z_O}{M_O} + + # :param m: + # The element based on which the mixture fraction is computed, + # may be specified by name or by index, or "Bilger" for the + # Bilger mixture fraction, which considers the elements C, + # H, S, and O + + # >>> f.mixture_fraction('H') + # >>> f.mixture_fraction('Bilger') + # """ + + # Yf = [self.value(self.flame, k, 0) for k in self.gas.species_names] + # Yo = [self.value(self.flame, k, self.flame.n_points - 1) + # for k in self.gas.species_names] + + # vals = np.empty(self.flame.n_points) + # for i in range(self.flame.n_points): + # self.set_gas_state(i) + # vals[i] = self.gas.mixture_fraction(Yf, Yo, 'mass', m) + # return vals + + # @property + # def equivalence_ratio(self): + # Yf = [self.value(self.flame, k, 0) for k in self.gas.species_names] + # Yo = [self.value(self.flame, k, self.flame.n_points - 1) + # for k in self.gas.species_names] + + # vals = np.empty(self.flame.n_points) + # for i in range(self.flame.n_points): + # self.set_gas_state(i) + # vals[i] = self.gas.equivalence_ratio(Yf, Yo, "mass") + # return vals \ No newline at end of file From a11b5661b64ff8536b8bf8b6578be6cad47d7a1b Mon Sep 17 00:00:00 2001 From: pestre Date: Fri, 24 Jan 2025 10:46:23 +0100 Subject: [PATCH 20/98] Merge differences in samples directory Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: new file: samples/clib/README.rst new file: samples/cxx/README.rst modified: samples/cxx/bvp/BoundaryValueProblem.h modified: samples/cxx/flamespeed/flamespeed.cpp new file: samples/f77/f77_demo.f new file: samples/f90/README.rst new file: samples/matlab_experimental/README.rst new file: samples/python/AVBP/1-runBurner.py new file: samples/python/AVBP/2-restoreBurner.py new file: samples/python/AVBP/3-plotBurner.py new file: samples/python/AVBP/ARC.py new file: samples/python/AVBP/FLAMELET.py new file: samples/python/AVBP/PEA.py new file: samples/python/AVBP/RESULTS/BISETTI.xml new file: samples/python/AVBP/RESULTS/BISETTI.yaml new file: samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml new file: samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.yaml new file: samples/python/AVBP/THICKENING.py new file: samples/python/AVBP/inputs/BFER_methane.cti new file: samples/python/AVBP/inputs/BFER_methane.yaml new file: samples/python/AVBP/inputs/BISETTI.cti new file: samples/python/AVBP/inputs/BISETTI.yaml new file: samples/python/AVBP/inputs/Lu.cti new file: samples/python/AVBP/inputs/Lu.yaml new file: samples/python/AVBP/inputs/Lu_ARC.cti new file: samples/python/AVBP/inputs/Lu_ARC.f90 new file: samples/python/AVBP/inputs/Lu_ARC.yaml new file: samples/python/AVBP/inputs/T_vs_x.dat new file: samples/python/AVBP/mech_lib/Makefile new file: samples/python/AVBP/mech_lib/customkinetics.f90 new file: samples/python/AVBP/mixture_database.dat new file: samples/python/AVBP/postproc.py new file: samples/python/AVBP/write_csv.py new file: samples/python/README.rst new file: samples/python/kinetics/README.rst new file: samples/python/multiphase/README.rst new file: samples/python/onedim/README.rst new file: samples/python/onedim/adiabatic_flame.csv new file: samples/python/onedim/adiabatic_flame.yaml new file: samples/python/reactors/README.rst new file: samples/python/surface_chemistry/README.rst new file: samples/python/thermo/README.rst new file: samples/python/transport/README.rst Author: pestre interactive rebase in progress; onto 7aec821a8 Last commands done (5 commands done): pick 20ede9daf Merge differences in interfaces directory pick 925ed423a Merge differences in samples directory Next commands to do (9 remaining commands): pick 68a09c47e Merge differences in src directory pick f298a7d4e Merge differences in test directory You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. Changes to be committed: modified: samples/cxx/bvp/BoundaryValueProblem.h modified: samples/cxx/flamespeed/flamespeed.cpp new file: samples/python/AVBP/1-runBurner.py new file: samples/python/AVBP/2-restoreBurner.py new file: samples/python/AVBP/3-plotBurner.py new file: samples/python/AVBP/ARC.py new file: samples/python/AVBP/FLAMELET.py new file: samples/python/AVBP/PEA.py new file: samples/python/AVBP/RESULTS/BISETTI.xml new file: samples/python/AVBP/RESULTS/BISETTI.yaml new file: samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml new file: samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.yaml new file: samples/python/AVBP/THICKENING.py new file: samples/python/AVBP/inputs/BFER_methane.cti new file: samples/python/AVBP/inputs/BFER_methane.yaml new file: samples/python/AVBP/inputs/BISETTI.cti new file: samples/python/AVBP/inputs/BISETTI.yaml new file: samples/python/AVBP/inputs/Lu.cti new file: samples/python/AVBP/inputs/Lu.yaml new file: samples/python/AVBP/inputs/Lu_ARC.cti new file: samples/python/AVBP/inputs/Lu_ARC.f90 new file: samples/python/AVBP/inputs/Lu_ARC.yaml new file: samples/python/AVBP/inputs/T_vs_x.dat new file: samples/python/AVBP/mech_lib/Makefile new file: samples/python/AVBP/mech_lib/customkinetics.f90 new file: samples/python/AVBP/mixture_database.dat new file: samples/python/AVBP/postproc.py new file: samples/python/AVBP/write_csv.py new file: samples/python/multiphase/README.rst new file: samples/python/onedim/adiabatic_flame.csv new file: samples/python/onedim/adiabatic_flame.yaml new file: samples/python/surface_chemistry/README.rst --- samples/cxx/bvp/BoundaryValueProblem.h | 2 +- samples/cxx/flamespeed/flamespeed.cpp | 6 +- samples/python/AVBP/1-runBurner.py | 62 + samples/python/AVBP/2-restoreBurner.py | 54 + samples/python/AVBP/3-plotBurner.py | 53 + samples/python/AVBP/ARC.py | 45 + samples/python/AVBP/FLAMELET.py | 111 + samples/python/AVBP/PEA.py | 50 + samples/python/AVBP/RESULTS/BISETTI.xml | 7624 +++++++++++++++++ samples/python/AVBP/RESULTS/BISETTI.yaml | 6778 +++++++++++++++ .../RESULTS/CH4-O2-converged-flamelet-Lu.xml | 1844 ++++ .../RESULTS/CH4-O2-converged-flamelet-Lu.yaml | 1565 ++++ samples/python/AVBP/THICKENING.py | 67 + samples/python/AVBP/inputs/BFER_methane.cti | 149 + samples/python/AVBP/inputs/BFER_methane.yaml | 151 + samples/python/AVBP/inputs/BISETTI.cti | 1537 ++++ samples/python/AVBP/inputs/BISETTI.yaml | 1367 +++ samples/python/AVBP/inputs/Lu.cti | 1351 +++ samples/python/AVBP/inputs/Lu.yaml | 997 +++ samples/python/AVBP/inputs/Lu_ARC.cti | 1338 +++ samples/python/AVBP/inputs/Lu_ARC.f90 | 2317 +++++ samples/python/AVBP/inputs/Lu_ARC.yaml | 2230 +++++ samples/python/AVBP/inputs/T_vs_x.dat | 203 + samples/python/AVBP/mech_lib/Makefile | 4 + .../python/AVBP/mech_lib/customkinetics.f90 | 2317 +++++ samples/python/AVBP/mixture_database.dat | 102 + samples/python/AVBP/postproc.py | 79 + samples/python/AVBP/write_csv.py | 37 + samples/python/multiphase/README.rst | 2 + samples/python/onedim/adiabatic_flame.csv | 141 + samples/python/onedim/adiabatic_flame.yaml | 1338 +++ samples/python/surface_chemistry/README.rst | 2 + 32 files changed, 33919 insertions(+), 4 deletions(-) create mode 100644 samples/python/AVBP/1-runBurner.py create mode 100644 samples/python/AVBP/2-restoreBurner.py create mode 100644 samples/python/AVBP/3-plotBurner.py create mode 100644 samples/python/AVBP/ARC.py create mode 100644 samples/python/AVBP/FLAMELET.py create mode 100644 samples/python/AVBP/PEA.py create mode 100644 samples/python/AVBP/RESULTS/BISETTI.xml create mode 100644 samples/python/AVBP/RESULTS/BISETTI.yaml create mode 100644 samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml create mode 100644 samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.yaml create mode 100644 samples/python/AVBP/THICKENING.py create mode 100755 samples/python/AVBP/inputs/BFER_methane.cti create mode 100644 samples/python/AVBP/inputs/BFER_methane.yaml create mode 100644 samples/python/AVBP/inputs/BISETTI.cti create mode 100644 samples/python/AVBP/inputs/BISETTI.yaml create mode 100755 samples/python/AVBP/inputs/Lu.cti create mode 100644 samples/python/AVBP/inputs/Lu.yaml create mode 100755 samples/python/AVBP/inputs/Lu_ARC.cti create mode 100755 samples/python/AVBP/inputs/Lu_ARC.f90 create mode 100644 samples/python/AVBP/inputs/Lu_ARC.yaml create mode 100644 samples/python/AVBP/inputs/T_vs_x.dat create mode 100644 samples/python/AVBP/mech_lib/Makefile create mode 100755 samples/python/AVBP/mech_lib/customkinetics.f90 create mode 100755 samples/python/AVBP/mixture_database.dat create mode 100644 samples/python/AVBP/postproc.py create mode 100644 samples/python/AVBP/write_csv.py create mode 100644 samples/python/multiphase/README.rst create mode 100644 samples/python/onedim/adiabatic_flame.csv create mode 100644 samples/python/onedim/adiabatic_flame.yaml create mode 100644 samples/python/surface_chemistry/README.rst diff --git a/samples/cxx/bvp/BoundaryValueProblem.h b/samples/cxx/bvp/BoundaryValueProblem.h index 2ae637e8fd8..82316f32f68 100644 --- a/samples/cxx/bvp/BoundaryValueProblem.h +++ b/samples/cxx/bvp/BoundaryValueProblem.h @@ -147,7 +147,7 @@ class BoundaryValueProblem : if (!m_sim) { start(); } - bool refine = true; + std::string refine = "refine"; m_sim->solve(loglevel, refine); } diff --git a/samples/cxx/flamespeed/flamespeed.cpp b/samples/cxx/flamespeed/flamespeed.cpp index 2859038d613..8c7ece4ff59 100644 --- a/samples/cxx/flamespeed/flamespeed.cpp +++ b/samples/cxx/flamespeed/flamespeed.cpp @@ -24,7 +24,7 @@ using namespace Cantera; using fmt::print; -int flamespeed(double phi, bool refine_grid, int loglevel) +int flamespeed(double phi, std::string refine_grid, int loglevel) { try { auto sol = newSolution("gri30.yaml", "gri30", "mixture-averaged"); @@ -199,7 +199,7 @@ int main(int argc, char** argv) { double phi; int loglevel = 1; - bool refine_grid = true; + std::string refine_grid = "refine"; if (argc >= 2) { phi = fpValue(argv[1]); } else { @@ -207,7 +207,7 @@ int main(int argc, char** argv) std::cin >> phi; } if (argc >= 3) { - refine_grid = bool(std::stoi(argv[2])); + refine_grid = std::string(argv[2]); } if (argc >= 4) { loglevel = std::stoi(argv[3]); diff --git a/samples/python/AVBP/1-runBurner.py b/samples/python/AVBP/1-runBurner.py new file mode 100644 index 00000000000..25902d7b859 --- /dev/null +++ b/samples/python/AVBP/1-runBurner.py @@ -0,0 +1,62 @@ +# Importing necessary libraries +import cantera as ct +import numpy as np +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Setting the mechanism name +mech = 'BISETTI' + +#Setting pressure +pressure = ct.one_atm + +# Setting temperature +temperature = 298.00 + +# Setting inlet velocity +velocity = 6.73e-2 + +# Setting flame initial composition +composition = 'C2H4:14.08, O2:18.05, N2:67.87' + +# Creating gas object +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/%s.yaml' % mech) +else: + gas = ct.Solution('./inputs/%s.cti' % mech) + +# Settng gas properties +gas.TPX = temperature, pressure, composition + +# Loading experimental data (temperature vs. height) +z, T = np.genfromtxt('./inputs/T_vs_x.dat').T + +# Creating flame object of the same size as the experimental flame +f = ct.BurnerFlame(gas=gas, width=z[-1]) + +# Setting the flame's mass flow rate +f.burner.mdot = velocity * gas.density + +# Disabling energy equation +f.energy_enabled = False + +#Imposing proposed temperature profile +f.flame.set_fixed_temp_profile(z/max(z), T) + +# Setting the transport model to mixture-averaged +f.transport_model = 'Mix' + +# Setting mesh refinement criteria +f.set_refine_criteria(ratio=2.0, slope=0.1, curve=0.1) + +# Solving the problem +f.solve(1, 'refine') + +# Showing the result +f.show_solution() + +# Saving the result +if ct.__version__ >= '2.5.0': + f.save('./RESULTS/%s.yaml' % mech, 'non-sooting',overwrite=True) +else: + f.save('./RESULTS/%s.xml' % mech, 'non-sooting') diff --git a/samples/python/AVBP/2-restoreBurner.py b/samples/python/AVBP/2-restoreBurner.py new file mode 100644 index 00000000000..3dd46de3365 --- /dev/null +++ b/samples/python/AVBP/2-restoreBurner.py @@ -0,0 +1,54 @@ +# Importing necessary libraries +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Setting the mechanism name +mech = 'BISETTI' + +# Creating gas object +#if cantera version is 2.5.0 or higher, use the following line instead +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/%s.yaml' % mech) +else: + gas = ct.Solution('./inputs/%s.cti' % mech) + +# Loading experimental data (temperature vs. height) +z, T = np.genfromtxt('./inputs/T_vs_x.dat').T + +# Creating flame object of the same size as the experimental flame with 25 soot sections +f = ct.BurnerFlame(gas=gas, width=z[-1], sections = 25) + +# Setting transport model +f.transport_model = 'Mix' + +# Setting up soot calculation +f.soot_setup(precursors =['A2'], + retroaction =True, + condensation =True, + coagulation =True, + surface_growth =True, + oxidation =True, + #fractal_aggregates=True, + radiation =True, + trash_section =-1, + #show_sections = True + ) + +# Restoring the non-sooting flame +if ct.__version__ >= '2.5.0': + f.restore('./RESULTS/%s.yaml' % mech, 'non-sooting') +else: + f.restore('./RESULTS/%s.xml' % mech, 'non-sooting') +f.radiation_enabled = True + +# Solving the sooting flame +f.solve(1,refine_grid='disabled') + +# # Saving the result +if ct.__version__ >= '2.5.0': + f.save('./RESULTS/%s.yaml' % mech,'sooting',overwrite=True) +else: + f.save('./RESULTS/%s.xml' % mech,'sooting') \ No newline at end of file diff --git a/samples/python/AVBP/3-plotBurner.py b/samples/python/AVBP/3-plotBurner.py new file mode 100644 index 00000000000..60388f4e7a8 --- /dev/null +++ b/samples/python/AVBP/3-plotBurner.py @@ -0,0 +1,53 @@ +# Importing necessary libraries +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Setting the mechanism name +mech = 'BISETTI' + +# Creating gas object +#if cantera version is 2.5.0 or higher, use the following line instead +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/%s.yaml' % mech) +else: + gas = ct.Solution('./inputs/%s.cti' % mech) + +# Loading experimental data (temperature vs. height) +z, T = np.genfromtxt('./inputs/T_vs_x.dat').T + +# Creating flame object of the same size as the experimental flame with 25 soot sections +f = ct.BurnerFlame(gas=gas, width=z[-1], sections=25) + +# Setting up soot computation +f.soot_setup(precursors =['A2'], + #fractal_aggregates=True, + trash_section =-1 + ) + +# Restoring the sooting flame +if ct.__version__ >= '2.5.0': + f.restore('./RESULTS/%s.yaml' % mech, 'sooting') +else: + f.restore('./RESULTS/%s.xml' % mech, 'sooting') + +# Plot volume fraction +# Particles under 2nm and in last section are excluded +plt.figure(0) +plt.plot(f.grid * 100, f.soot_fv(min=2e-7, last=-1)) +plt.yscale('log') +plt.ylabel('Volume fraction') +plt.xlabel('HAB ($cm$)') + +# Plot particles number density +# Particles under 2nm and in last section are excluded +plt.figure(1) +plt.plot(f.grid * 100, f.soot_Np(min=2e-7, last=-1)) +plt.yscale('log') +plt.ylabel('Soot particles number density ($cm^{-3}$)') +plt.xlabel('HAB ($cm$)') + +# Displaying graphs +plt.show() diff --git a/samples/python/AVBP/ARC.py b/samples/python/AVBP/ARC.py new file mode 100644 index 00000000000..edc2a530c53 --- /dev/null +++ b/samples/python/AVBP/ARC.py @@ -0,0 +1,45 @@ +import cantera as ct +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +p = 1e5 +tin = 400.0 +phi = 1.0 +fuel = {'CH4':1} +oxidizer = {'O2': 1, 'N2': 3.76} + +ct.compile_fortran('./inputs/Lu_ARC.f90') + +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/Lu_ARC.yaml') +else: + gas = ct.Solution('./inputs/Lu_ARC.cti') + +gas.TP = tin, p +gas.set_equivalence_ratio(phi, fuel, oxidizer) +# gas.transport_model = 'UnityLewis' + +loglevel = 1 +refine_grid = 'refine' + +f = ct.FreeFlame(gas, width=0.02) +f.inlet.X = gas.X +f.inlet.T = gas.T + +f.energy_enabled = True +f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05, prune=0.01) +f.set_max_jac_age(10, 10) +f.set_time_step(1e-8, [10, 20, 40, 80, 100, 100, 150,]) +f.max_time_step_count = 500 + +f.solve(loglevel, refine_grid) + +if ct.__version__ >= '2.5.0': + plt.plot(f.flame.grid, f.velocity) +else: + plt.plot(f.flame.grid, f.u) + +plt.xlabel('Flame grid [m]') +plt.ylabel('Velocity [m/s]') +plt.show() \ No newline at end of file diff --git a/samples/python/AVBP/FLAMELET.py b/samples/python/AVBP/FLAMELET.py new file mode 100644 index 00000000000..f7a367acad6 --- /dev/null +++ b/samples/python/AVBP/FLAMELET.py @@ -0,0 +1,111 @@ +import cantera as ct +import time +import numpy as np +from scipy.special import erfinv, erfcinv, erf +from scipy import integrate +import matplotlib.pyplot as plt + +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +#gas init + +T = 300.0 # temperature +P = 101325.0 # pressure + +rho_o = P / (8.314 / 0.032 * T) # oxidizer density +tin_o = 300.0 # oxidizer inlet temperature +mdot_o = 0.8 # kg/m^2/s +comp_o = 'O2:1' # oxidizer composition +u_o = mdot_o / rho_o # oxidizer speed + +rho_f = P / (8.314 / 0.016 * T) # fuel density +tin_f = 300.0 # fuel inlet temperature +mdot_f = 0.2 # kg/m^2/s +comp_f = 'CH4:1' # fuel composition +u_f = mdot_f / rho_f # fuel speed + +width = 1.0 # width +SR = (u_o + u_f) / (width) # strain rate + +if ct.__version__ >= '2.5.0': + ct.compile_fortran('./inputs/Lu_ARC.f90') + gas_1 = ct.Solution('./inputs/Lu_ARC.yaml') +else: + gas_1 = ct.Solution('./inputs/Lu.cti') + +gas_1.TP = T, P + +#flamelet creation +plt.rcParams['figure.figsize'] = (14, 10) + +initial_grid = np.linspace(0,width,11) # initial grid for the calculation + +f_1 = ct.Flamelet(gas_1) # Flamelet object creation + +f_1.fuel_inlet.mdot = mdot_f # Fuel inlet conditions +f_1.fuel_inlet.Y = comp_f +f_1.fuel_inlet.T = tin_f + # Oxidizer inlet conditions +f_1.oxidizer_inlet.mdot = mdot_o +f_1.oxidizer_inlet.Y = comp_o +f_1.oxidizer_inlet.T = tin_o +chist = SR/np.pi*(np.exp(-2*((erfinv(1-2*0.2))**2))) +f_1.ChiSt = chist # Stochiometric scalar dissipation rate + +f_1.set_initial_guess() + +# plt.plot(f_1.flame.grid, f_1.T) + +# Calculation properties + +loglevel = 1 +f_1.set_max_jac_age(1, 1) +f_1.set_time_step(1.e-9, [50, 100, 150]) +f_1.energy_enabled = True +f_1.set_refine_criteria(ratio=4, slope=0.1, curve=0.1) + +# Solver +t1_A = time.time() +f_1.solve(loglevel, refine_grid = 'refine') +t1_B = time.time() + +if ct.__version__ >= '2.5.0': + f_1.save('./RESULTS/CH4-O2-converged-flamelet-Lu.yaml', 'Lu.yaml-zspace',overwrite=True) +else: + f_1.save('./RESULTS/CH4-O2-converged-flamelet-Lu.xml') + +# Calculation of the heat release +hr_1 = -np.sum(f_1.standard_enthalpies_RT * f_1.net_production_rates, 0) * ct.gas_constant * f_1.T +# print('Heat release rate = ', hr_1) + +plt.rcParams['figure.figsize'] = (14, 10) + +# Get interesting indices for computation of species +fuel_species = 'CH4' +ifuel = gas_1.species_index(fuel_species) +io2 = gas_1.species_index('O2') +ico = gas_1.species_index('CO') + +# Initiate interesting vectors +ch4_1 = np.zeros(f_1.flame.n_points,'d') +o2_1 = np.zeros(f_1.flame.n_points,'d') +co_1 = np.zeros(f_1.flame.n_points,'d') + +# Computes interesting quantities for analyzing a counter-flow flame +for n in range(f_1.flame.n_points): + f_1.set_gas_state(n) + ch4_1[n]= gas_1.Y[ifuel] + o2_1[n]= gas_1.Y[io2] + co_1[n]= gas_1.Y[ico] + +T_1 = f_1.T + +plt.plot(f_1.flame.grid,T_1/np.max(T_1),f_1.flame.grid,ch4_1/np.max(ch4_1), + f_1.flame.grid,o2_1/np.max(o2_1),f_1.flame.grid,co_1/np.max(co_1), f_1.flame.grid,hr_1/np.max(hr_1)) +plt.title(r'$T_{adiabatic}, Y_{CH_4}, Y_{O_2}, Y_{CO}$, HR vs. Mixture fraction',fontsize=25) +plt.xlabel(r'Mixture fraction', fontsize=15) +plt.ylabel('Normalized values of different quantities',fontsize=15) +plt.legend(['Temperature','$Y_{CH_4}$', '$Y_{O_2}$', '$Y_{CO}$', 'HR'],fontsize=15) + +plt.show() \ No newline at end of file diff --git a/samples/python/AVBP/PEA.py b/samples/python/AVBP/PEA.py new file mode 100644 index 00000000000..98b248dcafd --- /dev/null +++ b/samples/python/AVBP/PEA.py @@ -0,0 +1,50 @@ +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Parameters of the solver +loglevel = 1 +refine_grid = 'refine' + +if ct.__version__ >= '2.5.0': + mechanism_list = ['gri30.yaml', './inputs/BFER_methane.yaml', './inputs/BFER_methane.yaml'] +else: + mechanism_list = ['gri30.cti', './inputs/BFER_methane.cti', './inputs/BFER_methane.cti'] +gas_list = ['', 'BFER_nopea', 'BFER_pea'] + +for mechanism_name, gas_name in zip(mechanism_list, gas_list): + # Setting up the gas object (operating conditions) + gas = ct.Solution(mechanism_name, gas_name) + p = 1e5 + tin = 473.0 + phi = 1.4 + fuel = {'CH4': 1} + oxidizer = {'O2': 1, 'N2': 3.76} + gas.TP = tin, p + gas.set_equivalence_ratio(phi, fuel, oxidizer) + + # Setting up the flame object + f = ct.FreeFlame(gas, width=0.2) # Careful about the domain size if you want to retrieve the same profile ! + f.inlet.X = gas.X + f.inlet.T = gas.T + + f.energy_enabled = True + f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05, prune=0.01) + f.set_max_jac_age(10, 10) + f.set_time_step(1e-8, [10, 20, 40, 80, 100, 100, 150]) + f.max_time_step_count = 5000 + + f.solve(loglevel, refine_grid) + + # Checking the results + if ct.__version__ >= '2.5.0': + plt.plot(f.flame.grid, f.velocity, label=mechanism_name + ' - ' + gas_name) + else: + plt.plot(f.grid, f.u, label=mechanism_name + ' - ' + gas_name) + +plt.xlabel('Flame grid [m]') +plt.ylabel('Veloctity [m/s]') +plt.legend() +plt.show() diff --git a/samples/python/AVBP/RESULTS/BISETTI.xml b/samples/python/AVBP/RESULTS/BISETTI.xml new file mode 100644 index 00000000000..239852c413e --- /dev/null +++ b/samples/python/AVBP/RESULTS/BISETTI.xml @@ -0,0 +1,7624 @@ + + + Thu Dec 28 11:45:10 2023 + none + + + + + + 2.980000000000000E+02 + 7.909433454451480E-02 + 0.000000000000000E+00 + 6.615775966700881E-01 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 2.009771930182301E-01 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 0.000000000000000E+00 + 1.374452103116817E-01 + 0.000000000000000E+00 + 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Dec 23 13:29:25 2023 + burner: + size: 1 + type: inlet + points: 1 + mass-flux: 0.07909499651938928 + temperature: 298.0 + pressure: 1.01325e+05 + mass-fractions: + N2: 0.6615842988823729 + O2: 0.2009704738662205 + C2H4: 0.1374452272514067 + flame: + Ys12: [-2.936810996752164e-22, -2.901974044126986e-22, -2.861412055025573e-22, + -2.845760420388120e-22, -2.791878899208235e-22, -2.753557512952252e-22, + -2.726182799211595e-22, -2.660333112178819e-22, -2.600526248356532e-22, + -2.539612806708918e-22, -2.476933850668903e-22, -2.389798597917e-22, + -2.346173730584655e-22, -2.318296553765535e-22, -2.274017101007241e-22, + -2.269700222665681e-22, -2.206624434491741e-22, -2.155700264763560e-22, + -2.111842260634649e-22, -2.080331121932468e-22, -2.033968591060562e-22, + -1.989903672008091e-22, -1.963815114933063e-22, -1.934461254633198e-22, + -1.891526970489431e-22, -1.863373490307378e-22, -1.864158323004905e-22, + -1.853630450219231e-22, -1.835246565635225e-22, -1.848100761964268e-22, + 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6.279295889559276e-17] + size: 154 + type: unstrained-flow + points: 154 + tolerances: + transient-abstol: 1.0e-11 + steady-reltol: 1.0e-04 + steady-abstol: 1.0e-09 + transient-reltol: 1.0e-04 + transport-model: mixture-averaged + phase: + name: gas + source: ./BISETTI.yaml + radiation-enabled: false + energy-enabled: false + Soret-enabled: false + species-enabled: true + refine-criteria: + ratio: 2.0 + slope: 0.1 + curve: 0.1 + prune: 0.0 + grid-min: 1.0e-10 + max-points: 1000 + basis: mass + components: [grid, velocity, T, D, AR, N2, S-CH2, T-CH2, O, H2, H, OH, H2O, O2, HO2, + CH, CO, HCO, CH2O, CH3, CO2, CH4, C2H3, C2H4, C2H5, C2H, HCCO, C2H2, + C3H3, A-C3H5, N-C3H7, C2H6, P-C3H4, A-C3H4, A1, A1-, C5H5, C3H6, C4H8, + C5H6, A2, C5H10, C5H11, A1C2H2, A1CH2, A1CHO, A1CH3, C7H15, N-C7H16, + A1C2H*, A2-, A1C2H] + outlet: + size: 0 + type: outlet + points: 1 diff --git a/samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml 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2.209004684050504e-12, 9.745178336063923e-13, 4.351065803884652e-13, + 1.959742036087853e-13, 8.877429299295270e-14, 4.033760971179704e-14, + 1.834531444376107e-14, 8.337372154444206e-15, 3.782440555268464e-15, + 1.712179079056678e-15, 7.733458046375476e-16, 3.486864330420177e-16, + 1.570538030743587e-16, 7.072998636725401e-17, 3.187935806731292e-17, + 1.439210423784746e-17, 6.511063151224956e-18, 2.945867167310686e-18, + 6.201938504786157e-19, 1.306772531749248e-19, 6.847637315797411e-21, + 3.970099950544625e-22, -1.716948145959151e-23, 2.097239934018185e-23, + 2.029223671651144e-23, 1.039150043002606e-22, 8.572315829734414e-25, + 9.969350204483684e-26, 2.206213741426378e-26, 8.491437863994048e-27, + 4.716602785763271e-27, 3.074147504932471e-27, 2.066824137239012e-27, + 1.340188612079251e-27, 7.845386992529860e-28, 3.490018573822431e-28, 0.0] + type: flamelet-flow + size: 144 + points: 145 + tolerances: + steady-reltol: 1.0e-04 + steady-abstol: 1.0e-09 + transient-reltol: 1.0e-04 + transient-abstol: 1.0e-11 + transport-model: mixture-averaged + phase: + name: gas + source: ././inputs/Lu.yaml + radiation-enabled: false + energy-enabled: true + Soret-enabled: false + species-enabled: true + refine-criteria: + ratio: 4.0 + slope: 0.1 + curve: 0.1 + prune: 0.0 + grid-min: 1.0e-10 + max-points: 1000 + basis: mass + components: [grid, T, D, H2, H, O, O2, OH, H2O, HO2, H2O2, CH3, CH4, CO, CO2, CH2O, + CH3OH, C2H2, C2H4, C2H6, CH2CO, N2] + fuel_inlet: + size: 1 + type: inlet + points: 1 + mass-flux: 0.2 + temperature: 300.0 + pressure: 1.01325e+05 + mass-fractions: + CH4: 1.0 diff --git a/samples/python/AVBP/THICKENING.py b/samples/python/AVBP/THICKENING.py new file mode 100644 index 00000000000..94ee0d1860a --- /dev/null +++ b/samples/python/AVBP/THICKENING.py @@ -0,0 +1,67 @@ +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +p = 101325 # pressure +tin = 300.0 # unburned gas temperature +phi = 0.8 # equivalence ratio + +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/BFER_methane.yaml') +else: + gas = ct.Solution('./inputs/BFER_methane.cti') + +m = gas.n_species +x = np.zeros(m,'d') +fuel_species = 'CH4' +ifuel = gas.species_index(fuel_species) +io2 = gas.species_index('O2') + +refine_grid = "disabled" +tol_ss = [1.0e-5, 1.0e-8] # [rtol atol] for steady-state problem +tol_ts = [1.0e-5, 1.0e-8] # [rtol atol] for time stepping +loglevel = 1 # amount of diagnostic output (0 to 5) + +n_points = 1000 +F = [1.0, 2.0, 5.0, 10.0, 15.0, 20.0] +temperature = [] +position = [] + +for ind_thick, thick in enumerate(F): + gas.set_equivalence_ratio(phi, 'CH4:1', 'O2:1.0, N2:3.76') + gas.TP = tin, p + initial_grid = np.linspace(0, 0.02, int(1000/thick)) + f = ct.FreeFlame(gas, grid=initial_grid) + + # This is where thickening is applied + f.flame.thick = thick + + f.energy_enabled = True + f.flame.set_steady_tolerances(default=tol_ss) + f.flame.set_transient_tolerances(default=tol_ts) + f.inlet.X = gas.X + f.inlet.T = tin + #f.set_refine_criteria(ratio = 7.0, slope = 1, curve = 1) + f.set_max_jac_age(50, 50) + f.set_time_step(5.e-06, [10, 20, 80]) #s + #f.set_refine_criteria(ratio = 2.0, slope = 0.02, curve = 0.02, prune = 0.01) + f.solve(loglevel, refine_grid) + + temperature.append(f.T) + position.append(f.flame.grid) + +fig = plt.figure(figsize=(18,16)) +a=fig.add_subplot(111) +for ind_thick, thick in enumerate(F): + a.plot(position[ind_thick],temperature[ind_thick], label="F = "+str(thick)) +plt.title(r'$T_{adiabatic}$ vs. Position', fontsize=25) +plt.xlabel(r'Position [m]', fontsize=20) +plt.ylabel("Adiabatic Flame Temperature [K]", fontsize=20) +plt.xticks(fontsize=15) +plt.yticks(fontsize=15) +#a.xaxis.set_major_locator(MaxNLocator(10)) # this controls the number of tick marks on the axis +plt.legend(fontsize=15) + +plt.show() \ No newline at end of file diff --git a/samples/python/AVBP/inputs/BFER_methane.cti b/samples/python/AVBP/inputs/BFER_methane.cti new file mode 100755 index 00000000000..d8fde74b17b --- /dev/null +++ b/samples/python/AVBP/inputs/BFER_methane.cti @@ -0,0 +1,149 @@ +# CH4_BFER mechanisme: CH4 + 1.5 O2 => CO +2H2O +# CO + 0.5 O2 <=> CO2 +# +# Transport data from file ../transport/gri30_tran.dat. + +units(length = "cm", time = "s", quantity = "mol", act_energy = "cal/mol") + +ideal_gas(name = "BFER_nopea", + elements = " O H C N Ar", + species = """ CH4 CO2 CO O2 H2O N2 """, + reactions = "all", + transport = "AVBP", + initial_state = state(temperature = 300.0, + pressure = OneAtm) ) + +ideal_gas(name = "BFER_pea", + elements = " O H C N Ar", + species = """ CH4 CO2 CO O2 H2O N2 """, + reactions = "all", + transport = "AVBP", + initial_state = state(temperature = 300.0, + pressure = OneAtm) ) + +#------------------------------------------------------------------------------- +# Species data +#------------------------------------------------------------------------------- + +species(name = "O2", + atoms = " O:2 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 3.782456360E+00, -2.996734160E-03, + 9.847302010E-06, -9.681295090E-09, 3.243728370E-12, + -1.063943560E+03, 3.657675730E+00] ), + NASA( [ 1000.00, 3500.00], [ 3.282537840E+00, 1.483087540E-03, + -7.579666690E-07, 2.094705550E-10, -2.167177940E-14, + -1.088457720E+03, 5.453231290E+00] ) + ), + transport = gas_transport( + geom = "linear", + diam = 3.46, + well_depth = 107.40, + polar = 1.60, + rot_relax = 3.80), + note = "TPIS89" + ) + +species(name = "H2O", + atoms = " H:2 O:1 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 4.198640560E+00, -2.036434100E-03, + 6.520402110E-06, -5.487970620E-09, 1.771978170E-12, + -3.029372670E+04, -8.490322080E-01] ), + NASA( [ 1000.00, 3500.00], [ 3.033992490E+00, 2.176918040E-03, + -1.640725180E-07, -9.704198700E-11, 1.682009920E-14, + -3.000429710E+04, 4.966770100E+00] ) + ), + transport = gas_transport( + geom = "nonlinear", + diam = 2.60, + well_depth = 572.40, + dipole = 1.84, + rot_relax = 4.00), + note = "L 8/89" + ) + +species(name = "CH4", + atoms = " C:1 H:4 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 5.149876130E+00, -1.367097880E-02, + 4.918005990E-05, -4.847430260E-08, 1.666939560E-11, + -1.024664760E+04, -4.641303760E+00] ), + NASA( [ 1000.00, 3500.00], [ 7.485149500E-02, 1.339094670E-02, + -5.732858090E-06, 1.222925350E-09, -1.018152300E-13, + -9.468344590E+03, 1.843731800E+01] ) + ), + transport = gas_transport( + geom = "nonlinear", + diam = 3.75, + well_depth = 141.40, + polar = 2.60, + rot_relax = 13.00), + note = "L 8/88" + ) + +species(name = "CO", + atoms = " C:1 O:1 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 3.579533470E+00, -6.103536800E-04, + 1.016814330E-06, 9.070058840E-10, -9.044244990E-13, + -1.434408600E+04, 3.508409280E+00] ), + NASA( [ 1000.00, 3500.00], [ 2.715185610E+00, 2.062527430E-03, + -9.988257710E-07, 2.300530080E-10, -2.036477160E-14, + -1.415187240E+04, 7.818687720E+00] ) + ), + transport = gas_transport( + geom = "linear", + diam = 3.65, + well_depth = 98.10, + polar = 1.95, + rot_relax = 1.80), + note = "TPIS79" + ) + +species(name = "CO2", + atoms = " C:1 O:2 ", + thermo = ( + NASA( [ 200.00, 1000.00], [ 2.356773520E+00, 8.984596770E-03, + -7.123562690E-06, 2.459190220E-09, -1.436995480E-13, + -4.837196970E+04, 9.901052220E+00] ), + NASA( [ 1000.00, 3500.00], [ 3.857460290E+00, 4.414370260E-03, + -2.214814040E-06, 5.234901880E-10, -4.720841640E-14, + -4.875916600E+04, 2.271638060E+00] ) + ), + transport = gas_transport( + geom = "linear", + diam = 3.76, + well_depth = 244.00, + polar = 2.65, + rot_relax = 2.10), + note = "L 7/88" + ) + +species(name = "N2", + atoms = " N:2 ", + thermo = ( + NASA( [ 300.00, 1000.00], [ 3.298677000E+00, 1.408240400E-03, + -3.963222000E-06, 5.641515000E-09, -2.444854000E-12, + -1.020899900E+03, 3.950372000E+00] ), + NASA( [ 1000.00, 5000.00], [ 2.926640000E+00, 1.487976800E-03, + -5.684760000E-07, 1.009703800E-10, -6.753351000E-15, + -9.227977000E+02, 5.980528000E+00] ) + ), + transport = gas_transport( + geom = "linear", + diam = 3.62, + well_depth = 97.53, + polar = 1.76, + rot_relax = 4.00), + note = "121286" + ) + +#------------------------------------------------------------------------------- +# Reaction data +#------------------------------------------------------------------------------- +# Reaction +reaction( " CH4 + 1.5 O2 => CO + 2 H2O ", [4.9E+09, 0.0, 35500], order="CH4:0.5 O2:0.65 ") + +# Reaction 2 +reaction( " CO + 0.5 O2 <=> CO2", [2.00E+08, 0.7, 12000]) \ No newline at end of file diff --git a/samples/python/AVBP/inputs/BFER_methane.yaml b/samples/python/AVBP/inputs/BFER_methane.yaml new file mode 100644 index 00000000000..e063132325b --- /dev/null +++ b/samples/python/AVBP/inputs/BFER_methane.yaml @@ -0,0 +1,151 @@ +description: |- + CH4_BFER mechanisme: CH4 + 1.5 O2 => CO +2H2O + CO + 0.5 O2 <=> CO2 + + Transport data from file ../transport/gri30_tran.dat. + +generator: cti2yaml +cantera-version: 3.0.0 +date: Tue, 19 Dec 2023 15:25:36 +0100 +input-files: [BFER_methane.cti] + +units: {length: cm, quantity: mol, activation-energy: cal/mol} + +phases: +- name: BFER_nopea + thermo: ideal-gas + elements: [O, H, C, N, Ar] + species: [CH4, CO2, CO, O2, H2O, N2] + kinetics: gas + reactions: all + transport: AVBP + state: + T: 300.0 + P: 1.01325e+05 +- name: BFER_pea + thermo: ideal-gas + elements: [O, H, C, N, Ar] + species: [CH4, CO2, CO, O2, H2O, N2] + kinetics: gas + reactions: all + transport: AVBP + state: + T: 300.0 + P: 1.01325e+05 + +species: +- name: O2 + composition: {O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.78245636, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09, 3.24372837e-12, + -1063.94356, 3.65767573] + - [3.28253784, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10, -2.16717794e-14, + -1088.45772, 5.45323129] + transport: + model: gas + geometry: linear + diameter: 3.46 + well-depth: 107.4 + polarizability: 1.6 + rotational-relaxation: 3.8 + note: TPIS89 +- name: H2O + composition: {H: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19864056, -2.0364341e-03, 6.52040211e-06, -5.48797062e-09, 1.77197817e-12, + -3.02937267e+04, -0.849032208] + - [3.03399249, 2.17691804e-03, -1.64072518e-07, -9.7041987e-11, 1.68200992e-14, + -3.00042971e+04, 4.9667701] + transport: + model: gas + geometry: nonlinear + diameter: 2.6 + well-depth: 572.4 + dipole: 1.84 + rotational-relaxation: 4.0 + note: L 8/89 +- name: CH4 + composition: {C: 1, H: 4} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.14987613, -0.0136709788, 4.91800599e-05, -4.84743026e-08, 1.66693956e-11, + -1.02466476e+04, -4.64130376] + - [0.074851495, 0.0133909467, -5.73285809e-06, 1.22292535e-09, -1.0181523e-13, + -9468.34459, 18.437318] + transport: + model: gas + geometry: nonlinear + diameter: 3.75 + well-depth: 141.4 + polarizability: 2.6 + rotational-relaxation: 13.0 + note: L 8/88 +- name: CO + composition: {C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.57953347, -6.1035368e-04, 1.01681433e-06, 9.07005884e-10, -9.04424499e-13, + -1.4344086e+04, 3.50840928] + - [2.71518561, 2.06252743e-03, -9.98825771e-07, 2.30053008e-10, -2.03647716e-14, + -1.41518724e+04, 7.81868772] + transport: + model: gas + geometry: linear + diameter: 3.65 + well-depth: 98.1 + polarizability: 1.95 + rotational-relaxation: 1.8 + note: TPIS79 +- name: CO2 + composition: {C: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.35677352, 8.98459677e-03, -7.12356269e-06, 2.45919022e-09, -1.43699548e-13, + -4.83719697e+04, 9.90105222] + - [3.85746029, 4.41437026e-03, -2.21481404e-06, 5.23490188e-10, -4.72084164e-14, + -4.8759166e+04, 2.27163806] + transport: + model: gas + geometry: linear + diameter: 3.76 + well-depth: 244.0 + polarizability: 2.65 + rotational-relaxation: 2.1 + note: L 7/88 +- name: N2 + composition: {N: 2} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12, + -1020.8999, 3.950372] + - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15, + -922.7977, 5.980528] + transport: + model: gas + geometry: linear + diameter: 3.62 + well-depth: 97.53 + polarizability: 1.76 + rotational-relaxation: 4.0 + note: '121286' + +reactions: +- equation: ' CH4 + 1.5 O2 => CO + 2 H2O ' # Reaction 1 + rate-constant: {A: 4.9e+09, b: 0.0, Ea: 35500} + orders: {CH4: 0.5, O2: 0.65} +- equation: ' CO + 0.5 O2 <=> CO2' # Reaction 2 + rate-constant: {A: 2.0e+08, b: 0.7, Ea: 12000} diff --git a/samples/python/AVBP/inputs/BISETTI.cti b/samples/python/AVBP/inputs/BISETTI.cti new file mode 100644 index 00000000000..5d440837551 --- /dev/null +++ b/samples/python/AVBP/inputs/BISETTI.cti @@ -0,0 +1,1537 @@ +units(length='cm', time='s', quantity='mol', act_energy='cal/mol') + +ideal_gas(name='gas', + elements="N C H O Ar", + species="""AR N2 S-CH2 T-CH2 O H2 H + OH H2O O2 HO2 CH CO + HCO CH2O CH3 CO2 CH4 C2H3 + C2H4 C2H5 C2H HCCO C2H2 C3H3 + A-C3H5 N-C3H7 C2H6 P-C3H4 A-C3H4 A1 + A1- C5H5 C3H6 C4H8 C5H6 A2 + C5H10 C5H11 A1C2H2 A1CH2 A1CHO A1CH3 + C7H15 N-C7H16 A1C2H* A2- A1C2H""", + reactions='all', + transport='Mix', + initial_state=state(temperature=300.0, pressure=OneAtm)) + +#------------------------------------------------------------------------------- +# Species data +#------------------------------------------------------------------------------- + +species(name='AR', + atoms='Ar:1', + thermo=(NASA([200.00, 1000.00], + [ 2.50000000E+00, 0.00000000E+00, 0.00000000E+00, + 0.00000000E+00, 0.00000000E+00, -7.45375000E+02, + 4.37967491E+00]), + NASA([1000.00, 6000.00], + [ 2.50000000E+00, 0.00000000E+00, 0.00000000E+00, + 0.00000000E+00, 0.00000000E+00, -7.45375000E+02, + 4.37967491E+00])), + transport=gas_transport(geom='atom', + diam=3.33, + well_depth=136.5), + note='REFELEMENTG5/97') + +species(name=u'N2', + atoms='N:2', + thermo=(NASA([300.00, 1000.00], + [ 3.29867700E+00, 1.40824040E-03, -3.96322200E-06, + 5.64151500E-09, -2.44485400E-12, -1.02089990E+03, + 3.95037200E+00]), + NASA([1000.00, 5000.00], + [ 2.92664000E+00, 1.48797680E-03, -5.68476000E-07, + 1.00970380E-10, -6.75335100E-15, -9.22797700E+02, + 5.98052800E+00])), + transport=gas_transport(geom='linear', + diam=3.621, + well_depth=97.53, + polar=1.76, + rot_relax=4.0), + note=u'121286') + +species(name=u'S-CH2', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19860411E+00, -2.36661419E-03, 8.23296220E-06, + -6.68815981E-09, 1.94314737E-12, 5.04968163E+04, + -7.69118967E-01]), + NASA([1000.00, 3500.00], + [ 2.29203842E+00, 4.65588637E-03, -2.01191947E-06, + 4.17906000E-10, -3.39716365E-14, 5.09259997E+04, + 8.62650169E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'LS/93') + +species(name=u'T-CH2', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.76267867E+00, 9.68872143E-04, 2.79489841E-06, + -3.85091153E-09, 1.68741719E-12, 4.60040401E+04, + 1.56253185E+00]), + NASA([1000.00, 3500.00], + [ 2.87410113E+00, 3.65639292E-03, -1.40894597E-06, + 2.60179549E-10, -1.87727567E-14, 4.62636040E+04, + 6.17119324E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'LS/93') + +species(name=u'O', + atoms='O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.16826710E+00, -3.27931884E-03, 6.64306396E-06, + -6.12806624E-09, 2.11265971E-12, 2.91222592E+04, + 2.05193346E+00]), + NASA([1000.00, 3500.00], + [ 2.56942078E+00, -8.59741137E-05, 4.19484589E-08, + -1.00177799E-11, 1.22833691E-15, 2.92175791E+04, + 4.78433864E+00])), + transport=gas_transport(geom='atom', + diam=2.75, + well_depth=80.0), + note=u'L1/90') + +species(name=u'H2', + atoms='H:2', + thermo=(NASA([200.00, 1000.00], + [ 2.34433112E+00, 7.98052075E-03, -1.94781510E-05, + 2.01572094E-08, -7.37611761E-12, -9.17935173E+02, + 6.83010238E-01]), + NASA([1000.00, 3500.00], + [ 3.33727920E+00, -4.94024731E-05, 4.99456778E-07, + -1.79566394E-10, 2.00255376E-14, -9.50158922E+02, + -3.20502331E+00])), + transport=gas_transport(geom='linear', + diam=2.92, + well_depth=38.0, + polar=0.79, + rot_relax=280.0), + note=u'TPIS78') + +species(name=u'H', + atoms='H:1', + thermo=(NASA([200.00, 1000.00], + [ 2.50000000E+00, 7.05332819E-13, -1.99591964E-15, + 2.30081632E-18, -9.27732332E-22, 2.54736599E+04, + -4.46682853E-01]), + NASA([1000.00, 3500.00], + [ 2.50000001E+00, -2.30842973E-11, 1.61561948E-14, + -4.73515235E-18, 4.98197357E-22, 2.54736599E+04, + -4.46682914E-01])), + transport=gas_transport(geom='atom', + diam=2.05, + well_depth=145.0), + note=u'L7/88') + +species(name=u'OH', + atoms='H:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.12530561E+00, -3.22544939E-03, 6.52764691E-06, + -5.79853643E-09, 2.06237379E-12, 3.38153812E+03, + -6.90432960E-01]), + NASA([1000.00, 6000.00], + [ 2.86472886E+00, 1.05650448E-03, -2.59082758E-07, + 3.05218674E-11, -1.33195876E-15, 3.71885774E+03, + 5.70164073E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note=u'S9/01') + +species(name=u'H2O', + atoms='H:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19864056E+00, -2.03643410E-03, 6.52040211E-06, + -5.48797062E-09, 1.77197817E-12, -3.02937267E+04, + -8.49032208E-01]), + NASA([1000.00, 3500.00], + [ 3.03399249E+00, 2.17691804E-03, -1.64072518E-07, + -9.70419870E-11, 1.68200992E-14, -3.00042971E+04, + 4.96677010E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.605, + well_depth=572.4, + dipole=1.844, + rot_relax=4.0), + note=u'L8/89') + +species(name=u'O2', + atoms='O:2', + thermo=(NASA([200.00, 1000.00], + [ 3.78245636E+00, -2.99673416E-03, 9.84730201E-06, + -9.68129509E-09, 3.24372837E-12, -1.06394356E+03, + 3.65767573E+00]), + NASA([1000.00, 3500.00], + [ 3.28253784E+00, 1.48308754E-03, -7.57966669E-07, + 2.09470555E-10, -2.16717794E-14, -1.08845772E+03, + 5.45323129E+00])), + transport=gas_transport(geom='linear', + diam=3.458, + well_depth=107.4, + polar=1.6, + rot_relax=3.8), + note=u'TPIS89') + +species(name=u'HO2', + atoms='H:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30179801E+00, -4.74912051E-03, 2.11582891E-05, + -2.42763894E-08, 9.29225124E-12, 2.94808040E+02, + 3.71666245E+00]), + NASA([1000.00, 3500.00], + [ 4.01721090E+00, 2.23982013E-03, -6.33658150E-07, + 1.14246370E-10, -1.07908535E-14, 1.11856713E+02, + 3.78510215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=1.0), + note=u'L5/89') + +species(name=u'CH', + atoms='H:1 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.48981665E+00, 3.23835541E-04, -1.68899065E-06, + 3.16217327E-09, -1.40609067E-12, 7.07972934E+04, + 2.08401108E+00]), + NASA([1000.00, 3500.00], + [ 2.87846473E+00, 9.70913681E-04, 1.44445655E-07, + -1.30687849E-10, 1.76079383E-14, 7.10124364E+04, + 5.48497999E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note=u'TPIS79') + +species(name=u'CO', + atoms='C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.57953347E+00, -6.10353680E-04, 1.01681433E-06, + 9.07005884E-10, -9.04424499E-13, -1.43440860E+04, + 3.50840928E+00]), + NASA([1000.00, 3500.00], + [ 2.71518561E+00, 2.06252743E-03, -9.98825771E-07, + 2.30053008E-10, -2.03647716E-14, -1.41518724E+04, + 7.81868772E+00])), + transport=gas_transport(geom='linear', + diam=3.65, + well_depth=98.1, + polar=1.95, + rot_relax=1.8), + note=u'TPIS79') + +species(name=u'HCO', + atoms='H:1 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.22118584E+00, -3.24392532E-03, 1.37799446E-05, + -1.33144093E-08, 4.33768865E-12, 3.83956496E+03, + 3.39437243E+00]), + NASA([1000.00, 3500.00], + [ 2.77217438E+00, 4.95695526E-03, -2.48445613E-06, + 5.89161778E-10, -5.33508711E-14, 4.01191815E+03, + 9.79834492E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0), + note=u'L12/89') + +species(name=u'CH2O', + atoms='H:2 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.79372315E+00, -9.90833369E-03, 3.73220008E-05, + -3.79285261E-08, 1.31772652E-11, -1.43089567E+04, + 6.02812900E-01]), + NASA([1000.00, 3500.00], + [ 1.76069008E+00, 9.20000082E-03, -4.42258813E-06, + 1.00641212E-09, -8.83855640E-14, -1.39958323E+04, + 1.36563230E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0, + rot_relax=2.0), + note=u'L8/88') + +species(name=u'CH3', + atoms='H:3 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.65717970E+00, 2.12659790E-03, 5.45838830E-06, + -6.61810030E-09, 2.46570740E-12, 1.64227160E+04, + 1.67353540E+00]), + NASA([1000.00, 6000.00], + [ 2.97812060E+00, 5.79785200E-03, -1.97558000E-06, + 3.07297900E-10, -1.79174160E-14, 1.65095130E+04, + 4.72247990E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'METHYLIU0702') + +species(name=u'CO2', + atoms='C:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 2.35677352E+00, 8.98459677E-03, -7.12356269E-06, + 2.45919022E-09, -1.43699548E-13, -4.83719697E+04, + 9.90105222E+00]), + NASA([1000.00, 3500.00], + [ 3.85746029E+00, 4.41437026E-03, -2.21481404E-06, + 5.23490188E-10, -4.72084164E-14, -4.87591660E+04, + 2.27163806E+00])), + transport=gas_transport(geom='linear', + diam=3.763, + well_depth=244.0, + polar=2.65, + rot_relax=2.1), + note=u'L7/88') + +species(name=u'CH4', + atoms='H:4 C:1', + thermo=(NASA([200.00, 1000.00], + [ 5.14911468E+00, -1.36622009E-02, 4.91453921E-05, + -4.84246767E-08, 1.66603441E-11, -1.02465983E+04, + -4.63848842E+00]), + NASA([1000.00, 6000.00], + [ 1.65326226E+00, 1.00263099E-02, -3.31661238E-06, + 5.36483138E-10, -3.14696758E-14, -1.00095936E+04, + 9.90506283E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.746, + well_depth=141.4, + polar=2.6, + rot_relax=13.0), + note=u'g8/99') + +species(name=u'C2H3', + atoms='H:3 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.21246645E+00, 1.51479162E-03, 2.59209412E-05, + -3.57657847E-08, 1.47150873E-11, 3.48598468E+04, + 8.51054025E+00]), + NASA([1000.00, 3500.00], + [ 3.01672400E+00, 1.03302292E-02, -4.68082349E-06, + 1.01763288E-09, -8.62607041E-14, 3.46128739E+04, + 7.78732378E+00])), + transport=gas_transport(geom='nonlinear', + diam=4.1, + well_depth=209.0, + rot_relax=1.0), + note=u'L2/92') + +species(name=u'C2H4', + atoms='H:4 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.95920148E+00, -7.57052247E-03, 5.70990292E-05, + -6.91588753E-08, 2.69884373E-11, 5.08977593E+03, + 4.09733096E+00]), + NASA([1000.00, 3500.00], + [ 2.03611116E+00, 1.46454151E-02, -6.71077915E-06, + 1.47222923E-09, -1.25706061E-13, 4.93988614E+03, + 1.03053693E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.971, + well_depth=280.8, + rot_relax=1.5), + note=u'L1/91') + +species(name=u'C2H5', + atoms='H:5 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30646568E+00, -4.18658892E-03, 4.97142807E-05, + -5.99126606E-08, 2.30509004E-11, 1.28416265E+04, + 4.70720924E+00]), + NASA([1000.00, 3500.00], + [ 1.95465642E+00, 1.73972722E-02, -7.98206668E-06, + 1.75217689E-09, -1.49641576E-13, 1.28575200E+04, + 1.34624343E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note=u'L12/92') + +species(name=u'C2H', + atoms='H:1 C:2', + thermo=(NASA([200.00, 1000.00], + [ 2.88965733E+00, 1.34099611E-02, -2.84769501E-05, + 2.94791045E-08, -1.09331511E-11, 6.68393932E+04, + 6.22296438E+00]), + NASA([1000.00, 3500.00], + [ 3.16780652E+00, 4.75221902E-03, -1.83787077E-06, + 3.04190252E-10, -1.77232770E-14, 6.71210650E+04, + 6.63589475E+00])), + transport=gas_transport(geom='linear', + diam=4.1, + well_depth=209.0, + rot_relax=2.5), + note=u'L1/91') + +species(name=u'HCCO', + atoms='H:1 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.25172140E+00, 1.76550210E-02, -2.37291010E-05, + 1.72757590E-08, -5.06648110E-12, 2.00594490E+04, + 1.24904170E+01]), + NASA([1000.00, 4000.00], + [ 5.62820580E+00, 4.08534010E-03, -1.59345470E-06, + 2.86260520E-10, -1.94078320E-14, 1.93272150E+04, + -3.93025950E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.5, + well_depth=150.0, + rot_relax=1.0), + note=u'SRIC91') + +species(name=u'C2H2', + atoms='H:2 C:2', + thermo=(NASA([200.00, 1000.00], + [ 8.08681094E-01, 2.33615629E-02, -3.55171815E-05, + 2.80152437E-08, -8.50072974E-12, 2.64289807E+04, + 1.39397051E+01]), + NASA([1000.00, 3500.00], + [ 4.14756964E+00, 5.96166664E-03, -2.37294852E-06, + 4.67412171E-10, -3.61235213E-14, 2.59359992E+04, + -1.23028121E+00])), + transport=gas_transport(geom='linear', + diam=4.1, + well_depth=209.0, + rot_relax=2.5), + note=u'L1/91') + +species(name=u'C3H3', + atoms='H:3 C:3', + thermo=(NASA([300.00, 1000.00], + [ 1.40299238E+00, 3.01773327E-02, -3.98449373E-05, + 2.93534629E-08, -8.70554579E-12, 3.93108220E+04, + 1.51527845E+01]), + NASA([1000.00, 3000.00], + [ 6.14915291E+00, 9.34063166E-03, -3.75055354E-06, + 6.90156316E-10, -4.60824994E-14, 3.83854848E+04, + -7.45345215E+00])), + transport=gas_transport(geom='nonlinear', + diam=4.76, + well_depth=252.0, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A-C3H5', + atoms='H:5 C:3', + thermo=(NASA([300.00, 1000.00], + [-1.03516444E+00, 3.75043366E-02, -3.26381242E-05, + 1.47662613E-08, -2.43741154E-12, 1.88792254E+04, + 2.71451071E+01]), + NASA([1000.00, 3000.00], + [ 2.28794927E+00, 2.36401575E-02, -1.27891450E-05, + 3.36838540E-09, -3.47449449E-13, 1.83033514E+04, + 1.14063418E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.982, + well_depth=266.8, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'N-C3H7', + atoms='H:7 C:3', + thermo=(NASA([298.15, 1000.00], + [ 1.04754730E+00, 2.60077940E-02, 2.35622520E-06, + -1.95923170E-08, 9.36801160E-12, 1.06326370E+04, + 2.11418760E+01]), + NASA([1000.00, 5000.00], + [ 7.70404050E+00, 1.60415400E-02, -5.28159670E-06, + 7.62544030E-10, -3.93534620E-14, 8.29795310E+03, + -1.54875140E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.982, + well_depth=266.8, + rot_relax=1.0), + note=u'N-L9/85') + +species(name=u'C2H6', + atoms='H:6 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.29142492E+00, -5.50154270E-03, 5.99438288E-05, + -7.08466285E-08, 2.68685771E-11, -1.15222055E+04, + 2.66682316E+00]), + NASA([1000.00, 3500.00], + [ 1.07188150E+00, 2.16852677E-02, -1.00256067E-05, + 2.21412001E-09, -1.90002890E-13, -1.14263932E+04, + 1.51156107E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note=u'L8/88') + +species(name=u'P-C3H4', + atoms='H:4 C:3', + thermo=(NASA([300.00, 1000.00], + [ 1.46175323E+00, 2.46026602E-02, -1.90219395E-05, + 8.60363422E-09, -1.66729240E-12, 2.09209793E+04, + 1.49262585E+01]), + NASA([1000.00, 3000.00], + [ 2.81460543E+00, 1.85524496E-02, -9.55026768E-06, + 2.39951370E-09, -2.37485257E-13, 2.07010771E+04, + 8.60604972E+00])), + transport=gas_transport(geom='nonlinear', + diam=4.76, + well_depth=252.0, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A-C3H4', + atoms='H:4 C:3', + thermo=(NASA([300.00, 1000.00], + [ 3.68928265E-01, 2.89351397E-02, -2.44386408E-05, + 1.12547166E-08, -2.03040262E-12, 2.17585256E+04, + 1.95267211E+01]), + NASA([1000.00, 3000.00], + [ 2.56128757E+00, 1.95080128E-02, -1.04061366E-05, + 2.70165173E-09, -2.75074329E-13, 2.13894289E+04, + 9.20550397E+00])), + transport=gas_transport(geom='nonlinear', + diam=4.76, + well_depth=252.0, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1', + atoms='H:6 C:6', + thermo=(NASA([300.00, 1000.00], + [-5.51558393E+00, 6.45453225E-02, -4.41402928E-05, + 7.47712161E-09, 3.10282254E-12, 9.11031457E+03, + 4.65332293E+01]), + NASA([1000.00, 3000.00], + [-2.06240612E-01, 4.64122440E-02, -2.77653536E-05, + 7.88910537E-09, -8.60365259E-13, 8.09883905E+03, + 2.06566629E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.29, + well_depth=464.8, + polar=10.32, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1-', + atoms='H:5 C:6', + thermo=(NASA([300.00, 1000.00], + [-4.87654845E+00, 6.26805782E-02, -4.87402286E-05, + 1.41122287E-08, 5.18518312E-13, 3.99269438E+04, + 4.59964173E+01]), + NASA([1000.00, 3000.00], + [ 1.38016336E+00, 4.04032009E-02, -2.42250885E-05, + 6.88723321E-09, -7.50960802E-13, 3.86973520E+04, + 1.55220921E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.29, + well_depth=464.8, + polar=10.32, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'C5H5', + atoms='H:5 C:5', + thermo=(NASA([300.00, 1000.00], + [-7.37844042E+00, 9.72391818E-02, -1.69579138E-04, + 1.51818667E-07, -5.12075479E-11, 3.05514662E+04, + 5.12829539E+01]), + NASA([1000.00, 3000.00], + [ 4.21464919E+00, 2.71834728E-02, -1.33173209E-05, + 3.08980119E-09, -2.77879873E-13, 2.88952416E+04, + -3.05999781E-02])), + transport=gas_transport(geom='nonlinear', + diam=5.2, + well_depth=400.0, + rot_relax=1.0), + note=u'Refitted') + +species(name=u'C3H6', + atoms='H:6 C:3', + thermo=(NASA([300.00, 1000.00], + [-2.29261670E-03, 3.10261065E-02, -1.67151548E-05, + 1.89594170E-09, 1.24957915E-12, 1.13437406E+03, + 2.35719601E+01]), + NASA([1000.00, 3000.00], + [ 4.71697982E-01, 2.89513070E-02, -1.56601819E-05, + 4.11443199E-09, -4.23075141E-13, 1.12603387E+03, + 2.15237289E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.982, + well_depth=266.8, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'C4H8', + atoms='H:8 C:4', + thermo=(NASA([300.00, 1000.00], + [-8.31372089E-01, 4.52580978E-02, -2.93658559E-05, + 1.00220436E-08, -1.43191680E-12, -1.57875035E+03, + 2.95084236E+01]), + NASA([1000.00, 5000.00], + [ 3.04470367E+00, 3.27451765E-02, -1.45363237E-05, + 2.39744017E-09, 0.00000000E+00, -2.52177534E+03, + 1.00151514E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.088, + well_depth=345.7, + dipole=0.3, + rot_relax=1.0), + note=u'000000') + +species(name=u'C5H6', + atoms='H:6 C:5', + thermo=(NASA([300.00, 1000.00], + [-5.13691194E+00, 6.06953453E-02, -4.60552837E-05, + 1.28457201E-08, 7.41214852E-13, 1.53675713E+04, + 4.61567559E+01]), + NASA([1000.00, 3000.00], + [ 2.30537462E-01, 4.09571826E-02, -2.41588958E-05, + 6.79763480E-09, -7.36374421E-13, 1.43779465E+04, + 2.02551234E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.2, + well_depth=400.0), + note=u'G3B3') + +species(name=u'A2', + atoms='H:8 C:10', + thermo=(NASA([300.00, 1000.00], + [-8.72434585E+00, 1.05376008E-01, -8.01710690E-05, + 2.18545974E-08, 1.42066606E-12, 1.48059774E+04, + 6.19827540E+01]), + NASA([1000.00, 3000.00], + [ 1.76826275E+00, 6.89143506E-02, -4.14322176E-05, + 1.17914309E-08, -1.28597061E-12, 1.26883657E+04, + 1.06256608E+01])), + transport=gas_transport(geom='nonlinear', + diam=6.18, + well_depth=630.4, + polar=16.5, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'C5H10', + atoms='H:10 C:5', + thermo=(NASA([300.00, 1000.00], + [-1.06223481E+00, 5.74218294E-02, -3.74486890E-05, + 1.27364989E-08, -1.79609789E-12, -4.46546666E+03, + 3.22739790E+01]), + NASA([1000.00, 5000.00], + [ 3.98580522E+00, 4.12429986E-02, -1.84390497E-05, + 3.06155241E-09, 0.00000000E+00, -5.70112071E+03, + 6.85332264E+00])), + transport=gas_transport(geom='nonlinear', + diam=5.489, + well_depth=386.2, + dipole=0.4, + rot_relax=1.0), + note=u'000000') + +species(name=u'C5H11', + atoms='H:11 C:5', + thermo=(NASA([300.00, 1000.00], + [-9.05255912E-01, 6.10632852E-02, -4.09491825E-05, + 1.46093470E-08, -2.18859615E-12, 4.83995303E+03, + 3.25574963E+01]), + NASA([1000.00, 5000.00], + [ 4.88920629E+00, 4.22834537E-02, -1.85843100E-05, + 3.04124763E-09, 0.00000000E+00, 3.43475468E+03, + 3.43704878E+00])), + transport=gas_transport(geom='nonlinear', + diam=5.041, + well_depth=440.735), + note=u'000000') + +species(name=u'A1C2H2', + atoms='H:7 C:8', + thermo=(NASA([300.00, 1000.00], + [-6.31199276E+00, 9.51097942E-02, -9.56352102E-05, + 4.97780207E-08, -1.02323717E-11, 4.57330975E+04, + 5.35475222E+01]), + NASA([1000.00, 3000.00], + [ 5.85935080E+00, 4.72571459E-02, -2.69864733E-05, + 7.35311775E-09, -7.74900830E-13, 4.33198974E+04, + -5.22359403E+00])), + transport=gas_transport(geom='nonlinear', + diam=6.0, + well_depth=546.2, + dipole=0.13, + polar=15.0, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1CH2', + atoms='H:7 C:7', + thermo=(NASA([300.00, 1000.00], + [-6.07053038E+00, 8.35201507E-02, -7.41700083E-05, + 3.13153847E-08, -4.23670868E-12, 2.35894712E+04, + 5.07932172E+01]), + NASA([1000.00, 3000.00], + [ 3.30049696E+00, 4.80055340E-02, -2.78443022E-05, + 7.72371356E-09, -8.27154136E-13, 2.17498572E+04, + 5.42371919E+00])), + transport=gas_transport(geom='nonlinear', + diam=5.68, + well_depth=495.3, + dipole=0.43, + polar=12.3, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1CHO', + atoms='H:6 C:7 O:1', + thermo=(NASA([300.00, 1000.00], + [-3.47171048E+00, 6.92891889E-02, -4.32603509E-05, + 3.43871096E-09, 4.81010261E-12, -6.14558774E+03, + 4.14094024E+01]), + NASA([1000.00, 3000.00], + [ 1.87355756E+00, 5.26231551E-02, -3.17644962E-05, + 9.06403069E-09, -9.90306123E-13, -7.23603865E+03, + 1.49787009E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.68, + well_depth=495.3, + dipole=0.43, + polar=12.3, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1CH3', + atoms='H:8 C:7', + thermo=(NASA([300.00, 1000.00], + [-4.54072038E+00, 6.85427145E-02, -3.57113024E-05, + -4.19397642E-09, 7.41779795E-12, 4.64121087E+03, + 4.57564849E+01]), + NASA([1000.00, 3000.00], + [-1.01117220E+00, 5.85301912E-02, -3.47595069E-05, + 9.82180993E-09, -1.06680870E-12, 3.99363395E+03, + 2.83610783E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.68, + well_depth=495.3, + dipole=0.43, + polar=12.3, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'C7H15', + atoms='H:15 C:7', + thermo=(NASA([300.00, 1000.00], + [-3.79155767E-02, 7.56726570E-02, -4.07473634E-05, + 9.32678943E-09, -4.92360745E-13, -2.35605303E+03, + 3.37321506E+01]), + NASA([1000.00, 5000.00], + [ 3.74721159E+00, 6.49345162E-02, -3.01341025E-05, + 5.17418142E-09, 0.00000000E+00, -3.37018357E+03, + 1.42780413E+01])), + transport=gas_transport(geom='nonlinear', + diam=6.253, + well_depth=459.6, + rot_relax=1.0), + note=u'000000') + +species(name=u'N-C7H16', + atoms='H:16 C:7', + thermo=(NASA([300.00, 1000.00], + [-1.26836187E+00, 8.54355820E-02, -5.25346786E-05, + 1.62945721E-08, -2.02394925E-12, -2.56586565E+04, + 3.53732912E+01]), + NASA([1000.00, 5000.00], + [ 5.14079241E+00, 6.53078671E-02, -2.94827624E-05, + 4.93726726E-09, 0.00000000E+00, -2.72533890E+04, + 2.98195967E+00])), + transport=gas_transport(geom='nonlinear', + diam=6.253, + well_depth=459.6, + rot_relax=1.0), + note=u'000000') + +species(name=u'A1C2H*', + atoms='H:5 C:8', + thermo=(NASA([300.00, 1000.00], + [-4.42757639E+00, 8.36668645E-02, -8.70106362E-05, + 4.70285661E-08, -1.01816985E-11, 6.73302359E+04, + 4.48118287E+01]), + NASA([1000.00, 3000.00], + [ 7.23812069E+00, 3.83812109E-02, -2.18850731E-05, + 5.97161247E-09, -6.30351467E-13, 6.49528135E+04, + -1.17512654E+01])), + transport=gas_transport(geom='nonlinear', + diam=5.72, + well_depth=535.6, + dipole=0.77, + polar=12.0, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A2-', + atoms='H:7 C:10', + thermo=(NASA([300.00, 1000.00], + [-8.02718034E+00, 1.02924518E-01, -8.34272010E-05, + 2.72135383E-08, -7.24559554E-13, 5.01363344E+04, + 6.08902264E+01]), + NASA([1000.00, 3000.00], + [ 3.22892303E+00, 6.31264486E-02, -3.80582381E-05, + 1.08454069E-08, -1.18342512E-12, 4.78400840E+04, + 5.82016697E+00])), + transport=gas_transport(geom='nonlinear', + diam=6.18, + well_depth=630.4, + polar=16.5, + rot_relax=1.0), + note=u'G3B3') + +species(name=u'A1C2H', + atoms='H:6 C:8', + thermo=(NASA([300.00, 1000.00], + [-5.21036925E+00, 8.65551944E-02, -8.45007483E-05, + 4.21920706E-08, -8.16766167E-12, 3.52488620E+04, + 4.69445057E+01]), + NASA([1000.00, 3000.00], + [ 5.81520488E+00, 4.40872933E-02, -2.52053858E-05, + 6.90275228E-09, -7.31378908E-13, 3.30271906E+04, + -6.49320690E+00])), + transport=gas_transport(geom='nonlinear', + diam=5.72, + well_depth=535.6, + dipole=0.77, + polar=12.0, + rot_relax=1.0), + note=u'G3B3') + +#------------------------------------------------------------------------------- +# Reaction data +#------------------------------------------------------------------------------- + +# Reaction 1 +reaction('S-CH2 + N2 <=> T-CH2 + N2', [1.500000e+13, 0.0, 599.9]) + +# Reaction 2 +reaction('O + H2 <=> H + OH', [4.590000e+04, 2.7, 6259.56]) + +# Reaction 3 +three_body_reaction('H + O + M => OH + M', [9.430000e+18, -1.0, 0.0], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0') + +# Reaction 4 +three_body_reaction('H + OH + M => H2O + M', [4.400000e+22, -2.0, 0.0], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:6.3 CH4:2.0 C2H6:3.0') + +# Reaction 5 +reaction('OH + H2 <=> H + H2O', [1.730000e+08, 1.51, 3429.73]) + +# Reaction 6 +reaction('2 OH <=> O + H2O', [3.970000e+04, 2.4, -2110.42]) + +# Reaction 7 +falloff_reaction('H + O2 (+ M) => HO2 (+ M)', + kf=[5.120000e+12, 0.44, 0.0], + kf0=[6.330000e+19, -1.4, 0.0], + efficiencies='H2:0.75 H2O:11.89 CO2:2.18 CO:1.09 O2:0.85', + falloff=Troe(A=0.5, T3=0.0, T1=10000000000.0, T2=10000000000.0)) + +# Reaction 8 +reaction('H + O2 <=> O + OH', [2.640000e+16, -0.67, 17041.11]) + +# Reaction 9 +reaction('HO2 + H => O2 + H2', [3.649000e+06, 2.07, -1092.26]) + +# Reaction 10 +reaction('HO2 + H => O + H2O', [3.970000e+12, 0.0, 671.61]) + +# Reaction 11 +reaction('HO2 + H => 2 OH', [7.490000e+13, 0.0, 635.76]) + +# Reaction 12 +reaction('HO2 + O => OH + O2', [4.000000e+13, 0.0, 0.0]) + +# Reaction 13 +reaction('HO2 + OH => H2O + O2', [2.380000e+13, 0.0, -499.52], + options='duplicate') + +# Reaction 14 +reaction('HO2 + OH => H2O + O2', [1.000000e+16, 0.0, 17330.31], + options='duplicate') + +# Reaction 15 +reaction('CH + O => CO + H', [5.700000e+13, 0.0, 0.0]) + +# Reaction 16 +reaction('CH + OH => HCO + H', [3.000000e+13, 0.0, 0.0]) + +# Reaction 17 +reaction('CH + H2 <=> T-CH2 + H', [1.080000e+14, 0.0, 3109.46]) + +# Reaction 18 +reaction('CH + H2O => CH2O + H', [5.710000e+12, 0.0, -755.26]) + +# Reaction 19 +reaction('CH + O2 => HCO + O', [6.710000e+13, 0.0, 0.0]) + +# Reaction 20 +reaction('T-CH2 + O => HCO + H', [8.000000e+13, 0.0, 0.0]) + +# Reaction 21 +reaction('T-CH2 + OH => CH2O + H', [2.000000e+13, 0.0, 0.0]) + +# Reaction 22 +reaction('T-CH2 + OH <=> CH + H2O', [1.130000e+07, 2.0, 2999.52]) + +# Reaction 23 +reaction('T-CH2 + H2 <=> H + CH3', [5.000000e+05, 2.0, 7229.92]) + +# Reaction 24 +reaction('T-CH2 + O2 => CO2 + 2 H', [5.800000e+12, 0.0, 1500.96]) + +# Reaction 25 +reaction('T-CH2 + O2 => CH2O + O', [2.400000e+12, 0.0, 1500.96]) + +# Reaction 26 +reaction('T-CH2 + O2 => OH + H + CO', [5.000000e+12, 0.0, 1500.96]) + +# Reaction 27 +reaction('S-CH2 + H2 <=> CH3 + H', [7.000000e+13, 0.0, 0.0]) + +# Reaction 28 +reaction('S-CH2 + O2 => H + OH + CO', [2.800000e+13, 0.0, 0.0]) + +# Reaction 29 +reaction('S-CH2 + O2 => CO + H2O', [1.200000e+13, 0.0, 0.0]) + +# Reaction 30 +falloff_reaction('S-CH2 + H2O (+ M) => CH2O + H2 (+ M)', + kf=[4.820000e+17, -1.16, 1144.84], + kf0=[1.880000e+38, -6.36, 5040.63], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.6027, T3=208.0, T1=3922.0, T2=10180.0)) + +# Reaction 31 +reaction('S-CH2 + H2O <=> T-CH2 + H2O', [3.000000e+13, 0.0, 0.0]) + +# Reaction 32 +reaction('S-CH2 + H2O => H2 + CH2O', [6.820000e+10, 0.25, -934.51]) + +# Reaction 33 +falloff_reaction('CH3 + H (+ M) <=> CH4 (+ M)', + kf=[6.920000e+13, 0.18, 0.0], + kf0=[3.470000e+38, -6.3, 5074.09], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:3.0 C2H6:3.0') + +# Reaction 34 +reaction('CH3 + O => CH2O + H', [5.060000e+13, 0.0, 0.0]) + +# Reaction 35 +reaction('CH3 + O => H + H2 + CO', [3.370000e+13, 0.0, 0.0]) + +# Reaction 36 +falloff_reaction('CH3 + OH (+ M) => CH2O + H2 (+ M)', + kf=[2.790000e+18, -1.43, 1331.26], + kf0=[4.000000e+36, -5.92, 3140.54], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.412, T3=195.0, T1=5900.0, T2=6394.0)) + +# Reaction 37 +reaction('CH3 + OH <=> T-CH2 + H2O', [5.600000e+07, 1.6, 5420.65]) + +# Reaction 38 +reaction('CH3 + OH <=> S-CH2 + H2O', [6.440000e+17, -1.34, 1417.3]) + +# Reaction 39 +reaction('CH3 + O2 => CH2O + O + H', [1.380000e+13, 0.0, 30480.4]) + +# Reaction 40 +reaction('CH3 + O2 => CH2O + OH', [5.870000e+11, 0.0, 13840.82]) + +# Reaction 41 +reaction('CH3 + HO2 => CH2O + OH + H', [1.000000e+13, 0.0, 0.0]) + +# Reaction 42 +reaction('CH3 + HO2 => CH4 + O2', [3.610000e+12, 0.0, 0.0]) + +# Reaction 43 +reaction('CH3 + CH => C2H3 + H', [3.000000e+13, 0.0, 0.0]) + +# Reaction 44 +reaction('CH3 + T-CH2 => C2H4 + H', [1.000000e+14, 0.0, 0.0]) + +# Reaction 45 +reaction('2 CH3 <=> C2H5 + H', [6.840000e+12, 0.1, 10599.9]) + +# Reaction 46 +reaction('2 CH3 => S-CH2 + CH4', [2.632000e+12, -0.06, 13661.57]) + +# Reaction 47 +reaction('CH4 + H <=> CH3 + H2', [6.600000e+08, 1.62, 10841.3]) + +# Reaction 48 +reaction('CH4 + O <=> CH3 + OH', [1.020000e+09, 1.5, 8599.43]) + +# Reaction 49 +reaction('CH4 + OH <=> CH3 + H2O', [1.000000e+08, 1.6, 3119.02]) + +# Reaction 50 +reaction('CH4 + CH => C2H4 + H', [6.000000e+13, 0.0, 0.0]) + +# Reaction 51 +reaction('CH4 + T-CH2 <=> 2 CH3', [2.460000e+06, 2.0, 8269.6]) + +# Reaction 52 +falloff_reaction('CO + O (+ M) => CO2 (+ M)', + kf=[1.360000e+10, 0.0, 2385.28], + kf0=[1.170000e+24, -2.79, 4192.16], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=1.0, T3=1.0, T1=10000000.0, T2=10000000.0)) + +# Reaction 53 +reaction('CO + OH <=> CO2 + H', [8.000000e+11, 0.14, 7351.82], + options='duplicate') + +# Reaction 54 +reaction('CO + OH <=> CO2 + H', [8.780000e+10, 0.03, -16.73], + options='duplicate') + +# Reaction 55 +reaction('CO + HO2 => CO2 + OH', [3.010000e+13, 0.0, 22999.52]) + +# Reaction 56 +reaction('CO + S-CH2 <=> CO + T-CH2', [9.000000e+12, 0.0, 0.0]) + +# Reaction 57 +reaction('HCO + H => CO + H2', [1.200000e+14, 0.0, 0.0]) + +# Reaction 58 +reaction('HCO + O => CO + OH', [3.000000e+13, 0.0, 0.0]) + +# Reaction 59 +reaction('HCO + O => CO2 + H', [3.000000e+13, 0.0, 0.0]) + +# Reaction 60 +reaction('HCO + OH => CO + H2O', [3.020000e+13, 0.0, 0.0]) + +# Reaction 61 +three_body_reaction('HCO + M <=> CO + H + M', [1.870000e+17, -1.0, 17000.48], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:0.0 CH4:2.0 C2H6:3.0') + +# Reaction 62 +reaction('HCO + H2O <=> CO + H + H2O', [2.240000e+18, -1.0, 17000.48]) + +# Reaction 63 +reaction('HCO + O2 => CO + HO2', [1.200000e+10, 0.81, -726.58]) + +# Reaction 64 +reaction('CH3 + HCO => CH4 + CO', [2.650000e+13, 0.0, 0.0]) + +# Reaction 65 +reaction('CH2O + H <=> HCO + H2', [5.740000e+07, 1.9, 2741.4]) + +# Reaction 66 +reaction('CH2O + O => HCO + OH', [3.900000e+13, 0.0, 3539.67]) + +# Reaction 67 +reaction('CH2O + OH => HCO + H2O', [3.430000e+09, 1.18, -446.94]) + +# Reaction 68 +reaction('CH3 + CH2O => CH4 + HCO', [3.320000e+03, 2.81, 5860.42]) + +# Reaction 69 +reaction('CO2 + CH => HCO + CO', [1.900000e+14, 0.0, 15791.11]) + +# Reaction 70 +reaction('CO2 + S-CH2 <=> CO2 + T-CH2', [7.000000e+12, 0.0, 0.0]) + +# Reaction 71 +reaction('CO2 + S-CH2 => CH2O + CO', [1.400000e+13, 0.0, 0.0]) + +# Reaction 72 +reaction('C2H + O => CH + CO', [5.000000e+13, 0.0, 0.0]) + +# Reaction 73 +reaction('C2H + OH => HCCO + H', [2.000000e+13, 0.0, 0.0]) + +# Reaction 74 +reaction('C2H + O2 => HCO + CO', [1.000000e+13, 0.0, -755.26]) + +# Reaction 75 +reaction('C2H + H2 <=> C2H2 + H', [3.310000e+06, 2.26, 901.05]) + +# Reaction 76 +falloff_reaction('C2H2 + H (+ M) <=> C2H3 (+ M)', + kf=[1.710000e+10, 1.27, 2707.93], + kf0=[6.340000e+31, -4.66, 3781.07], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.2122, T3=1.0, T1=-10210.0)) + +# Reaction 77 +reaction('C2H2 + O => HCCO + H', [8.100000e+06, 2.0, 1900.1]) + +# Reaction 78 +reaction('C2H2 + O => T-CH2 + CO', [1.250000e+07, 2.0, 1900.1]) + +# Reaction 79 +reaction('C2H2 + O => C2H + OH', [3.324000e+16, -0.44, 30697.9]) + +# Reaction 80 +reaction('C2H2 + OH => C2H + H2O', [2.630000e+06, 2.14, 17060.23]) + +# Reaction 81 +reaction('C2H2 + OH => CH3 + CO', [7.530000e+06, 1.55, 2105.64], + options='duplicate') + +# Reaction 82 +reaction('C2H2 + OH => CH3 + CO', [1.280000e+09, 0.73, 2578.87], + options='duplicate') + +# Reaction 83 +reaction('C2H2 + S-CH2 <=> C3H3 + H', [1.900000e+14, 0.0, 0.0]) + +# Reaction 84 +falloff_reaction('C2H3 + H (+ M) => C2H4 (+ M)', + kf=[6.080000e+12, 0.27, 279.64], + kf0=[1.400000e+30, -3.86, 3319.79], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.782, T3=207.5, T1=2663.0, T2=6095.0)) + +# Reaction 85 +reaction('C2H3 + H => C2H2 + H2', [3.000000e+13, 0.0, 0.0]) + +# Reaction 86 +reaction('C2H3 + O => CH3 + CO', [1.030000e+13, 0.21, -427.82]) + +# Reaction 87 +reaction('C2H3 + OH => C2H2 + H2O', [5.000000e+12, 0.0, 0.0]) + +# Reaction 88 +reaction('C2H3 + O2 => C2H2 + HO2', [1.340000e+06, 1.61, -384.8]) + +# Reaction 89 +reaction('C2H3 + O2 => CH3 + CO + O', [3.030000e+11, 0.29, 11.95]) + +# Reaction 90 +reaction('C2H3 + O2 => HCO + CH2O', [4.580000e+16, -1.39, 1015.77]) + +# Reaction 91 +reaction('C2H3 + HCO => C2H4 + CO', [9.000000e+13, 0.0, 0.0]) + +# Reaction 92 +reaction('C2H3 + CH3 => C2H2 + CH4', [9.030000e+12, 0.0, -764.82]) + +# Reaction 93 +reaction('C2H3 + CH3 <=> A-C3H5 + H', [1.930000e+18, -1.25, 7669.69]) + +# Reaction 94 +falloff_reaction('C2H4 + H (+ M) <=> C2H5 (+ M)', + kf=[1.370000e+09, 1.46, 1355.16], + kf0=[2.030000e+39, -6.64, 5769.6], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=-0.569, T3=299.0, T1=-9147.0, T2=152.4)) + +# Reaction 95 +reaction('C2H4 + H => C2H3 + H2', [1.330000e+06, 2.53, 12239.48]) + +# Reaction 96 +reaction('C2H4 + O => CH3 + CO + H', [7.660000e+09, 0.88, 1140.06]) + +# Reaction 97 +reaction('C2H4 + O => T-CH2 + CH2O', [7.150000e+04, 2.47, 929.73]) + +# Reaction 98 +reaction('C2H4 + O => CH3 + HCO', [3.890000e+08, 1.36, 886.71]) + +# Reaction 99 +reaction('C2H4 + OH => C2H3 + H2O', [1.310000e-01, 4.2, -860.42]) + +# Reaction 100 +reaction('C2H4 + OH => CH3 + CH2O', [3.750000e+36, -7.8, 7060.23]) + +# Reaction 101 +reaction('C2H4 + CH3 => C2H3 + CH4', [2.270000e+05, 2.0, 9199.33]) + +# Reaction 102 +falloff_reaction('C2H4 + CH3 (+ M) <=> N-C3H7 (+ M)', + kf=[2.550000e+06, 1.6, 5700.29], + kf0=[3.000000e+63, -14.6, 18169.22], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.1894, T3=277.0, T1=8748.0, T2=7891.0)) + +# Reaction 103 +falloff_reaction('C2H5 + H (+ M) <=> C2H6 (+ M)', + kf=[5.210000e+17, -0.99, 1579.83], + kf0=[1.990000e+41, -7.08, 6684.99], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.8422, T3=125.0, T1=2219.0, T2=6882.0)) + +# Reaction 104 +reaction('C2H5 + O => CH3 + CH2O', [3.170000e+13, 0.03, -394.36]) + +# Reaction 105 +reaction('C2H5 + O2 => C2H4 + HO2', [1.920000e+07, 1.02, -2033.94]) + +# Reaction 106 +reaction('C2H5 + HCO => C2H6 + CO', [1.200000e+14, 0.0, 0.0]) + +# Reaction 107 +reaction('C2H5 + HO2 => C2H6 + O2', [3.000000e+11, 0.0, 0.0]) + +# Reaction 108 +reaction('C2H5 + HO2 => CH3 + CH2O + OH', [3.100000e+13, 0.0, 0.0]) + +# Reaction 109 +falloff_reaction('C2H6 (+ M) <=> 2 CH3 (+ M)', + kf=[1.880000e+50, -9.72, 107342.26], + kf0=[3.720000e+65, -13.14, 101579.83], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.39, T3=100.0, T1=1900.0, T2=6000.0)) + +# Reaction 110 +reaction('C2H6 + H => C2H5 + H2', [1.700000e+05, 2.7, 5740.92]) + +# Reaction 111 +reaction('C2H6 + O => C2H5 + OH', [8.980000e+07, 1.92, 5690.73]) + +# Reaction 112 +reaction('C2H6 + OH => C2H5 + H2O', [1.610000e+06, 2.22, 740.92]) + +# Reaction 113 +reaction('C2H6 + CH3 => C2H5 + CH4', [8.430000e+14, 0.0, 22256.21]) + +# Reaction 114 +falloff_reaction('HCCO (+ M) => CO + CH (+ M)', + kf=[2.255000e+20, -1.44, 74732.31], + kf0=[1.213000e+35, -5.18, 76668.26], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.5757, T3=237.0, T1=1652.0, T2=5069.0)) + +# Reaction 115 +reaction('HCCO + H => S-CH2 + CO', [1.000000e+14, 0.0, 0.0]) + +# Reaction 116 +reaction('HCCO + O => H + 2 CO', [1.000000e+14, 0.0, 0.0]) + +# Reaction 117 +reaction('HCCO + O2 => OH + 2 CO', [4.200000e+10, 0.0, 853.25]) + +# Reaction 118 +reaction('2 HCCO => C2H2 + 2 CO', [1.000000e+13, 0.0, 0.0]) + +# Reaction 119 +reaction('HCCO + C2H2 => C3H3 + CO', [1.000000e+11, 0.0, 2999.52]) + +# Reaction 120 +reaction('HCCO + CH3 => C2H4 + CO', [5.000000e+13, 0.0, 0.0]) + +# Reaction 121 +reaction('HCCO + OH => 2 HCO', [1.000000e+13, 0.0, 0.0]) + +# Reaction 122 +reaction('C3H3 + H <=> P-C3H4', [7.940000e+29, -5.06, 4861.38]) + +# Reaction 123 +reaction('C3H3 + H <=> A-C3H4', [3.160000e+29, -5.0, 4710.8]) + +# Reaction 124 +reaction('C3H3 + OH => C2H4 + CO', [1.280000e+09, 0.73, 2578.87]) + +# Reaction 125 +reaction('C3H3 + O => C2H2 + CO + H', [6.950000e+13, 0.0, 0.0]) + +# Reaction 126 +reaction('C3H3 + O2 => CH3 + 2 CO', [1.700000e+05, 1.7, 1500.96]) + +# Reaction 127 +reaction('C3H3 + HO2 => OH + CO + C2H3', [8.000000e+11, 0.0, 0.0]) + +# Reaction 128 +reaction('2 C3H3 <=> A1', [1.870000e+46, -9.84, 16804.49]) + +# Reaction 129 +reaction('2 C3H3 <=> A1- + H', [5.770000e+37, -7.0, 31505.74]) + +# Reaction 130 +reaction('C3H3 + C2H2 <=> C5H5', [2.350000e+11, 0.0, 9995.22]) + +# Reaction 131 +reaction('P-C3H4 + H <=> C2H2 + CH3', [3.460000e+12, 0.44, 5463.67]) + +# Reaction 132 +reaction('P-C3H4 + H <=> C3H3 + H2', [8.500000e+04, 2.7, 5740.92]) + +# Reaction 133 +reaction('P-C3H4 + OH => C3H3 + H2O', [8.050000e+05, 2.22, 740.92]) + +# Reaction 134 +reaction('P-C3H4 + CH3 => C3H3 + CH4', [4.220000e+14, 0.0, 22256.21]) + +# Reaction 135 +reaction('P-C3H4 + O => HCCO + CH3', [4.050000e+06, 2.0, 1900.1]) + +# Reaction 136 +reaction('P-C3H4 + O => C2H4 + CO', [6.250000e+06, 2.0, 1900.1]) + +# Reaction 137 +reaction('P-C3H4 + OH => C2H5 + CO', [1.280000e+09, 0.73, 2578.87]) + +# Reaction 138 +reaction('A-C3H4 + H <=> C2H2 + CH3', [8.950000e+13, -0.02, 11250.0]) + +# Reaction 139 +reaction('A-C3H4 <=> P-C3H4', [7.760000e+39, -7.8, 78446.46]) + +# Reaction 140 +reaction('A-C3H4 + H <=> P-C3H4 + H', [2.470000e+15, -0.33, 6436.42]) + +# Reaction 141 +reaction('A-C3H4 + H => C3H3 + H2', [1.330000e+06, 2.53, 12239.48]) + +# Reaction 142 +reaction('A-C3H4 + OH => C3H3 + H2O', [1.310000e-01, 4.2, -860.42]) + +# Reaction 143 +reaction('A-C3H4 + CH3 => C3H3 + CH4', [2.270000e+05, 2.0, 9199.33]) + +# Reaction 144 +reaction('A-C3H4 + H <=> A-C3H5', [2.010000e+49, -10.77, 19622.37]) + +# Reaction 145 +reaction('A-C3H5 + H => A-C3H4 + H2', [9.560000e+03, 2.8, 3291.11]) + +# Reaction 146 +reaction('A-C3H5 + OH => A-C3H4 + H2O', [6.030000e+12, 0.0, 0.0]) + +# Reaction 147 +reaction('A-C3H5 + CH3 => A-C3H4 + CH4', [4.860000e+11, -0.32, -131.45]) + +# Reaction 148 +reaction('A-C3H5 + O2 => C2H2 + CH2O + OH', [9.710000e+20, -2.7, 24980.88]) + +# Reaction 149 +reaction('A-C3H5 + C3H3 => A1 + 2 H', [2.160000e+39, -7.74, 23852.77]) + +# Reaction 150 +falloff_reaction('C3H6 + H (+ M) <=> N-C3H7 (+ M)', + kf=[3.060000e+14, -0.37, 4032.03], + kf0=[6.260000e+38, -6.66, 7000.48], + efficiencies='CO2:3.6 CO:1.75 H2:2.0 H2O:12.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=1.0, T3=1000.0, T1=1310.0, T2=48100.0)) + +# Reaction 151 +reaction('C3H6 <=> C2H3 + CH3', [4.040000e+42, -7.67, 111830.78]) + +# Reaction 152 +reaction('A-C3H5 + H <=> C3H6', [5.930000e+54, -11.76, 23549.24]) + +# Reaction 153 +reaction('C3H6 + H <=> C2H4 + CH3', [8.000000e+21, -2.39, 11180.69]) + +# Reaction 154 +reaction('C3H6 + O => 2 CH3 + CO', [1.200000e+08, 1.6, 327.44]) + +# Reaction 155 +reaction('C3H6 + O => C2H5 + HCO', [3.500000e+07, 1.6, -972.75]) + +# Reaction 156 +reaction('C3H6 + H => A-C3H5 + H2', [6.600000e+05, 2.54, 6756.69]) + +# Reaction 157 +reaction('C3H6 + O => A-C3H5 + OH', [9.650000e+04, 2.68, 3716.54]) + +# Reaction 158 +reaction('C3H6 + OH => A-C3H5 + H2O', [2.000000e+08, 1.46, 537.76]) + +# Reaction 159 +reaction('C3H6 + CH3 => A-C3H5 + CH4', [4.520000e-01, 3.65, 7153.44]) + +# Reaction 160 +reaction('C4H8 + H => C2H5 + C2H4', [7.680000e+12, 0.11, 1479.45]) + +# Reaction 161 +reaction('C4H8 => A-C3H5 + CH3', [5.000000e+15, 0.0, 70999.04]) + +# Reaction 162 +reaction('C5H5 + HO2 => O2 + C5H6', [2.561000e+12, 0.06, 3116.63]) + +# Reaction 163 +reaction('2 C5H5 => A2 + 2 H', [6.390000e+29, -4.03, 35205.54]) + +# Reaction 164 +reaction('C5H5 + O => C2H3 + C2H2 + CO', [7.000000e+13, 0.0, 0.0]) + +# Reaction 165 +reaction('C5H5 + HO2 => C2H3 + C2H2 + CO + OH', [6.776000e+29, -4.7, 11658.7]) + +# Reaction 166 +reaction('C5H5 + HO2 => 2 C2H2 + CO + H2O', [1.190000e+33, -6.52, 13401.05]) + +# Reaction 167 +reaction('C5H5 + OH => C2H3 + C2H2 + CO + H', [3.020000e+13, 0.0, 0.0]) + +# Reaction 168 +reaction('C5H6 <=> C5H5 + H', [1.730000e+68, -15.16, 116371.89]) + +# Reaction 169 +reaction('C5H6 + H => C5H5 + H2', [2.800000e+13, 0.0, 2258.6]) + +# Reaction 170 +reaction('C5H6 + H => A-C3H5 + C2H2', [6.600000e+14, 0.0, 12344.65]) + +# Reaction 171 +reaction('C5H6 + O => C5H5 + OH', [4.770000e+04, 2.71, 1106.6]) + +# Reaction 172 +reaction('C5H6 + OH => C5H5 + H2O', [3.080000e+06, 2.0, 0.0]) + +# Reaction 173 +reaction('C5H6 + CH3 => C5H5 + CH4', [1.800000e-01, 4.0, 0.0]) + +# Reaction 174 +reaction('C5H10 + H => C5H11', [7.100000e+12, 0.12, 1460.33]) + +# Reaction 175 +reaction('C5H10 => C2H5 + A-C3H5', [9.170000e+20, -1.63, 73989.01]) + +# Reaction 176 +reaction('C5H11 => C2H4 + N-C3H7', [7.460000e+21, -2.61, 32026.77]) + +# Reaction 177 +reaction('C5H11 => H + C5H10', [8.460000e+14, -0.47, 37617.11]) + +# Reaction 178 +reaction('C5H11 => C3H6 + C2H5', [3.150000e-19, 8.84, 7105.64]) + +# Reaction 179 +reaction('A1- + O2 => C5H5 + CO + O', [2.600000e+13, 0.0, 6120.94]) + +# Reaction 180 +reaction('A1- + O2 => 2 CO + 2 C2H2 + H', [3.000000e+13, 0.0, 8979.45]) + +# Reaction 181 +reaction('A1- + O => C5H5 + CO', [1.000000e+14, 0.0, 0.0]) + +# Reaction 182 +reaction('A1- + OH => C5H6 + CO', [3.000000e+13, 0.0, 0.0]) + +# Reaction 183 +reaction('A1- + HO2 => C5H5 + CO + OH', [3.000000e+13, 0.0, 0.0]) + +# Reaction 184 +reaction('A1- + C2H2 <=> A1C2H2', [3.290000e+06, 2.05, 3162.05]) + +# Reaction 185 +reaction('A1 <=> A1- + H', [1.290000e+61, -12.48, 148085.56]) + +# Reaction 186 +reaction('A1 + H => A1- + H2', [6.020000e+08, 1.8, 16352.77]) + +# Reaction 187 +reaction('A1 + OH => A1- + H2O', [4.030000e+02, 3.33, 1455.54]) + +# Reaction 188 +reaction('A1 + CH3 => A1- + CH4', [2.752000e-02, 4.46, 13637.67]) + +# Reaction 189 +reaction('A1 + O => C5H5 + CO + H', [2.220000e+13, 0.0, 4531.55]) + +# Reaction 190 +reaction('A1 + OH => C5H6 + CO + H', [1.320000e+02, 3.25, 5590.34]) + +# Reaction 191 +reaction('A1CH2 <=> C5H5 + C2H2', [8.200000e+14, 0.0, 80676.39]) + +# Reaction 192 +reaction('A1CH2 + H <=> A1- + CH3', [5.830000e+67, -14.15, 68329.35]) + +# Reaction 193 +reaction('A1CH2 + O => A1CHO + H', [3.310000e+14, 0.0, 0.0]) + +# Reaction 194 +reaction('A1CH2 + HO2 => A1CHO + OH + H', [1.060000e+16, -0.94, 2523.9]) + +# Reaction 195 +reaction('A1CH2 + C3H3 => A2 + 2 H', [4.320000e+39, -7.74, 23852.77]) + +# Reaction 196 +reaction('A1CH3 + H <=> A1 + CH3', [2.310000e+06, 2.17, 4163.48]) + +# Reaction 197 +reaction('A1CH3 <=> A1CH2 + H', [1.250000e+18, -0.6, 94787.28]) + +# Reaction 198 +reaction('A1CH3 <=> A1- + CH3', [2.160000e+29, -3.58, 110164.91]) + +# Reaction 199 +reaction('A1CH3 + H => A1CH2 + H2', [6.470000e+00, 3.98, 3384.32]) + +# Reaction 200 +reaction('A1CH3 + OH => A1CH2 + H2O', [1.620000e+13, 0.0, 2770.08]) + +# Reaction 201 +reaction('A1CH3 + CH3 => A1CH2 + CH4', [4.220000e+14, 0.0, 22256.21]) + +# Reaction 202 +reaction('C7H15 => C5H11 + C2H4', [1.890000e+12, 0.02, 27784.42]) + +# Reaction 203 +reaction('C7H15 => C2H5 + C2H4 + C3H6', [7.730000e+18, -1.75, 31974.19]) + +# Reaction 204 +reaction('C7H15 => C4H8 + N-C3H7', [2.530000e+18, -1.65, 31682.6]) + +# Reaction 205 +reaction('C7H15 => C2H5 + C5H10', [2.490000e+16, -1.18, 29517.21]) + +# Reaction 206 +reaction('N-C7H16 => C5H11 + C2H5', [8.100000e+77, -17.62, 120399.14]) + +# Reaction 207 +reaction('N-C7H16 => C2H5 + C2H4 + N-C3H7', [1.420000e+78, -17.71, 120700.29]) + +# Reaction 208 +reaction('N-C7H16 + H => C7H15 + H2', [1.750000e+06, 2.6, 4361.85]) + +# Reaction 209 +reaction('N-C7H16 + O => C7H15 + OH', [1.720000e+05, 2.81, 2260.99]) + +# Reaction 210 +reaction('N-C7H16 + OH => C7H15 + H2O', [7.400000e+08, 1.5, 258.13]) + +# Reaction 211 +reaction('N-C7H16 + CH3 => C7H15 + CH4', [1.460000e+04, 2.57, 6933.56]) + +# Reaction 212 +reaction('A1CHO => A1- + HCO', [2.610000e+15, 0.15, 80549.71]) + +# Reaction 213 +reaction('A1CHO + H => A1- + CO + H2', [2.050000e+09, 1.16, 2404.4]) + +# Reaction 214 +reaction('A1CHO + CH3 => A1- + CO + CH4', [2.720000e+06, 1.77, 5920.17]) + +# Reaction 215 +reaction('A1C2H* + C2H2 <=> A2-', [1.340000e+04, 2.5, 1283.46]) + +# Reaction 216 +reaction('A1C2H* + C2H4 <=> A2 + H', [3.620000e+28, -4.24, 23864.72]) + +# Reaction 217 +reaction('A1C2H <=> A1C2H* + H', [2.100000e+60, -12.4, 148076.0]) + +# Reaction 218 +reaction('A1C2H + H <=> A1C2H* + H2', [1.320000e+08, 1.88, 16821.22]) + +# Reaction 219 +reaction('A1C2H + OH <=> A1C2H* + H2O', [1.340000e+02, 3.33, 1455.54]) + +# Reaction 220 +reaction('A1C2H2 <=> A1C2H + H', [1.340000e+17, -0.86, 41238.05]) + +# Reaction 221 +reaction('A1C2H2 + C2H2 <=> A2 + H', [7.091000e+13, -0.26, 7002.87]) + +# Reaction 222 +reaction('A2 <=> A2- + H', [8.600000e+60, -12.48, 148076.0]) + +# Reaction 223 +reaction('A2 + H <=> A2- + H2', [2.650000e+08, 1.87, 17096.08]) + +# Reaction 224 +reaction('A2 + OH <=> A2- + H2O', [9.630000e+02, 3.02, 4373.8]) diff --git a/samples/python/AVBP/inputs/BISETTI.yaml b/samples/python/AVBP/inputs/BISETTI.yaml new file mode 100644 index 00000000000..fe0e0b7e836 --- /dev/null +++ b/samples/python/AVBP/inputs/BISETTI.yaml @@ -0,0 +1,1367 @@ +description: |- + nits(length='cm', time='s', quantity='mol', act_energy='cal/mol') + +generator: cti2yaml +cantera-version: 3.0.0 +date: Wed, 20 Dec 2023 16:58:00 +0100 +input-files: [BISETTI.cti] + +units: {length: cm, quantity: mol, activation-energy: cal/mol} + +phases: +- name: gas + thermo: ideal-gas + elements: [N, C, H, O, Ar] + species: [AR, N2, S-CH2, T-CH2, O, H2, H, OH, H2O, O2, HO2, CH, CO, HCO, + CH2O, CH3, CO2, CH4, C2H3, C2H4, C2H5, C2H, HCCO, C2H2, C3H3, A-C3H5, + N-C3H7, C2H6, P-C3H4, A-C3H4, A1, A1-, C5H5, C3H6, C4H8, C5H6, A2, C5H10, + C5H11, A1C2H2, A1CH2, A1CHO, A1CH3, C7H15, N-C7H16, A1C2H*, A2-, A1C2H] + kinetics: gas + reactions: all + transport: mixture-averaged + state: + T: 300.0 + P: 1.01325e+05 + +species: +- name: AR + composition: {Ar: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 6000.0] + data: + - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.37967491] + - [2.5, 0.0, 0.0, 0.0, 0.0, -745.375, 4.37967491] + transport: + model: gas + geometry: atom + diameter: 3.33 + well-depth: 136.5 + note: REFELEMENTG5/97 +- name: N2 + composition: {N: 2} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12, + -1020.8999, 3.950372] + - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15, + -922.7977, 5.980528] + transport: + model: gas + geometry: linear + diameter: 3.621 + well-depth: 97.53 + polarizability: 1.76 + rotational-relaxation: 4.0 + note: '121286' +- name: S-CH2 + composition: {H: 2, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19860411, -2.36661419e-03, 8.2329622e-06, -6.68815981e-09, 1.94314737e-12, + 5.04968163e+04, -0.769118967] + - [2.29203842, 4.65588637e-03, -2.01191947e-06, 4.17906e-10, -3.39716365e-14, + 5.09259997e+04, 8.62650169] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 +- name: T-CH2 + composition: {H: 2, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.76267867, 9.68872143e-04, 2.79489841e-06, -3.85091153e-09, 1.68741719e-12, + 4.60040401e+04, 1.56253185] + - [2.87410113, 3.65639292e-03, -1.40894597e-06, 2.60179549e-10, -1.87727567e-14, + 4.6263604e+04, 6.17119324] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 +- name: O + composition: {O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.1682671, -3.27931884e-03, 6.64306396e-06, -6.12806624e-09, 2.11265971e-12, + 2.91222592e+04, 2.05193346] + - [2.56942078, -8.59741137e-05, 4.19484589e-08, -1.00177799e-11, 1.22833691e-15, + 2.92175791e+04, 4.78433864] + transport: + model: gas + geometry: atom + diameter: 2.75 + well-depth: 80.0 + note: L1/90 +- name: H2 + composition: {H: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.34433112, 7.98052075e-03, -1.9478151e-05, 2.01572094e-08, -7.37611761e-12, + -917.935173, 0.683010238] + - [3.3372792, -4.94024731e-05, 4.99456778e-07, -1.79566394e-10, 2.00255376e-14, + -950.158922, -3.20502331] + transport: + model: gas + geometry: linear + diameter: 2.92 + well-depth: 38.0 + polarizability: 0.79 + rotational-relaxation: 280.0 + note: TPIS78 +- name: H + composition: {H: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18, -9.27732332e-22, + 2.54736599e+04, -0.446682853] + - [2.50000001, -2.30842973e-11, 1.61561948e-14, -4.73515235e-18, 4.98197357e-22, + 2.54736599e+04, -0.446682914] + transport: + model: gas + geometry: atom + diameter: 2.05 + well-depth: 145.0 + note: L7/88 +- name: OH + composition: {H: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 6000.0] + data: + - [4.12530561, -3.22544939e-03, 6.52764691e-06, -5.79853643e-09, 2.06237379e-12, + 3381.53812, -0.69043296] + - [2.86472886, 1.05650448e-03, -2.59082758e-07, 3.05218674e-11, -1.33195876e-15, + 3718.85774, 5.70164073] + transport: + model: gas + geometry: linear + diameter: 2.75 + well-depth: 80.0 + note: S9/01 +- name: H2O + composition: {H: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19864056, -2.0364341e-03, 6.52040211e-06, -5.48797062e-09, 1.77197817e-12, + -3.02937267e+04, -0.849032208] + - [3.03399249, 2.17691804e-03, -1.64072518e-07, -9.7041987e-11, 1.68200992e-14, + -3.00042971e+04, 4.9667701] + transport: + model: gas + geometry: nonlinear + diameter: 2.605 + well-depth: 572.4 + dipole: 1.844 + rotational-relaxation: 4.0 + note: L8/89 +- name: O2 + composition: {O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.78245636, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09, 3.24372837e-12, + -1063.94356, 3.65767573] + - [3.28253784, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10, -2.16717794e-14, + -1088.45772, 5.45323129] + transport: + model: gas + geometry: linear + diameter: 3.458 + well-depth: 107.4 + polarizability: 1.6 + rotational-relaxation: 3.8 + note: TPIS89 +- name: HO2 + composition: {H: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30179801, -4.74912051e-03, 2.11582891e-05, -2.42763894e-08, 9.29225124e-12, + 294.80804, 3.71666245] + - [4.0172109, 2.23982013e-03, -6.3365815e-07, 1.1424637e-10, -1.07908535e-14, + 111.856713, 3.78510215] + transport: + model: gas + geometry: nonlinear + diameter: 3.458 + well-depth: 107.4 + rotational-relaxation: 1.0 + note: L5/89 +- name: CH + composition: {H: 1, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.48981665, 3.23835541e-04, -1.68899065e-06, 3.16217327e-09, -1.40609067e-12, + 7.07972934e+04, 2.08401108] + - [2.87846473, 9.70913681e-04, 1.44445655e-07, -1.30687849e-10, 1.76079383e-14, + 7.10124364e+04, 5.48497999] + transport: + model: gas + geometry: linear + diameter: 2.75 + well-depth: 80.0 + note: TPIS79 +- name: CO + composition: {C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.57953347, -6.1035368e-04, 1.01681433e-06, 9.07005884e-10, -9.04424499e-13, + -1.4344086e+04, 3.50840928] + - [2.71518561, 2.06252743e-03, -9.98825771e-07, 2.30053008e-10, -2.03647716e-14, + -1.41518724e+04, 7.81868772] + transport: + model: gas + geometry: linear + diameter: 3.65 + well-depth: 98.1 + polarizability: 1.95 + rotational-relaxation: 1.8 + note: TPIS79 +- name: HCO + composition: {H: 1, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.22118584, -3.24392532e-03, 1.37799446e-05, -1.33144093e-08, 4.33768865e-12, + 3839.56496, 3.39437243] + - [2.77217438, 4.95695526e-03, -2.48445613e-06, 5.89161778e-10, -5.33508711e-14, + 4011.91815, 9.79834492] + transport: + model: gas + geometry: nonlinear + diameter: 3.59 + well-depth: 498.0 + note: L12/89 +- name: CH2O + composition: {H: 2, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.79372315, -9.90833369e-03, 3.73220008e-05, -3.79285261e-08, 1.31772652e-11, + -1.43089567e+04, 0.6028129] + - [1.76069008, 9.20000082e-03, -4.42258813e-06, 1.00641212e-09, -8.8385564e-14, + -1.39958323e+04, 13.656323] + transport: + model: gas + geometry: nonlinear + diameter: 3.59 + well-depth: 498.0 + rotational-relaxation: 2.0 + note: L8/88 +- name: CH3 + composition: {H: 3, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 6000.0] + data: + - [3.6571797, 2.1265979e-03, 5.4583883e-06, -6.6181003e-09, 2.4657074e-12, + 1.6422716e+04, 1.6735354] + - [2.9781206, 5.797852e-03, -1.97558e-06, 3.072979e-10, -1.7917416e-14, + 1.6509513e+04, 4.7224799] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: METHYLIU0702 +- name: CO2 + composition: {C: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.35677352, 8.98459677e-03, -7.12356269e-06, 2.45919022e-09, -1.43699548e-13, + -4.83719697e+04, 9.90105222] + - [3.85746029, 4.41437026e-03, -2.21481404e-06, 5.23490188e-10, -4.72084164e-14, + -4.8759166e+04, 2.27163806] + transport: + model: gas + geometry: linear + diameter: 3.763 + well-depth: 244.0 + polarizability: 2.65 + rotational-relaxation: 2.1 + note: L7/88 +- name: CH4 + composition: {H: 4, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 6000.0] + data: + - [5.14911468, -0.0136622009, 4.91453921e-05, -4.84246767e-08, 1.66603441e-11, + -1.02465983e+04, -4.63848842] + - [1.65326226, 0.0100263099, -3.31661238e-06, 5.36483138e-10, -3.14696758e-14, + -1.00095936e+04, 9.90506283] + transport: + model: gas + geometry: nonlinear + diameter: 3.746 + well-depth: 141.4 + polarizability: 2.6 + rotational-relaxation: 13.0 + note: g8/99 +- name: C2H3 + composition: {H: 3, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.21246645, 1.51479162e-03, 2.59209412e-05, -3.57657847e-08, 1.47150873e-11, + 3.48598468e+04, 8.51054025] + - [3.016724, 0.0103302292, -4.68082349e-06, 1.01763288e-09, -8.62607041e-14, + 3.46128739e+04, 7.78732378] + transport: + model: gas + geometry: nonlinear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 1.0 + note: L2/92 +- name: C2H4 + composition: {H: 4, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.95920148, -7.57052247e-03, 5.70990292e-05, -6.91588753e-08, 2.69884373e-11, + 5089.77593, 4.09733096] + - [2.03611116, 0.0146454151, -6.71077915e-06, 1.47222923e-09, -1.25706061e-13, + 4939.88614, 10.3053693] + transport: + model: gas + geometry: nonlinear + diameter: 3.971 + well-depth: 280.8 + rotational-relaxation: 1.5 + note: L1/91 +- name: C2H5 + composition: {H: 5, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30646568, -4.18658892e-03, 4.97142807e-05, -5.99126606e-08, 2.30509004e-11, + 1.28416265e+04, 4.70720924] + - [1.95465642, 0.0173972722, -7.98206668e-06, 1.75217689e-09, -1.49641576e-13, + 1.285752e+04, 13.4624343] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L12/92 +- name: C2H + composition: {H: 1, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.88965733, 0.0134099611, -2.84769501e-05, 2.94791045e-08, -1.09331511e-11, + 6.68393932e+04, 6.22296438] + - [3.16780652, 4.75221902e-03, -1.83787077e-06, 3.04190252e-10, -1.7723277e-14, + 6.7121065e+04, 6.63589475] + transport: + model: gas + geometry: linear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 2.5 + note: L1/91 +- name: HCCO + composition: {H: 1, C: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 4000.0] + data: + - [2.2517214, 0.017655021, -2.3729101e-05, 1.7275759e-08, -5.0664811e-12, + 2.0059449e+04, 12.490417] + - [5.6282058, 4.0853401e-03, -1.5934547e-06, 2.8626052e-10, -1.9407832e-14, + 1.9327215e+04, -3.9302595] + transport: + model: gas + geometry: nonlinear + diameter: 2.5 + well-depth: 150.0 + rotational-relaxation: 1.0 + note: SRIC91 +- name: C2H2 + composition: {H: 2, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [0.808681094, 0.0233615629, -3.55171815e-05, 2.80152437e-08, -8.50072974e-12, + 2.64289807e+04, 13.9397051] + - [4.14756964, 5.96166664e-03, -2.37294852e-06, 4.67412171e-10, -3.61235213e-14, + 2.59359992e+04, -1.23028121] + transport: + model: gas + geometry: linear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 2.5 + note: L1/91 +- name: C3H3 + composition: {H: 3, C: 3} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [1.40299238, 0.0301773327, -3.98449373e-05, 2.93534629e-08, -8.70554579e-12, + 3.9310822e+04, 15.1527845] + - [6.14915291, 9.34063166e-03, -3.75055354e-06, 6.90156316e-10, -4.60824994e-14, + 3.83854848e+04, -7.45345215] + transport: + model: gas + geometry: nonlinear + diameter: 4.76 + well-depth: 252.0 + rotational-relaxation: 1.0 + note: G3B3 +- name: A-C3H5 + composition: {H: 5, C: 3} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-1.03516444, 0.0375043366, -3.26381242e-05, 1.47662613e-08, -2.43741154e-12, + 1.88792254e+04, 27.1451071] + - [2.28794927, 0.0236401575, -1.2789145e-05, 3.3683854e-09, -3.47449449e-13, + 1.83033514e+04, 11.4063418] + transport: + model: gas + geometry: nonlinear + diameter: 4.982 + well-depth: 266.8 + rotational-relaxation: 1.0 + note: G3B3 +- name: N-C3H7 + composition: {H: 7, C: 3} + thermo: + model: NASA7 + temperature-ranges: [298.15, 1000.0, 5000.0] + data: + - [1.0475473, 0.026007794, 2.3562252e-06, -1.9592317e-08, 9.3680116e-12, + 1.0632637e+04, 21.141876] + - [7.7040405, 0.01604154, -5.2815967e-06, 7.6254403e-10, -3.9353462e-14, + 8297.9531, -15.487514] + transport: + model: gas + geometry: nonlinear + diameter: 4.982 + well-depth: 266.8 + rotational-relaxation: 1.0 + note: N-L9/85 +- name: C2H6 + composition: {H: 6, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.29142492, -5.5015427e-03, 5.99438288e-05, -7.08466285e-08, 2.68685771e-11, + -1.15222055e+04, 2.66682316] + - [1.0718815, 0.0216852677, -1.00256067e-05, 2.21412001e-09, -1.9000289e-13, + -1.14263932e+04, 15.1156107] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L8/88 +- name: P-C3H4 + composition: {H: 4, C: 3} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [1.46175323, 0.0246026602, -1.90219395e-05, 8.60363422e-09, -1.6672924e-12, + 2.09209793e+04, 14.9262585] + - [2.81460543, 0.0185524496, -9.55026768e-06, 2.3995137e-09, -2.37485257e-13, + 2.07010771e+04, 8.60604972] + transport: + model: gas + geometry: nonlinear + diameter: 4.76 + well-depth: 252.0 + rotational-relaxation: 1.0 + note: G3B3 +- name: A-C3H4 + composition: {H: 4, C: 3} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [0.368928265, 0.0289351397, -2.44386408e-05, 1.12547166e-08, -2.03040262e-12, + 2.17585256e+04, 19.5267211] + - [2.56128757, 0.0195080128, -1.04061366e-05, 2.70165173e-09, -2.75074329e-13, + 2.13894289e+04, 9.20550397] + transport: + model: gas + geometry: nonlinear + diameter: 4.76 + well-depth: 252.0 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1 + composition: {H: 6, C: 6} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-5.51558393, 0.0645453225, -4.41402928e-05, 7.47712161e-09, 3.10282254e-12, + 9110.31457, 46.5332293] + - [-0.206240612, 0.046412244, -2.77653536e-05, 7.88910537e-09, -8.60365259e-13, + 8098.83905, 20.6566629] + transport: + model: gas + geometry: nonlinear + diameter: 5.29 + well-depth: 464.8 + polarizability: 10.32 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1- + composition: {H: 5, C: 6} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-4.87654845, 0.0626805782, -4.87402286e-05, 1.41122287e-08, 5.18518312e-13, + 3.99269438e+04, 45.9964173] + - [1.38016336, 0.0404032009, -2.42250885e-05, 6.88723321e-09, -7.50960802e-13, + 3.8697352e+04, 15.5220921] + transport: + model: gas + geometry: nonlinear + diameter: 5.29 + well-depth: 464.8 + polarizability: 10.32 + rotational-relaxation: 1.0 + note: G3B3 +- name: C5H5 + composition: {H: 5, C: 5} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-7.37844042, 0.0972391818, -1.69579138e-04, 1.51818667e-07, -5.12075479e-11, + 3.05514662e+04, 51.2829539] + - [4.21464919, 0.0271834728, -1.33173209e-05, 3.08980119e-09, -2.77879873e-13, + 2.88952416e+04, -0.0305999781] + transport: + model: gas + geometry: nonlinear + diameter: 5.2 + well-depth: 400.0 + rotational-relaxation: 1.0 + note: Refitted +- name: C3H6 + composition: {H: 6, C: 3} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-2.2926167e-03, 0.0310261065, -1.67151548e-05, 1.8959417e-09, 1.24957915e-12, + 1134.37406, 23.5719601] + - [0.471697982, 0.028951307, -1.56601819e-05, 4.11443199e-09, -4.23075141e-13, + 1126.03387, 21.5237289] + transport: + model: gas + geometry: nonlinear + diameter: 4.982 + well-depth: 266.8 + rotational-relaxation: 1.0 + note: G3B3 +- name: C4H8 + composition: {H: 8, C: 4} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-0.831372089, 0.0452580978, -2.93658559e-05, 1.00220436e-08, -1.4319168e-12, + -1578.75035, 29.5084236] + - [3.04470367, 0.0327451765, -1.45363237e-05, 2.39744017e-09, 0.0, -2521.77534, + 10.0151514] + transport: + model: gas + geometry: nonlinear + diameter: 5.088 + well-depth: 345.7 + dipole: 0.3 + rotational-relaxation: 1.0 + note: '000000' +- name: C5H6 + composition: {H: 6, C: 5} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-5.13691194, 0.0606953453, -4.60552837e-05, 1.28457201e-08, 7.41214852e-13, + 1.53675713e+04, 46.1567559] + - [0.230537462, 0.0409571826, -2.41588958e-05, 6.7976348e-09, -7.36374421e-13, + 1.43779465e+04, 20.2551234] + transport: + model: gas + geometry: nonlinear + diameter: 5.2 + well-depth: 400.0 + note: G3B3 +- name: A2 + composition: {H: 8, C: 10} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-8.72434585, 0.105376008, -8.0171069e-05, 2.18545974e-08, 1.42066606e-12, + 1.48059774e+04, 61.982754] + - [1.76826275, 0.0689143506, -4.14322176e-05, 1.17914309e-08, -1.28597061e-12, + 1.26883657e+04, 10.6256608] + transport: + model: gas + geometry: nonlinear + diameter: 6.18 + well-depth: 630.4 + polarizability: 16.5 + rotational-relaxation: 1.0 + note: G3B3 +- name: C5H10 + composition: {H: 10, C: 5} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-1.06223481, 0.0574218294, -3.7448689e-05, 1.27364989e-08, -1.79609789e-12, + -4465.46666, 32.273979] + - [3.98580522, 0.0412429986, -1.84390497e-05, 3.06155241e-09, 0.0, -5701.12071, + 6.85332264] + transport: + model: gas + geometry: nonlinear + diameter: 5.489 + well-depth: 386.2 + dipole: 0.4 + rotational-relaxation: 1.0 + note: '000000' +- name: C5H11 + composition: {H: 11, C: 5} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-0.905255912, 0.0610632852, -4.09491825e-05, 1.4609347e-08, -2.18859615e-12, + 4839.95303, 32.5574963] + - [4.88920629, 0.0422834537, -1.858431e-05, 3.04124763e-09, 0.0, 3434.75468, + 3.43704878] + transport: + model: gas + geometry: nonlinear + diameter: 5.041 + well-depth: 440.735 + note: '000000' +- name: A1C2H2 + composition: {H: 7, C: 8} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-6.31199276, 0.0951097942, -9.56352102e-05, 4.97780207e-08, -1.02323717e-11, + 4.57330975e+04, 53.5475222] + - [5.8593508, 0.0472571459, -2.69864733e-05, 7.35311775e-09, -7.7490083e-13, + 4.33198974e+04, -5.22359403] + transport: + model: gas + geometry: nonlinear + diameter: 6.0 + well-depth: 546.2 + dipole: 0.13 + polarizability: 15.0 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1CH2 + composition: {H: 7, C: 7} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-6.07053038, 0.0835201507, -7.41700083e-05, 3.13153847e-08, -4.23670868e-12, + 2.35894712e+04, 50.7932172] + - [3.30049696, 0.048005534, -2.78443022e-05, 7.72371356e-09, -8.27154136e-13, + 2.17498572e+04, 5.42371919] + transport: + model: gas + geometry: nonlinear + diameter: 5.68 + well-depth: 495.3 + dipole: 0.43 + polarizability: 12.3 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1CHO + composition: {H: 6, C: 7, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-3.47171048, 0.0692891889, -4.32603509e-05, 3.43871096e-09, 4.81010261e-12, + -6145.58774, 41.4094024] + - [1.87355756, 0.0526231551, -3.17644962e-05, 9.06403069e-09, -9.90306123e-13, + -7236.03865, 14.9787009] + transport: + model: gas + geometry: nonlinear + diameter: 5.68 + well-depth: 495.3 + dipole: 0.43 + polarizability: 12.3 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1CH3 + composition: {H: 8, C: 7} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-4.54072038, 0.0685427145, -3.57113024e-05, -4.19397642e-09, 7.41779795e-12, + 4641.21087, 45.7564849] + - [-1.0111722, 0.0585301912, -3.47595069e-05, 9.82180993e-09, -1.0668087e-12, + 3993.63395, 28.3610783] + transport: + model: gas + geometry: nonlinear + diameter: 5.68 + well-depth: 495.3 + dipole: 0.43 + polarizability: 12.3 + rotational-relaxation: 1.0 + note: G3B3 +- name: C7H15 + composition: {H: 15, C: 7} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-0.0379155767, 0.075672657, -4.07473634e-05, 9.32678943e-09, -4.92360745e-13, + -2356.05303, 33.7321506] + - [3.74721159, 0.0649345162, -3.01341025e-05, 5.17418142e-09, 0.0, -3370.18357, + 14.2780413] + transport: + model: gas + geometry: nonlinear + diameter: 6.253 + well-depth: 459.6 + rotational-relaxation: 1.0 + note: '000000' +- name: N-C7H16 + composition: {H: 16, C: 7} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [-1.26836187, 0.085435582, -5.25346786e-05, 1.62945721e-08, -2.02394925e-12, + -2.56586565e+04, 35.3732912] + - [5.14079241, 0.0653078671, -2.94827624e-05, 4.93726726e-09, 0.0, -2.7253389e+04, + 2.98195967] + transport: + model: gas + geometry: nonlinear + diameter: 6.253 + well-depth: 459.6 + rotational-relaxation: 1.0 + note: '000000' +- name: A1C2H* + composition: {H: 5, C: 8} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-4.42757639, 0.0836668645, -8.70106362e-05, 4.70285661e-08, -1.01816985e-11, + 6.73302359e+04, 44.8118287] + - [7.23812069, 0.0383812109, -2.18850731e-05, 5.97161247e-09, -6.30351467e-13, + 6.49528135e+04, -11.7512654] + transport: + model: gas + geometry: nonlinear + diameter: 5.72 + well-depth: 535.6 + dipole: 0.77 + polarizability: 12.0 + rotational-relaxation: 1.0 + note: G3B3 +- name: A2- + composition: {H: 7, C: 10} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-8.02718034, 0.102924518, -8.3427201e-05, 2.72135383e-08, -7.24559554e-13, + 5.01363344e+04, 60.8902264] + - [3.22892303, 0.0631264486, -3.80582381e-05, 1.08454069e-08, -1.18342512e-12, + 4.7840084e+04, 5.82016697] + transport: + model: gas + geometry: nonlinear + diameter: 6.18 + well-depth: 630.4 + polarizability: 16.5 + rotational-relaxation: 1.0 + note: G3B3 +- name: A1C2H + composition: {H: 6, C: 8} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [-5.21036925, 0.0865551944, -8.45007483e-05, 4.21920706e-08, -8.16766167e-12, + 3.5248862e+04, 46.9445057] + - [5.81520488, 0.0440872933, -2.52053858e-05, 6.90275228e-09, -7.31378908e-13, + 3.30271906e+04, -6.4932069] + transport: + model: gas + geometry: nonlinear + diameter: 5.72 + well-depth: 535.6 + dipole: 0.77 + polarizability: 12.0 + rotational-relaxation: 1.0 + note: G3B3 + +reactions: +- equation: S-CH2 + N2 <=> T-CH2 + N2 # Reaction 1 + rate-constant: {A: 1.5e+13, b: 0.0, Ea: 599.9} +- equation: O + H2 <=> H + OH # Reaction 2 + rate-constant: {A: 4.59e+04, b: 2.7, Ea: 6259.56} +- equation: H + O + M => OH + M # Reaction 3 + type: three-body + rate-constant: {A: 9.43e+18, b: -1.0, Ea: 0.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: H + OH + M => H2O + M # Reaction 4 + type: three-body + rate-constant: {A: 4.4e+22, b: -2.0, Ea: 0.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 6.3, CH4: 2.0, C2H6: 3.0} +- equation: OH + H2 <=> H + H2O # Reaction 5 + rate-constant: {A: 1.73e+08, b: 1.51, Ea: 3429.73} +- equation: 2 OH <=> O + H2O # Reaction 6 + rate-constant: {A: 3.97e+04, b: 2.4, Ea: -2110.42} +- equation: H + O2 (+ M) => HO2 (+ M) # Reaction 7 + type: falloff + low-P-rate-constant: {A: 6.33e+19, b: -1.4, Ea: 0.0} + high-P-rate-constant: {A: 5.12e+12, b: 0.44, Ea: 0.0} + Troe: {A: 0.5, T3: 0.0, T1: 1.0e+10, T2: 1.0e+10} + efficiencies: {H2: 0.75, H2O: 11.89, CO2: 2.18, CO: 1.09, O2: 0.85} +- equation: H + O2 <=> O + OH # Reaction 8 + rate-constant: {A: 2.64e+16, b: -0.67, Ea: 1.704111e+04} +- equation: HO2 + H => O2 + H2 # Reaction 9 + rate-constant: {A: 3.649e+06, b: 2.07, Ea: -1092.26} +- equation: HO2 + H => O + H2O # Reaction 10 + rate-constant: {A: 3.97e+12, b: 0.0, Ea: 671.61} +- equation: HO2 + H => 2 OH # Reaction 11 + rate-constant: {A: 7.49e+13, b: 0.0, Ea: 635.76} +- equation: HO2 + O => OH + O2 # Reaction 12 + rate-constant: {A: 4.0e+13, b: 0.0, Ea: 0.0} +- equation: HO2 + OH => H2O + O2 # Reaction 13 + rate-constant: {A: 2.38e+13, b: 0.0, Ea: -499.52} + duplicate: true +- equation: HO2 + OH => H2O + O2 # Reaction 14 + rate-constant: {A: 1.0e+16, b: 0.0, Ea: 1.733031e+04} + duplicate: true +- equation: CH + O => CO + H # Reaction 15 + rate-constant: {A: 5.7e+13, b: 0.0, Ea: 0.0} +- equation: CH + OH => HCO + H # Reaction 16 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: CH + H2 <=> T-CH2 + H # Reaction 17 + rate-constant: {A: 1.08e+14, b: 0.0, Ea: 3109.46} +- equation: CH + H2O => CH2O + H # Reaction 18 + rate-constant: {A: 5.71e+12, b: 0.0, Ea: -755.26} +- equation: CH + O2 => HCO + O # Reaction 19 + rate-constant: {A: 6.71e+13, b: 0.0, Ea: 0.0} +- equation: T-CH2 + O => HCO + H # Reaction 20 + rate-constant: {A: 8.0e+13, b: 0.0, Ea: 0.0} +- equation: T-CH2 + OH => CH2O + H # Reaction 21 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: T-CH2 + OH <=> CH + H2O # Reaction 22 + rate-constant: {A: 1.13e+07, b: 2.0, Ea: 2999.52} +- equation: T-CH2 + H2 <=> H + CH3 # Reaction 23 + rate-constant: {A: 5.0e+05, b: 2.0, Ea: 7229.92} +- equation: T-CH2 + O2 => CO2 + 2 H # Reaction 24 + rate-constant: {A: 5.8e+12, b: 0.0, Ea: 1500.96} +- equation: T-CH2 + O2 => CH2O + O # Reaction 25 + rate-constant: {A: 2.4e+12, b: 0.0, Ea: 1500.96} +- equation: T-CH2 + O2 => OH + H + CO # Reaction 26 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 1500.96} +- equation: S-CH2 + H2 <=> CH3 + H # Reaction 27 + rate-constant: {A: 7.0e+13, b: 0.0, Ea: 0.0} +- equation: S-CH2 + O2 => H + OH + CO # Reaction 28 + rate-constant: {A: 2.8e+13, b: 0.0, Ea: 0.0} +- equation: S-CH2 + O2 => CO + H2O # Reaction 29 + rate-constant: {A: 1.2e+13, b: 0.0, Ea: 0.0} +- equation: S-CH2 + H2O (+ M) => CH2O + H2 (+ M) # Reaction 30 + type: falloff + low-P-rate-constant: {A: 1.88e+38, b: -6.36, Ea: 5040.63} + high-P-rate-constant: {A: 4.82e+17, b: -1.16, Ea: 1144.84} + Troe: {A: 0.6027, T3: 208.0, T1: 3922.0, T2: 1.018e+04} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: S-CH2 + H2O <=> T-CH2 + H2O # Reaction 31 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: S-CH2 + H2O => H2 + CH2O # Reaction 32 + rate-constant: {A: 6.82e+10, b: 0.25, Ea: -934.51} +- equation: CH3 + H (+ M) <=> CH4 (+ M) # Reaction 33 + type: falloff + low-P-rate-constant: {A: 3.47e+38, b: -6.3, Ea: 5074.09} + high-P-rate-constant: {A: 6.92e+13, b: 0.18, Ea: 0.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 3.0, C2H6: 3.0} +- equation: CH3 + O => CH2O + H # Reaction 34 + rate-constant: {A: 5.06e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + O => H + H2 + CO # Reaction 35 + rate-constant: {A: 3.37e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + OH (+ M) => CH2O + H2 (+ M) # Reaction 36 + type: falloff + low-P-rate-constant: {A: 4.0e+36, b: -5.92, Ea: 3140.54} + high-P-rate-constant: {A: 2.79e+18, b: -1.43, Ea: 1331.26} + Troe: {A: 0.412, T3: 195.0, T1: 5900.0, T2: 6394.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: CH3 + OH <=> T-CH2 + H2O # Reaction 37 + rate-constant: {A: 5.6e+07, b: 1.6, Ea: 5420.65} +- equation: CH3 + OH <=> S-CH2 + H2O # Reaction 38 + rate-constant: {A: 6.44e+17, b: -1.34, Ea: 1417.3} +- equation: CH3 + O2 => CH2O + O + H # Reaction 39 + rate-constant: {A: 1.38e+13, b: 0.0, Ea: 3.04804e+04} +- equation: CH3 + O2 => CH2O + OH # Reaction 40 + rate-constant: {A: 5.87e+11, b: 0.0, Ea: 1.384082e+04} +- equation: CH3 + HO2 => CH2O + OH + H # Reaction 41 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + HO2 => CH4 + O2 # Reaction 42 + rate-constant: {A: 3.61e+12, b: 0.0, Ea: 0.0} +- equation: CH3 + CH => C2H3 + H # Reaction 43 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + T-CH2 => C2H4 + H # Reaction 44 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: 2 CH3 <=> C2H5 + H # Reaction 45 + rate-constant: {A: 6.84e+12, b: 0.1, Ea: 1.05999e+04} +- equation: 2 CH3 => S-CH2 + CH4 # Reaction 46 + rate-constant: {A: 2.632e+12, b: -0.06, Ea: 1.366157e+04} +- equation: CH4 + H <=> CH3 + H2 # Reaction 47 + rate-constant: {A: 6.6e+08, b: 1.62, Ea: 1.08413e+04} +- equation: CH4 + O <=> CH3 + OH # Reaction 48 + rate-constant: {A: 1.02e+09, b: 1.5, Ea: 8599.43} +- equation: CH4 + OH <=> CH3 + H2O # Reaction 49 + rate-constant: {A: 1.0e+08, b: 1.6, Ea: 3119.02} +- equation: CH4 + CH => C2H4 + H # Reaction 50 + rate-constant: {A: 6.0e+13, b: 0.0, Ea: 0.0} +- equation: CH4 + T-CH2 <=> 2 CH3 # Reaction 51 + rate-constant: {A: 2.46e+06, b: 2.0, Ea: 8269.6} +- equation: CO + O (+ M) => CO2 (+ M) # Reaction 52 + type: falloff + low-P-rate-constant: {A: 1.17e+24, b: -2.79, Ea: 4192.16} + high-P-rate-constant: {A: 1.36e+10, b: 0.0, Ea: 2385.28} + Troe: {A: 1.0, T3: 1.0, T1: 1.0e+07, T2: 1.0e+07} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: CO + OH <=> CO2 + H # Reaction 53 + rate-constant: {A: 8.0e+11, b: 0.14, Ea: 7351.82} + duplicate: true +- equation: CO + OH <=> CO2 + H # Reaction 54 + rate-constant: {A: 8.78e+10, b: 0.03, Ea: -16.73} + duplicate: true +- equation: CO + HO2 => CO2 + OH # Reaction 55 + rate-constant: {A: 3.01e+13, b: 0.0, Ea: 2.299952e+04} +- equation: CO + S-CH2 <=> CO + T-CH2 # Reaction 56 + rate-constant: {A: 9.0e+12, b: 0.0, Ea: 0.0} +- equation: HCO + H => CO + H2 # Reaction 57 + rate-constant: {A: 1.2e+14, b: 0.0, Ea: 0.0} +- equation: HCO + O => CO + OH # Reaction 58 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: HCO + O => CO2 + H # Reaction 59 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: HCO + OH => CO + H2O # Reaction 60 + rate-constant: {A: 3.02e+13, b: 0.0, Ea: 0.0} +- equation: HCO + M <=> CO + H + M # Reaction 61 + type: three-body + rate-constant: {A: 1.87e+17, b: -1.0, Ea: 1.700048e+04} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 0.0, CH4: 2.0, C2H6: 3.0} +- equation: HCO + H2O <=> CO + H + H2O # Reaction 62 + rate-constant: {A: 2.24e+18, b: -1.0, Ea: 1.700048e+04} +- equation: HCO + O2 => CO + HO2 # Reaction 63 + rate-constant: {A: 1.2e+10, b: 0.81, Ea: -726.58} +- equation: CH3 + HCO => CH4 + CO # Reaction 64 + rate-constant: {A: 2.65e+13, b: 0.0, Ea: 0.0} +- equation: CH2O + H <=> HCO + H2 # Reaction 65 + rate-constant: {A: 5.74e+07, b: 1.9, Ea: 2741.4} +- equation: CH2O + O => HCO + OH # Reaction 66 + rate-constant: {A: 3.9e+13, b: 0.0, Ea: 3539.67} +- equation: CH2O + OH => HCO + H2O # Reaction 67 + rate-constant: {A: 3.43e+09, b: 1.18, Ea: -446.94} +- equation: CH3 + CH2O => CH4 + HCO # Reaction 68 + rate-constant: {A: 3320.0, b: 2.81, Ea: 5860.42} +- equation: CO2 + CH => HCO + CO # Reaction 69 + rate-constant: {A: 1.9e+14, b: 0.0, Ea: 1.579111e+04} +- equation: CO2 + S-CH2 <=> CO2 + T-CH2 # Reaction 70 + rate-constant: {A: 7.0e+12, b: 0.0, Ea: 0.0} +- equation: CO2 + S-CH2 => CH2O + CO # Reaction 71 + rate-constant: {A: 1.4e+13, b: 0.0, Ea: 0.0} +- equation: C2H + O => CH + CO # Reaction 72 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: C2H + OH => HCCO + H # Reaction 73 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: C2H + O2 => HCO + CO # Reaction 74 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: -755.26} +- equation: C2H + H2 <=> C2H2 + H # Reaction 75 + rate-constant: {A: 3.31e+06, b: 2.26, Ea: 901.05} +- equation: C2H2 + H (+ M) <=> C2H3 (+ M) # Reaction 76 + type: falloff + low-P-rate-constant: {A: 6.34e+31, b: -4.66, Ea: 3781.07} + high-P-rate-constant: {A: 1.71e+10, b: 1.27, Ea: 2707.93} + Troe: {A: 0.2122, T3: 1.0, T1: -1.021e+04} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H2 + O => HCCO + H # Reaction 77 + rate-constant: {A: 8.1e+06, b: 2.0, Ea: 1900.1} +- equation: C2H2 + O => T-CH2 + CO # Reaction 78 + rate-constant: {A: 1.25e+07, b: 2.0, Ea: 1900.1} +- equation: C2H2 + O => C2H + OH # Reaction 79 + rate-constant: {A: 3.324e+16, b: -0.44, Ea: 3.06979e+04} +- equation: C2H2 + OH => C2H + H2O # Reaction 80 + rate-constant: {A: 2.63e+06, b: 2.14, Ea: 1.706023e+04} +- equation: C2H2 + OH => CH3 + CO # Reaction 81 + rate-constant: {A: 7.53e+06, b: 1.55, Ea: 2105.64} + duplicate: true +- equation: C2H2 + OH => CH3 + CO # Reaction 82 + rate-constant: {A: 1.28e+09, b: 0.73, Ea: 2578.87} + duplicate: true +- equation: C2H2 + S-CH2 <=> C3H3 + H # Reaction 83 + rate-constant: {A: 1.9e+14, b: 0.0, Ea: 0.0} +- equation: C2H3 + H (+ M) => C2H4 (+ M) # Reaction 84 + type: falloff + low-P-rate-constant: {A: 1.4e+30, b: -3.86, Ea: 3319.79} + high-P-rate-constant: {A: 6.08e+12, b: 0.27, Ea: 279.64} + Troe: {A: 0.782, T3: 207.5, T1: 2663.0, T2: 6095.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H3 + H => C2H2 + H2 # Reaction 85 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: C2H3 + O => CH3 + CO # Reaction 86 + rate-constant: {A: 1.03e+13, b: 0.21, Ea: -427.82} +- equation: C2H3 + OH => C2H2 + H2O # Reaction 87 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0} +- equation: C2H3 + O2 => C2H2 + HO2 # Reaction 88 + rate-constant: {A: 1.34e+06, b: 1.61, Ea: -384.8} +- equation: C2H3 + O2 => CH3 + CO + O # Reaction 89 + rate-constant: {A: 3.03e+11, b: 0.29, Ea: 11.95} +- equation: C2H3 + O2 => HCO + CH2O # Reaction 90 + rate-constant: {A: 4.58e+16, b: -1.39, Ea: 1015.77} +- equation: C2H3 + HCO => C2H4 + CO # Reaction 91 + rate-constant: {A: 9.0e+13, b: 0.0, Ea: 0.0} +- equation: C2H3 + CH3 => C2H2 + CH4 # Reaction 92 + rate-constant: {A: 9.03e+12, b: 0.0, Ea: -764.82} +- equation: C2H3 + CH3 <=> A-C3H5 + H # Reaction 93 + rate-constant: {A: 1.93e+18, b: -1.25, Ea: 7669.69} +- equation: C2H4 + H (+ M) <=> C2H5 (+ M) # Reaction 94 + type: falloff + low-P-rate-constant: {A: 2.03e+39, b: -6.64, Ea: 5769.6} + high-P-rate-constant: {A: 1.37e+09, b: 1.46, Ea: 1355.16} + Troe: {A: -0.569, T3: 299.0, T1: -9147.0, T2: 152.4} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H4 + H => C2H3 + H2 # Reaction 95 + rate-constant: {A: 1.33e+06, b: 2.53, Ea: 1.223948e+04} +- equation: C2H4 + O => CH3 + CO + H # Reaction 96 + rate-constant: {A: 7.66e+09, b: 0.88, Ea: 1140.06} +- equation: C2H4 + O => T-CH2 + CH2O # Reaction 97 + rate-constant: {A: 7.15e+04, b: 2.47, Ea: 929.73} +- equation: C2H4 + O => CH3 + HCO # Reaction 98 + rate-constant: {A: 3.89e+08, b: 1.36, Ea: 886.71} +- equation: C2H4 + OH => C2H3 + H2O # Reaction 99 + rate-constant: {A: 0.131, b: 4.2, Ea: -860.42} +- equation: C2H4 + OH => CH3 + CH2O # Reaction 100 + rate-constant: {A: 3.75e+36, b: -7.8, Ea: 7060.23} +- equation: C2H4 + CH3 => C2H3 + CH4 # Reaction 101 + rate-constant: {A: 2.27e+05, b: 2.0, Ea: 9199.33} +- equation: C2H4 + CH3 (+ M) <=> N-C3H7 (+ M) # Reaction 102 + type: falloff + low-P-rate-constant: {A: 3.0e+63, b: -14.6, Ea: 1.816922e+04} + high-P-rate-constant: {A: 2.55e+06, b: 1.6, Ea: 5700.29} + Troe: {A: 0.1894, T3: 277.0, T1: 8748.0, T2: 7891.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H5 + H (+ M) <=> C2H6 (+ M) # Reaction 103 + type: falloff + low-P-rate-constant: {A: 1.99e+41, b: -7.08, Ea: 6684.99} + high-P-rate-constant: {A: 5.21e+17, b: -0.99, Ea: 1579.83} + Troe: {A: 0.8422, T3: 125.0, T1: 2219.0, T2: 6882.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H5 + O => CH3 + CH2O # Reaction 104 + rate-constant: {A: 3.17e+13, b: 0.03, Ea: -394.36} +- equation: C2H5 + O2 => C2H4 + HO2 # Reaction 105 + rate-constant: {A: 1.92e+07, b: 1.02, Ea: -2033.94} +- equation: C2H5 + HCO => C2H6 + CO # Reaction 106 + rate-constant: {A: 1.2e+14, b: 0.0, Ea: 0.0} +- equation: C2H5 + HO2 => C2H6 + O2 # Reaction 107 + rate-constant: {A: 3.0e+11, b: 0.0, Ea: 0.0} +- equation: C2H5 + HO2 => CH3 + CH2O + OH # Reaction 108 + rate-constant: {A: 3.1e+13, b: 0.0, Ea: 0.0} +- equation: C2H6 (+ M) <=> 2 CH3 (+ M) # Reaction 109 + type: falloff + low-P-rate-constant: {A: 3.72e+65, b: -13.14, Ea: 1.0157983e+05} + high-P-rate-constant: {A: 1.88e+50, b: -9.72, Ea: 1.0734226e+05} + Troe: {A: 0.39, T3: 100.0, T1: 1900.0, T2: 6000.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H6 + H => C2H5 + H2 # Reaction 110 + rate-constant: {A: 1.7e+05, b: 2.7, Ea: 5740.92} +- equation: C2H6 + O => C2H5 + OH # Reaction 111 + rate-constant: {A: 8.98e+07, b: 1.92, Ea: 5690.73} +- equation: C2H6 + OH => C2H5 + H2O # Reaction 112 + rate-constant: {A: 1.61e+06, b: 2.22, Ea: 740.92} +- equation: C2H6 + CH3 => C2H5 + CH4 # Reaction 113 + rate-constant: {A: 8.43e+14, b: 0.0, Ea: 2.225621e+04} +- equation: HCCO (+ M) => CO + CH (+ M) # Reaction 114 + type: falloff + low-P-rate-constant: {A: 1.213e+35, b: -5.18, Ea: 7.666826e+04} + high-P-rate-constant: {A: 2.255e+20, b: -1.44, Ea: 7.473231e+04} + Troe: {A: 0.5757, T3: 237.0, T1: 1652.0, T2: 5069.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: HCCO + H => S-CH2 + CO # Reaction 115 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: HCCO + O => H + 2 CO # Reaction 116 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: HCCO + O2 => OH + 2 CO # Reaction 117 + rate-constant: {A: 4.2e+10, b: 0.0, Ea: 853.25} +- equation: 2 HCCO => C2H2 + 2 CO # Reaction 118 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: HCCO + C2H2 => C3H3 + CO # Reaction 119 + rate-constant: {A: 1.0e+11, b: 0.0, Ea: 2999.52} +- equation: HCCO + CH3 => C2H4 + CO # Reaction 120 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: HCCO + OH => 2 HCO # Reaction 121 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: C3H3 + H <=> P-C3H4 # Reaction 122 + rate-constant: {A: 7.94e+29, b: -5.06, Ea: 4861.38} +- equation: C3H3 + H <=> A-C3H4 # Reaction 123 + rate-constant: {A: 3.16e+29, b: -5.0, Ea: 4710.8} +- equation: C3H3 + OH => C2H4 + CO # Reaction 124 + rate-constant: {A: 1.28e+09, b: 0.73, Ea: 2578.87} +- equation: C3H3 + O => C2H2 + CO + H # Reaction 125 + rate-constant: {A: 6.95e+13, b: 0.0, Ea: 0.0} +- equation: C3H3 + O2 => CH3 + 2 CO # Reaction 126 + rate-constant: {A: 1.7e+05, b: 1.7, Ea: 1500.96} +- equation: C3H3 + HO2 => OH + CO + C2H3 # Reaction 127 + rate-constant: {A: 8.0e+11, b: 0.0, Ea: 0.0} +- equation: 2 C3H3 <=> A1 # Reaction 128 + rate-constant: {A: 1.87e+46, b: -9.84, Ea: 1.680449e+04} +- equation: 2 C3H3 <=> A1- + H # Reaction 129 + rate-constant: {A: 5.77e+37, b: -7.0, Ea: 3.150574e+04} +- equation: C3H3 + C2H2 <=> C5H5 # Reaction 130 + rate-constant: {A: 2.35e+11, b: 0.0, Ea: 9995.22} +- equation: P-C3H4 + H <=> C2H2 + CH3 # Reaction 131 + rate-constant: {A: 3.46e+12, b: 0.44, Ea: 5463.67} +- equation: P-C3H4 + H <=> C3H3 + H2 # Reaction 132 + rate-constant: {A: 8.5e+04, b: 2.7, Ea: 5740.92} +- equation: P-C3H4 + OH => C3H3 + H2O # Reaction 133 + rate-constant: {A: 8.05e+05, b: 2.22, Ea: 740.92} +- equation: P-C3H4 + CH3 => C3H3 + CH4 # Reaction 134 + rate-constant: {A: 4.22e+14, b: 0.0, Ea: 2.225621e+04} +- equation: P-C3H4 + O => HCCO + CH3 # Reaction 135 + rate-constant: {A: 4.05e+06, b: 2.0, Ea: 1900.1} +- equation: P-C3H4 + O => C2H4 + CO # Reaction 136 + rate-constant: {A: 6.25e+06, b: 2.0, Ea: 1900.1} +- equation: P-C3H4 + OH => C2H5 + CO # Reaction 137 + rate-constant: {A: 1.28e+09, b: 0.73, Ea: 2578.87} +- equation: A-C3H4 + H <=> C2H2 + CH3 # Reaction 138 + rate-constant: {A: 8.95e+13, b: -0.02, Ea: 1.125e+04} +- equation: A-C3H4 <=> P-C3H4 # Reaction 139 + rate-constant: {A: 7.76e+39, b: -7.8, Ea: 7.844646e+04} +- equation: A-C3H4 + H <=> P-C3H4 + H # Reaction 140 + rate-constant: {A: 2.47e+15, b: -0.33, Ea: 6436.42} +- equation: A-C3H4 + H => C3H3 + H2 # Reaction 141 + rate-constant: {A: 1.33e+06, b: 2.53, Ea: 1.223948e+04} +- equation: A-C3H4 + OH => C3H3 + H2O # Reaction 142 + rate-constant: {A: 0.131, b: 4.2, Ea: -860.42} +- equation: A-C3H4 + CH3 => C3H3 + CH4 # Reaction 143 + rate-constant: {A: 2.27e+05, b: 2.0, Ea: 9199.33} +- equation: A-C3H4 + H <=> A-C3H5 # Reaction 144 + rate-constant: {A: 2.01e+49, b: -10.77, Ea: 1.962237e+04} +- equation: A-C3H5 + H => A-C3H4 + H2 # Reaction 145 + rate-constant: {A: 9560.0, b: 2.8, Ea: 3291.11} +- equation: A-C3H5 + OH => A-C3H4 + H2O # Reaction 146 + rate-constant: {A: 6.03e+12, b: 0.0, Ea: 0.0} +- equation: A-C3H5 + CH3 => A-C3H4 + CH4 # Reaction 147 + rate-constant: {A: 4.86e+11, b: -0.32, Ea: -131.45} +- equation: A-C3H5 + O2 => C2H2 + CH2O + OH # Reaction 148 + rate-constant: {A: 9.71e+20, b: -2.7, Ea: 2.498088e+04} +- equation: A-C3H5 + C3H3 => A1 + 2 H # Reaction 149 + rate-constant: {A: 2.16e+39, b: -7.74, Ea: 2.385277e+04} +- equation: C3H6 + H (+ M) <=> N-C3H7 (+ M) # Reaction 150 + type: falloff + low-P-rate-constant: {A: 6.26e+38, b: -6.66, Ea: 7000.48} + high-P-rate-constant: {A: 3.06e+14, b: -0.37, Ea: 4032.03} + Troe: {A: 1.0, T3: 1000.0, T1: 1310.0, T2: 4.81e+04} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.0, H2O: 12.0, CH4: 2.0, C2H6: 3.0} +- equation: C3H6 <=> C2H3 + CH3 # Reaction 151 + rate-constant: {A: 4.04e+42, b: -7.67, Ea: 1.1183078e+05} +- equation: A-C3H5 + H <=> C3H6 # Reaction 152 + rate-constant: {A: 5.93e+54, b: -11.76, Ea: 2.354924e+04} +- equation: C3H6 + H <=> C2H4 + CH3 # Reaction 153 + rate-constant: {A: 8.0e+21, b: -2.39, Ea: 1.118069e+04} +- equation: C3H6 + O => 2 CH3 + CO # Reaction 154 + rate-constant: {A: 1.2e+08, b: 1.6, Ea: 327.44} +- equation: C3H6 + O => C2H5 + HCO # Reaction 155 + rate-constant: {A: 3.5e+07, b: 1.6, Ea: -972.75} +- equation: C3H6 + H => A-C3H5 + H2 # Reaction 156 + rate-constant: {A: 6.6e+05, b: 2.54, Ea: 6756.69} +- equation: C3H6 + O => A-C3H5 + OH # Reaction 157 + rate-constant: {A: 9.65e+04, b: 2.68, Ea: 3716.54} +- equation: C3H6 + OH => A-C3H5 + H2O # Reaction 158 + rate-constant: {A: 2.0e+08, b: 1.46, Ea: 537.76} +- equation: C3H6 + CH3 => A-C3H5 + CH4 # Reaction 159 + rate-constant: {A: 0.452, b: 3.65, Ea: 7153.44} +- equation: C4H8 + H => C2H5 + C2H4 # Reaction 160 + rate-constant: {A: 7.68e+12, b: 0.11, Ea: 1479.45} +- equation: C4H8 => A-C3H5 + CH3 # Reaction 161 + rate-constant: {A: 5.0e+15, b: 0.0, Ea: 7.099904e+04} +- equation: C5H5 + HO2 => O2 + C5H6 # Reaction 162 + rate-constant: {A: 2.561e+12, b: 0.06, Ea: 3116.63} +- equation: 2 C5H5 => A2 + 2 H # Reaction 163 + rate-constant: {A: 6.39e+29, b: -4.03, Ea: 3.520554e+04} +- equation: C5H5 + O => C2H3 + C2H2 + CO # Reaction 164 + rate-constant: {A: 7.0e+13, b: 0.0, Ea: 0.0} +- equation: C5H5 + HO2 => C2H3 + C2H2 + CO + OH # Reaction 165 + rate-constant: {A: 6.776e+29, b: -4.7, Ea: 1.16587e+04} +- equation: C5H5 + HO2 => 2 C2H2 + CO + H2O # Reaction 166 + rate-constant: {A: 1.19e+33, b: -6.52, Ea: 1.340105e+04} +- equation: C5H5 + OH => C2H3 + C2H2 + CO + H # Reaction 167 + rate-constant: {A: 3.02e+13, b: 0.0, Ea: 0.0} +- equation: C5H6 <=> C5H5 + H # Reaction 168 + rate-constant: {A: 1.73e+68, b: -15.16, Ea: 1.1637189e+05} +- equation: C5H6 + H => C5H5 + H2 # Reaction 169 + rate-constant: {A: 2.8e+13, b: 0.0, Ea: 2258.6} +- equation: C5H6 + H => A-C3H5 + C2H2 # Reaction 170 + rate-constant: {A: 6.6e+14, b: 0.0, Ea: 1.234465e+04} +- equation: C5H6 + O => C5H5 + OH # Reaction 171 + rate-constant: {A: 4.77e+04, b: 2.71, Ea: 1106.6} +- equation: C5H6 + OH => C5H5 + H2O # Reaction 172 + rate-constant: {A: 3.08e+06, b: 2.0, Ea: 0.0} +- equation: C5H6 + CH3 => C5H5 + CH4 # Reaction 173 + rate-constant: {A: 0.18, b: 4.0, Ea: 0.0} +- equation: C5H10 + H => C5H11 # Reaction 174 + rate-constant: {A: 7.1e+12, b: 0.12, Ea: 1460.33} +- equation: C5H10 => C2H5 + A-C3H5 # Reaction 175 + rate-constant: {A: 9.17e+20, b: -1.63, Ea: 7.398901e+04} +- equation: C5H11 => C2H4 + N-C3H7 # Reaction 176 + rate-constant: {A: 7.46e+21, b: -2.61, Ea: 3.202677e+04} +- equation: C5H11 => H + C5H10 # Reaction 177 + rate-constant: {A: 8.46e+14, b: -0.47, Ea: 3.761711e+04} +- equation: C5H11 => C3H6 + C2H5 # Reaction 178 + rate-constant: {A: 3.15e-19, b: 8.84, Ea: 7105.64} +- equation: A1- + O2 => C5H5 + CO + O # Reaction 179 + rate-constant: {A: 2.6e+13, b: 0.0, Ea: 6120.94} +- equation: A1- + O2 => 2 CO + 2 C2H2 + H # Reaction 180 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 8979.45} +- equation: A1- + O => C5H5 + CO # Reaction 181 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: A1- + OH => C5H6 + CO # Reaction 182 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: A1- + HO2 => C5H5 + CO + OH # Reaction 183 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: A1- + C2H2 <=> A1C2H2 # Reaction 184 + rate-constant: {A: 3.29e+06, b: 2.05, Ea: 3162.05} +- equation: A1 <=> A1- + H # Reaction 185 + rate-constant: {A: 1.29e+61, b: -12.48, Ea: 1.4808556e+05} +- equation: A1 + H => A1- + H2 # Reaction 186 + rate-constant: {A: 6.02e+08, b: 1.8, Ea: 1.635277e+04} +- equation: A1 + OH => A1- + H2O # Reaction 187 + rate-constant: {A: 403.0, b: 3.33, Ea: 1455.54} +- equation: A1 + CH3 => A1- + CH4 # Reaction 188 + rate-constant: {A: 0.02752, b: 4.46, Ea: 1.363767e+04} +- equation: A1 + O => C5H5 + CO + H # Reaction 189 + rate-constant: {A: 2.22e+13, b: 0.0, Ea: 4531.55} +- equation: A1 + OH => C5H6 + CO + H # Reaction 190 + rate-constant: {A: 132.0, b: 3.25, Ea: 5590.34} +- equation: A1CH2 <=> C5H5 + C2H2 # Reaction 191 + rate-constant: {A: 8.2e+14, b: 0.0, Ea: 8.067639e+04} +- equation: A1CH2 + H <=> A1- + CH3 # Reaction 192 + rate-constant: {A: 5.83e+67, b: -14.15, Ea: 6.832935e+04} +- equation: A1CH2 + O => A1CHO + H # Reaction 193 + rate-constant: {A: 3.31e+14, b: 0.0, Ea: 0.0} +- equation: A1CH2 + HO2 => A1CHO + OH + H # Reaction 194 + rate-constant: {A: 1.06e+16, b: -0.94, Ea: 2523.9} +- equation: A1CH2 + C3H3 => A2 + 2 H # Reaction 195 + rate-constant: {A: 4.32e+39, b: -7.74, Ea: 2.385277e+04} +- equation: A1CH3 + H <=> A1 + CH3 # Reaction 196 + rate-constant: {A: 2.31e+06, b: 2.17, Ea: 4163.48} +- equation: A1CH3 <=> A1CH2 + H # Reaction 197 + rate-constant: {A: 1.25e+18, b: -0.6, Ea: 9.478728e+04} +- equation: A1CH3 <=> A1- + CH3 # Reaction 198 + rate-constant: {A: 2.16e+29, b: -3.58, Ea: 1.1016491e+05} +- equation: A1CH3 + H => A1CH2 + H2 # Reaction 199 + rate-constant: {A: 6.47, b: 3.98, Ea: 3384.32} +- equation: A1CH3 + OH => A1CH2 + H2O # Reaction 200 + rate-constant: {A: 1.62e+13, b: 0.0, Ea: 2770.08} +- equation: A1CH3 + CH3 => A1CH2 + CH4 # Reaction 201 + rate-constant: {A: 4.22e+14, b: 0.0, Ea: 2.225621e+04} +- equation: C7H15 => C5H11 + C2H4 # Reaction 202 + rate-constant: {A: 1.89e+12, b: 0.02, Ea: 2.778442e+04} +- equation: C7H15 => C2H5 + C2H4 + C3H6 # Reaction 203 + rate-constant: {A: 7.73e+18, b: -1.75, Ea: 3.197419e+04} +- equation: C7H15 => C4H8 + N-C3H7 # Reaction 204 + rate-constant: {A: 2.53e+18, b: -1.65, Ea: 3.16826e+04} +- equation: C7H15 => C2H5 + C5H10 # Reaction 205 + rate-constant: {A: 2.49e+16, b: -1.18, Ea: 2.951721e+04} +- equation: N-C7H16 => C5H11 + C2H5 # Reaction 206 + rate-constant: {A: 8.1e+77, b: -17.62, Ea: 1.2039914e+05} +- equation: N-C7H16 => C2H5 + C2H4 + N-C3H7 # Reaction 207 + rate-constant: {A: 1.42e+78, b: -17.71, Ea: 1.2070029e+05} +- equation: N-C7H16 + H => C7H15 + H2 # Reaction 208 + rate-constant: {A: 1.75e+06, b: 2.6, Ea: 4361.85} +- equation: N-C7H16 + O => C7H15 + OH # Reaction 209 + rate-constant: {A: 1.72e+05, b: 2.81, Ea: 2260.99} +- equation: N-C7H16 + OH => C7H15 + H2O # Reaction 210 + rate-constant: {A: 7.4e+08, b: 1.5, Ea: 258.13} +- equation: N-C7H16 + CH3 => C7H15 + CH4 # Reaction 211 + rate-constant: {A: 1.46e+04, b: 2.57, Ea: 6933.56} +- equation: A1CHO => A1- + HCO # Reaction 212 + rate-constant: {A: 2.61e+15, b: 0.15, Ea: 8.054971e+04} +- equation: A1CHO + H => A1- + CO + H2 # Reaction 213 + rate-constant: {A: 2.05e+09, b: 1.16, Ea: 2404.4} +- equation: A1CHO + CH3 => A1- + CO + CH4 # Reaction 214 + rate-constant: {A: 2.72e+06, b: 1.77, Ea: 5920.17} +- equation: A1C2H* + C2H2 <=> A2- # Reaction 215 + rate-constant: {A: 1.34e+04, b: 2.5, Ea: 1283.46} +- equation: A1C2H* + C2H4 <=> A2 + H # Reaction 216 + rate-constant: {A: 3.62e+28, b: -4.24, Ea: 2.386472e+04} +- equation: A1C2H <=> A1C2H* + H # Reaction 217 + rate-constant: {A: 2.1e+60, b: -12.4, Ea: 1.48076e+05} +- equation: A1C2H + H <=> A1C2H* + H2 # Reaction 218 + rate-constant: {A: 1.32e+08, b: 1.88, Ea: 1.682122e+04} +- equation: A1C2H + OH <=> A1C2H* + H2O # Reaction 219 + rate-constant: {A: 134.0, b: 3.33, Ea: 1455.54} +- equation: A1C2H2 <=> A1C2H + H # Reaction 220 + rate-constant: {A: 1.34e+17, b: -0.86, Ea: 4.123805e+04} +- equation: A1C2H2 + C2H2 <=> A2 + H # Reaction 221 + rate-constant: {A: 7.091e+13, b: -0.26, Ea: 7002.87} +- equation: A2 <=> A2- + H # Reaction 222 + rate-constant: {A: 8.6e+60, b: -12.48, Ea: 1.48076e+05} +- equation: A2 + H <=> A2- + H2 # Reaction 223 + rate-constant: {A: 2.65e+08, b: 1.87, Ea: 1.709608e+04} +- equation: A2 + OH <=> A2- + H2O # Reaction 224 + rate-constant: {A: 963.0, b: 3.02, Ea: 4373.8} diff --git a/samples/python/AVBP/inputs/Lu.cti b/samples/python/AVBP/inputs/Lu.cti new file mode 100755 index 00000000000..66a81d9203c --- /dev/null +++ b/samples/python/AVBP/inputs/Lu.cti @@ -0,0 +1,1351 @@ +""" + A 30-species skeletal mechanism based on GRI3.0 + + by Tianfeng Lu + Email: tlu@engr.uconn.edu + + Reference: + Tianfeng Lu and Chung K. Law, + "A criterion based on computational singular perturbation + for the identification of quasi steady state species: + A reduced mechanism for methane oxidation with NO chemistry," + Combustion and Flame, Vol.154 No.4 pp.761774, 2008. + + +""" + +units(length='cm', time='s', quantity='mol', act_energy='cal/mol') + +ideal_gas(name='gas', + elements="O H C N Ar", + species="""H2 H O O2 OH H2O HO2 + H2O2 C CH CH2 CH2(S) CH3 CH4 + CO CO2 HCO CH2O CH2OH CH3O CH3OH + C2H2 C2H3 C2H4 C2H5 C2H6 HCCO CH2CO + CH2CHO N2""", + reactions='all', + transport='Mix', + initial_state=state(temperature=300.0, pressure=OneAtm)) + +#------------------------------------------------------------------------------- +# Species data +#------------------------------------------------------------------------------- + +species(name=u'H2', + atoms='H:2', + thermo=(NASA([200.00, 1000.00], + [ 2.34433112E+00, 7.98052075E-03, -1.94781510E-05, + 2.01572094E-08, -7.37611761E-12, -9.17935173E+02, + 6.83010238E-01]), + NASA([1000.00, 3500.00], + [ 3.33727920E+00, -4.94024731E-05, 4.99456778E-07, + -1.79566394E-10, 2.00255376E-14, -9.50158922E+02, + -3.20502331E+00])), + transport=gas_transport(geom='linear', + diam=2.92, + well_depth=38.0, + polar=0.79, + rot_relax=280.0), + note=u'TPIS78') + +species(name=u'H', + atoms='H:1', + thermo=(NASA([200.00, 1000.00], + [ 2.50000000E+00, 7.05332819E-13, -1.99591964E-15, + 2.30081632E-18, -9.27732332E-22, 2.54736599E+04, + -4.46682853E-01]), + NASA([1000.00, 3500.00], + [ 2.50000001E+00, -2.30842973E-11, 1.61561948E-14, + -4.73515235E-18, 4.98197357E-22, 2.54736599E+04, + -4.46682914E-01])), + transport=gas_transport(geom='atom', + diam=2.05, + well_depth=145.0), + note=u'L7/88') + +species(name=u'O', + atoms='O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.16826710E+00, -3.27931884E-03, 6.64306396E-06, + -6.12806624E-09, 2.11265971E-12, 2.91222592E+04, + 2.05193346E+00]), + NASA([1000.00, 3500.00], + [ 2.56942078E+00, -8.59741137E-05, 4.19484589E-08, + -1.00177799E-11, 1.22833691E-15, 2.92175791E+04, + 4.78433864E+00])), + transport=gas_transport(geom='atom', + diam=2.75, + well_depth=80.0), + note=u'L1/90') + +species(name=u'O2', + atoms='O:2', + thermo=(NASA([200.00, 1000.00], + [ 3.78245636E+00, -2.99673416E-03, 9.84730201E-06, + -9.68129509E-09, 3.24372837E-12, -1.06394356E+03, + 3.65767573E+00]), + NASA([1000.00, 3500.00], + [ 3.28253784E+00, 1.48308754E-03, -7.57966669E-07, + 2.09470555E-10, -2.16717794E-14, -1.08845772E+03, + 5.45323129E+00])), + transport=gas_transport(geom='linear', + diam=3.458, + well_depth=107.4, + polar=1.6, + rot_relax=3.8), + note=u'TPIS89') + +species(name=u'OH', + atoms='H:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.99201543E+00, -2.40131752E-03, 4.61793841E-06, + -3.88113333E-09, 1.36411470E-12, 3.61508056E+03, + -1.03925458E-01]), + NASA([1000.00, 3500.00], + [ 3.09288767E+00, 5.48429716E-04, 1.26505228E-07, + -8.79461556E-11, 1.17412376E-14, 3.85865700E+03, + 4.47669610E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note=u'RUS78') + +species(name=u'H2O', + atoms='H:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19864056E+00, -2.03643410E-03, 6.52040211E-06, + -5.48797062E-09, 1.77197817E-12, -3.02937267E+04, + -8.49032208E-01]), + NASA([1000.00, 3500.00], + [ 3.03399249E+00, 2.17691804E-03, -1.64072518E-07, + -9.70419870E-11, 1.68200992E-14, -3.00042971E+04, + 4.96677010E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.605, + well_depth=572.4, + dipole=1.844, + rot_relax=4.0), + note=u'L8/89') + +species(name=u'HO2', + atoms='H:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30179801E+00, -4.74912051E-03, 2.11582891E-05, + -2.42763894E-08, 9.29225124E-12, 2.94808040E+02, + 3.71666245E+00]), + NASA([1000.00, 3500.00], + [ 4.01721090E+00, 2.23982013E-03, -6.33658150E-07, + 1.14246370E-10, -1.07908535E-14, 1.11856713E+02, + 3.78510215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=1.0), + note=u'L5/89') + +species(name=u'H2O2', + atoms='H:2 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.27611269E+00, -5.42822417E-04, 1.67335701E-05, + -2.15770813E-08, 8.62454363E-12, -1.77025821E+04, + 3.43505074E+00]), + NASA([1000.00, 3500.00], + [ 4.16500285E+00, 4.90831694E-03, -1.90139225E-06, + 3.71185986E-10, -2.87908305E-14, -1.78617877E+04, + 2.91615662E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=3.8), + note=u'L7/88') + +species(name=u'C', + atoms='C:1', + thermo=(NASA([200.00, 1000.00], + [ 2.55423955E+00, -3.21537724E-04, 7.33792245E-07, + -7.32234889E-10, 2.66521446E-13, 8.54438832E+04, + 4.53130848E+00]), + NASA([1000.00, 3500.00], + [ 2.49266888E+00, 4.79889284E-05, -7.24335020E-08, + 3.74291029E-11, -4.87277893E-15, 8.54512953E+04, + 4.80150373E+00])), + transport=gas_transport(geom='atom', + diam=3.298, + well_depth=71.4), + note=u'L11/88') + +species(name=u'CH', + atoms='H:1 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.48981665E+00, 3.23835541E-04, -1.68899065E-06, + 3.16217327E-09, -1.40609067E-12, 7.07972934E+04, + 2.08401108E+00]), + NASA([1000.00, 3500.00], + [ 2.87846473E+00, 9.70913681E-04, 1.44445655E-07, + -1.30687849E-10, 1.76079383E-14, 7.10124364E+04, + 5.48497999E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note=u'TPIS79') + +species(name=u'CH2', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.76267867E+00, 9.68872143E-04, 2.79489841E-06, + -3.85091153E-09, 1.68741719E-12, 4.60040401E+04, + 1.56253185E+00]), + NASA([1000.00, 3500.00], + [ 2.87410113E+00, 3.65639292E-03, -1.40894597E-06, + 2.60179549E-10, -1.87727567E-14, 4.62636040E+04, + 6.17119324E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'LS/93') + +species(name=u'CH2(S)', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19860411E+00, -2.36661419E-03, 8.23296220E-06, + -6.68815981E-09, 1.94314737E-12, 5.04968163E+04, + -7.69118967E-01]), + NASA([1000.00, 3500.00], + [ 2.29203842E+00, 4.65588637E-03, -2.01191947E-06, + 4.17906000E-10, -3.39716365E-14, 5.09259997E+04, + 8.62650169E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'LS/93') + +species(name=u'CH3', + atoms='H:3 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.67359040E+00, 2.01095175E-03, 5.73021856E-06, + -6.87117425E-09, 2.54385734E-12, 1.64449988E+04, + 1.60456433E+00]), + NASA([1000.00, 3500.00], + [ 2.28571772E+00, 7.23990037E-03, -2.98714348E-06, + 5.95684644E-10, -4.67154394E-14, 1.67755843E+04, + 8.48007179E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note=u'L11/89') + +species(name=u'CH4', + atoms='H:4 C:1', + thermo=(NASA([200.00, 1000.00], + [ 5.14987613E+00, -1.36709788E-02, 4.91800599E-05, + -4.84743026E-08, 1.66693956E-11, -1.02466476E+04, + -4.64130376E+00]), + NASA([1000.00, 3500.00], + [ 7.48514950E-02, 1.33909467E-02, -5.73285809E-06, + 1.22292535E-09, -1.01815230E-13, -9.46834459E+03, + 1.84373180E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.746, + well_depth=141.4, + polar=2.6, + rot_relax=13.0), + note=u'L8/88') + +species(name=u'CO', + atoms='C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.57953347E+00, -6.10353680E-04, 1.01681433E-06, + 9.07005884E-10, -9.04424499E-13, -1.43440860E+04, + 3.50840928E+00]), + NASA([1000.00, 3500.00], + [ 2.71518561E+00, 2.06252743E-03, -9.98825771E-07, + 2.30053008E-10, -2.03647716E-14, -1.41518724E+04, + 7.81868772E+00])), + transport=gas_transport(geom='linear', + diam=3.65, + well_depth=98.1, + polar=1.95, + rot_relax=1.8), + note=u'TPIS79') + +species(name=u'CO2', + atoms='C:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 2.35677352E+00, 8.98459677E-03, -7.12356269E-06, + 2.45919022E-09, -1.43699548E-13, -4.83719697E+04, + 9.90105222E+00]), + NASA([1000.00, 3500.00], + [ 3.85746029E+00, 4.41437026E-03, -2.21481404E-06, + 5.23490188E-10, -4.72084164E-14, -4.87591660E+04, + 2.27163806E+00])), + transport=gas_transport(geom='linear', + diam=3.763, + well_depth=244.0, + polar=2.65, + rot_relax=2.1), + note=u'L7/88') + +species(name=u'HCO', + atoms='H:1 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.22118584E+00, -3.24392532E-03, 1.37799446E-05, + -1.33144093E-08, 4.33768865E-12, 3.83956496E+03, + 3.39437243E+00]), + NASA([1000.00, 3500.00], + [ 2.77217438E+00, 4.95695526E-03, -2.48445613E-06, + 5.89161778E-10, -5.33508711E-14, 4.01191815E+03, + 9.79834492E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0), + note=u'L12/89') + +species(name=u'CH2O', + atoms='H:2 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.79372315E+00, -9.90833369E-03, 3.73220008E-05, + -3.79285261E-08, 1.31772652E-11, -1.43089567E+04, + 6.02812900E-01]), + NASA([1000.00, 3500.00], + [ 1.76069008E+00, 9.20000082E-03, -4.42258813E-06, + 1.00641212E-09, -8.83855640E-14, -1.39958323E+04, + 1.36563230E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0, + rot_relax=2.0), + note=u'L8/88') + +species(name=u'CH2OH', + atoms='H:3 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.86388918E+00, 5.59672304E-03, 5.93271791E-06, + -1.04532012E-08, 4.36967278E-12, -3.19391367E+03, + 5.47302243E+00]), + NASA([1000.00, 3500.00], + [ 3.69266569E+00, 8.64576797E-03, -3.75101120E-06, + 7.87234636E-10, -6.48554201E-14, -3.24250627E+03, + 5.81043215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.69, + well_depth=417.0, + dipole=1.7, + rot_relax=2.0), + note=u'GUNL93') + +species(name=u'CH3O', + atoms='H:3 C:1 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.10620400E+00, 7.21659500E-03, 5.33847200E-06, + -7.37763600E-09, 2.07561000E-12, 9.78601100E+02, + 1.31521770E+01]), + NASA([1000.00, 3000.00], + [ 3.77079900E+00, 7.87149700E-03, -2.65638400E-06, + 3.94443100E-10, -2.11261600E-14, 1.27832520E+02, + 2.92957500E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.69, + well_depth=417.0, + dipole=1.7, + rot_relax=2.0), + note=u'121686') + +species(name=u'CH3OH', + atoms='H:4 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 5.71539582E+00, -1.52309129E-02, 6.52441155E-05, + -7.10806889E-08, 2.61352698E-11, -2.56427656E+04, + -1.50409823E+00]), + NASA([1000.00, 3500.00], + [ 1.78970791E+00, 1.40938292E-02, -6.36500835E-06, + 1.38171085E-09, -1.17060220E-13, -2.53748747E+04, + 1.45023623E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.626, + well_depth=481.8, + rot_relax=1.0), + note=u'L8/88') + +species(name=u'C2H2', + atoms='H:2 C:2', + thermo=(NASA([200.00, 1000.00], + [ 8.08681094E-01, 2.33615629E-02, -3.55171815E-05, + 2.80152437E-08, -8.50072974E-12, 2.64289807E+04, + 1.39397051E+01]), + NASA([1000.00, 3500.00], + [ 4.14756964E+00, 5.96166664E-03, -2.37294852E-06, + 4.67412171E-10, -3.61235213E-14, 2.59359992E+04, + -1.23028121E+00])), + transport=gas_transport(geom='linear', + diam=4.1, + well_depth=209.0, + rot_relax=2.5), + note=u'L1/91') + +species(name=u'C2H3', + atoms='H:3 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.21246645E+00, 1.51479162E-03, 2.59209412E-05, + -3.57657847E-08, 1.47150873E-11, 3.48598468E+04, + 8.51054025E+00]), + NASA([1000.00, 3500.00], + [ 3.01672400E+00, 1.03302292E-02, -4.68082349E-06, + 1.01763288E-09, -8.62607041E-14, 3.46128739E+04, + 7.78732378E+00])), + transport=gas_transport(geom='nonlinear', + diam=4.1, + well_depth=209.0, + rot_relax=1.0), + note=u'L2/92') + +species(name=u'C2H4', + atoms='H:4 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.95920148E+00, -7.57052247E-03, 5.70990292E-05, + -6.91588753E-08, 2.69884373E-11, 5.08977593E+03, + 4.09733096E+00]), + NASA([1000.00, 3500.00], + [ 2.03611116E+00, 1.46454151E-02, -6.71077915E-06, + 1.47222923E-09, -1.25706061E-13, 4.93988614E+03, + 1.03053693E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.971, + well_depth=280.8, + rot_relax=1.5), + note=u'L1/91') + +species(name=u'C2H5', + atoms='H:5 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30646568E+00, -4.18658892E-03, 4.97142807E-05, + -5.99126606E-08, 2.30509004E-11, 1.28416265E+04, + 4.70720924E+00]), + NASA([1000.00, 3500.00], + [ 1.95465642E+00, 1.73972722E-02, -7.98206668E-06, + 1.75217689E-09, -1.49641576E-13, 1.28575200E+04, + 1.34624343E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note=u'L12/92') + +species(name=u'C2H6', + atoms='H:6 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.29142492E+00, -5.50154270E-03, 5.99438288E-05, + -7.08466285E-08, 2.68685771E-11, -1.15222055E+04, + 2.66682316E+00]), + NASA([1000.00, 3500.00], + [ 1.07188150E+00, 2.16852677E-02, -1.00256067E-05, + 2.21412001E-09, -1.90002890E-13, -1.14263932E+04, + 1.51156107E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note=u'L8/88') + +species(name=u'HCCO', + atoms='H:1 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.25172140E+00, 1.76550210E-02, -2.37291010E-05, + 1.72757590E-08, -5.06648110E-12, 2.00594490E+04, + 1.24904170E+01]), + NASA([1000.00, 4000.00], + [ 5.62820580E+00, 4.08534010E-03, -1.59345470E-06, + 2.86260520E-10, -1.94078320E-14, 1.93272150E+04, + -3.93025950E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.5, + well_depth=150.0, + rot_relax=1.0), + note=u'SRIC91') + +species(name=u'CH2CO', + atoms='H:2 C:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 2.13583630E+00, 1.81188721E-02, -1.73947474E-05, + 9.34397568E-09, -2.01457615E-12, -7.04291804E+03, + 1.22156480E+01]), + NASA([1000.00, 3500.00], + [ 4.51129732E+00, 9.00359745E-03, -4.16939635E-06, + 9.23345882E-10, -7.94838201E-14, -7.55105311E+03, + 6.32247205E-01])), + transport=gas_transport(geom='nonlinear', + diam=3.97, + well_depth=436.0, + rot_relax=2.0), + note=u'L5/90') + +species(name=u'CH2CHO', + atoms='H:3 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 3.40906200E+00, 1.07385740E-02, 1.89149200E-06, + -7.15858300E-09, 2.86738500E-12, 1.52147660E+03, + 9.55829000E+00]), + NASA([1000.00, 5000.00], + [ 5.97567000E+00, 8.13059100E-03, -2.74362400E-06, + 4.07030400E-10, -2.17601700E-14, 4.90321800E+02, + -5.04525100E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.97, + well_depth=436.0, + rot_relax=2.0), + note=u'SAND86') + +species(name=u'N2', + atoms='N:2', + thermo=(NASA([300.00, 1000.00], + [ 3.29867700E+00, 1.40824040E-03, -3.96322200E-06, + 5.64151500E-09, -2.44485400E-12, -1.02089990E+03, + 3.95037200E+00]), + NASA([1000.00, 5000.00], + [ 2.92664000E+00, 1.48797680E-03, -5.68476000E-07, + 1.00970380E-10, -6.75335100E-15, -9.22797700E+02, + 5.98052800E+00])), + transport=gas_transport(geom='linear', + diam=3.621, + well_depth=97.53, + polar=1.76, + rot_relax=4.0), + note=u'121286') + +#------------------------------------------------------------------------------- +# Reaction data +#------------------------------------------------------------------------------- +# R1 + +# Reaction 1 +three_body_reaction('2 O + M <=> O2 + M', [1.200000e+17, -1.0, 0.0], + efficiencies='CO2:3.6 CO:1.75 H2:2.4 H2O:15.4 CH4:2.0 C2H6:3.0') +# R2 + +# Reaction 2 +three_body_reaction('O + H + M <=> OH + M', [5.000000e+17, -1.0, 0.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0') +# R3 + +# Reaction 3 +reaction('O + H2 <=> H + OH', [3.870000e+04, 2.7, 6260.0]) +# R4 + +# Reaction 4 +reaction('O + HO2 <=> OH + O2', [2.000000e+13, 0.0, 0.0]) +# R5 + +# Reaction 5 +reaction('O + H2O2 <=> OH + HO2', [9.630000e+06, 2.0, 4000.0]) +# R6 + +# Reaction 6 +reaction('O + CH <=> H + CO', [5.700000e+13, 0.0, 0.0]) +# R7 + +# Reaction 7 +reaction('O + CH2 <=> H + HCO', [8.000000e+13, 0.0, 0.0]) +# R8 + +# Reaction 8 +reaction('O + CH2(S) <=> H2 + CO', [1.500000e+13, 0.0, 0.0]) +# R9 + +# Reaction 9 +reaction('O + CH2(S) <=> H + HCO', [1.500000e+13, 0.0, 0.0]) +# R10 + +# Reaction 10 +reaction('O + CH3 <=> H + CH2O', [5.060000e+13, 0.0, 0.0]) +# R11 + +# Reaction 11 +reaction('O + CH4 <=> OH + CH3', [1.020000e+09, 1.5, 8600.0]) +# R12 + +# Reaction 12 +falloff_reaction('O + CO (+ M) <=> CO2 (+ M)', + kf=[1.800000e+10, 0.0, 2385.0], + kf0=[6.020000e+14, 0.0, 3000.0], + efficiencies='CO2:3.5 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0 O2:6.0') +# R13 + +# Reaction 13 +reaction('O + HCO <=> OH + CO', [3.000000e+13, 0.0, 0.0]) +# R14 + +# Reaction 14 +reaction('O + HCO <=> H + CO2', [3.000000e+13, 0.0, 0.0]) +# R15 + +# Reaction 15 +reaction('O + CH2O <=> OH + HCO', [3.900000e+13, 0.0, 3540.0]) +# R16 + +# Reaction 16 +reaction('O + CH2OH <=> OH + CH2O', [1.000000e+13, 0.0, 0.0]) +# R17 + +# Reaction 17 +reaction('O + CH3O <=> OH + CH2O', [1.000000e+13, 0.0, 0.0]) +# R18 + +# Reaction 18 +reaction('O + CH3OH <=> OH + CH2OH', [3.880000e+05, 2.5, 3100.0]) +# R19 + +# Reaction 19 +reaction('O + CH3OH <=> OH + CH3O', [1.300000e+05, 2.5, 5000.0]) +# R20 + +# Reaction 20 +reaction('O + C2H2 <=> H + HCCO', [1.350000e+07, 2.0, 1900.0]) +# R21 + +# Reaction 21 +reaction('O + C2H2 <=> CO + CH2', [6.940000e+06, 2.0, 1900.0]) +# R22 + +# Reaction 22 +reaction('O + C2H3 <=> H + CH2CO', [3.000000e+13, 0.0, 0.0]) +# R23 + +# Reaction 23 +reaction('O + C2H4 <=> CH3 + HCO', [1.250000e+07, 1.83, 220.0]) +# R24 + +# Reaction 24 +reaction('O + C2H5 <=> CH3 + CH2O', [2.240000e+13, 0.0, 0.0]) +# R25 + +# Reaction 25 +reaction('O + C2H6 <=> OH + C2H5', [8.980000e+07, 1.92, 5690.0]) +# R26 + +# Reaction 26 +reaction('O + HCCO <=> H + 2 CO', [1.000000e+14, 0.0, 0.0]) +# R27 + +# Reaction 27 +reaction('O + CH2CO <=> OH + HCCO', [1.000000e+13, 0.0, 8000.0]) +# R28 + +# Reaction 28 +reaction('O + CH2CO <=> CH2 + CO2', [1.750000e+12, 0.0, 1350.0]) +# R29 + +# Reaction 29 +reaction('O2 + CO <=> O + CO2', [2.500000e+12, 0.0, 47800.0]) +# R30 + +# Reaction 30 +reaction('O2 + CH2O <=> HO2 + HCO', [1.000000e+14, 0.0, 40000.0]) +# R31 + +# Reaction 31 +three_body_reaction('H + O2 + M <=> HO2 + M', [2.800000e+18, -0.86, 0.0], + efficiencies='CO2:1.5 CO:0.75 H2O:0.0 C2H6:1.5 N2:0.0 O2:0.0') +# R32 + +# Reaction 32 +reaction('H + 2 O2 <=> HO2 + O2', [2.080000e+19, -1.24, 0.0]) +# R33 + +# Reaction 33 +reaction('H + O2 + H2O <=> HO2 + H2O', [1.126000e+19, -0.76, 0.0]) +# R34 + +# Reaction 34 +reaction('H + O2 + N2 <=> HO2 + N2', [2.600000e+19, -1.24, 0.0]) +# R35 + +# Reaction 35 +reaction('H + O2 <=> O + OH', [2.650000e+16, -0.6707, 17041.0]) +# R36 + +# Reaction 36 +three_body_reaction('2 H + M <=> H2 + M', [1.000000e+18, -1.0, 0.0], + efficiencies='H2:0.0 C2H6:3.0 H2O:0.0 CO2:0.0 CH4:2.0') +# R37 + +# Reaction 37 +reaction('2 H + H2 <=> 2 H2', [9.000000e+16, -0.6, 0.0]) +# R38 + +# Reaction 38 +reaction('2 H + H2O <=> H2 + H2O', [6.000000e+19, -1.25, 0.0]) +# R39 + +# Reaction 39 +reaction('2 H + CO2 <=> H2 + CO2', [5.500000e+20, -2.0, 0.0]) +# R40 + +# Reaction 40 +three_body_reaction('H + OH + M <=> H2O + M', [2.200000e+22, -2.0, 0.0], + efficiencies='H2:0.73 C2H6:3.0 H2O:3.65 CH4:2.0') +# R41 + +# Reaction 41 +reaction('H + HO2 <=> O + H2O', [3.970000e+12, 0.0, 671.0]) +# R42 + +# Reaction 42 +reaction('H + HO2 <=> O2 + H2', [4.480000e+13, 0.0, 1068.0]) +# R43 + +# Reaction 43 +reaction('H + HO2 <=> 2 OH', [8.400000e+13, 0.0, 635.0]) +# R44 + +# Reaction 44 +reaction('H + H2O2 <=> HO2 + H2', [1.210000e+07, 2.0, 5200.0]) +# R45 + +# Reaction 45 +reaction('H + H2O2 <=> OH + H2O', [1.000000e+13, 0.0, 3600.0]) +# R46 + +# Reaction 46 +reaction('H + CH <=> C + H2', [1.650000e+14, 0.0, 0.0]) +# R47 + +# Reaction 47 +falloff_reaction('H + CH2 (+ M) <=> CH3 (+ M)', + kf=[6.000000e+14, 0.0, 0.0], + kf0=[1.040000e+26, -2.76, 1600.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.562, T3=91.0, T1=5836.0, T2=8552.0)) +# R48 + +# Reaction 48 +reaction('H + CH2(S) <=> CH + H2', [3.000000e+13, 0.0, 0.0]) +# R49 + +# Reaction 49 +falloff_reaction('H + CH3 (+ M) <=> CH4 (+ M)', + kf=[1.390000e+16, -0.534, 536.0], + kf0=[2.620000e+33, -4.76, 2440.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:3.0 C2H6:3.0', + falloff=Troe(A=0.783, T3=74.0, T1=2941.0, T2=6964.0)) +# R50 + +# Reaction 50 +reaction('H + CH4 <=> CH3 + H2', [6.600000e+08, 1.62, 10840.0]) +# R51 + +# Reaction 51 +falloff_reaction('H + HCO (+ M) <=> CH2O (+ M)', + kf=[1.090000e+12, 0.48, -260.0], + kf0=[2.470000e+24, -2.57, 425.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7824, T3=271.0, T1=2755.0, T2=6570.0)) +# R52 + +# Reaction 52 +reaction('H + HCO <=> H2 + CO', [7.340000e+13, 0.0, 0.0]) +# R53 + +# Reaction 53 +falloff_reaction('H + CH2O (+ M) <=> CH2OH (+ M)', + kf=[5.400000e+11, 0.454, 3600.0], + kf0=[1.270000e+32, -4.82, 6530.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7187, T3=103.0, T1=1291.0, T2=4160.0)) +# R54 + +# Reaction 54 +falloff_reaction('H + CH2O (+ M) <=> CH3O (+ M)', + kf=[5.400000e+11, 0.454, 2600.0], + kf0=[2.200000e+30, -4.8, 5560.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.758, T3=94.0, T1=1555.0, T2=4200.0)) +# R55 + +# Reaction 55 +reaction('H + CH2O <=> HCO + H2', [5.740000e+07, 1.9, 2742.0]) +# R56 + +# Reaction 56 +falloff_reaction('H + CH2OH (+ M) <=> CH3OH (+ M)', + kf=[1.055000e+12, 0.5, 86.0], + kf0=[4.360000e+31, -4.65, 5080.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.6, T3=100.0, T1=90000.0, T2=10000.0)) +# R57 + +# Reaction 57 +reaction('H + CH2OH <=> H2 + CH2O', [2.000000e+13, 0.0, 0.0]) +# R58 + +# Reaction 58 +reaction('H + CH2OH <=> OH + CH3', [1.650000e+11, 0.65, -284.0]) +# R59 + +# Reaction 59 +reaction('H + CH2OH <=> CH2(S) + H2O', [3.280000e+13, -0.09, 610.0]) +# R60 + +# Reaction 60 +falloff_reaction('H + CH3O (+ M) <=> CH3OH (+ M)', + kf=[2.430000e+12, 0.515, 50.0], + kf0=[4.660000e+41, -7.44, 14080.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7, T3=100.0, T1=90000.0, T2=10000.0)) +# R61 + +# Reaction 61 +reaction('H + CH3O <=> H + CH2OH', [4.150000e+07, 1.63, 1924.0]) +# R62 + +# Reaction 62 +reaction('H + CH3O <=> H2 + CH2O', [2.000000e+13, 0.0, 0.0]) +# R63 + +# Reaction 63 +reaction('H + CH3O <=> OH + CH3', [1.500000e+12, 0.5, -110.0]) +# R64 + +# Reaction 64 +reaction('H + CH3O <=> CH2(S) + H2O', [2.620000e+14, -0.23, 1070.0]) +# R65 + +# Reaction 65 +reaction('H + CH3OH <=> CH2OH + H2', [1.700000e+07, 2.1, 4870.0]) +# R66 + +# Reaction 66 +reaction('H + CH3OH <=> CH3O + H2', [4.200000e+06, 2.1, 4870.0]) +# R67 + +# Reaction 67 +falloff_reaction('H + C2H2 (+ M) <=> C2H3 (+ M)', + kf=[5.600000e+12, 0.0, 2400.0], + kf0=[3.800000e+40, -7.27, 7220.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7507, T3=98.5, T1=1302.0, T2=4167.0)) +# R68 + +# Reaction 68 +falloff_reaction('H + C2H3 (+ M) <=> C2H4 (+ M)', + kf=[6.080000e+12, 0.27, 280.0], + kf0=[1.400000e+30, -3.86, 3320.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.782, T3=207.5, T1=2663.0, T2=6095.0)) +# R69 + +# Reaction 69 +reaction('H + C2H3 <=> H2 + C2H2', [3.000000e+13, 0.0, 0.0]) +# R70 + +# Reaction 70 +falloff_reaction('H + C2H4 (+ M) <=> C2H5 (+ M)', + kf=[5.400000e+11, 0.454, 1820.0], + kf0=[6.000000e+41, -7.62, 6970.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.9753, T3=210.0, T1=984.0, T2=4374.0)) +# R71 + +# Reaction 71 +reaction('H + C2H4 <=> C2H3 + H2', [1.325000e+06, 2.53, 12240.0]) +# R72 + +# Reaction 72 +falloff_reaction('H + C2H5 (+ M) <=> C2H6 (+ M)', + kf=[5.210000e+17, -0.99, 1580.0], + kf0=[1.990000e+41, -7.08, 6685.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.8422, T3=125.0, T1=2219.0, T2=6882.0)) +# R73 + +# Reaction 73 +reaction('H + C2H5 <=> H2 + C2H4', [2.000000e+12, 0.0, 0.0]) +# R74 + +# Reaction 74 +reaction('H + C2H6 <=> C2H5 + H2', [1.150000e+08, 1.9, 7530.0]) +# R75 + +# Reaction 75 +reaction('H + HCCO <=> CH2(S) + CO', [1.000000e+14, 0.0, 0.0]) +# R76 + +# Reaction 76 +reaction('H + CH2CO <=> HCCO + H2', [5.000000e+13, 0.0, 8000.0]) +# R77 + +# Reaction 77 +reaction('H + CH2CO <=> CH3 + CO', [1.130000e+13, 0.0, 3428.0]) +# R78 + +# Reaction 78 +falloff_reaction('H2 + CO (+ M) <=> CH2O (+ M)', + kf=[4.300000e+07, 1.5, 79600.0], + kf0=[5.070000e+27, -3.42, 84350.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.932, T3=197.0, T1=1540.0, T2=10300.0)) +# R79 + +# Reaction 79 +reaction('OH + H2 <=> H + H2O', [2.160000e+08, 1.51, 3430.0]) +# R80 + +# Reaction 80 +falloff_reaction('2 OH (+ M) <=> H2O2 (+ M)', + kf=[7.400000e+13, -0.37, 0.0], + kf0=[2.300000e+18, -0.9, -1700.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7346, T3=94.0, T1=1756.0, T2=5182.0)) +# R81 + +# Reaction 81 +reaction('2 OH <=> O + H2O', [3.570000e+04, 2.4, -2110.0]) +# R82 + +# Reaction 82 +reaction('OH + HO2 <=> O2 + H2O', [1.450000e+13, 0.0, -500.0], + options='duplicate') +# R83 + +# Reaction 83 +reaction('OH + H2O2 <=> HO2 + H2O', [2.000000e+12, 0.0, 427.0], + options='duplicate') +# R84 + +# Reaction 84 +reaction('OH + H2O2 <=> HO2 + H2O', [1.700000e+18, 0.0, 29410.0], + options='duplicate') +# R85 + +# Reaction 85 +reaction('OH + C <=> H + CO', [5.000000e+13, 0.0, 0.0]) +# R86 + +# Reaction 86 +reaction('OH + CH <=> H + HCO', [3.000000e+13, 0.0, 0.0]) +# R87 + +# Reaction 87 +reaction('OH + CH2 <=> H + CH2O', [2.000000e+13, 0.0, 0.0]) +# R88 + +# Reaction 88 +reaction('OH + CH2 <=> CH + H2O', [1.130000e+07, 2.0, 3000.0]) +# R89 + +# Reaction 89 +reaction('OH + CH2(S) <=> H + CH2O', [3.000000e+13, 0.0, 0.0]) +# R90 + +# Reaction 90 +falloff_reaction('OH + CH3 (+ M) <=> CH3OH (+ M)', + kf=[2.790000e+18, -1.43, 1330.0], + kf0=[4.000000e+36, -5.92, 3140.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.412, T3=195.0, T1=5900.0, T2=6394.0)) +# R91 + +# Reaction 91 +reaction('OH + CH3 <=> CH2 + H2O', [5.600000e+07, 1.6, 5420.0]) +# R92 + +# Reaction 92 +reaction('OH + CH3 <=> CH2(S) + H2O', [6.440000e+17, -1.34, 1417.0]) +# R93 + +# Reaction 93 +reaction('OH + CH4 <=> CH3 + H2O', [1.000000e+08, 1.6, 3120.0]) +# R94 + +# Reaction 94 +reaction('OH + CO <=> H + CO2', [4.760000e+07, 1.228, 70.0]) +# R95 + +# Reaction 95 +reaction('OH + HCO <=> H2O + CO', [5.000000e+13, 0.0, 0.0]) +# R96 + +# Reaction 96 +reaction('OH + CH2O <=> HCO + H2O', [3.430000e+09, 1.18, -447.0]) +# R97 + +# Reaction 97 +reaction('OH + CH2OH <=> H2O + CH2O', [5.000000e+12, 0.0, 0.0]) +# R98 + +# Reaction 98 +reaction('OH + CH3O <=> H2O + CH2O', [5.000000e+12, 0.0, 0.0]) +# R99 + +# Reaction 99 +reaction('OH + CH3OH <=> CH2OH + H2O', [1.440000e+06, 2.0, -840.0]) +# R100 + +# Reaction 100 +reaction('OH + CH3OH <=> CH3O + H2O', [6.300000e+06, 2.0, 1500.0]) +# R101 + +# Reaction 101 +reaction('OH + C2H2 <=> H + CH2CO', [2.180000e-04, 4.5, -1000.0]) +# R102 + +# Reaction 102 +reaction('OH + C2H2 <=> CH3 + CO', [4.830000e-04, 4.0, -2000.0]) +# R103 + +# Reaction 103 +reaction('OH + C2H3 <=> H2O + C2H2', [5.000000e+12, 0.0, 0.0]) +# R104 + +# Reaction 104 +reaction('OH + C2H4 <=> C2H3 + H2O', [3.600000e+06, 2.0, 2500.0]) +# R105 + +# Reaction 105 +reaction('OH + C2H6 <=> C2H5 + H2O', [3.540000e+06, 2.12, 870.0]) +# R106 + +# Reaction 106 +reaction('OH + CH2CO <=> HCCO + H2O', [7.500000e+12, 0.0, 2000.0]) +# R107 + +# Reaction 107 +reaction('2 HO2 <=> O2 + H2O2', [1.300000e+11, 0.0, -1630.0], + options='duplicate') +# R108 + +# Reaction 108 +reaction('2 HO2 <=> O2 + H2O2', [4.200000e+14, 0.0, 12000.0], + options='duplicate') +# R109 + +# Reaction 109 +reaction('HO2 + CH2 <=> OH + CH2O', [2.000000e+13, 0.0, 0.0]) +# R110 + +# Reaction 110 +reaction('HO2 + CH3 <=> O2 + CH4', [1.000000e+12, 0.0, 0.0]) +# R111 + +# Reaction 111 +reaction('HO2 + CH3 <=> OH + CH3O', [3.780000e+13, 0.0, 0.0]) +# R112 + +# Reaction 112 +reaction('HO2 + CO <=> OH + CO2', [1.500000e+14, 0.0, 23600.0]) +# R113 + +# Reaction 113 +reaction('HO2 + CH2O <=> HCO + H2O2', [5.600000e+06, 2.0, 12000.0]) +# R114 + +# Reaction 114 +reaction('C + O2 <=> O + CO', [5.800000e+13, 0.0, 576.0]) +# R115 + +# Reaction 115 +reaction('C + CH3 <=> H + C2H2', [5.000000e+13, 0.0, 0.0]) +# R116 + +# Reaction 116 +reaction('CH + O2 <=> O + HCO', [6.710000e+13, 0.0, 0.0]) +# R117 + +# Reaction 117 +reaction('CH + H2 <=> H + CH2', [1.080000e+14, 0.0, 3110.0]) +# R118 + +# Reaction 118 +reaction('CH + H2O <=> H + CH2O', [5.710000e+12, 0.0, -755.0]) +# R119 + +# Reaction 119 +# reaction('CH + CH2 <=> H + C2H2', [4.000000e+13, 0.0, 0.0]) +# R120 + +# Reaction 120 +reaction('CH + CH3 <=> H + C2H3', [3.000000e+13, 0.0, 0.0]) +# R121 + +# Reaction 121 +reaction('CH + CH4 <=> H + C2H4', [6.000000e+13, 0.0, 0.0]) +# R122 + +# Reaction 122 +falloff_reaction('CH + CO (+ M) <=> HCCO (+ M)', + kf=[5.000000e+13, 0.0, 0.0], + kf0=[2.690000e+28, -3.74, 1936.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.5757, T3=237.0, T1=1652.0, T2=5069.0)) +# R123 + +# Reaction 123 +reaction('CH + CO2 <=> HCO + CO', [1.900000e+14, 0.0, 15792.0]) +# R124 + +# Reaction 124 +reaction('CH + CH2O <=> H + CH2CO', [9.460000e+13, 0.0, -515.0]) +# R125 + +# Reaction 125 +# reaction('CH + HCCO <=> CO + C2H2', [5.000000e+13, 0.0, 0.0]) +# R126 + +# Reaction 126 +reaction('CH2 + O2 => OH + H + CO', [5.000000e+12, 0.0, 1500.0]) +# R127 + +# Reaction 127 +reaction('CH2 + H2 <=> H + CH3', [5.000000e+05, 2.0, 7230.0]) +# R128 + +# Reaction 128 +# reaction('2 CH2 <=> H2 + C2H2', [1.600000e+15, 0.0, 11944.0]) +# R129 + +# Reaction 129 +reaction('CH2 + CH3 <=> H + C2H4', [4.000000e+13, 0.0, 0.0]) +# R130 + +# Reaction 130 +reaction('CH2 + CH4 <=> 2 CH3', [2.460000e+06, 2.0, 8270.0]) +# R131 + +# Reaction 131 +falloff_reaction('CH2 + CO (+ M) <=> CH2CO (+ M)', + kf=[8.100000e+11, 0.5, 4510.0], + kf0=[2.690000e+33, -5.11, 7095.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.5907, T3=275.0, T1=1226.0, T2=5185.0)) +# R132 + +# Reaction 132 +# reaction('CH2 + HCCO <=> C2H3 + CO', [3.000000e+13, 0.0, 0.0]) +# R133 + +# Reaction 133 +reaction('CH2(S) + N2 <=> CH2 + N2', [1.500000e+13, 0.0, 600.0]) +# R134 + +# Reaction 134 +reaction('CH2(S) + O2 <=> H + OH + CO', [2.800000e+13, 0.0, 0.0]) +# R135 + +# Reaction 135 +reaction('CH2(S) + O2 <=> CO + H2O', [1.200000e+13, 0.0, 0.0]) +# R136 + +# Reaction 136 +reaction('CH2(S) + H2 <=> CH3 + H', [7.000000e+13, 0.0, 0.0]) +# R137 + +# Reaction 137 +falloff_reaction('CH2(S) + H2O (+ M) <=> CH3OH (+ M)', + kf=[4.820000e+17, -1.16, 1145.0], + kf0=[1.880000e+38, -6.36, 5040.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.6027, T3=208.0, T1=3922.0, T2=10180.0)) +# R138 + +# Reaction 138 +reaction('CH2(S) + H2O <=> CH2 + H2O', [3.000000e+13, 0.0, 0.0]) +# R139 + +# Reaction 139 +reaction('CH2(S) + CH3 <=> H + C2H4', [1.200000e+13, 0.0, -570.0]) +# R140 + +# Reaction 140 +reaction('CH2(S) + CH4 <=> 2 CH3', [1.600000e+13, 0.0, -570.0]) +# R141 + +# Reaction 141 +reaction('CH2(S) + CO <=> CH2 + CO', [9.000000e+12, 0.0, 0.0]) +# R142 + +# Reaction 142 +reaction('CH2(S) + CO2 <=> CH2 + CO2', [7.000000e+12, 0.0, 0.0]) +# R143 + +# Reaction 143 +reaction('CH2(S) + CO2 <=> CO + CH2O', [1.400000e+13, 0.0, 0.0]) +# R144 + +# Reaction 144 +reaction('CH2(S) + C2H6 <=> CH3 + C2H5', [4.000000e+13, 0.0, -550.0]) +# R145 + +# Reaction 145 +reaction('CH3 + O2 <=> O + CH3O', [3.560000e+13, 0.0, 30480.0]) +# R146 + +# Reaction 146 +reaction('CH3 + O2 <=> OH + CH2O', [2.310000e+12, 0.0, 20315.0]) +# R147 + +# Reaction 147 +reaction('CH3 + H2O2 <=> HO2 + CH4', [2.450000e+04, 2.47, 5180.0]) +# R148 + +# Reaction 148 +falloff_reaction('2 CH3 (+ M) <=> C2H6 (+ M)', + kf=[6.770000e+16, -1.18, 654.0], + kf0=[3.400000e+41, -7.03, 2762.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.619, T3=73.2, T1=1180.0, T2=9999.0)) +# R149 + +# Reaction 149 +reaction('2 CH3 <=> H + C2H5', [6.840000e+12, 0.1, 10600.0]) +# R150 + +# Reaction 150 +reaction('CH3 + HCO <=> CH4 + CO', [2.648000e+13, 0.0, 0.0]) +# R151 + +# Reaction 151 +reaction('CH3 + CH2O <=> HCO + CH4', [3.320000e+03, 2.81, 5860.0]) +# R152 + +# Reaction 152 +reaction('CH3 + CH3OH <=> CH2OH + CH4', [3.000000e+07, 1.5, 9940.0]) +# R153 + +# Reaction 153 +reaction('CH3 + CH3OH <=> CH3O + CH4', [1.000000e+07, 1.5, 9940.0]) +# R154 + +# Reaction 154 +reaction('CH3 + C2H4 <=> C2H3 + CH4', [2.270000e+05, 2.0, 9200.0]) +# R155 + +# Reaction 155 +reaction('CH3 + C2H6 <=> C2H5 + CH4', [6.140000e+06, 1.74, 10450.0]) +# R156 + +# Reaction 156 +reaction('HCO + H2O <=> H + CO + H2O', [1.500000e+18, -1.0, 17000.0]) +# R157 + +# Reaction 157 +three_body_reaction('HCO + M <=> H + CO + M', [1.870000e+17, -1.0, 17000.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:0.0 CH4:2.0 C2H6:3.0') +# R158 + +# Reaction 158 +reaction('HCO + O2 <=> HO2 + CO', [1.345000e+13, 0.0, 400.0]) +# R159 + +# Reaction 159 +reaction('CH2OH + O2 <=> HO2 + CH2O', [1.800000e+13, 0.0, 900.0]) +# R160 + +# Reaction 160 +reaction('CH3O + O2 <=> HO2 + CH2O', [4.280000e-13, 7.6, -3530.0]) +# R161 + +# Reaction 161 +reaction('C2H3 + O2 <=> HCO + CH2O', [4.580000e+16, -1.39, 1015.0]) +# R162 + +# Reaction 162 +falloff_reaction('C2H4 (+ M) <=> H2 + C2H2 (+ M)', + kf=[8.000000e+12, 0.44, 86770.0], + kf0=[1.580000e+51, -9.3, 97800.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.7345, T3=180.0, T1=1035.0, T2=5417.0)) +# R163 + +# Reaction 163 +reaction('C2H5 + O2 <=> HO2 + C2H4', [8.400000e+11, 0.0, 3875.0]) +# R164 + +# Reaction 164 +reaction('HCCO + O2 <=> OH + 2 CO', [3.200000e+12, 0.0, 854.0]) +# R165 + +# Reaction 165 +# reaction('2 HCCO <=> 2 CO + C2H2', [1.000000e+13, 0.0, 0.0]) +# R166 + +# Reaction 166 +reaction('O + CH3 => H + H2 + CO', [3.370000e+13, 0.0, 0.0]) +# R167 + +# Reaction 167 +reaction('O + C2H4 <=> H + CH2CHO', [6.700000e+06, 1.83, 220.0]) +# R168 + +# Reaction 168 +reaction('OH + HO2 <=> O2 + H2O', [5.000000e+15, 0.0, 17330.0], + options='duplicate') +# R169 + +# Reaction 169 +reaction('OH + CH3 => H2 + CH2O', [8.000000e+09, 0.5, -1755.0]) +# R170 + +# Reaction 170 +falloff_reaction('CH + H2 (+ M) <=> CH3 (+ M)', + kf=[1.970000e+12, 0.43, -370.0], + kf0=[4.820000e+25, -2.8, 590.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.578, T3=122.0, T1=2535.0, T2=9365.0)) +# R171 + +# Reaction 171 +reaction('CH2 + O2 => 2 H + CO2', [5.800000e+12, 0.0, 1500.0]) +# R172 + +# Reaction 172 +reaction('CH2 + O2 <=> O + CH2O', [2.400000e+12, 0.0, 1500.0]) +# R173 + +# Reaction 173 +# reaction('CH2 + CH2 => 2 H + C2H2', [2.000000e+14, 0.0, 10989.0]) +# R174 + +# Reaction 174 +reaction('CH2(S) + H2O => H2 + CH2O', [6.820000e+10, 0.25, -935.0]) +# R175 + +# Reaction 175 +reaction('C2H3 + O2 <=> O + CH2CHO', [3.030000e+11, 0.29, 11.0]) +# R176 + +# Reaction 176 +reaction('C2H3 + O2 <=> HO2 + C2H2', [1.337000e+06, 1.61, -384.0]) +# R177 + +# Reaction 177 +falloff_reaction('H + CH2CO (+ M) <=> CH2CHO (+ M)', + kf=[4.865000e+11, 0.422, -1755.0], + kf0=[1.012000e+42, -7.63, 3854.0], + efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', + falloff=Troe(A=0.465, T3=201.0, T1=1773.0, T2=5333.0)) +# R178 + +# Reaction 178 +reaction('O + CH2CHO => H + CH2 + CO2', [1.500000e+14, 0.0, 0.0]) +# R179 + +# Reaction 179 +reaction('O2 + CH2CHO => OH + CO + CH2O', [1.810000e+10, 0.0, 0.0]) +# R180 + +# Reaction 180 +reaction('O2 + CH2CHO => OH + 2 HCO', [2.350000e+10, 0.0, 0.0]) +# R181 + +# Reaction 181 +reaction('H + CH2CHO <=> CH3 + HCO', [2.200000e+13, 0.0, 0.0]) +# R182 + +# Reaction 182 +reaction('H + CH2CHO <=> CH2CO + H2', [1.100000e+13, 0.0, 0.0]) +# R183 + +# Reaction 183 +reaction('OH + CH2CHO <=> H2O + CH2CO', [1.200000e+13, 0.0, 0.0]) +# R184 + +# Reaction 184 +# reaction('OH + CH2CHO <=> HCO + CH2OH', [3.010000e+13, 0.0, 0.0]) diff --git a/samples/python/AVBP/inputs/Lu.yaml b/samples/python/AVBP/inputs/Lu.yaml new file mode 100644 index 00000000000..3dcf578a23c --- /dev/null +++ b/samples/python/AVBP/inputs/Lu.yaml @@ -0,0 +1,997 @@ +description: |- + "" + +generator: cti2yaml +cantera-version: 3.0.0 +date: Tue, 26 Dec 2023 00:54:57 +0100 +input-files: [Lu.cti] + +units: {length: cm, quantity: mol, activation-energy: cal/mol} + +phases: +- name: gas + thermo: ideal-gas + elements: [O, H, C, N, Ar] + species: [H2, H, O, O2, OH, H2O, HO2, H2O2, C, CH, CH2, CH2(S), CH3, CH4, + CO, CO2, HCO, CH2O, CH2OH, CH3O, CH3OH, C2H2, C2H3, C2H4, C2H5, C2H6, + HCCO, CH2CO, CH2CHO, N2] + kinetics: gas + reactions: all + transport: mixture-averaged + state: + T: 300.0 + P: 1.01325e+05 + +species: +- name: H2 + composition: {H: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.34433112, 7.98052075e-03, -1.9478151e-05, 2.01572094e-08, -7.37611761e-12, + -917.935173, 0.683010238] + - [3.3372792, -4.94024731e-05, 4.99456778e-07, -1.79566394e-10, 2.00255376e-14, + -950.158922, -3.20502331] + transport: + model: gas + geometry: linear + diameter: 2.92 + well-depth: 38.0 + polarizability: 0.79 + rotational-relaxation: 280.0 + note: TPIS78 +- name: H + composition: {H: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18, -9.27732332e-22, + 2.54736599e+04, -0.446682853] + - [2.50000001, -2.30842973e-11, 1.61561948e-14, -4.73515235e-18, 4.98197357e-22, + 2.54736599e+04, -0.446682914] + transport: + model: gas + geometry: atom + diameter: 2.05 + well-depth: 145.0 + note: L7/88 +- name: O + composition: {O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.1682671, -3.27931884e-03, 6.64306396e-06, -6.12806624e-09, 2.11265971e-12, + 2.91222592e+04, 2.05193346] + - [2.56942078, -8.59741137e-05, 4.19484589e-08, -1.00177799e-11, 1.22833691e-15, + 2.92175791e+04, 4.78433864] + transport: + model: gas + geometry: atom + diameter: 2.75 + well-depth: 80.0 + note: L1/90 +- name: O2 + composition: {O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.78245636, -2.99673416e-03, 9.84730201e-06, -9.68129509e-09, 3.24372837e-12, + -1063.94356, 3.65767573] + - [3.28253784, 1.48308754e-03, -7.57966669e-07, 2.09470555e-10, -2.16717794e-14, + -1088.45772, 5.45323129] + transport: + model: gas + geometry: linear + diameter: 3.458 + well-depth: 107.4 + polarizability: 1.6 + rotational-relaxation: 3.8 + note: TPIS89 +- name: OH + composition: {H: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.99201543, -2.40131752e-03, 4.61793841e-06, -3.88113333e-09, 1.3641147e-12, + 3615.08056, -0.103925458] + - [3.09288767, 5.48429716e-04, 1.26505228e-07, -8.79461556e-11, 1.17412376e-14, + 3858.657, 4.4766961] + transport: + model: gas + geometry: linear + diameter: 2.75 + well-depth: 80.0 + note: RUS78 +- name: H2O + composition: {H: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19864056, -2.0364341e-03, 6.52040211e-06, -5.48797062e-09, 1.77197817e-12, + -3.02937267e+04, -0.849032208] + - [3.03399249, 2.17691804e-03, -1.64072518e-07, -9.7041987e-11, 1.68200992e-14, + -3.00042971e+04, 4.9667701] + transport: + model: gas + geometry: nonlinear + diameter: 2.605 + well-depth: 572.4 + dipole: 1.844 + rotational-relaxation: 4.0 + note: L8/89 +- name: HO2 + composition: {H: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30179801, -4.74912051e-03, 2.11582891e-05, -2.42763894e-08, 9.29225124e-12, + 294.80804, 3.71666245] + - [4.0172109, 2.23982013e-03, -6.3365815e-07, 1.1424637e-10, -1.07908535e-14, + 111.856713, 3.78510215] + transport: + model: gas + geometry: nonlinear + diameter: 3.458 + well-depth: 107.4 + rotational-relaxation: 1.0 + note: L5/89 +- name: H2O2 + composition: {H: 2, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.27611269, -5.42822417e-04, 1.67335701e-05, -2.15770813e-08, 8.62454363e-12, + -1.77025821e+04, 3.43505074] + - [4.16500285, 4.90831694e-03, -1.90139225e-06, 3.71185986e-10, -2.87908305e-14, + -1.78617877e+04, 2.91615662] + transport: + model: gas + geometry: nonlinear + diameter: 3.458 + well-depth: 107.4 + rotational-relaxation: 3.8 + note: L7/88 +- name: C + composition: {C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.55423955, -3.21537724e-04, 7.33792245e-07, -7.32234889e-10, 2.66521446e-13, + 8.54438832e+04, 4.53130848] + - [2.49266888, 4.79889284e-05, -7.2433502e-08, 3.74291029e-11, -4.87277893e-15, + 8.54512953e+04, 4.80150373] + transport: + model: gas + geometry: atom + diameter: 3.298 + well-depth: 71.4 + note: L11/88 +- name: CH + composition: {H: 1, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.48981665, 3.23835541e-04, -1.68899065e-06, 3.16217327e-09, -1.40609067e-12, + 7.07972934e+04, 2.08401108] + - [2.87846473, 9.70913681e-04, 1.44445655e-07, -1.30687849e-10, 1.76079383e-14, + 7.10124364e+04, 5.48497999] + transport: + model: gas + geometry: linear + diameter: 2.75 + well-depth: 80.0 + note: TPIS79 +- name: CH2 + composition: {H: 2, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.76267867, 9.68872143e-04, 2.79489841e-06, -3.85091153e-09, 1.68741719e-12, + 4.60040401e+04, 1.56253185] + - [2.87410113, 3.65639292e-03, -1.40894597e-06, 2.60179549e-10, -1.87727567e-14, + 4.6263604e+04, 6.17119324] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 +- name: CH2(S) + composition: {H: 2, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.19860411, -2.36661419e-03, 8.2329622e-06, -6.68815981e-09, 1.94314737e-12, + 5.04968163e+04, -0.769118967] + - [2.29203842, 4.65588637e-03, -2.01191947e-06, 4.17906e-10, -3.39716365e-14, + 5.09259997e+04, 8.62650169] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: LS/93 +- name: CH3 + composition: {H: 3, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.6735904, 2.01095175e-03, 5.73021856e-06, -6.87117425e-09, 2.54385734e-12, + 1.64449988e+04, 1.60456433] + - [2.28571772, 7.23990037e-03, -2.98714348e-06, 5.95684644e-10, -4.67154394e-14, + 1.67755843e+04, 8.48007179] + transport: + model: gas + geometry: linear + diameter: 3.8 + well-depth: 144.0 + note: L11/89 +- name: CH4 + composition: {H: 4, C: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.14987613, -0.0136709788, 4.91800599e-05, -4.84743026e-08, 1.66693956e-11, + -1.02466476e+04, -4.64130376] + - [0.074851495, 0.0133909467, -5.73285809e-06, 1.22292535e-09, -1.0181523e-13, + -9468.34459, 18.437318] + transport: + model: gas + geometry: nonlinear + diameter: 3.746 + well-depth: 141.4 + polarizability: 2.6 + rotational-relaxation: 13.0 + note: L8/88 +- name: CO + composition: {C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.57953347, -6.1035368e-04, 1.01681433e-06, 9.07005884e-10, -9.04424499e-13, + -1.4344086e+04, 3.50840928] + - [2.71518561, 2.06252743e-03, -9.98825771e-07, 2.30053008e-10, -2.03647716e-14, + -1.41518724e+04, 7.81868772] + transport: + model: gas + geometry: linear + diameter: 3.65 + well-depth: 98.1 + polarizability: 1.95 + rotational-relaxation: 1.8 + note: TPIS79 +- name: CO2 + composition: {C: 1, O: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.35677352, 8.98459677e-03, -7.12356269e-06, 2.45919022e-09, -1.43699548e-13, + -4.83719697e+04, 9.90105222] + - [3.85746029, 4.41437026e-03, -2.21481404e-06, 5.23490188e-10, -4.72084164e-14, + -4.8759166e+04, 2.27163806] + transport: + model: gas + geometry: linear + diameter: 3.763 + well-depth: 244.0 + polarizability: 2.65 + rotational-relaxation: 2.1 + note: L7/88 +- name: HCO + composition: {H: 1, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.22118584, -3.24392532e-03, 1.37799446e-05, -1.33144093e-08, 4.33768865e-12, + 3839.56496, 3.39437243] + - [2.77217438, 4.95695526e-03, -2.48445613e-06, 5.89161778e-10, -5.33508711e-14, + 4011.91815, 9.79834492] + transport: + model: gas + geometry: nonlinear + diameter: 3.59 + well-depth: 498.0 + note: L12/89 +- name: CH2O + composition: {H: 2, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.79372315, -9.90833369e-03, 3.73220008e-05, -3.79285261e-08, 1.31772652e-11, + -1.43089567e+04, 0.6028129] + - [1.76069008, 9.20000082e-03, -4.42258813e-06, 1.00641212e-09, -8.8385564e-14, + -1.39958323e+04, 13.656323] + transport: + model: gas + geometry: nonlinear + diameter: 3.59 + well-depth: 498.0 + rotational-relaxation: 2.0 + note: L8/88 +- name: CH2OH + composition: {H: 3, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.86388918, 5.59672304e-03, 5.93271791e-06, -1.04532012e-08, 4.36967278e-12, + -3193.91367, 5.47302243] + - [3.69266569, 8.64576797e-03, -3.7510112e-06, 7.87234636e-10, -6.48554201e-14, + -3242.50627, 5.81043215] + transport: + model: gas + geometry: nonlinear + diameter: 3.69 + well-depth: 417.0 + dipole: 1.7 + rotational-relaxation: 2.0 + note: GUNL93 +- name: CH3O + composition: {H: 3, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 3000.0] + data: + - [2.106204, 7.216595e-03, 5.338472e-06, -7.377636e-09, 2.07561e-12, + 978.6011, 13.152177] + - [3.770799, 7.871497e-03, -2.656384e-06, 3.944431e-10, -2.112616e-14, + 127.83252, 2.929575] + transport: + model: gas + geometry: nonlinear + diameter: 3.69 + well-depth: 417.0 + dipole: 1.7 + rotational-relaxation: 2.0 + note: '121686' +- name: CH3OH + composition: {H: 4, C: 1, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [5.71539582, -0.0152309129, 6.52441155e-05, -7.10806889e-08, 2.61352698e-11, + -2.56427656e+04, -1.50409823] + - [1.78970791, 0.0140938292, -6.36500835e-06, 1.38171085e-09, -1.1706022e-13, + -2.53748747e+04, 14.5023623] + transport: + model: gas + geometry: nonlinear + diameter: 3.626 + well-depth: 481.8 + rotational-relaxation: 1.0 + note: L8/88 +- name: C2H2 + composition: {H: 2, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [0.808681094, 0.0233615629, -3.55171815e-05, 2.80152437e-08, -8.50072974e-12, + 2.64289807e+04, 13.9397051] + - [4.14756964, 5.96166664e-03, -2.37294852e-06, 4.67412171e-10, -3.61235213e-14, + 2.59359992e+04, -1.23028121] + transport: + model: gas + geometry: linear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 2.5 + note: L1/91 +- name: C2H3 + composition: {H: 3, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.21246645, 1.51479162e-03, 2.59209412e-05, -3.57657847e-08, 1.47150873e-11, + 3.48598468e+04, 8.51054025] + - [3.016724, 0.0103302292, -4.68082349e-06, 1.01763288e-09, -8.62607041e-14, + 3.46128739e+04, 7.78732378] + transport: + model: gas + geometry: nonlinear + diameter: 4.1 + well-depth: 209.0 + rotational-relaxation: 1.0 + note: L2/92 +- name: C2H4 + composition: {H: 4, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [3.95920148, -7.57052247e-03, 5.70990292e-05, -6.91588753e-08, 2.69884373e-11, + 5089.77593, 4.09733096] + - [2.03611116, 0.0146454151, -6.71077915e-06, 1.47222923e-09, -1.25706061e-13, + 4939.88614, 10.3053693] + transport: + model: gas + geometry: nonlinear + diameter: 3.971 + well-depth: 280.8 + rotational-relaxation: 1.5 + note: L1/91 +- name: C2H5 + composition: {H: 5, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30646568, -4.18658892e-03, 4.97142807e-05, -5.99126606e-08, 2.30509004e-11, + 1.28416265e+04, 4.70720924] + - [1.95465642, 0.0173972722, -7.98206668e-06, 1.75217689e-09, -1.49641576e-13, + 1.285752e+04, 13.4624343] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L12/92 +- name: C2H6 + composition: {H: 6, C: 2} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.29142492, -5.5015427e-03, 5.99438288e-05, -7.08466285e-08, 2.68685771e-11, + -1.15222055e+04, 2.66682316] + - [1.0718815, 0.0216852677, -1.00256067e-05, 2.21412001e-09, -1.9000289e-13, + -1.14263932e+04, 15.1156107] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L8/88 +- name: HCCO + composition: {H: 1, C: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 4000.0] + data: + - [2.2517214, 0.017655021, -2.3729101e-05, 1.7275759e-08, -5.0664811e-12, + 2.0059449e+04, 12.490417] + - [5.6282058, 4.0853401e-03, -1.5934547e-06, 2.8626052e-10, -1.9407832e-14, + 1.9327215e+04, -3.9302595] + transport: + model: gas + geometry: nonlinear + diameter: 2.5 + well-depth: 150.0 + rotational-relaxation: 1.0 + note: SRIC91 +- name: CH2CO + composition: {H: 2, C: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.1358363, 0.0181188721, -1.73947474e-05, 9.34397568e-09, -2.01457615e-12, + -7042.91804, 12.215648] + - [4.51129732, 9.00359745e-03, -4.16939635e-06, 9.23345882e-10, -7.94838201e-14, + -7551.05311, 0.632247205] + transport: + model: gas + geometry: nonlinear + diameter: 3.97 + well-depth: 436.0 + rotational-relaxation: 2.0 + note: L5/90 +- name: CH2CHO + composition: {H: 3, C: 2, O: 1} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.409062, 0.010738574, 1.891492e-06, -7.158583e-09, 2.867385e-12, + 1521.4766, 9.55829] + - [5.97567, 8.130591e-03, -2.743624e-06, 4.070304e-10, -2.176017e-14, + 490.3218, -5.045251] + transport: + model: gas + geometry: nonlinear + diameter: 3.97 + well-depth: 436.0 + rotational-relaxation: 2.0 + note: SAND86 +- name: N2 + composition: {N: 2} + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 5000.0] + data: + - [3.298677, 1.4082404e-03, -3.963222e-06, 5.641515e-09, -2.444854e-12, + -1020.8999, 3.950372] + - [2.92664, 1.4879768e-03, -5.68476e-07, 1.0097038e-10, -6.753351e-15, + -922.7977, 5.980528] + transport: + model: gas + geometry: linear + diameter: 3.621 + well-depth: 97.53 + polarizability: 1.76 + rotational-relaxation: 4.0 + note: '121286' + +reactions: +- equation: 2 O + M <=> O2 + M # Reaction 1 + type: three-body + rate-constant: {A: 1.2e+17, b: -1.0, Ea: 0.0} + efficiencies: {CO2: 3.6, CO: 1.75, H2: 2.4, H2O: 15.4, CH4: 2.0, C2H6: 3.0} +- equation: O + H + M <=> OH + M # Reaction 2 + type: three-body + rate-constant: {A: 5.0e+17, b: -1.0, Ea: 0.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: O + H2 <=> H + OH # Reaction 3 + rate-constant: {A: 3.87e+04, b: 2.7, Ea: 6260.0} +- equation: O + HO2 <=> OH + O2 # Reaction 4 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: O + H2O2 <=> OH + HO2 # Reaction 5 + rate-constant: {A: 9.63e+06, b: 2.0, Ea: 4000.0} +- equation: O + CH <=> H + CO # Reaction 6 + rate-constant: {A: 5.7e+13, b: 0.0, Ea: 0.0} +- equation: O + CH2 <=> H + HCO # Reaction 7 + rate-constant: {A: 8.0e+13, b: 0.0, Ea: 0.0} +- equation: O + CH2(S) <=> H2 + CO # Reaction 8 + rate-constant: {A: 1.5e+13, b: 0.0, Ea: 0.0} +- equation: O + CH2(S) <=> H + HCO # Reaction 9 + rate-constant: {A: 1.5e+13, b: 0.0, Ea: 0.0} +- equation: O + CH3 <=> H + CH2O # Reaction 10 + rate-constant: {A: 5.06e+13, b: 0.0, Ea: 0.0} +- equation: O + CH4 <=> OH + CH3 # Reaction 11 + rate-constant: {A: 1.02e+09, b: 1.5, Ea: 8600.0} +- equation: O + CO (+ M) <=> CO2 (+ M) # Reaction 12 + type: falloff + low-P-rate-constant: {A: 6.02e+14, b: 0.0, Ea: 3000.0} + high-P-rate-constant: {A: 1.8e+10, b: 0.0, Ea: 2385.0} + efficiencies: {CO2: 3.5, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0, + O2: 6.0} +- equation: O + HCO <=> OH + CO # Reaction 13 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: O + HCO <=> H + CO2 # Reaction 14 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: O + CH2O <=> OH + HCO # Reaction 15 + rate-constant: {A: 3.9e+13, b: 0.0, Ea: 3540.0} +- equation: O + CH2OH <=> OH + CH2O # Reaction 16 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: O + CH3O <=> OH + CH2O # Reaction 17 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 0.0} +- equation: O + CH3OH <=> OH + CH2OH # Reaction 18 + rate-constant: {A: 3.88e+05, b: 2.5, Ea: 3100.0} +- equation: O + CH3OH <=> OH + CH3O # Reaction 19 + rate-constant: {A: 1.3e+05, b: 2.5, Ea: 5000.0} +- equation: O + C2H2 <=> H + HCCO # Reaction 20 + rate-constant: {A: 1.35e+07, b: 2.0, Ea: 1900.0} +- equation: O + C2H2 <=> CO + CH2 # Reaction 21 + rate-constant: {A: 6.94e+06, b: 2.0, Ea: 1900.0} +- equation: O + C2H3 <=> H + CH2CO # Reaction 22 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: O + C2H4 <=> CH3 + HCO # Reaction 23 + rate-constant: {A: 1.25e+07, b: 1.83, Ea: 220.0} +- equation: O + C2H5 <=> CH3 + CH2O # Reaction 24 + rate-constant: {A: 2.24e+13, b: 0.0, Ea: 0.0} +- equation: O + C2H6 <=> OH + C2H5 # Reaction 25 + rate-constant: {A: 8.98e+07, b: 1.92, Ea: 5690.0} +- equation: O + HCCO <=> H + 2 CO # Reaction 26 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: O + CH2CO <=> OH + HCCO # Reaction 27 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 8000.0} +- equation: O + CH2CO <=> CH2 + CO2 # Reaction 28 + rate-constant: {A: 1.75e+12, b: 0.0, Ea: 1350.0} +- equation: O2 + CO <=> O + CO2 # Reaction 29 + rate-constant: {A: 2.5e+12, b: 0.0, Ea: 4.78e+04} +- equation: O2 + CH2O <=> HO2 + HCO # Reaction 30 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 4.0e+04} +- equation: H + O2 + M <=> HO2 + M # Reaction 31 + type: three-body + rate-constant: {A: 2.8e+18, b: -0.86, Ea: 0.0} + efficiencies: {CO2: 1.5, CO: 0.75, H2O: 0.0, C2H6: 1.5, N2: 0.0, O2: 0.0} +- equation: H + 2 O2 <=> HO2 + O2 # Reaction 32 + rate-constant: {A: 2.08e+19, b: -1.24, Ea: 0.0} +- equation: H + O2 + H2O <=> HO2 + H2O # Reaction 33 + rate-constant: {A: 1.126e+19, b: -0.76, Ea: 0.0} +- equation: H + O2 + N2 <=> HO2 + N2 # Reaction 34 + rate-constant: {A: 2.6e+19, b: -1.24, Ea: 0.0} +- equation: H + O2 <=> O + OH # Reaction 35 + rate-constant: {A: 2.65e+16, b: -0.6707, Ea: 1.7041e+04} +- equation: 2 H + M <=> H2 + M # Reaction 36 + type: three-body + rate-constant: {A: 1.0e+18, b: -1.0, Ea: 0.0} + efficiencies: {H2: 0.0, C2H6: 3.0, H2O: 0.0, CO2: 0.0, CH4: 2.0} +- equation: 2 H + H2 <=> 2 H2 # Reaction 37 + rate-constant: {A: 9.0e+16, b: -0.6, Ea: 0.0} +- equation: 2 H + H2O <=> H2 + H2O # Reaction 38 + rate-constant: {A: 6.0e+19, b: -1.25, Ea: 0.0} +- equation: 2 H + CO2 <=> H2 + CO2 # Reaction 39 + rate-constant: {A: 5.5e+20, b: -2.0, Ea: 0.0} +- equation: H + OH + M <=> H2O + M # Reaction 40 + type: three-body + rate-constant: {A: 2.2e+22, b: -2.0, Ea: 0.0} + efficiencies: {H2: 0.73, C2H6: 3.0, H2O: 3.65, CH4: 2.0} +- equation: H + HO2 <=> O + H2O # Reaction 41 + rate-constant: {A: 3.97e+12, b: 0.0, Ea: 671.0} +- equation: H + HO2 <=> O2 + H2 # Reaction 42 + rate-constant: {A: 4.48e+13, b: 0.0, Ea: 1068.0} +- equation: H + HO2 <=> 2 OH # Reaction 43 + rate-constant: {A: 8.4e+13, b: 0.0, Ea: 635.0} +- equation: H + H2O2 <=> HO2 + H2 # Reaction 44 + rate-constant: {A: 1.21e+07, b: 2.0, Ea: 5200.0} +- equation: H + H2O2 <=> OH + H2O # Reaction 45 + rate-constant: {A: 1.0e+13, b: 0.0, Ea: 3600.0} +- equation: H + CH <=> C + H2 # Reaction 46 + rate-constant: {A: 1.65e+14, b: 0.0, Ea: 0.0} +- equation: H + CH2 (+ M) <=> CH3 (+ M) # Reaction 47 + type: falloff + low-P-rate-constant: {A: 1.04e+26, b: -2.76, Ea: 1600.0} + high-P-rate-constant: {A: 6.0e+14, b: 0.0, Ea: 0.0} + Troe: {A: 0.562, T3: 91.0, T1: 5836.0, T2: 8552.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH2(S) <=> CH + H2 # Reaction 48 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: H + CH3 (+ M) <=> CH4 (+ M) # Reaction 49 + type: falloff + low-P-rate-constant: {A: 2.62e+33, b: -4.76, Ea: 2440.0} + high-P-rate-constant: {A: 1.39e+16, b: -0.534, Ea: 536.0} + Troe: {A: 0.783, T3: 74.0, T1: 2941.0, T2: 6964.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 3.0, C2H6: 3.0} +- equation: H + CH4 <=> CH3 + H2 # Reaction 50 + rate-constant: {A: 6.6e+08, b: 1.62, Ea: 1.084e+04} +- equation: H + HCO (+ M) <=> CH2O (+ M) # Reaction 51 + type: falloff + low-P-rate-constant: {A: 2.47e+24, b: -2.57, Ea: 425.0} + high-P-rate-constant: {A: 1.09e+12, b: 0.48, Ea: -260.0} + Troe: {A: 0.7824, T3: 271.0, T1: 2755.0, T2: 6570.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + HCO <=> H2 + CO # Reaction 52 + rate-constant: {A: 7.34e+13, b: 0.0, Ea: 0.0} +- equation: H + CH2O (+ M) <=> CH2OH (+ M) # Reaction 53 + type: falloff + low-P-rate-constant: {A: 1.27e+32, b: -4.82, Ea: 6530.0} + high-P-rate-constant: {A: 5.4e+11, b: 0.454, Ea: 3600.0} + Troe: {A: 0.7187, T3: 103.0, T1: 1291.0, T2: 4160.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH2O (+ M) <=> CH3O (+ M) # Reaction 54 + type: falloff + low-P-rate-constant: {A: 2.2e+30, b: -4.8, Ea: 5560.0} + high-P-rate-constant: {A: 5.4e+11, b: 0.454, Ea: 2600.0} + Troe: {A: 0.758, T3: 94.0, T1: 1555.0, T2: 4200.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH2O <=> HCO + H2 # Reaction 55 + rate-constant: {A: 5.74e+07, b: 1.9, Ea: 2742.0} +- equation: H + CH2OH (+ M) <=> CH3OH (+ M) # Reaction 56 + type: falloff + low-P-rate-constant: {A: 4.36e+31, b: -4.65, Ea: 5080.0} + high-P-rate-constant: {A: 1.055e+12, b: 0.5, Ea: 86.0} + Troe: {A: 0.6, T3: 100.0, T1: 9.0e+04, T2: 1.0e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH2OH <=> H2 + CH2O # Reaction 57 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: H + CH2OH <=> OH + CH3 # Reaction 58 + rate-constant: {A: 1.65e+11, b: 0.65, Ea: -284.0} +- equation: H + CH2OH <=> CH2(S) + H2O # Reaction 59 + rate-constant: {A: 3.28e+13, b: -0.09, Ea: 610.0} +- equation: H + CH3O (+ M) <=> CH3OH (+ M) # Reaction 60 + type: falloff + low-P-rate-constant: {A: 4.66e+41, b: -7.44, Ea: 1.408e+04} + high-P-rate-constant: {A: 2.43e+12, b: 0.515, Ea: 50.0} + Troe: {A: 0.7, T3: 100.0, T1: 9.0e+04, T2: 1.0e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + CH3O <=> H + CH2OH # Reaction 61 + rate-constant: {A: 4.15e+07, b: 1.63, Ea: 1924.0} +- equation: H + CH3O <=> H2 + CH2O # Reaction 62 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: H + CH3O <=> OH + CH3 # Reaction 63 + rate-constant: {A: 1.5e+12, b: 0.5, Ea: -110.0} +- equation: H + CH3O <=> CH2(S) + H2O # Reaction 64 + rate-constant: {A: 2.62e+14, b: -0.23, Ea: 1070.0} +- equation: H + CH3OH <=> CH2OH + H2 # Reaction 65 + rate-constant: {A: 1.7e+07, b: 2.1, Ea: 4870.0} +- equation: H + CH3OH <=> CH3O + H2 # Reaction 66 + rate-constant: {A: 4.2e+06, b: 2.1, Ea: 4870.0} +- equation: H + C2H2 (+ M) <=> C2H3 (+ M) # Reaction 67 + type: falloff + low-P-rate-constant: {A: 3.8e+40, b: -7.27, Ea: 7220.0} + high-P-rate-constant: {A: 5.6e+12, b: 0.0, Ea: 2400.0} + Troe: {A: 0.7507, T3: 98.5, T1: 1302.0, T2: 4167.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + C2H3 (+ M) <=> C2H4 (+ M) # Reaction 68 + type: falloff + low-P-rate-constant: {A: 1.4e+30, b: -3.86, Ea: 3320.0} + high-P-rate-constant: {A: 6.08e+12, b: 0.27, Ea: 280.0} + Troe: {A: 0.782, T3: 207.5, T1: 2663.0, T2: 6095.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + C2H3 <=> H2 + C2H2 # Reaction 69 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: H + C2H4 (+ M) <=> C2H5 (+ M) # Reaction 70 + type: falloff + low-P-rate-constant: {A: 6.0e+41, b: -7.62, Ea: 6970.0} + high-P-rate-constant: {A: 5.4e+11, b: 0.454, Ea: 1820.0} + Troe: {A: 0.9753, T3: 210.0, T1: 984.0, T2: 4374.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + C2H4 <=> C2H3 + H2 # Reaction 71 + rate-constant: {A: 1.325e+06, b: 2.53, Ea: 1.224e+04} +- equation: H + C2H5 (+ M) <=> C2H6 (+ M) # Reaction 72 + type: falloff + low-P-rate-constant: {A: 1.99e+41, b: -7.08, Ea: 6685.0} + high-P-rate-constant: {A: 5.21e+17, b: -0.99, Ea: 1580.0} + Troe: {A: 0.8422, T3: 125.0, T1: 2219.0, T2: 6882.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: H + C2H5 <=> H2 + C2H4 # Reaction 73 + rate-constant: {A: 2.0e+12, b: 0.0, Ea: 0.0} +- equation: H + C2H6 <=> C2H5 + H2 # Reaction 74 + rate-constant: {A: 1.15e+08, b: 1.9, Ea: 7530.0} +- equation: H + HCCO <=> CH2(S) + CO # Reaction 75 + rate-constant: {A: 1.0e+14, b: 0.0, Ea: 0.0} +- equation: H + CH2CO <=> HCCO + H2 # Reaction 76 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 8000.0} +- equation: H + CH2CO <=> CH3 + CO # Reaction 77 + rate-constant: {A: 1.13e+13, b: 0.0, Ea: 3428.0} +- equation: H2 + CO (+ M) <=> CH2O (+ M) # Reaction 78 + type: falloff + low-P-rate-constant: {A: 5.07e+27, b: -3.42, Ea: 8.435e+04} + high-P-rate-constant: {A: 4.3e+07, b: 1.5, Ea: 7.96e+04} + Troe: {A: 0.932, T3: 197.0, T1: 1540.0, T2: 1.03e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: OH + H2 <=> H + H2O # Reaction 79 + rate-constant: {A: 2.16e+08, b: 1.51, Ea: 3430.0} +- equation: 2 OH (+ M) <=> H2O2 (+ M) # Reaction 80 + type: falloff + low-P-rate-constant: {A: 2.3e+18, b: -0.9, Ea: -1700.0} + high-P-rate-constant: {A: 7.4e+13, b: -0.37, Ea: 0.0} + Troe: {A: 0.7346, T3: 94.0, T1: 1756.0, T2: 5182.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: 2 OH <=> O + H2O # Reaction 81 + rate-constant: {A: 3.57e+04, b: 2.4, Ea: -2110.0} +- equation: OH + HO2 <=> O2 + H2O # Reaction 82 + rate-constant: {A: 1.45e+13, b: 0.0, Ea: -500.0} + duplicate: true +- equation: OH + H2O2 <=> HO2 + H2O # Reaction 83 + rate-constant: {A: 2.0e+12, b: 0.0, Ea: 427.0} + duplicate: true +- equation: OH + H2O2 <=> HO2 + H2O # Reaction 84 + rate-constant: {A: 1.7e+18, b: 0.0, Ea: 2.941e+04} + duplicate: true +- equation: OH + C <=> H + CO # Reaction 85 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH <=> H + HCO # Reaction 86 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH2 <=> H + CH2O # Reaction 87 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH2 <=> CH + H2O # Reaction 88 + rate-constant: {A: 1.13e+07, b: 2.0, Ea: 3000.0} +- equation: OH + CH2(S) <=> H + CH2O # Reaction 89 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH3 (+ M) <=> CH3OH (+ M) # Reaction 90 + type: falloff + low-P-rate-constant: {A: 4.0e+36, b: -5.92, Ea: 3140.0} + high-P-rate-constant: {A: 2.79e+18, b: -1.43, Ea: 1330.0} + Troe: {A: 0.412, T3: 195.0, T1: 5900.0, T2: 6394.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: OH + CH3 <=> CH2 + H2O # Reaction 91 + rate-constant: {A: 5.6e+07, b: 1.6, Ea: 5420.0} +- equation: OH + CH3 <=> CH2(S) + H2O # Reaction 92 + rate-constant: {A: 6.44e+17, b: -1.34, Ea: 1417.0} +- equation: OH + CH4 <=> CH3 + H2O # Reaction 93 + rate-constant: {A: 1.0e+08, b: 1.6, Ea: 3120.0} +- equation: OH + CO <=> H + CO2 # Reaction 94 + rate-constant: {A: 4.76e+07, b: 1.228, Ea: 70.0} +- equation: OH + HCO <=> H2O + CO # Reaction 95 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH2O <=> HCO + H2O # Reaction 96 + rate-constant: {A: 3.43e+09, b: 1.18, Ea: -447.0} +- equation: OH + CH2OH <=> H2O + CH2O # Reaction 97 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0} +- equation: OH + CH3O <=> H2O + CH2O # Reaction 98 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0} +- equation: OH + CH3OH <=> CH2OH + H2O # Reaction 99 + rate-constant: {A: 1.44e+06, b: 2.0, Ea: -840.0} +- equation: OH + CH3OH <=> CH3O + H2O # Reaction 100 + rate-constant: {A: 6.3e+06, b: 2.0, Ea: 1500.0} +- equation: OH + C2H2 <=> H + CH2CO # Reaction 101 + rate-constant: {A: 2.18e-04, b: 4.5, Ea: -1000.0} +- equation: OH + C2H2 <=> CH3 + CO # Reaction 102 + rate-constant: {A: 4.83e-04, b: 4.0, Ea: -2000.0} +- equation: OH + C2H3 <=> H2O + C2H2 # Reaction 103 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 0.0} +- equation: OH + C2H4 <=> C2H3 + H2O # Reaction 104 + rate-constant: {A: 3.6e+06, b: 2.0, Ea: 2500.0} +- equation: OH + C2H6 <=> C2H5 + H2O # Reaction 105 + rate-constant: {A: 3.54e+06, b: 2.12, Ea: 870.0} +- equation: OH + CH2CO <=> HCCO + H2O # Reaction 106 + rate-constant: {A: 7.5e+12, b: 0.0, Ea: 2000.0} +- equation: 2 HO2 <=> O2 + H2O2 # Reaction 107 + rate-constant: {A: 1.3e+11, b: 0.0, Ea: -1630.0} + duplicate: true +- equation: 2 HO2 <=> O2 + H2O2 # Reaction 108 + rate-constant: {A: 4.2e+14, b: 0.0, Ea: 1.2e+04} + duplicate: true +- equation: HO2 + CH2 <=> OH + CH2O # Reaction 109 + rate-constant: {A: 2.0e+13, b: 0.0, Ea: 0.0} +- equation: HO2 + CH3 <=> O2 + CH4 # Reaction 110 + rate-constant: {A: 1.0e+12, b: 0.0, Ea: 0.0} +- equation: HO2 + CH3 <=> OH + CH3O # Reaction 111 + rate-constant: {A: 3.78e+13, b: 0.0, Ea: 0.0} +- equation: HO2 + CO <=> OH + CO2 # Reaction 112 + rate-constant: {A: 1.5e+14, b: 0.0, Ea: 2.36e+04} +- equation: HO2 + CH2O <=> HCO + H2O2 # Reaction 113 + rate-constant: {A: 5.6e+06, b: 2.0, Ea: 1.2e+04} +- equation: C + O2 <=> O + CO # Reaction 114 + rate-constant: {A: 5.8e+13, b: 0.0, Ea: 576.0} +- equation: C + CH3 <=> H + C2H2 # Reaction 115 + rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} +- equation: CH + O2 <=> O + HCO # Reaction 116 + rate-constant: {A: 6.71e+13, b: 0.0, Ea: 0.0} +- equation: CH + H2 <=> H + CH2 # Reaction 117 + rate-constant: {A: 1.08e+14, b: 0.0, Ea: 3110.0} +- equation: CH + H2O <=> H + CH2O # Reaction 118 + rate-constant: {A: 5.71e+12, b: 0.0, Ea: -755.0} +- equation: CH + CH3 <=> H + C2H3 # Reaction 119 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: CH + CH4 <=> H + C2H4 # Reaction 120 + rate-constant: {A: 6.0e+13, b: 0.0, Ea: 0.0} +- equation: CH + CO (+ M) <=> HCCO (+ M) # Reaction 121 + type: falloff + low-P-rate-constant: {A: 2.69e+28, b: -3.74, Ea: 1936.0} + high-P-rate-constant: {A: 5.0e+13, b: 0.0, Ea: 0.0} + Troe: {A: 0.5757, T3: 237.0, T1: 1652.0, T2: 5069.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: CH + CO2 <=> HCO + CO # Reaction 122 + rate-constant: {A: 1.9e+14, b: 0.0, Ea: 1.5792e+04} +- equation: CH + CH2O <=> H + CH2CO # Reaction 123 + rate-constant: {A: 9.46e+13, b: 0.0, Ea: -515.0} +- equation: CH2 + O2 => OH + H + CO # Reaction 124 + rate-constant: {A: 5.0e+12, b: 0.0, Ea: 1500.0} +- equation: CH2 + H2 <=> H + CH3 # Reaction 125 + rate-constant: {A: 5.0e+05, b: 2.0, Ea: 7230.0} +- equation: CH2 + CH3 <=> H + C2H4 # Reaction 126 + rate-constant: {A: 4.0e+13, b: 0.0, Ea: 0.0} +- equation: CH2 + CH4 <=> 2 CH3 # Reaction 127 + rate-constant: {A: 2.46e+06, b: 2.0, Ea: 8270.0} +- equation: CH2 + CO (+ M) <=> CH2CO (+ M) # Reaction 128 + type: falloff + low-P-rate-constant: {A: 2.69e+33, b: -5.11, Ea: 7095.0} + high-P-rate-constant: {A: 8.1e+11, b: 0.5, Ea: 4510.0} + Troe: {A: 0.5907, T3: 275.0, T1: 1226.0, T2: 5185.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: CH2(S) + N2 <=> CH2 + N2 # Reaction 129 + rate-constant: {A: 1.5e+13, b: 0.0, Ea: 600.0} +- equation: CH2(S) + O2 <=> H + OH + CO # Reaction 130 + rate-constant: {A: 2.8e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + O2 <=> CO + H2O # Reaction 131 + rate-constant: {A: 1.2e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + H2 <=> CH3 + H # Reaction 132 + rate-constant: {A: 7.0e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + H2O (+ M) <=> CH3OH (+ M) # Reaction 133 + type: falloff + low-P-rate-constant: {A: 1.88e+38, b: -6.36, Ea: 5040.0} + high-P-rate-constant: {A: 4.82e+17, b: -1.16, Ea: 1145.0} + Troe: {A: 0.6027, T3: 208.0, T1: 3922.0, T2: 1.018e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: CH2(S) + H2O <=> CH2 + H2O # Reaction 134 + rate-constant: {A: 3.0e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + CH3 <=> H + C2H4 # Reaction 135 + rate-constant: {A: 1.2e+13, b: 0.0, Ea: -570.0} +- equation: CH2(S) + CH4 <=> 2 CH3 # Reaction 136 + rate-constant: {A: 1.6e+13, b: 0.0, Ea: -570.0} +- equation: CH2(S) + CO <=> CH2 + CO # Reaction 137 + rate-constant: {A: 9.0e+12, b: 0.0, Ea: 0.0} +- equation: CH2(S) + CO2 <=> CH2 + CO2 # Reaction 138 + rate-constant: {A: 7.0e+12, b: 0.0, Ea: 0.0} +- equation: CH2(S) + CO2 <=> CO + CH2O # Reaction 139 + rate-constant: {A: 1.4e+13, b: 0.0, Ea: 0.0} +- equation: CH2(S) + C2H6 <=> CH3 + C2H5 # Reaction 140 + rate-constant: {A: 4.0e+13, b: 0.0, Ea: -550.0} +- equation: CH3 + O2 <=> O + CH3O # Reaction 141 + rate-constant: {A: 3.56e+13, b: 0.0, Ea: 3.048e+04} +- equation: CH3 + O2 <=> OH + CH2O # Reaction 142 + rate-constant: {A: 2.31e+12, b: 0.0, Ea: 2.0315e+04} +- equation: CH3 + H2O2 <=> HO2 + CH4 # Reaction 143 + rate-constant: {A: 2.45e+04, b: 2.47, Ea: 5180.0} +- equation: 2 CH3 (+ M) <=> C2H6 (+ M) # Reaction 144 + type: falloff + low-P-rate-constant: {A: 3.4e+41, b: -7.03, Ea: 2762.0} + high-P-rate-constant: {A: 6.77e+16, b: -1.18, Ea: 654.0} + Troe: {A: 0.619, T3: 73.2, T1: 1180.0, T2: 9999.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: 2 CH3 <=> H + C2H5 # Reaction 145 + rate-constant: {A: 6.84e+12, b: 0.1, Ea: 1.06e+04} +- equation: CH3 + HCO <=> CH4 + CO # Reaction 146 + rate-constant: {A: 2.648e+13, b: 0.0, Ea: 0.0} +- equation: CH3 + CH2O <=> HCO + CH4 # Reaction 147 + rate-constant: {A: 3320.0, b: 2.81, Ea: 5860.0} +- equation: CH3 + CH3OH <=> CH2OH + CH4 # Reaction 148 + rate-constant: {A: 3.0e+07, b: 1.5, Ea: 9940.0} +- equation: CH3 + CH3OH <=> CH3O + CH4 # Reaction 149 + rate-constant: {A: 1.0e+07, b: 1.5, Ea: 9940.0} +- equation: CH3 + C2H4 <=> C2H3 + CH4 # Reaction 150 + rate-constant: {A: 2.27e+05, b: 2.0, Ea: 9200.0} +- equation: CH3 + C2H6 <=> C2H5 + CH4 # Reaction 151 + rate-constant: {A: 6.14e+06, b: 1.74, Ea: 1.045e+04} +- equation: HCO + H2O <=> H + CO + H2O # Reaction 152 + rate-constant: {A: 1.5e+18, b: -1.0, Ea: 1.7e+04} +- equation: HCO + M <=> H + CO + M # Reaction 153 + type: three-body + rate-constant: {A: 1.87e+17, b: -1.0, Ea: 1.7e+04} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 0.0, CH4: 2.0, C2H6: 3.0} +- equation: HCO + O2 <=> HO2 + CO # Reaction 154 + rate-constant: {A: 1.345e+13, b: 0.0, Ea: 400.0} +- equation: CH2OH + O2 <=> HO2 + CH2O # Reaction 155 + rate-constant: {A: 1.8e+13, b: 0.0, Ea: 900.0} +- equation: CH3O + O2 <=> HO2 + CH2O # Reaction 156 + rate-constant: {A: 4.28e-13, b: 7.6, Ea: -3530.0} +- equation: C2H3 + O2 <=> HCO + CH2O # Reaction 157 + rate-constant: {A: 4.58e+16, b: -1.39, Ea: 1015.0} +- equation: C2H4 (+ M) <=> H2 + C2H2 (+ M) # Reaction 158 + type: falloff + low-P-rate-constant: {A: 1.58e+51, b: -9.3, Ea: 9.78e+04} + high-P-rate-constant: {A: 8.0e+12, b: 0.44, Ea: 8.677e+04} + Troe: {A: 0.7345, T3: 180.0, T1: 1035.0, T2: 5417.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: C2H5 + O2 <=> HO2 + C2H4 # Reaction 159 + rate-constant: {A: 8.4e+11, b: 0.0, Ea: 3875.0} +- equation: HCCO + O2 <=> OH + 2 CO # Reaction 160 + rate-constant: {A: 3.2e+12, b: 0.0, Ea: 854.0} +- equation: O + CH3 => H + H2 + CO # Reaction 161 + rate-constant: {A: 3.37e+13, b: 0.0, Ea: 0.0} +- equation: O + C2H4 <=> H + CH2CHO # Reaction 162 + rate-constant: {A: 6.7e+06, b: 1.83, Ea: 220.0} +- equation: OH + HO2 <=> O2 + H2O # Reaction 163 + rate-constant: {A: 5.0e+15, b: 0.0, Ea: 1.733e+04} + duplicate: true +- equation: OH + CH3 => H2 + CH2O # Reaction 164 + rate-constant: {A: 8.0e+09, b: 0.5, Ea: -1755.0} +- equation: CH + H2 (+ M) <=> CH3 (+ M) # Reaction 165 + type: falloff + low-P-rate-constant: {A: 4.82e+25, b: -2.8, Ea: 590.0} + high-P-rate-constant: {A: 1.97e+12, b: 0.43, Ea: -370.0} + Troe: {A: 0.578, T3: 122.0, T1: 2535.0, T2: 9365.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: CH2 + O2 => 2 H + CO2 # Reaction 166 + rate-constant: {A: 5.8e+12, b: 0.0, Ea: 1500.0} +- equation: CH2 + O2 <=> O + CH2O # Reaction 167 + rate-constant: {A: 2.4e+12, b: 0.0, Ea: 1500.0} +- equation: CH2(S) + H2O => H2 + CH2O # Reaction 168 + rate-constant: {A: 6.82e+10, b: 0.25, Ea: -935.0} +- equation: C2H3 + O2 <=> O + CH2CHO # Reaction 169 + rate-constant: {A: 3.03e+11, b: 0.29, Ea: 11.0} +- equation: C2H3 + O2 <=> HO2 + C2H2 # Reaction 170 + rate-constant: {A: 1.337e+06, b: 1.61, Ea: -384.0} +- equation: H + CH2CO (+ M) <=> CH2CHO (+ M) # Reaction 171 + type: falloff + low-P-rate-constant: {A: 1.012e+42, b: -7.63, Ea: 3854.0} + high-P-rate-constant: {A: 4.865e+11, b: 0.422, Ea: -1755.0} + Troe: {A: 0.465, T3: 201.0, T1: 1773.0, T2: 5333.0} + efficiencies: {CO2: 2.0, CO: 1.5, H2: 2.0, H2O: 6.0, CH4: 2.0, C2H6: 3.0} +- equation: O + CH2CHO => H + CH2 + CO2 # Reaction 172 + rate-constant: {A: 1.5e+14, b: 0.0, Ea: 0.0} +- equation: O2 + CH2CHO => OH + CO + CH2O # Reaction 173 + rate-constant: {A: 1.81e+10, b: 0.0, Ea: 0.0} +- equation: O2 + CH2CHO => OH + 2 HCO # Reaction 174 + rate-constant: {A: 2.35e+10, b: 0.0, Ea: 0.0} +- equation: H + CH2CHO <=> CH3 + HCO # Reaction 175 + rate-constant: {A: 2.2e+13, b: 0.0, Ea: 0.0} +- equation: H + CH2CHO <=> CH2CO + H2 # Reaction 176 + rate-constant: {A: 1.1e+13, b: 0.0, Ea: 0.0} +- equation: OH + CH2CHO <=> H2O + CH2CO # Reaction 177 + rate-constant: {A: 1.2e+13, b: 0.0, Ea: 0.0} diff --git a/samples/python/AVBP/inputs/Lu_ARC.cti b/samples/python/AVBP/inputs/Lu_ARC.cti new file mode 100755 index 00000000000..d31c4b10100 --- /dev/null +++ b/samples/python/AVBP/inputs/Lu_ARC.cti @@ -0,0 +1,1338 @@ +#--------------------------------------------------------------------------- +# CTI File converted from Solution Object +#--------------------------------------------------------------------------- +units(length='cm', time='s', quantity='mol', act_energy='cal/mol') + +ideal_gas(name = "gas", + elements = "N O H C", + species = """H2 H O O2 OH H2O HO2 H2O2 CH3 CH4 CO CO2 CH2O + CH3OH C2H2 C2H4 C2H6 CH2CO N2""", +# species_qss = """ C CH CH2 CH2(S) HCO CH2OH CH3O C2H3 C2H5 +# HCCO CH2CHO """, + reactions = "all", + kinetics = "custom", + initial_state = state(temperature = 3.000000E+02, pressure= 1.013250E+05) ) +#------------------------------------------------------------------------------- +# Species data +#------------------------------------------------------------------------------- + +species(name='H2', + atoms='H:2', + thermo=(NASA([200.00, 1000.00], + [ 2.34433112E+00, 7.98052075E-03, -1.94781510E-05, + 2.01572094E-08, -7.37611761E-12, -9.17935173E+02, + 6.83010238E-01]), + NASA([1000.00, 3500.00], + [ 3.33727920E+00, -4.94024731E-05, 4.99456778E-07, + -1.79566394E-10, 2.00255376E-14, -9.50158922E+02, + -3.20502331E+00])), + transport=gas_transport(geom='linear', + diam=2.92, + well_depth=38.0, + polar=0.79, + rot_relax=280.0), + note=u'TPIS78') + +species(name='H', + atoms='H:1', + thermo=(NASA([200.00, 1000.00], + [ 2.50000000E+00, 7.05332819E-13, -1.99591964E-15, + 2.30081632E-18, -9.27732332E-22, 2.54736599E+04, + -4.46682853E-01]), + NASA([1000.00, 3500.00], + [ 2.50000001E+00, -2.30842973E-11, 1.61561948E-14, + -4.73515235E-18, 4.98197357E-22, 2.54736599E+04, + -4.46682914E-01])), + transport=gas_transport(geom='atom', + diam=2.05, + well_depth=145.0), + note=u'L7/88') + +species(name='O', + atoms='O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.16826710E+00, -3.27931884E-03, 6.64306396E-06, + -6.12806624E-09, 2.11265971E-12, 2.91222592E+04, + 2.05193346E+00]), + NASA([1000.00, 3500.00], + [ 2.56942078E+00, -8.59741137E-05, 4.19484589E-08, + -1.00177799E-11, 1.22833691E-15, 2.92175791E+04, + 4.78433864E+00])), + transport=gas_transport(geom='atom', + diam=2.75, + well_depth=80.0), + note=u'L1/90') + +species(name='O2', + atoms='O:2', + thermo=(NASA([200.00, 1000.00], + [ 3.78245636E+00, -2.99673416E-03, 9.84730201E-06, + -9.68129509E-09, 3.24372837E-12, -1.06394356E+03, + 3.65767573E+00]), + NASA([1000.00, 3500.00], + [ 3.28253784E+00, 1.48308754E-03, -7.57966669E-07, + 2.09470555E-10, -2.16717794E-14, -1.08845772E+03, + 5.45323129E+00])), + transport=gas_transport(geom='linear', + diam=3.458, + well_depth=107.4, + polar=1.6, + rot_relax=3.8), + note=u'TPIS89') + +species(name='OH', + atoms='H:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.99201543E+00, -2.40131752E-03, 4.61793841E-06, + -3.88113333E-09, 1.36411470E-12, 3.61508056E+03, + -1.03925458E-01]), + NASA([1000.00, 3500.00], + [ 3.09288767E+00, 5.48429716E-04, 1.26505228E-07, + -8.79461556E-11, 1.17412376E-14, 3.85865700E+03, + 4.47669610E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note='RUS78') + +species(name='H2O', + atoms='H:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19864056E+00, -2.03643410E-03, 6.52040211E-06, + -5.48797062E-09, 1.77197817E-12, -3.02937267E+04, + -8.49032208E-01]), + NASA([1000.00, 3500.00], + [ 3.03399249E+00, 2.17691804E-03, -1.64072518E-07, + -9.70419870E-11, 1.68200992E-14, -3.00042971E+04, + 4.96677010E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.605, + well_depth=572.4, + dipole=1.844, + rot_relax=4.0), + note='L8/89') + +species(name='HO2', + atoms='H:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30179801E+00, -4.74912051E-03, 2.11582891E-05, + -2.42763894E-08, 9.29225124E-12, 2.94808040E+02, + 3.71666245E+00]), + NASA([1000.00, 3500.00], + [ 4.01721090E+00, 2.23982013E-03, -6.33658150E-07, + 1.14246370E-10, -1.07908535E-14, 1.11856713E+02, + 3.78510215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=1.0), + note='L5/89') + +species(name='H2O2', + atoms='H:2 O:2', + thermo=(NASA([200.00, 1000.00], + [ 4.27611269E+00, -5.42822417E-04, 1.67335701E-05, + -2.15770813E-08, 8.62454363E-12, -1.77025821E+04, + 3.43505074E+00]), + NASA([1000.00, 3500.00], + [ 4.16500285E+00, 4.90831694E-03, -1.90139225E-06, + 3.71185986E-10, -2.87908305E-14, -1.78617877E+04, + 2.91615662E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.458, + well_depth=107.4, + rot_relax=3.8), + note='L7/88') + +species(name='C', + atoms='C:1', + thermo=(NASA([200.00, 1000.00], + [ 2.55423955E+00, -3.21537724E-04, 7.33792245E-07, + -7.32234889E-10, 2.66521446E-13, 8.54438832E+04, + 4.53130848E+00]), + NASA([1000.00, 3500.00], + [ 2.49266888E+00, 4.79889284E-05, -7.24335020E-08, + 3.74291029E-11, -4.87277893E-15, 8.54512953E+04, + 4.80150373E+00])), + transport=gas_transport(geom='atom', + diam=3.298, + well_depth=71.4), + note='L11/88') + +species(name='CH', + atoms='H:1 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.48981665E+00, 3.23835541E-04, -1.68899065E-06, + 3.16217327E-09, -1.40609067E-12, 7.07972934E+04, + 2.08401108E+00]), + NASA([1000.00, 3500.00], + [ 2.87846473E+00, 9.70913681E-04, 1.44445655E-07, + -1.30687849E-10, 1.76079383E-14, 7.10124364E+04, + 5.48497999E+00])), + transport=gas_transport(geom='linear', + diam=2.75, + well_depth=80.0), + note='TPIS79') + +species(name='CH2', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.76267867E+00, 9.68872143E-04, 2.79489841E-06, + -3.85091153E-09, 1.68741719E-12, 4.60040401E+04, + 1.56253185E+00]), + NASA([1000.00, 3500.00], + [ 2.87410113E+00, 3.65639292E-03, -1.40894597E-06, + 2.60179549E-10, -1.87727567E-14, 4.62636040E+04, + 6.17119324E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note='LS/93') + +species(name='CH2(S)', + atoms='H:2 C:1', + thermo=(NASA([200.00, 1000.00], + [ 4.19860411E+00, -2.36661419E-03, 8.23296220E-06, + -6.68815981E-09, 1.94314737E-12, 5.04968163E+04, + -7.69118967E-01]), + NASA([1000.00, 3500.00], + [ 2.29203842E+00, 4.65588637E-03, -2.01191947E-06, + 4.17906000E-10, -3.39716365E-14, 5.09259997E+04, + 8.62650169E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note='LS/93') + +species(name='CH3', + atoms='H:3 C:1', + thermo=(NASA([200.00, 1000.00], + [ 3.67359040E+00, 2.01095175E-03, 5.73021856E-06, + -6.87117425E-09, 2.54385734E-12, 1.64449988E+04, + 1.60456433E+00]), + NASA([1000.00, 3500.00], + [ 2.28571772E+00, 7.23990037E-03, -2.98714348E-06, + 5.95684644E-10, -4.67154394E-14, 1.67755843E+04, + 8.48007179E+00])), + transport=gas_transport(geom='linear', + diam=3.8, + well_depth=144.0), + note='L11/89') + +species(name='CH4', + atoms='H:4 C:1', + thermo=(NASA([200.00, 1000.00], + [ 5.14987613E+00, -1.36709788E-02, 4.91800599E-05, + -4.84743026E-08, 1.66693956E-11, -1.02466476E+04, + -4.64130376E+00]), + NASA([1000.00, 3500.00], + [ 7.48514950E-02, 1.33909467E-02, -5.73285809E-06, + 1.22292535E-09, -1.01815230E-13, -9.46834459E+03, + 1.84373180E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.746, + well_depth=141.4, + polar=2.6, + rot_relax=13.0), + note='L8/88') + +species(name='CO', + atoms='C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.57953347E+00, -6.10353680E-04, 1.01681433E-06, + 9.07005884E-10, -9.04424499E-13, -1.43440860E+04, + 3.50840928E+00]), + NASA([1000.00, 3500.00], + [ 2.71518561E+00, 2.06252743E-03, -9.98825771E-07, + 2.30053008E-10, -2.03647716E-14, -1.41518724E+04, + 7.81868772E+00])), + transport=gas_transport(geom='linear', + diam=3.65, + well_depth=98.1, + polar=1.95, + rot_relax=1.8), + note='TPIS79') + +species(name='CO2', + atoms='C:1 O:2', + thermo=(NASA([200.00, 1000.00], + [ 2.35677352E+00, 8.98459677E-03, -7.12356269E-06, + 2.45919022E-09, -1.43699548E-13, -4.83719697E+04, + 9.90105222E+00]), + NASA([1000.00, 3500.00], + [ 3.85746029E+00, 4.41437026E-03, -2.21481404E-06, + 5.23490188E-10, -4.72084164E-14, -4.87591660E+04, + 2.27163806E+00])), + transport=gas_transport(geom='linear', + diam=3.763, + well_depth=244.0, + polar=2.65, + rot_relax=2.1), + note='L7/88') + +species(name='HCO', + atoms='H:1 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.22118584E+00, -3.24392532E-03, 1.37799446E-05, + -1.33144093E-08, 4.33768865E-12, 3.83956496E+03, + 3.39437243E+00]), + NASA([1000.00, 3500.00], + [ 2.77217438E+00, 4.95695526E-03, -2.48445613E-06, + 5.89161778E-10, -5.33508711E-14, 4.01191815E+03, + 9.79834492E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0), + note='L12/89') + +species(name='CH2O', + atoms='H:2 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 4.79372315E+00, -9.90833369E-03, 3.73220008E-05, + -3.79285261E-08, 1.31772652E-11, -1.43089567E+04, + 6.02812900E-01]), + NASA([1000.00, 3500.00], + [ 1.76069008E+00, 9.20000082E-03, -4.42258813E-06, + 1.00641212E-09, -8.83855640E-14, -1.39958323E+04, + 1.36563230E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.59, + well_depth=498.0, + rot_relax=2.0), + note='L8/88') + +species(name='CH2OH', + atoms='H:3 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 3.86388918E+00, 5.59672304E-03, 5.93271791E-06, + -1.04532012E-08, 4.36967278E-12, -3.19391367E+03, + 5.47302243E+00]), + NASA([1000.00, 3500.00], + [ 3.69266569E+00, 8.64576797E-03, -3.75101120E-06, + 7.87234636E-10, -6.48554201E-14, -3.24250627E+03, + 5.81043215E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.69, + well_depth=417.0, + dipole=1.7, + rot_relax=2.0), + note='GUNL93') + +species(name='CH3O', + atoms='H:3 C:1 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.10620400E+00, 7.21659500E-03, 5.33847200E-06, + -7.37763600E-09, 2.07561000E-12, 9.78601100E+02, + 1.31521770E+01]), + NASA([1000.00, 3000.00], + [ 3.77079900E+00, 7.87149700E-03, -2.65638400E-06, + 3.94443100E-10, -2.11261600E-14, 1.27832520E+02, + 2.92957500E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.69, + well_depth=417.0, + dipole=1.7, + rot_relax=2.0), + note='121686') + +species(name='CH3OH', + atoms='H:4 C:1 O:1', + thermo=(NASA([200.00, 1000.00], + [ 5.71539582E+00, -1.52309129E-02, 6.52441155E-05, + -7.10806889E-08, 2.61352698E-11, -2.56427656E+04, + -1.50409823E+00]), + NASA([1000.00, 3500.00], + [ 1.78970791E+00, 1.40938292E-02, -6.36500835E-06, + 1.38171085E-09, -1.17060220E-13, -2.53748747E+04, + 1.45023623E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.626, + well_depth=481.8, + rot_relax=1.0), + note='L8/88') + +species(name='C2H2', + atoms='H:2 C:2', + thermo=(NASA([200.00, 1000.00], + [ 8.08681094E-01, 2.33615629E-02, -3.55171815E-05, + 2.80152437E-08, -8.50072974E-12, 2.64289807E+04, + 1.39397051E+01]), + NASA([1000.00, 3500.00], + [ 4.14756964E+00, 5.96166664E-03, -2.37294852E-06, + 4.67412171E-10, -3.61235213E-14, 2.59359992E+04, + -1.23028121E+00])), + transport=gas_transport(geom='linear', + diam=4.1, + well_depth=209.0, + rot_relax=2.5), + note='L1/91') + +species(name='C2H3', + atoms='H:3 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.21246645E+00, 1.51479162E-03, 2.59209412E-05, + -3.57657847E-08, 1.47150873E-11, 3.48598468E+04, + 8.51054025E+00]), + NASA([1000.00, 3500.00], + [ 3.01672400E+00, 1.03302292E-02, -4.68082349E-06, + 1.01763288E-09, -8.62607041E-14, 3.46128739E+04, + 7.78732378E+00])), + transport=gas_transport(geom='nonlinear', + diam=4.1, + well_depth=209.0, + rot_relax=1.0), + note='L2/92') + +species(name='C2H4', + atoms='H:4 C:2', + thermo=(NASA([200.00, 1000.00], + [ 3.95920148E+00, -7.57052247E-03, 5.70990292E-05, + -6.91588753E-08, 2.69884373E-11, 5.08977593E+03, + 4.09733096E+00]), + NASA([1000.00, 3500.00], + [ 2.03611116E+00, 1.46454151E-02, -6.71077915E-06, + 1.47222923E-09, -1.25706061E-13, 4.93988614E+03, + 1.03053693E+01])), + transport=gas_transport(geom='nonlinear', + diam=3.971, + well_depth=280.8, + rot_relax=1.5), + note='L1/91') + +species(name='C2H5', + atoms='H:5 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.30646568E+00, -4.18658892E-03, 4.97142807E-05, + -5.99126606E-08, 2.30509004E-11, 1.28416265E+04, + 4.70720924E+00]), + NASA([1000.00, 3500.00], + [ 1.95465642E+00, 1.73972722E-02, -7.98206668E-06, + 1.75217689E-09, -1.49641576E-13, 1.28575200E+04, + 1.34624343E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note='L12/92') + +species(name='C2H6', + atoms='H:6 C:2', + thermo=(NASA([200.00, 1000.00], + [ 4.29142492E+00, -5.50154270E-03, 5.99438288E-05, + -7.08466285E-08, 2.68685771E-11, -1.15222055E+04, + 2.66682316E+00]), + NASA([1000.00, 3500.00], + [ 1.07188150E+00, 2.16852677E-02, -1.00256067E-05, + 2.21412001E-09, -1.90002890E-13, -1.14263932E+04, + 1.51156107E+01])), + transport=gas_transport(geom='nonlinear', + diam=4.302, + well_depth=252.3, + rot_relax=1.5), + note='L8/88') + +species(name='HCCO', + atoms='H:1 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 2.25172140E+00, 1.76550210E-02, -2.37291010E-05, + 1.72757590E-08, -5.06648110E-12, 2.00594490E+04, + 1.24904170E+01]), + NASA([1000.00, 4000.00], + [ 5.62820580E+00, 4.08534010E-03, -1.59345470E-06, + 2.86260520E-10, -1.94078320E-14, 1.93272150E+04, + -3.93025950E+00])), + transport=gas_transport(geom='nonlinear', + diam=2.5, + well_depth=150.0, + rot_relax=1.0), + note='SRIC91') + +species(name='CH2CO', + atoms='H:2 C:2 O:1', + thermo=(NASA([200.00, 1000.00], + [ 2.13583630E+00, 1.81188721E-02, -1.73947474E-05, + 9.34397568E-09, -2.01457615E-12, -7.04291804E+03, + 1.22156480E+01]), + NASA([1000.00, 3500.00], + [ 4.51129732E+00, 9.00359745E-03, -4.16939635E-06, + 9.23345882E-10, -7.94838201E-14, -7.55105311E+03, + 6.32247205E-01])), + transport=gas_transport(geom='nonlinear', + diam=3.97, + well_depth=436.0, + rot_relax=2.0), + note='L5/90') + +species(name='CH2CHO', + atoms='H:3 C:2 O:1', + thermo=(NASA([300.00, 1000.00], + [ 3.40906200E+00, 1.07385740E-02, 1.89149200E-06, + -7.15858300E-09, 2.86738500E-12, 1.52147660E+03, + 9.55829000E+00]), + NASA([1000.00, 5000.00], + [ 5.97567000E+00, 8.13059100E-03, -2.74362400E-06, + 4.07030400E-10, -2.17601700E-14, 4.90321800E+02, + -5.04525100E+00])), + transport=gas_transport(geom='nonlinear', + diam=3.97, + well_depth=436.0, + rot_relax=2.0), + note='SAND86') + +species(name='N2', + atoms='N:2', + thermo=(NASA([300.00, 1000.00], + [ 3.29867700E+00, 1.40824040E-03, -3.96322200E-06, + 5.64151500E-09, -2.44485400E-12, -1.02089990E+03, + 3.95037200E+00]), + NASA([1000.00, 5000.00], + [ 2.92664000E+00, 1.48797680E-03, -5.68476000E-07, + 1.00970380E-10, -6.75335100E-15, -9.22797700E+02, + 5.98052800E+00])), + transport=gas_transport(geom='linear', + diam=3.621, + well_depth=97.53, + polar=1.76, + rot_relax=4.0), + note='121286') + +#------------------------------------------------------------------------------- +# Reaction data +#------------------------------------------------------------------------------- + +# Dummy Reaction +reaction('O + H2 <=> H + OH', [0.0, 0.0, 0.0]) + +## Reaction 1 +#three_body_reaction('2 O + M <=> O2 + M', [1.200000e+17, -1.0, 0.0], +# efficiencies='CO2:3.6 CO:1.75 H2:2.4 H2O:15.4 CH4:2.0 C2H6:3.0') + +## Reaction 2 +#three_body_reaction('O + H + M <=> OH + M', [5.000000e+17, -1.0, 0.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0') + +## Reaction 3 +#reaction('O + H2 <=> H + OH', [3.870000e+04, 2.7, 6260.0]) +## R4 +# + +## Reaction 4 +#reaction('O + HO2 <=> OH + O2', [2.000000e+13, 0.0, 0.0]) +## R5 +# +## Reaction 5 +#reaction('O + H2O2 <=> OH + HO2', [9.630000e+06, 2.0, 4000.0]) +## R6 +# +## Reaction 6 +#reaction('O + CH <=> H + CO', [5.700000e+13, 0.0, 0.0]) +## R7 +# +## Reaction 7 +#reaction('O + CH2 <=> H + HCO', [8.000000e+13, 0.0, 0.0]) +## R8 +# +## Reaction 8 +#reaction('O + CH2(S) <=> H2 + CO', [1.500000e+13, 0.0, 0.0]) +## R9 +# +## Reaction 9 +#reaction('O + CH2(S) <=> H + HCO', [1.500000e+13, 0.0, 0.0]) +## R10 +# +## Reaction 10 +#reaction('O + CH3 <=> H + CH2O', [5.060000e+13, 0.0, 0.0]) +## R11 +# +## Reaction 11 +#reaction('O + CH4 <=> OH + CH3', [1.020000e+09, 1.5, 8600.0]) +## R12 +# +## Reaction 12 +#falloff_reaction('O + CO (+ M) <=> CO2 (+ M)', +# kf=[1.800000e+10, 0.0, 2385.0], +# kf0=[6.020000e+14, 0.0, 3000.0], +# efficiencies='CO2:3.5 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0 O2:6.0') +## R13 +# +## Reaction 13 +#reaction('O + HCO <=> OH + CO', [3.000000e+13, 0.0, 0.0]) +## R14 +# +## Reaction 14 +#reaction('O + HCO <=> H + CO2', [3.000000e+13, 0.0, 0.0]) +## R15 +# +## Reaction 15 +#reaction('O + CH2O <=> OH + HCO', [3.900000e+13, 0.0, 3540.0]) +## R16 +# +## Reaction 16 +#reaction('O + CH2OH <=> OH + CH2O', [1.000000e+13, 0.0, 0.0]) +## R17 +# +## Reaction 17 +#reaction('O + CH3O <=> OH + CH2O', [1.000000e+13, 0.0, 0.0]) +## R18 +# +## Reaction 18 +#reaction('O + CH3OH <=> OH + CH2OH', [3.880000e+05, 2.5, 3100.0]) +## R19 +# +## Reaction 19 +#reaction('O + CH3OH <=> OH + CH3O', [1.300000e+05, 2.5, 5000.0]) +## R20 +# +## Reaction 20 +#reaction('O + C2H2 <=> H + HCCO', [1.350000e+07, 2.0, 1900.0]) +## R21 +# +## Reaction 21 +#reaction('O + C2H2 <=> CO + CH2', [6.940000e+06, 2.0, 1900.0]) +## R22 +# +## Reaction 22 +#reaction('O + C2H3 <=> H + CH2CO', [3.000000e+13, 0.0, 0.0]) +## R23 +# +## Reaction 23 +#reaction('O + C2H4 <=> CH3 + HCO', [1.250000e+07, 1.83, 220.0]) +## R24 +# +## Reaction 24 +#reaction('O + C2H5 <=> CH3 + CH2O', [2.240000e+13, 0.0, 0.0]) +## R25 +# +## Reaction 25 +#reaction('O + C2H6 <=> OH + C2H5', [8.980000e+07, 1.92, 5690.0]) +## R26 +# +## Reaction 26 +#reaction('O + HCCO <=> H + 2 CO', [1.000000e+14, 0.0, 0.0]) +## R27 +# +## Reaction 27 +#reaction('O + CH2CO <=> OH + HCCO', [1.000000e+13, 0.0, 8000.0]) +## R28 +# +## Reaction 28 +#reaction('O + CH2CO <=> CH2 + CO2', [1.750000e+12, 0.0, 1350.0]) +## R29 +# +## Reaction 29 +#reaction('O2 + CO <=> O + CO2', [2.500000e+12, 0.0, 47800.0]) +## R30 +# +## Reaction 30 +#reaction('O2 + CH2O <=> HO2 + HCO', [1.000000e+14, 0.0, 40000.0]) +## R31 +# +## Reaction 31 +#three_body_reaction('H + O2 + M <=> HO2 + M', [2.800000e+18, -0.86, 0.0], +# efficiencies='CO2:1.5 CO:0.75 H2O:0.0 C2H6:1.5 N2:0.0 O2:0.0') +## R32 +# +## Reaction 32 +#reaction('H + 2 O2 <=> HO2 + O2', [2.080000e+19, -1.24, 0.0]) +## R33 +# +## Reaction 33 +#reaction('H + O2 + H2O <=> HO2 + H2O', [1.126000e+19, -0.76, 0.0]) +## R34 +# +## Reaction 34 +#reaction('H + O2 + N2 <=> HO2 + N2', [2.600000e+19, -1.24, 0.0]) +## R35 +# +## Reaction 35 +#reaction('H + O2 <=> O + OH', [2.650000e+16, -0.6707, 17041.0]) +## R36 +# +## Reaction 36 +#three_body_reaction('2 H + M <=> H2 + M', [1.000000e+18, -1.0, 0.0], +# efficiencies='H2:0.0 C2H6:3.0 H2O:0.0 CO2:0.0 CH4:2.0') +## R37 +# +## Reaction 37 +#reaction('2 H + H2 <=> 2 H2', [9.000000e+16, -0.6, 0.0]) +## R38 +# +## Reaction 38 +#reaction('2 H + H2O <=> H2 + H2O', [6.000000e+19, -1.25, 0.0]) +## R39 +# +## Reaction 39 +#reaction('2 H + CO2 <=> H2 + CO2', [5.500000e+20, -2.0, 0.0]) +## R40 +# +## Reaction 40 +#three_body_reaction('H + OH + M <=> H2O + M', [2.200000e+22, -2.0, 0.0], +# efficiencies='H2:0.73 C2H6:3.0 H2O:3.65 CH4:2.0') +## R41 +# +## Reaction 41 +#reaction('H + HO2 <=> O + H2O', [3.970000e+12, 0.0, 671.0]) +## R42 +# +## Reaction 42 +#reaction('H + HO2 <=> O2 + H2', [4.480000e+13, 0.0, 1068.0]) +## R43 +# +## Reaction 43 +#reaction('H + HO2 <=> 2 OH', [8.400000e+13, 0.0, 635.0]) +## R44 +# +## Reaction 44 +#reaction('H + H2O2 <=> HO2 + H2', [1.210000e+07, 2.0, 5200.0]) +## R45 +# +## Reaction 45 +#reaction('H + H2O2 <=> OH + H2O', [1.000000e+13, 0.0, 3600.0]) +## R46 +# +## Reaction 46 +#reaction('H + CH <=> C + H2', [1.650000e+14, 0.0, 0.0]) +## R47 +# +## Reaction 47 +#falloff_reaction('H + CH2 (+ M) <=> CH3 (+ M)', +# kf=[6.000000e+14, 0.0, 0.0], +# kf0=[1.040000e+26, -2.76, 1600.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.562, T3=91.0, T1=5836.0, T2=8552.0)) +## R48 +# +## Reaction 48 +#reaction('H + CH2(S) <=> CH + H2', [3.000000e+13, 0.0, 0.0]) +## R49 +# +## Reaction 49 +#falloff_reaction('H + CH3 (+ M) <=> CH4 (+ M)', +# kf=[1.390000e+16, -0.534, 536.0], +# kf0=[2.620000e+33, -4.76, 2440.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:3.0 C2H6:3.0', +# falloff=Troe(A=0.783, T3=74.0, T1=2941.0, T2=6964.0)) +## R50 +# +## Reaction 50 +#reaction('H + CH4 <=> CH3 + H2', [6.600000e+08, 1.62, 10840.0]) +## R51 +# +## Reaction 51 +#falloff_reaction('H + HCO (+ M) <=> CH2O (+ M)', +# kf=[1.090000e+12, 0.48, -260.0], +# kf0=[2.470000e+24, -2.57, 425.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7824, T3=271.0, T1=2755.0, T2=6570.0)) +## R52 +# +## Reaction 52 +#reaction('H + HCO <=> H2 + CO', [7.340000e+13, 0.0, 0.0]) +## R53 +# +## Reaction 53 +#falloff_reaction('H + CH2O (+ M) <=> CH2OH (+ M)', +# kf=[5.400000e+11, 0.454, 3600.0], +# kf0=[1.270000e+32, -4.82, 6530.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7187, T3=103.0, T1=1291.0, T2=4160.0)) +## R54 +# +## Reaction 54 +#falloff_reaction('H + CH2O (+ M) <=> CH3O (+ M)', +# kf=[5.400000e+11, 0.454, 2600.0], +# kf0=[2.200000e+30, -4.8, 5560.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.758, T3=94.0, T1=1555.0, T2=4200.0)) +## R55 +# +## Reaction 55 +#reaction('H + CH2O <=> HCO + H2', [5.740000e+07, 1.9, 2742.0]) +## R56 +# +## Reaction 56 +#falloff_reaction('H + CH2OH (+ M) <=> CH3OH (+ M)', +# kf=[1.055000e+12, 0.5, 86.0], +# kf0=[4.360000e+31, -4.65, 5080.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.6, T3=100.0, T1=90000.0, T2=10000.0)) +## R57 +# +## Reaction 57 +#reaction('H + CH2OH <=> H2 + CH2O', [2.000000e+13, 0.0, 0.0]) +## R58 +# +## Reaction 58 +#reaction('H + CH2OH <=> OH + CH3', [1.650000e+11, 0.65, -284.0]) +## R59 +# +## Reaction 59 +#reaction('H + CH2OH <=> CH2(S) + H2O', [3.280000e+13, -0.09, 610.0]) +## R60 +# +## Reaction 60 +#falloff_reaction('H + CH3O (+ M) <=> CH3OH (+ M)', +# kf=[2.430000e+12, 0.515, 50.0], +# kf0=[4.660000e+41, -7.44, 14080.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7, T3=100.0, T1=90000.0, T2=10000.0)) +## R61 +# +## Reaction 61 +#reaction('H + CH3O <=> H + CH2OH', [4.150000e+07, 1.63, 1924.0]) +## R62 +# +## Reaction 62 +#reaction('H + CH3O <=> H2 + CH2O', [2.000000e+13, 0.0, 0.0]) +## R63 +# +## Reaction 63 +#reaction('H + CH3O <=> OH + CH3', [1.500000e+12, 0.5, -110.0]) +## R64 +# +## Reaction 64 +#reaction('H + CH3O <=> CH2(S) + H2O', [2.620000e+14, -0.23, 1070.0]) +## R65 +# +## Reaction 65 +#reaction('H + CH3OH <=> CH2OH + H2', [1.700000e+07, 2.1, 4870.0]) +## R66 +# +## Reaction 66 +#reaction('H + CH3OH <=> CH3O + H2', [4.200000e+06, 2.1, 4870.0]) +## R67 +# +## Reaction 67 +#falloff_reaction('H + C2H2 (+ M) <=> C2H3 (+ M)', +# kf=[5.600000e+12, 0.0, 2400.0], +# kf0=[3.800000e+40, -7.27, 7220.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7507, T3=98.5, T1=1302.0, T2=4167.0)) +## R68 +# +## Reaction 68 +#falloff_reaction('H + C2H3 (+ M) <=> C2H4 (+ M)', +# kf=[6.080000e+12, 0.27, 280.0], +# kf0=[1.400000e+30, -3.86, 3320.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.782, T3=207.5, T1=2663.0, T2=6095.0)) +## R69 +# +## Reaction 69 +#reaction('H + C2H3 <=> H2 + C2H2', [3.000000e+13, 0.0, 0.0]) +## R70 +# +## Reaction 70 +#falloff_reaction('H + C2H4 (+ M) <=> C2H5 (+ M)', +# kf=[5.400000e+11, 0.454, 1820.0], +# kf0=[6.000000e+41, -7.62, 6970.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.9753, T3=210.0, T1=984.0, T2=4374.0)) +## R71 +# +## Reaction 71 +#reaction('H + C2H4 <=> C2H3 + H2', [1.325000e+06, 2.53, 12240.0]) +## R72 +# +## Reaction 72 +#falloff_reaction('H + C2H5 (+ M) <=> C2H6 (+ M)', +# kf=[5.210000e+17, -0.99, 1580.0], +# kf0=[1.990000e+41, -7.08, 6685.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.8422, T3=125.0, T1=2219.0, T2=6882.0)) +## R73 +# +## Reaction 73 +#reaction('H + C2H5 <=> H2 + C2H4', [2.000000e+12, 0.0, 0.0]) +## R74 +# +## Reaction 74 +#reaction('H + C2H6 <=> C2H5 + H2', [1.150000e+08, 1.9, 7530.0]) +## R75 +# +## Reaction 75 +#reaction('H + HCCO <=> CH2(S) + CO', [1.000000e+14, 0.0, 0.0]) +## R76 +# +## Reaction 76 +#reaction('H + CH2CO <=> HCCO + H2', [5.000000e+13, 0.0, 8000.0]) +## R77 +# +## Reaction 77 +#reaction('H + CH2CO <=> CH3 + CO', [1.130000e+13, 0.0, 3428.0]) +## R78 +# +## Reaction 78 +#falloff_reaction('H2 + CO (+ M) <=> CH2O (+ M)', +# kf=[4.300000e+07, 1.5, 79600.0], +# kf0=[5.070000e+27, -3.42, 84350.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.932, T3=197.0, T1=1540.0, T2=10300.0)) +## R79 +# +## Reaction 79 +#reaction('OH + H2 <=> H + H2O', [2.160000e+08, 1.51, 3430.0]) +## R80 +# +## Reaction 80 +#falloff_reaction('2 OH (+ M) <=> H2O2 (+ M)', +# kf=[7.400000e+13, -0.37, 0.0], +# kf0=[2.300000e+18, -0.9, -1700.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7346, T3=94.0, T1=1756.0, T2=5182.0)) +## R81 +# +## Reaction 81 +#reaction('2 OH <=> O + H2O', [3.570000e+04, 2.4, -2110.0]) +## R82 +# +## Reaction 82 +#reaction('OH + HO2 <=> O2 + H2O', [1.450000e+13, 0.0, -500.0], +# options='duplicate') +## R83 +# +## Reaction 83 +#reaction('OH + H2O2 <=> HO2 + H2O', [2.000000e+12, 0.0, 427.0], +# options='duplicate') +## R84 +# +## Reaction 84 +#reaction('OH + H2O2 <=> HO2 + H2O', [1.700000e+18, 0.0, 29410.0], +# options='duplicate') +## R85 +# +## Reaction 85 +#reaction('OH + C <=> H + CO', [5.000000e+13, 0.0, 0.0]) +## R86 +# +## Reaction 86 +#reaction('OH + CH <=> H + HCO', [3.000000e+13, 0.0, 0.0]) +## R87 +# +## Reaction 87 +#reaction('OH + CH2 <=> H + CH2O', [2.000000e+13, 0.0, 0.0]) +## R88 +# +## Reaction 88 +#reaction('OH + CH2 <=> CH + H2O', [1.130000e+07, 2.0, 3000.0]) +## R89 +# +## Reaction 89 +#reaction('OH + CH2(S) <=> H + CH2O', [3.000000e+13, 0.0, 0.0]) +## R90 +# +## Reaction 90 +#falloff_reaction('OH + CH3 (+ M) <=> CH3OH (+ M)', +# kf=[2.790000e+18, -1.43, 1330.0], +# kf0=[4.000000e+36, -5.92, 3140.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.412, T3=195.0, T1=5900.0, T2=6394.0)) +## R91 +# +## Reaction 91 +#reaction('OH + CH3 <=> CH2 + H2O', [5.600000e+07, 1.6, 5420.0]) +## R92 +# +## Reaction 92 +#reaction('OH + CH3 <=> CH2(S) + H2O', [6.440000e+17, -1.34, 1417.0]) +## R93 +# +## Reaction 93 +#reaction('OH + CH4 <=> CH3 + H2O', [1.000000e+08, 1.6, 3120.0]) +## R94 +# +## Reaction 94 +#reaction('OH + CO <=> H + CO2', [4.760000e+07, 1.228, 70.0]) +## R95 +# +## Reaction 95 +#reaction('OH + HCO <=> H2O + CO', [5.000000e+13, 0.0, 0.0]) +## R96 +# +## Reaction 96 +#reaction('OH + CH2O <=> HCO + H2O', [3.430000e+09, 1.18, -447.0]) +## R97 +# +## Reaction 97 +#reaction('OH + CH2OH <=> H2O + CH2O', [5.000000e+12, 0.0, 0.0]) +## R98 +# +## Reaction 98 +#reaction('OH + CH3O <=> H2O + CH2O', [5.000000e+12, 0.0, 0.0]) +## R99 +# +## Reaction 99 +#reaction('OH + CH3OH <=> CH2OH + H2O', [1.440000e+06, 2.0, -840.0]) +## R100 +# +## Reaction 100 +#reaction('OH + CH3OH <=> CH3O + H2O', [6.300000e+06, 2.0, 1500.0]) +## R101 +# +## Reaction 101 +#reaction('OH + C2H2 <=> H + CH2CO', [2.180000e-04, 4.5, -1000.0]) +## R102 +# +## Reaction 102 +#reaction('OH + C2H2 <=> CH3 + CO', [4.830000e-04, 4.0, -2000.0]) +## R103 +# +## Reaction 103 +#reaction('OH + C2H3 <=> H2O + C2H2', [5.000000e+12, 0.0, 0.0]) +## R104 +# +## Reaction 104 +#reaction('OH + C2H4 <=> C2H3 + H2O', [3.600000e+06, 2.0, 2500.0]) +## R105 +# +## Reaction 105 +#reaction('OH + C2H6 <=> C2H5 + H2O', [3.540000e+06, 2.12, 870.0]) +## R106 +# +## Reaction 106 +#reaction('OH + CH2CO <=> HCCO + H2O', [7.500000e+12, 0.0, 2000.0]) +## R107 +# +## Reaction 107 +#reaction('2 HO2 <=> O2 + H2O2', [1.300000e+11, 0.0, -1630.0], +# options='duplicate') +## R108 +# +## Reaction 108 +#reaction('2 HO2 <=> O2 + H2O2', [4.200000e+14, 0.0, 12000.0], +# options='duplicate') +## R109 +# +## Reaction 109 +#reaction('HO2 + CH2 <=> OH + CH2O', [2.000000e+13, 0.0, 0.0]) +## R110 +# +## Reaction 110 +#reaction('HO2 + CH3 <=> O2 + CH4', [1.000000e+12, 0.0, 0.0]) +## R111 +# +## Reaction 111 +#reaction('HO2 + CH3 <=> OH + CH3O', [3.780000e+13, 0.0, 0.0]) +## R112 +# +## Reaction 112 +#reaction('HO2 + CO <=> OH + CO2', [1.500000e+14, 0.0, 23600.0]) +## R113 +# +## Reaction 113 +#reaction('HO2 + CH2O <=> HCO + H2O2', [5.600000e+06, 2.0, 12000.0]) +## R114 +# +## Reaction 114 +#reaction('C + O2 <=> O + CO', [5.800000e+13, 0.0, 576.0]) +## R115 +# +## Reaction 115 +#reaction('C + CH3 <=> H + C2H2', [5.000000e+13, 0.0, 0.0]) +## R116 +# +## Reaction 116 +#reaction('CH + O2 <=> O + HCO', [6.710000e+13, 0.0, 0.0]) +## R117 +# +## Reaction 117 +#reaction('CH + H2 <=> H + CH2', [1.080000e+14, 0.0, 3110.0]) +## R118 +# +## Reaction 118 +#reaction('CH + H2O <=> H + CH2O', [5.710000e+12, 0.0, -755.0]) +## R119 +# +## Reaction 119 +## reaction('CH + CH2 <=> H + C2H2', [4.000000e+13, 0.0, 0.0]) +## R120 +# +## Reaction 120 +#reaction('CH + CH3 <=> H + C2H3', [3.000000e+13, 0.0, 0.0]) +## R121 +# +## Reaction 121 +#reaction('CH + CH4 <=> H + C2H4', [6.000000e+13, 0.0, 0.0]) +## R122 +# +## Reaction 122 +#falloff_reaction('CH + CO (+ M) <=> HCCO (+ M)', +# kf=[5.000000e+13, 0.0, 0.0], +# kf0=[2.690000e+28, -3.74, 1936.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.5757, T3=237.0, T1=1652.0, T2=5069.0)) +## R123 +# +## Reaction 123 +#reaction('CH + CO2 <=> HCO + CO', [1.900000e+14, 0.0, 15792.0]) +## R124 +# +## Reaction 124 +#reaction('CH + CH2O <=> H + CH2CO', [9.460000e+13, 0.0, -515.0]) +## R125 +# +## Reaction 125 +## reaction('CH + HCCO <=> CO + C2H2', [5.000000e+13, 0.0, 0.0]) +## R126 +# +## Reaction 126 +#reaction('CH2 + O2 => OH + H + CO', [5.000000e+12, 0.0, 1500.0]) +## R127 +# +## Reaction 127 +#reaction('CH2 + H2 <=> H + CH3', [5.000000e+05, 2.0, 7230.0]) +## R128 +# +## Reaction 128 +## reaction('2 CH2 <=> H2 + C2H2', [1.600000e+15, 0.0, 11944.0]) +## R129 +# +## Reaction 129 +#reaction('CH2 + CH3 <=> H + C2H4', [4.000000e+13, 0.0, 0.0]) +## R130 +# +## Reaction 130 +#reaction('CH2 + CH4 <=> 2 CH3', [2.460000e+06, 2.0, 8270.0]) +## R131 +# +## Reaction 131 +#falloff_reaction('CH2 + CO (+ M) <=> CH2CO (+ M)', +# kf=[8.100000e+11, 0.5, 4510.0], +# kf0=[2.690000e+33, -5.11, 7095.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.5907, T3=275.0, T1=1226.0, T2=5185.0)) +## R132 +# +## Reaction 132 +## reaction('CH2 + HCCO <=> C2H3 + CO', [3.000000e+13, 0.0, 0.0]) +## R133 +# +## Reaction 133 +#reaction('CH2(S) + N2 <=> CH2 + N2', [1.500000e+13, 0.0, 600.0]) +## R134 +# +## Reaction 134 +#reaction('CH2(S) + O2 <=> H + OH + CO', [2.800000e+13, 0.0, 0.0]) +## R135 +# +## Reaction 135 +#reaction('CH2(S) + O2 <=> CO + H2O', [1.200000e+13, 0.0, 0.0]) +## R136 +# +## Reaction 136 +#reaction('CH2(S) + H2 <=> CH3 + H', [7.000000e+13, 0.0, 0.0]) +## R137 +# +## Reaction 137 +#falloff_reaction('CH2(S) + H2O (+ M) <=> CH3OH (+ M)', +# kf=[4.820000e+17, -1.16, 1145.0], +# kf0=[1.880000e+38, -6.36, 5040.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.6027, T3=208.0, T1=3922.0, T2=10180.0)) +## R138 +# +## Reaction 138 +#reaction('CH2(S) + H2O <=> CH2 + H2O', [3.000000e+13, 0.0, 0.0]) +## R139 +# +## Reaction 139 +#reaction('CH2(S) + CH3 <=> H + C2H4', [1.200000e+13, 0.0, -570.0]) +## R140 +# +## Reaction 140 +#reaction('CH2(S) + CH4 <=> 2 CH3', [1.600000e+13, 0.0, -570.0]) +## R141 +# +## Reaction 141 +#reaction('CH2(S) + CO <=> CH2 + CO', [9.000000e+12, 0.0, 0.0]) +## R142 +# +## Reaction 142 +#reaction('CH2(S) + CO2 <=> CH2 + CO2', [7.000000e+12, 0.0, 0.0]) +## R143 +# +## Reaction 143 +#reaction('CH2(S) + CO2 <=> CO + CH2O', [1.400000e+13, 0.0, 0.0]) +## R144 +# +## Reaction 144 +#reaction('CH2(S) + C2H6 <=> CH3 + C2H5', [4.000000e+13, 0.0, -550.0]) +## R145 +# +## Reaction 145 +#reaction('CH3 + O2 <=> O + CH3O', [3.560000e+13, 0.0, 30480.0]) +## R146 +# +## Reaction 146 +#reaction('CH3 + O2 <=> OH + CH2O', [2.310000e+12, 0.0, 20315.0]) +## R147 +# +## Reaction 147 +#reaction('CH3 + H2O2 <=> HO2 + CH4', [2.450000e+04, 2.47, 5180.0]) +## R148 +# +## Reaction 148 +#falloff_reaction('2 CH3 (+ M) <=> C2H6 (+ M)', +# kf=[6.770000e+16, -1.18, 654.0], +# kf0=[3.400000e+41, -7.03, 2762.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.619, T3=73.2, T1=1180.0, T2=9999.0)) +## R149 +# +## Reaction 149 +#reaction('2 CH3 <=> H + C2H5', [6.840000e+12, 0.1, 10600.0]) +## R150 +# +## Reaction 150 +#reaction('CH3 + HCO <=> CH4 + CO', [2.648000e+13, 0.0, 0.0]) +## R151 +# +## Reaction 151 +#reaction('CH3 + CH2O <=> HCO + CH4', [3.320000e+03, 2.81, 5860.0]) +## R152 +# +## Reaction 152 +#reaction('CH3 + CH3OH <=> CH2OH + CH4', [3.000000e+07, 1.5, 9940.0]) +## R153 +# +## Reaction 153 +#reaction('CH3 + CH3OH <=> CH3O + CH4', [1.000000e+07, 1.5, 9940.0]) +## R154 +# +## Reaction 154 +#reaction('CH3 + C2H4 <=> C2H3 + CH4', [2.270000e+05, 2.0, 9200.0]) +## R155 +# +## Reaction 155 +#reaction('CH3 + C2H6 <=> C2H5 + CH4', [6.140000e+06, 1.74, 10450.0]) +## R156 +# +## Reaction 156 +#reaction('HCO + H2O <=> H + CO + H2O', [1.500000e+18, -1.0, 17000.0]) +## R157 +# +## Reaction 157 +#three_body_reaction('HCO + M <=> H + CO + M', [1.870000e+17, -1.0, 17000.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:0.0 CH4:2.0 C2H6:3.0') +## R158 +# +## Reaction 158 +#reaction('HCO + O2 <=> HO2 + CO', [1.345000e+13, 0.0, 400.0]) +## R159 +# +## Reaction 159 +#reaction('CH2OH + O2 <=> HO2 + CH2O', [1.800000e+13, 0.0, 900.0]) +## R160 +# +## Reaction 160 +#reaction('CH3O + O2 <=> HO2 + CH2O', [4.280000e-13, 7.6, -3530.0]) +## R161 +# +## Reaction 161 +#reaction('C2H3 + O2 <=> HCO + CH2O', [4.580000e+16, -1.39, 1015.0]) +## R162 +# +## Reaction 162 +#falloff_reaction('C2H4 (+ M) <=> H2 + C2H2 (+ M)', +# kf=[8.000000e+12, 0.44, 86770.0], +# kf0=[1.580000e+51, -9.3, 97800.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.7345, T3=180.0, T1=1035.0, T2=5417.0)) +## R163 +# +## Reaction 163 +#reaction('C2H5 + O2 <=> HO2 + C2H4', [8.400000e+11, 0.0, 3875.0]) +## R164 +# +## Reaction 164 +#reaction('HCCO + O2 <=> OH + 2 CO', [3.200000e+12, 0.0, 854.0]) +## R165 +# +## Reaction 165 +## reaction('2 HCCO <=> 2 CO + C2H2', [1.000000e+13, 0.0, 0.0]) +## R166 +# +## Reaction 166 +#reaction('O + CH3 => H + H2 + CO', [3.370000e+13, 0.0, 0.0]) +## R167 +# +## Reaction 167 +#reaction('O + C2H4 <=> H + CH2CHO', [6.700000e+06, 1.83, 220.0]) +## R168 +# +## Reaction 168 +#reaction('OH + HO2 <=> O2 + H2O', [5.000000e+15, 0.0, 17330.0], +# options='duplicate') +## R169 +# +## Reaction 169 +#reaction('OH + CH3 => H2 + CH2O', [8.000000e+09, 0.5, -1755.0]) +## R170 +# +## Reaction 170 +#falloff_reaction('CH + H2 (+ M) <=> CH3 (+ M)', +# kf=[1.970000e+12, 0.43, -370.0], +# kf0=[4.820000e+25, -2.8, 590.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.578, T3=122.0, T1=2535.0, T2=9365.0)) +## R171 +# +## Reaction 171 +#reaction('CH2 + O2 => 2 H + CO2', [5.800000e+12, 0.0, 1500.0]) +## R172 +# +## Reaction 172 +#reaction('CH2 + O2 <=> O + CH2O', [2.400000e+12, 0.0, 1500.0]) +## R173 +# +## Reaction 173 +## reaction('CH2 + CH2 => 2 H + C2H2', [2.000000e+14, 0.0, 10989.0]) +## R174 +# +## Reaction 174 +#reaction('CH2(S) + H2O => H2 + CH2O', [6.820000e+10, 0.25, -935.0]) +## R175 +# +## Reaction 175 +#reaction('C2H3 + O2 <=> O + CH2CHO', [3.030000e+11, 0.29, 11.0]) +## R176 +# +## Reaction 176 +#reaction('C2H3 + O2 <=> HO2 + C2H2', [1.337000e+06, 1.61, -384.0]) +## R177 +# +## Reaction 177 +#falloff_reaction('H + CH2CO (+ M) <=> CH2CHO (+ M)', +# kf=[4.865000e+11, 0.422, -1755.0], +# kf0=[1.012000e+42, -7.63, 3854.0], +# efficiencies='CO2:2.0 CO:1.5 H2:2.0 H2O:6.0 CH4:2.0 C2H6:3.0', +# falloff=Troe(A=0.465, T3=201.0, T1=1773.0, T2=5333.0)) +## R178 +# +## Reaction 178 +#reaction('O + CH2CHO => H + CH2 + CO2', [1.500000e+14, 0.0, 0.0]) +## R179 +# +## Reaction 179 +#reaction('O2 + CH2CHO => OH + CO + CH2O', [1.810000e+10, 0.0, 0.0]) +## R180 +# +## Reaction 180 +#reaction('O2 + CH2CHO => OH + 2 HCO', [2.350000e+10, 0.0, 0.0]) +## R181 +# +## Reaction 181 +#reaction('H + CH2CHO <=> CH3 + HCO', [2.200000e+13, 0.0, 0.0]) +## R182 +# +## Reaction 182 +#reaction('H + CH2CHO <=> CH2CO + H2', [1.100000e+13, 0.0, 0.0]) +## R183 +# +## Reaction 183 +#reaction('OH + CH2CHO <=> H2O + CH2CO', [1.200000e+13, 0.0, 0.0]) +## R184 +# +## Reaction 184 +## reaction('OH + CH2CHO <=> HCO + CH2OH', [3.010000e+13, 0.0, 0.0]) +# \ No newline at end of file diff --git a/samples/python/AVBP/inputs/Lu_ARC.f90 b/samples/python/AVBP/inputs/Lu_ARC.f90 new file mode 100755 index 00000000000..355e516069d --- /dev/null +++ b/samples/python/AVBP/inputs/Lu_ARC.f90 @@ -0,0 +1,2317 @@ +! +! A 15-step reduced mechanism based on GRI3.0 +! +! by Tianfeng Lu +! Email: tlu@engr.uconn.edu +! +! Reference: +! Tianfeng Lu and Chung K. Law, +! "A criterion based on computational singular perturbation +! for the identification of quasi steady state species: +! A reduced mechanism for methane oxidation with NO chemistry," +! Combustion and Flame, Vol.154 No.4 pp.761�774, 2008. +! +! SUBROUTINE CKWYP (P, T, Y, ICKWRK, RCKWRK, WDOT) + SUBROUTINE customkinetics(P, T, Y, WDOT) + IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! +! DIMENSION ICKWRK(*), RCKWRK(*), WDOT(*), Y(*) + PARAMETER (RU=8.314510D7, PATM=1.01325D6, SMALL = 1.D-200) + DIMENSION WDOT(19), Y(19) + DIMENSION TN(5), ROP(184), CTB(184) + DIMENSION RF(184), RB(184), RKLOW(22), XQ(11), C(19) + DIMENSION EQK(184), SMH(30), EG(30) + + ! Correction for units compatibility in Cantera + P = P*10.D0 +! +! CALL YTCP(P, T, Y, C) +! CALL RATT(T, RF, RB, RKLOW) +! CALL RATX(T, C, RF, RB, RKLOW) +! CALL QSSA(RF, RB, XQ) +! CALL RDOT(RF, RB, WDOT) +! END +! +! ----------------------------------------------------------------------! +! +! SUBROUTINE YTCP (P, T, Y, C) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION Y(*), C(*) +! +! +! convert Y to ! + + C(1) = Y(1)*4.96046521D-1 + C(2) = Y(2)*9.92093043D-1 + C(3) = Y(3)*6.25023433D-2 + C(4) = Y(4)*3.12511716D-2 + C(5) = Y(5)*5.87980383D-2 + C(6) = Y(6)*5.55082499D-2 + C(7) = Y(7)*3.02968146D-2 + C(8) = Y(8)*2.93990192D-2 + C(9) = Y(9)*6.65112065D-2 + C(10) = Y(10)*6.23323639D-2 + C(11) = Y(11)*3.57008335D-2 + C(12) = Y(12)*2.27221341D-2 + C(13) = Y(13)*3.33039255D-2 + C(14) = Y(14)*3.12086189D-2 + C(15) = Y(15)*3.84050525D-2 + C(16) = Y(16)*3.56453112D-2 + C(17) = Y(17)*3.32556033D-2 + C(18) = Y(18)*2.37882046D-2 + C(19) = Y(19)*3.56972032D-2 +! + SUM = 0.0 + DO K = 1, 19 + SUM = SUM + C(K) + ENDDO + SUM = P/(SUM*T*8.314510D7) +! + DO K = 1, 19 + C(K) = MAX(C(K),SMALL) * SUM + ENDDO +! END +! +! ----------------------------------------------------------------------! +! +! +! forward reaction rates +! +! SUBROUTINE RATT (T, RF, RB, RKLOW) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION RF(*), RB(*), RKLOW(*), EQK(184), SMH(30), EG(30) +! + ALOGT = LOG(T) + TI = 1.0D0/T + TI2 = TI*TI +! + RF(1) = 1.2D17*TI + RF(2) = 5.D17*TI + RF(3) = EXP(1.05635949D1 +2.7D0*ALOGT -3.15013634D3*TI) + RF(4) = 2.D13 + RF(5) = EXP(1.60803938D1 +2.D0*ALOGT -2.01286667D3*TI) + RF(6) = 5.7D13 + RF(7) = 8.D13 + RF(8) = 1.5D13 + RF(9) = 1.5D13 + RF(10) = 5.06D13 + RF(11) = EXP(2.07430685D1 +1.5D0*ALOGT -4.32766334D3*TI) + RF(12) = EXP(2.36136376D1 -1.20017175D3*TI) + RF(13) = 3.D13 + RF(14) = 3.D13 + RF(15) = EXP(3.12945828D1 -1.781387D3*TI) + RF(16) = 1.D13 + RF(17) = 1.D13 + RF(18) = EXP(1.28687606D1 +2.5D0*ALOGT -1.55997167D3*TI) + RF(19) = EXP(1.17752897D1 +2.5D0*ALOGT -2.51608334D3*TI) + TMP = EXP(2.D0*ALOGT -9.56111669D2*TI ) + RF(20) = 1.35D7 * TMP + RF(21) = 6.94D6 * TMP + RF(22) = 3.D13 + TMP = EXP(1.83D0*ALOGT -1.10707667D2*TI ) + RF(23) = 1.25D7 * TMP + RF(167) = 6.7D6 * TMP + RF(24) = 2.24D13 + RF(25) = EXP(1.83130955D1 +1.92D0*ALOGT -2.86330284D3*TI) + RF(26) = 1.D14 + TMP = EXP(-4.02573334D3*TI) + RF(27) = 1.D13 * TMP + RF(76) = 5.D13 * TMP + RF(28) = EXP(2.81906369D1 -6.79342501D2*TI) + RF(29) = EXP(2.85473118D1 -2.40537567D4*TI) + RF(30) = EXP(3.22361913D1 -2.01286667D4*TI) + RF(31) = EXP(4.24761511D1 -8.6D-1*ALOGT) + TMP = EXP(-1.24D0*ALOGT) + RF(32) = 2.08D19 * TMP + RF(34) = 2.6D19 * TMP + RF(33) = EXP(4.38677883D1 -7.6D-1*ALOGT) + RF(35) = EXP(3.78159211D1 -6.707D-1*ALOGT -8.57531523D3*TI) + RF(36) = 1.D18*TI + RF(37) = EXP(3.90385861D1 -6.D-1*ALOGT) + RF(38) = EXP(4.55408762D1 -1.25D0*ALOGT) + RF(39) = 5.5D20*TI2 + RF(40) = 2.2D22*TI2 + RF(41) = EXP(2.90097872D1 -3.37658384D2*TI) + RF(42) = EXP(3.14332293D1 -5.37435401D2*TI) + RF(43) = EXP(3.20618379D1 -3.19542584D2*TI) + RF(44) = EXP(1.6308716D1 +2.D0*ALOGT -2.61672667D3*TI) + RF(45) = EXP(2.99336062D1 -1.81158D3*TI) + RF(46) = 1.65D14 + RF(47) = 6.D14 + RF(48) = 3.D13 + RF(49) = EXP(3.71706652D1 -5.34D-1*ALOGT -2.69724134D2*TI) + RF(50) = EXP(2.03077504D1 +1.62D0*ALOGT -5.45486868D3*TI) + RF(51) = EXP(2.77171988D1 +4.8D-1*ALOGT +1.30836334D2*TI) + RF(52) = 7.34D13 + RF(53) = EXP(2.7014835D1 +4.54D-1*ALOGT -1.81158D3*TI) + RF(54) = EXP(2.7014835D1 +4.54D-1*ALOGT -1.30836334D3*TI) + RF(55) = EXP(1.78655549D1 +1.9D0*ALOGT -1.3798201D3*TI) + RF(56) = EXP(2.76845619D1 +5.D-1*ALOGT -4.32766334D1*TI) + RF(57) = 2.D13 + RF(58) = EXP(2.58292113D1 +6.5D-1*ALOGT +1.42913534D2*TI) + RF(59) = EXP(3.11214496D1 -9.D-2*ALOGT -3.06962167D2*TI) + RF(60) = EXP(2.85189124D1 +5.15D-1*ALOGT -2.51608334D1*TI) + RF(61) = EXP(1.7541204D1 +1.63D0*ALOGT -9.68188869D2*TI) + RF(62) = 2.D13 + RF(63) = EXP(2.80364862D1 +5.D-1*ALOGT +5.53538334D1*TI) + RF(64) = EXP(3.31993656D1 -2.3D-1*ALOGT -5.38441834D2*TI) + TMP = EXP(2.1D0*ALOGT -2.45066517D3*TI ) + RF(65) = 1.7D7 * TMP + RF(66) = 4.2D6 * TMP + RF(67) = EXP(2.93537877D1 -1.20772D3*TI) + RF(68) = EXP(2.94360258D1 +2.7D-1*ALOGT -1.40900667D2*TI) + RF(69) = 3.D13 + RF(70) = EXP(2.7014835D1 +4.54D-1*ALOGT -9.15854335D2*TI) + RF(71) = EXP(1.4096923D1 +2.53D0*ALOGT -6.15937201D3*TI) + RF(72) = EXP(4.07945264D1 -9.9D-1*ALOGT -7.95082335D2*TI) + RF(73) = 2.D12 + RF(74) = EXP(1.85604427D1 +1.9D0*ALOGT -3.78922151D3*TI) + RF(75) = 1.D14 + RF(77) = EXP(3.00558238D1 -1.72502674D3*TI) + RF(78) = EXP(1.75767107D1 +1.5D0*ALOGT -4.00560467D4*TI) + RF(79) = EXP(1.9190789D1 +1.51D0*ALOGT -1.72603317D3*TI) + RF(80) = EXP(3.19350862D1 -3.7D-1*ALOGT) + RF(81) = EXP(1.0482906D1 +2.4D0*ALOGT +1.06178717D3*TI) + RF(82) = EXP(3.03051698D1 +2.51608334D2*TI) + RF(83) = EXP(2.83241683D1 -2.14873517D2*TI) + RF(84) = EXP(4.19771599D1 -1.47996022D4*TI) + RF(85) = 5.D13 + RF(86) = 3.D13 + RF(87) = 2.D13 + RF(88) = EXP(1.62403133D1 +2.D0*ALOGT -1.50965D3*TI) + RF(89) = 3.D13 + RF(90) = EXP(4.24725733D1 -1.43D0*ALOGT -6.69278168D2*TI) + RF(91) = EXP(1.78408622D1 +1.6D0*ALOGT -2.72743434D3*TI) + RF(92) = EXP(4.10064751D1 -1.34D0*ALOGT -7.13058018D2*TI) + RF(93) = EXP(1.84206807D1 +1.6D0*ALOGT -1.570036D3*TI) + RF(94) = EXP(1.76783433D1 +1.228D0*ALOGT -3.52251667D1*TI) + RF(95) = 5.D13 + RF(96) = EXP(2.19558261D1 +1.18D0*ALOGT +2.2493785D2*TI) + RF(97) = 5.D12 + RF(98) = 5.D12 + RF(99) = EXP(1.41801537D1 +2.D0*ALOGT +4.22702001D2*TI) + RF(100) = EXP(1.56560602D1 +2.D0*ALOGT -7.54825001D2*TI) + RF(101) = EXP(-8.4310155D0 +4.5D0*ALOGT +5.03216668D2*TI) + RF(102) = EXP(-7.6354939D0 +4.D0*ALOGT +1.00643334D3*TI) + RF(103) = 5.D12 + RF(104) = EXP(1.50964444D1 +2.D0*ALOGT -1.25804167D3*TI) + RF(105) = EXP(1.50796373D1 +2.12D0*ALOGT -4.37798501D2*TI) + RF(106) = EXP(2.96459241D1 -1.00643334D3*TI) + RF(107) = EXP(2.55908003D1 +8.20243168D2*TI) + RF(108) = EXP(3.36712758D1 -6.03860001D3*TI) + RF(109) = 2.D13 + RF(110) = 1.D12 + RF(111) = 3.78D13 + RF(112) = EXP(3.26416564D1 -1.18759134D4*TI) + RF(113) = EXP(1.55382772D1 +2.D0*ALOGT -6.03860001D3*TI) + RF(114) = EXP(3.16914641D1 -2.89852801D2*TI) + RF(115) = 5.D13 + RF(116) = 6.71D13 + RF(117) = EXP(3.23131523D1 -1.56500384D3*TI) + RF(118) = EXP(2.93732401D1 +3.79928584D2*TI) + RF(119) = 4.D13 + RF(120) = 3.D13 + RF(121) = 6.D13 + RF(122) = 5.D13 + RF(123) = EXP(3.28780452D1 -7.94679762D3*TI) + RF(124) = EXP(3.21806786D1 +2.59156584D2*TI) + RF(125) = 5.D13 + TMP = EXP(-7.54825001D2*TI) + RF(126) = 5.D12 * TMP + RF(171) = 5.8D12 * TMP + RF(172) = 2.4D12 * TMP + RF(127) = EXP(1.31223634D1 +2.D0*ALOGT -3.63825651D3*TI) + RF(128) = EXP(3.500878D1 -6.01041988D3*TI) + RF(129) = 4.D13 + RF(130) = EXP(1.47156719D1 +2.D0*ALOGT -4.16160184D3*TI) + RF(131) = EXP(2.74203001D1 +5.D-1*ALOGT -2.26950717D3*TI) + RF(132) = 3.D13 + RF(133) = EXP(3.03390713D1 -3.01930001D2*TI) + RF(134) = 2.8D13 + RF(135) = 1.2D13 + RF(136) = 7.D13 + RF(137) = EXP(4.07167205D1 -1.16D0*ALOGT -5.76183084D2*TI) + RF(138) = 3.D13 + TMP = EXP(2.86833501D2*TI) + RF(139) = 1.2D13 * TMP + RF(140) = 1.6D13 * TMP + RF(141) = 9.D12 + RF(142) = 7.D12 + RF(143) = 1.4D13 + RF(144) = EXP(3.13199006D1 +2.76769167D2*TI) + RF(145) = EXP(3.12033668D1 -1.5338044D4*TI) + RF(146) = EXP(2.84682686D1 -1.02228466D4*TI) + RF(147) = EXP(1.01064284D1 +2.47D0*ALOGT -2.60666234D3*TI) + RF(148) = EXP(3.87538626D1 -1.18D0*ALOGT -3.29103701D2*TI) + RF(149) = EXP(2.95538088D1 +1.D-1*ALOGT -5.33409668D3*TI) + RF(150) = 2.648D13 + RF(151) = EXP(8.10772006D0 +2.81D0*ALOGT -2.94884967D3*TI) + TMP = EXP(1.5D0*ALOGT -5.00197368D3*TI) + RF(152) = 3.D7 * TMP + RF(153) = 1.D7 * TMP + RF(154) = EXP(1.23327053D1 +2.D0*ALOGT -4.62959334D3*TI) + RF(155) = EXP(1.56303353D1 +1.74D0*ALOGT -5.25861418D3*TI) + TMP = EXP(-1.D0*ALOGT -8.55468335D3*TI) + RF(156) = 1.5D18 * TMP + RF(157) = 1.87D17 * TMP + RF(158) = EXP(3.02300002D1 -2.01286667D2*TI) + RF(159) = EXP(3.05213929D1 -4.52895001D2*TI) + RF(160) = EXP(-2.84796532D1 +7.6D0*ALOGT +1.77635484D3*TI) + RF(161) = EXP(3.83630605D1 -1.39D0*ALOGT -5.10764918D2*TI) + RF(162) = EXP(2.97104627D1 +4.4D-1*ALOGT -4.36641103D4*TI) + RF(163) = EXP(2.74566677D1 -1.94996459D3*TI) + RF(164) = EXP(2.87941719D1 -4.29747034D2*TI) + RF(165) = 1.D13 + RF(166) = 3.37D13 + RF(168) = EXP(3.61482143D1 -8.72074485D3*TI) + RF(169) = EXP(2.28027074D1 +5.D-1*ALOGT +8.83145252D2*TI) + RF(170) = EXP(2.83090547D1 +4.3D-1*ALOGT +1.86190167D2*TI) + RF(173) = EXP(3.29293385D1 -5.52984796D3*TI) + RF(174) = EXP(2.49457104D1 +2.5D-1*ALOGT +4.70507584D2*TI) + RF(175) = EXP(2.64369986D1 +2.9D-1*ALOGT -5.53538334D0*TI) + RF(176) = EXP(1.41059389D1 +1.61D0*ALOGT +1.932352D2*TI) + RF(177) = EXP(2.69105027D1 +4.22D-1*ALOGT +8.83145252D2*TI) + RF(178) = 1.5D14 + RF(179) = 1.81D10 + RF(180) = 2.35D10 + RF(181) = 2.2D13 + RF(182) = 1.1D13 + RF(183) = 1.2D13 + RF(184) = 3.01D13 +! +! +! thermal data +! +! + TLOG = LOG(T) + TI = 1.0D0/T + TN(1) = TLOG - 1.0 + TN(2) = T + TN(3) = TN(2)*T + TN(4) = TN(3)*T + TN(5) = TN(4)*T +! + IF (T .GT. 1.D3) THEN +! + SMH(1) = -3.20502331D+00 + 9.50158922D+02*TI & + + 3.33727920D+00*TN(1) - 2.47012365D-05*TN(2) & + + 8.32427963D-08*TN(3) - 1.49638662D-11*TN(4) & + + 1.00127688D-15*TN(5) + SMH(2) = -4.46682914D-01 - 2.54736599D+04*TI & + + 2.50000001D+00*TN(1) - 1.15421486D-11*TN(2) & + + 2.69269913D-15*TN(3) - 3.94596029D-19*TN(4) & + + 2.49098679D-23*TN(5) + SMH(3) = 4.78433864D+00 - 2.92175791D+04*TI & + + 2.56942078D+00*TN(1) - 4.29870569D-05*TN(2) & + + 6.99140982D-09*TN(3) - 8.34814992D-13*TN(4) & + + 6.14168455D-17*TN(5) + SMH(4) = 5.45323129D+00 + 1.08845772D+03*TI & + + 3.28253784D+00*TN(1) + 7.41543770D-04*TN(2) & + - 1.26327778D-07*TN(3) + 1.74558796D-11*TN(4) & + - 1.08358897D-15*TN(5) + SMH(5) = 4.47669610D+00 - 3.85865700D+03*TI & + + 3.09288767D+00*TN(1) + 2.74214858D-04*TN(2) & + + 2.10842047D-08*TN(3) - 7.32884630D-12*TN(4) & + + 5.87061880D-16*TN(5) + SMH(6) = 4.96677010D+00 + 3.00042971D+04*TI & + + 3.03399249D+00*TN(1) + 1.08845902D-03*TN(2) & + - 2.73454197D-08*TN(3) - 8.08683225D-12*TN(4) & + + 8.41004960D-16*TN(5) + SMH(7) = 3.78510215D+00 - 1.11856713D+02*TI & + + 4.01721090D+00*TN(1) + 1.11991007D-03*TN(2) & + - 1.05609692D-07*TN(3) + 9.52053083D-12*TN(4) & + - 5.39542675D-16*TN(5) + SMH(8) = 2.91615662D+00 + 1.78617877D+04*TI & + + 4.16500285D+00*TN(1) + 2.45415847D-03*TN(2) & + - 3.16898708D-07*TN(3) + 3.09321655D-11*TN(4) & + - 1.43954153D-15*TN(5) + SMH(9) = 4.80150373D+00 - 8.54512953D+04*TI & + + 2.49266888D+00*TN(1) + 2.39944642D-05*TN(2) & + - 1.20722503D-08*TN(3) + 3.11909191D-12*TN(4) & + - 2.43638946D-16*TN(5) + SMH(10) = 5.48497999D+00 - 7.10124364D+04*TI & + + 2.87846473D+00*TN(1) + 4.85456841D-04*TN(2) & + + 2.40742758D-08*TN(3) - 1.08906541D-11*TN(4) & + + 8.80396915D-16*TN(5) + SMH(11) = 6.17119324D+00 - 4.62636040D+04*TI & + + 2.87410113D+00*TN(1) + 1.82819646D-03*TN(2) & + - 2.34824328D-07*TN(3) + 2.16816291D-11*TN(4) & + - 9.38637835D-16*TN(5) + SMH(12) = 8.62650169D+00 - 5.09259997D+04*TI & + + 2.29203842D+00*TN(1) + 2.32794319D-03*TN(2) & + - 3.35319912D-07*TN(3) + 3.48255000D-11*TN(4) & + - 1.69858183D-15*TN(5) + SMH(13) = 8.48007179D+00 - 1.67755843D+04*TI & + + 2.28571772D+00*TN(1) + 3.61995018D-03*TN(2) & + - 4.97857247D-07*TN(3) + 4.96403870D-11*TN(4) & + - 2.33577197D-15*TN(5) + SMH(14) = 1.84373180D+01 + 9.46834459D+03*TI & + + 7.48514950D-02*TN(1) + 6.69547335D-03*TN(2) & + - 9.55476348D-07*TN(3) + 1.01910446D-10*TN(4) & + - 5.09076150D-15*TN(5) + SMH(15) = 7.81868772D+00 + 1.41518724D+04*TI & + + 2.71518561D+00*TN(1) + 1.03126372D-03*TN(2) & + - 1.66470962D-07*TN(3) + 1.91710840D-11*TN(4) & + - 1.01823858D-15*TN(5) + SMH(16) = 2.27163806D+00 + 4.87591660D+04*TI & + + 3.85746029D+00*TN(1) + 2.20718513D-03*TN(2) & + - 3.69135673D-07*TN(3) + 4.36241823D-11*TN(4) & + - 2.36042082D-15*TN(5) + SMH(17) = 9.79834492D+00 - 4.01191815D+03*TI & + + 2.77217438D+00*TN(1) + 2.47847763D-03*TN(2) & + - 4.14076022D-07*TN(3) + 4.90968148D-11*TN(4) & + - 2.66754356D-15*TN(5) + SMH(18) = 1.36563230D+01 + 1.39958323D+04*TI & + + 1.76069008D+00*TN(1) + 4.60000041D-03*TN(2) & + - 7.37098022D-07*TN(3) + 8.38676767D-11*TN(4) & + - 4.41927820D-15*TN(5) + SMH(19) = 5.81043215D+00 + 3.24250627D+03*TI & + + 3.69266569D+00*TN(1) + 4.32288399D-03*TN(2) & + - 6.25168533D-07*TN(3) + 6.56028863D-11*TN(4) & + - 3.24277101D-15*TN(5) + SMH(20) = 2.92957500D+00 - 1.27832520D+02*TI & + + 3.77079900D+00*TN(1) + 3.93574850D-03*TN(2) & + - 4.42730667D-07*TN(3) + 3.28702583D-11*TN(4) & + - 1.05630800D-15*TN(5) + + SMH(21) = 1.45023623D+01 + 2.53748747D+04*TI & + + 1.78970791D+00*TN(1) + 7.04691460D-03*TN(2) & + - 1.06083472D-06*TN(3) + 1.15142571D-10*TN(4) & + - 5.85301100D-15*TN(5) + SMH(22) = -1.23028121D+00 - 2.59359992D+04*TI & + + 4.14756964D+00*TN(1) + 2.98083332D-03*TN(2) & + - 3.95491420D-07*TN(3) + 3.89510143D-11*TN(4) & + - 1.80617607D-15*TN(5) + SMH(23) = 7.78732378D+00 - 3.46128739D+04*TI & + + 3.01672400D+00*TN(1) + 5.16511460D-03*TN(2) & + - 7.80137248D-07*TN(3) + 8.48027400D-11*TN(4) & + - 4.31303520D-15*TN(5) + SMH(24) = 1.03053693D+01 - 4.93988614D+03*TI & + + 2.03611116D+00*TN(1) + 7.32270755D-03*TN(2) & + - 1.11846319D-06*TN(3) + 1.22685769D-10*TN(4) & + - 6.28530305D-15*TN(5) + SMH(25) = 1.34624343D+01 - 1.28575200D+04*TI & + + 1.95465642D+00*TN(1) + 8.69863610D-03*TN(2) & + - 1.33034445D-06*TN(3) + 1.46014741D-10*TN(4) & + - 7.48207880D-15*TN(5) + SMH(26) = 1.51156107D+01 + 1.14263932D+04*TI & + + 1.07188150D+00*TN(1) + 1.08426339D-02*TN(2) & + - 1.67093445D-06*TN(3) + 1.84510001D-10*TN(4) & + - 9.50014450D-15*TN(5) + SMH(27) = -3.93025950D+00 - 1.93272150D+04*TI & + + 5.62820580D+00*TN(1) + 2.04267005D-03*TN(2) & + - 2.65575783D-07*TN(3) + 2.38550433D-11*TN(4) & + - 9.70391600D-16*TN(5) + SMH(28) = 6.32247205D-01 + 7.55105311D+03*TI & + + 4.51129732D+00*TN(1) + 4.50179872D-03*TN(2) & + - 6.94899392D-07*TN(3) + 7.69454902D-11*TN(4) & + - 3.97419100D-15*TN(5) + SMH(29) = -5.04525100D+00 - 4.90321800D+02*TI & + + 5.97567000D+00*TN(1) + 4.06529550D-03*TN(2) & + - 4.57270667D-07*TN(3) + 3.39192000D-11*TN(4) & + - 1.08800850D-15*TN(5) +! + ELSE +! + SMH(1) = 6.83010238D-01 + 9.17935173D+02*TI & + + 2.34433112D+00*TN(1) + 3.99026037D-03*TN(2) & + - 3.24635850D-06*TN(3) + 1.67976745D-09*TN(4) & + - 3.68805881D-13*TN(5) + SMH(2) = -4.46682853D-01 - 2.54736599D+04*TI & + + 2.50000000D+00*TN(1) + 3.52666409D-13*TN(2) & + - 3.32653273D-16*TN(3) + 1.91734693D-19*TN(4) & + - 4.63866166D-23*TN(5) + SMH(3) = 2.05193346D+00 - 2.91222592D+04*TI & + + 3.16826710D+00*TN(1) - 1.63965942D-03*TN(2) & + + 1.10717733D-06*TN(3) - 5.10672187D-10*TN(4) & + + 1.05632986D-13*TN(5) + SMH(4) = 3.65767573D+00 + 1.06394356D+03*TI & + + 3.78245636D+00*TN(1) - 1.49836708D-03*TN(2) & + + 1.64121700D-06*TN(3) - 8.06774591D-10*TN(4) & + + 1.62186419D-13*TN(5) + SMH(5) = -1.03925458D-01 - 3.61508056D+03*TI & + + 3.99201543D+00*TN(1) - 1.20065876D-03*TN(2) & + + 7.69656402D-07*TN(3) - 3.23427778D-10*TN(4) & + + 6.82057350D-14*TN(5) + SMH(6) = -8.49032208D-01 + 3.02937267D+04*TI & + + 4.19864056D+00*TN(1) - 1.01821705D-03*TN(2) & + + 1.08673369D-06*TN(3) - 4.57330885D-10*TN(4) & + + 8.85989085D-14*TN(5) + SMH(7) = 3.71666245D+00 - 2.94808040D+02*TI & + + 4.30179801D+00*TN(1) - 2.37456025D-03*TN(2) & + + 3.52638152D-06*TN(3) - 2.02303245D-09*TN(4) & + + 4.64612562D-13*TN(5) + SMH(8) = 3.43505074D+00 + 1.77025821D+04*TI & + + 4.27611269D+00*TN(1) - 2.71411208D-04*TN(2) & + + 2.78892835D-06*TN(3) - 1.79809011D-09*TN(4) & + + 4.31227182D-13*TN(5) + SMH(9) = 4.53130848D+00 - 8.54438832D+04*TI & + + 2.55423955D+00*TN(1) - 1.60768862D-04*TN(2) & + + 1.22298708D-07*TN(3) - 6.10195741D-11*TN(4) & + + 1.33260723D-14*TN(5) + SMH(10) = 2.08401108D+00 - 7.07972934D+04*TI & + + 3.48981665D+00*TN(1) + 1.61917771D-04*TN(2) & + - 2.81498442D-07*TN(3) + 2.63514439D-10*TN(4) & + - 7.03045335D-14*TN(5) + SMH(11) = 1.56253185D+00 - 4.60040401D+04*TI & + + 3.76267867D+00*TN(1) + 4.84436072D-04*TN(2) & + + 4.65816402D-07*TN(3) - 3.20909294D-10*TN(4) & + + 8.43708595D-14*TN(5) + SMH(12) = -7.69118967D-01 - 5.04968163D+04*TI & + + 4.19860411D+00*TN(1) - 1.18330710D-03*TN(2) & + + 1.37216037D-06*TN(3) - 5.57346651D-10*TN(4) & + + 9.71573685D-14*TN(5) + SMH(13) = 1.60456433D+00 - 1.64449988D+04*TI & + + 3.67359040D+00*TN(1) + 1.00547588D-03*TN(2) & + + 9.55036427D-07*TN(3) - 5.72597854D-10*TN(4) & + + 1.27192867D-13*TN(5) + SMH(14) = -4.64130376D+00 + 1.02466476D+04*TI & + + 5.14987613D+00*TN(1) - 6.83548940D-03*TN(2) & + + 8.19667665D-06*TN(3) - 4.03952522D-09*TN(4) & + + 8.33469780D-13*TN(5) + SMH(15) = 3.50840928D+00 + 1.43440860D+04*TI & + + 3.57953347D+00*TN(1) - 3.05176840D-04*TN(2) & + + 1.69469055D-07*TN(3) + 7.55838237D-11*TN(4) & + - 4.52212249D-14*TN(5) + SMH(16) = 9.90105222D+00 + 4.83719697D+04*TI & + + 2.35677352D+00*TN(1) + 4.49229839D-03*TN(2) & + - 1.18726045D-06*TN(3) + 2.04932518D-10*TN(4) & + - 7.18497740D-15*TN(5) + SMH(17) = 3.39437243D+00 - 3.83956496D+03*TI & + + 4.22118584D+00*TN(1) - 1.62196266D-03*TN(2) & + + 2.29665743D-06*TN(3) - 1.10953411D-09*TN(4) & + + 2.16884433D-13*TN(5) + SMH(18) = 6.02812900D-01 + 1.43089567D+04*TI & + + 4.79372315D+00*TN(1) - 4.95416685D-03*TN(2) & + + 6.22033347D-06*TN(3) - 3.16071051D-09*TN(4) & + + 6.58863260D-13*TN(5) + SMH(19) = 5.47302243D+00 + 3.19391367D+03*TI & + + 3.86388918D+00*TN(1) + 2.79836152D-03*TN(2) & + + 9.88786318D-07*TN(3) - 8.71100100D-10*TN(4) & + + 2.18483639D-13*TN(5) + SMH(20) = 1.31521770D+01 - 9.78601100D+02*TI & + + 2.10620400D+00*TN(1) + 3.60829750D-03*TN(2) & + + 8.89745333D-07*TN(3) - 6.14803000D-10*TN(4) & + + 1.03780500D-13*TN(5) + SMH(21) = -1.50409823D+00 + 2.56427656D+04*TI & + + 5.71539582D+00*TN(1) - 7.61545645D-03*TN(2) & + + 1.08740193D-05*TN(3) - 5.92339074D-09*TN(4) & + + 1.30676349D-12*TN(5) + SMH(22) = 1.39397051D+01 - 2.64289807D+04*TI & + + 8.08681094D-01*TN(1) + 1.16807815D-02*TN(2) & + - 5.91953025D-06*TN(3) + 2.33460364D-09*TN(4) & + - 4.25036487D-13*TN(5) + SMH(23) = 8.51054025D+00 - 3.48598468D+04*TI & + + 3.21246645D+00*TN(1) + 7.57395810D-04*TN(2) & + + 4.32015687D-06*TN(3) - 2.98048206D-09*TN(4) & + + 7.35754365D-13*TN(5) + SMH(24) = 4.09733096D+00 - 5.08977593D+03*TI & + + 3.95920148D+00*TN(1) - 3.78526124D-03*TN(2) & + + 9.51650487D-06*TN(3) - 5.76323961D-09*TN(4) & + + 1.34942187D-12*TN(5) + SMH(25) = 4.70720924D+00 - 1.28416265D+04*TI & + + 4.30646568D+00*TN(1) - 2.09329446D-03*TN(2) & + + 8.28571345D-06*TN(3) - 4.99272172D-09*TN(4) & + + 1.15254502D-12*TN(5) + SMH(26) = 2.66682316D+00 + 1.15222055D+04*TI & + + 4.29142492D+00*TN(1) - 2.75077135D-03*TN(2) & + + 9.99063813D-06*TN(3) - 5.90388571D-09*TN(4) & + + 1.34342886D-12*TN(5) + SMH(27) = 1.24904170D+01 - 2.00594490D+04*TI & + + 2.25172140D+00*TN(1) + 8.82751050D-03*TN(2) & + - 3.95485017D-06*TN(3) + 1.43964658D-09*TN(4) & + - 2.53324055D-13*TN(5) + SMH(28) = 1.22156480D+01 + 7.04291804D+03*TI & + + 2.13583630D+00*TN(1) + 9.05943605D-03*TN(2) & + - 2.89912457D-06*TN(3) + 7.78664640D-10*TN(4) & + - 1.00728807D-13*TN(5) + SMH(29) = 9.55829000D+00 - 1.52147660D+03*TI & + + 3.40906200D+00*TN(1) + 5.36928700D-03*TN(2) & + + 3.15248667D-07*TN(3) - 5.96548583D-10*TN(4) & + + 1.43369250D-13*TN(5) + ENDIF +! CALL RDSMH (T, SMH) +! +! equilibrium constants +! + DO N = 1, 29 + EG(N) = EXP(SMH(N)) + ENDDO +! + PFAC = PATM / (RU*T) + PFAC2 = PFAC*PFAC + PFAC3 = PFAC2*PFAC +! + EQK(1)=EG(4)/EG(3)/EG(3)/PFAC + EQK(2)=EG(5)/EG(2)/EG(3)/PFAC + EQK(3)=EG(2)*EG(5)/EG(1)/EG(3) + EQK(4)=EG(4)*EG(5)/EG(3)/EG(7) + EQK(5)=EG(5)*EG(7)/EG(3)/EG(8) + EQK(6)=EG(2)*EG(15)/EG(3)/EG(10) + EQK(7)=EG(2)*EG(17)/EG(3)/EG(11) + EQK(8)=EG(1)*EG(15)/EG(3)/EG(12) + EQK(9)=EG(2)*EG(17)/EG(3)/EG(12) + EQK(10)=EG(2)*EG(18)/EG(3)/EG(13) + EQK(11)=EG(5)*EG(13)/EG(3)/EG(14) + EQK(12)=EG(16)/EG(3)/EG(15)/PFAC + EQK(13)=EG(5)*EG(15)/EG(3)/EG(17) + EQK(14)=EG(2)*EG(16)/EG(3)/EG(17) + EQK(15)=EG(5)*EG(17)/EG(3)/EG(18) + EQK(16)=EG(5)*EG(18)/EG(3)/EG(19) + EQK(17)=EG(5)*EG(18)/EG(3)/EG(20) + EQK(18)=EG(5)*EG(19)/EG(3)/EG(21) + EQK(19)=EG(5)*EG(20)/EG(3)/EG(21) + EQK(20)=EG(2)*EG(27)/EG(3)/EG(22) + EQK(21)=EG(11)*EG(15)/EG(3)/EG(22) + EQK(22)=EG(2)*EG(28)/EG(3)/EG(23) + EQK(23)=EG(13)*EG(17)/EG(3)/EG(24) + EQK(24)=EG(13)*EG(18)/EG(3)/EG(25) + EQK(25)=EG(5)*EG(25)/EG(3)/EG(26) + EQK(26)=EG(2)*EG(15)*EG(15)/EG(3)/EG(27)*PFAC + EQK(27)=EG(5)*EG(27)/EG(3)/EG(28) + EQK(28)=EG(11)*EG(16)/EG(3)/EG(28) + EQK(29)=EG(3)*EG(16)/EG(4)/EG(15) + EQK(30)=EG(7)*EG(17)/EG(4)/EG(18) + EQK(31)=EG(7)/EG(2)/EG(4)/PFAC + EQK(32)=EQK(31) + EQK(33)=EQK(31) + EQK(34)=EQK(31) + EQK(35)=EG(3)*EG(5)/EG(2)/EG(4) + EQK(36)=EG(1)/EG(2)/EG(2)/PFAC + EQK(37)=EQK(36) + EQK(38)=EQK(36) + EQK(39)=EQK(36) + EQK(40)=EG(6)/EG(2)/EG(5)/PFAC + EQK(41)=EG(3)*EG(6)/EG(2)/EG(7) + EQK(42)=EG(1)*EG(4)/EG(2)/EG(7) + EQK(43)=EG(5)*EG(5)/EG(2)/EG(7) + EQK(44)=EG(1)*EG(7)/EG(2)/EG(8) + EQK(45)=EG(5)*EG(6)/EG(2)/EG(8) + EQK(46)=EG(1)*EG(9)/EG(2)/EG(10) + EQK(47)=EG(13)/EG(2)/EG(11)/PFAC + EQK(48)=EG(1)*EG(10)/EG(2)/EG(12) + EQK(49)=EG(14)/EG(2)/EG(13)/PFAC + EQK(50)=EG(1)*EG(13)/EG(2)/EG(14) + EQK(51)=EG(18)/EG(2)/EG(17)/PFAC + EQK(52)=EG(1)*EG(15)/EG(2)/EG(17) + EQK(53)=EG(19)/EG(2)/EG(18)/PFAC + EQK(54)=EG(20)/EG(2)/EG(18)/PFAC + EQK(55)=EG(1)*EG(17)/EG(2)/EG(18) + EQK(56)=EG(21)/EG(2)/EG(19)/PFAC + EQK(57)=EG(1)*EG(18)/EG(2)/EG(19) + EQK(58)=EG(5)*EG(13)/EG(2)/EG(19) + EQK(59)=EG(6)*EG(12)/EG(2)/EG(19) + EQK(60)=EG(21)/EG(2)/EG(20)/PFAC + EQK(61)=EG(19)/EG(20) + EQK(62)=EG(1)*EG(18)/EG(2)/EG(20) + EQK(63)=EG(5)*EG(13)/EG(2)/EG(20) + EQK(64)=EG(6)*EG(12)/EG(2)/EG(20) + EQK(65)=EG(1)*EG(19)/EG(2)/EG(21) + EQK(66)=EG(1)*EG(20)/EG(2)/EG(21) + EQK(67)=EG(23)/EG(2)/EG(22)/PFAC + EQK(68)=EG(24)/EG(2)/EG(23)/PFAC + EQK(69)=EG(1)*EG(22)/EG(2)/EG(23) + EQK(70)=EG(25)/EG(2)/EG(24)/PFAC + EQK(71)=EG(1)*EG(23)/EG(2)/EG(24) + EQK(72)=EG(26)/EG(2)/EG(25)/PFAC + EQK(73)=EG(1)*EG(24)/EG(2)/EG(25) + EQK(74)=EG(1)*EG(25)/EG(2)/EG(26) + EQK(75)=EG(12)*EG(15)/EG(2)/EG(27) + EQK(76)=EG(1)*EG(27)/EG(2)/EG(28) + EQK(77)=EG(13)*EG(15)/EG(2)/EG(28) + EQK(78)=EG(18)/EG(1)/EG(15)/PFAC + EQK(79)=EG(2)*EG(6)/EG(1)/EG(5) + EQK(80)=EG(8)/EG(5)/EG(5)/PFAC + EQK(81)=EG(3)*EG(6)/EG(5)/EG(5) + EQK(82)=EG(4)*EG(6)/EG(5)/EG(7) + EQK(168)=EQK(82) + EQK(83)=EG(6)*EG(7)/EG(5)/EG(8) + EQK(84)=EQK(83) + EQK(85)=EG(2)*EG(15)/EG(5)/EG(9) + EQK(86)=EG(2)*EG(17)/EG(5)/EG(10) + EQK(87)=EG(2)*EG(18)/EG(5)/EG(11) + EQK(88)=EG(6)*EG(10)/EG(5)/EG(11) + EQK(89)=EG(2)*EG(18)/EG(5)/EG(12) + EQK(90)=EG(21)/EG(5)/EG(13)/PFAC + EQK(91)=EG(6)*EG(11)/EG(5)/EG(13) + EQK(92)=EG(6)*EG(12)/EG(5)/EG(13) + EQK(93)=EG(6)*EG(13)/EG(5)/EG(14) + EQK(94)=EG(2)*EG(16)/EG(5)/EG(15) + EQK(95)=EG(6)*EG(15)/EG(5)/EG(17) + EQK(96)=EG(6)*EG(17)/EG(5)/EG(18) + EQK(97)=EG(6)*EG(18)/EG(5)/EG(19) + EQK(98)=EG(6)*EG(18)/EG(5)/EG(20) + EQK(99)=EG(6)*EG(19)/EG(5)/EG(21) + EQK(100)=EG(6)*EG(20)/EG(5)/EG(21) + EQK(101)=EG(2)*EG(28)/EG(5)/EG(22) + EQK(102)=EG(13)*EG(15)/EG(5)/EG(22) + EQK(103)=EG(6)*EG(22)/EG(5)/EG(23) + EQK(104)=EG(6)*EG(23)/EG(5)/EG(24) + EQK(105)=EG(6)*EG(25)/EG(5)/EG(26) + EQK(106)=EG(6)*EG(27)/EG(5)/EG(28) + EQK(107)=EG(4)*EG(8)/EG(7)/EG(7) + EQK(108)=EQK(107) + EQK(109)=EG(5)*EG(18)/EG(7)/EG(11) + EQK(110)=EG(4)*EG(14)/EG(7)/EG(13) + EQK(111)=EG(5)*EG(20)/EG(7)/EG(13) + EQK(112)=EG(5)*EG(16)/EG(7)/EG(15) + EQK(113)=EG(8)*EG(17)/EG(7)/EG(18) + EQK(114)=EG(3)*EG(15)/EG(4)/EG(9) + EQK(115)=EG(2)*EG(22)/EG(9)/EG(13) + EQK(116)=EG(3)*EG(17)/EG(4)/EG(10) + EQK(117)=EG(2)*EG(11)/EG(1)/EG(10) + EQK(118)=EG(2)*EG(18)/EG(6)/EG(10) + EQK(119)=EG(2)*EG(22)/EG(10)/EG(11) + EQK(120)=EG(2)*EG(23)/EG(10)/EG(13) + EQK(121)=EG(2)*EG(24)/EG(10)/EG(14) + EQK(122)=EG(27)/EG(10)/EG(15)/PFAC + EQK(123)=EG(15)*EG(17)/EG(10)/EG(16) + EQK(124)=EG(2)*EG(28)/EG(10)/EG(18) + EQK(125)=EG(15)*EG(22)/EG(10)/EG(27) + EQK(127)=EG(2)*EG(13)/EG(1)/EG(11) + EQK(128)=EG(1)*EG(22)/EG(11)/EG(11) + EQK(129)=EG(2)*EG(24)/EG(11)/EG(13) + EQK(130)=EG(13)*EG(13)/EG(11)/EG(14) + EQK(131)=EG(28)/EG(11)/EG(15)/PFAC + EQK(132)=EG(15)*EG(23)/EG(11)/EG(27) + EQK(133)=EG(11)/EG(12) + EQK(138)=EQK(133) + EQK(141)=EQK(133) + EQK(142)=EQK(133) + EQK(134)=EG(2)*EG(5)*EG(15)/EG(4)/EG(12)*PFAC + EQK(135)=EG(6)*EG(15)/EG(4)/EG(12) + EQK(136)=EG(2)*EG(13)/EG(1)/EG(12) + EQK(137)=EG(21)/EG(6)/EG(12)/PFAC + EQK(139)=EG(2)*EG(24)/EG(12)/EG(13) + EQK(140)=EG(13)*EG(13)/EG(12)/EG(14) + EQK(143)=EG(15)*EG(18)/EG(12)/EG(16) + EQK(144)=EG(13)*EG(25)/EG(12)/EG(26) + EQK(145)=EG(3)*EG(20)/EG(4)/EG(13) + EQK(146)=EG(5)*EG(18)/EG(4)/EG(13) + EQK(147)=EG(7)*EG(14)/EG(8)/EG(13) + EQK(148)=EG(26)/EG(13)/EG(13)/PFAC + EQK(149)=EG(2)*EG(25)/EG(13)/EG(13) + EQK(150)=EG(14)*EG(15)/EG(13)/EG(17) + EQK(151)=EG(14)*EG(17)/EG(13)/EG(18) + EQK(152)=EG(14)*EG(19)/EG(13)/EG(21) + EQK(153)=EG(14)*EG(20)/EG(13)/EG(21) + EQK(154)=EG(14)*EG(23)/EG(13)/EG(24) + EQK(155)=EG(14)*EG(25)/EG(13)/EG(26) + EQK(156)=EG(2)*EG(15)/EG(17)*PFAC + EQK(157)=EQK(156) + EQK(158)=EG(7)*EG(15)/EG(4)/EG(17) + EQK(159)=EG(7)*EG(18)/EG(4)/EG(19) + EQK(160)=EG(7)*EG(18)/EG(4)/EG(20) + EQK(161)=EG(17)*EG(18)/EG(4)/EG(23) + EQK(162)=EG(1)*EG(22)/EG(24)*PFAC + EQK(163)=EG(7)*EG(24)/EG(4)/EG(25) + EQK(164)=EG(5)*EG(15)*EG(15)/EG(4)/EG(27)*PFAC + EQK(165)=EG(15)*EG(15)*EG(22)/EG(27)/EG(27)*PFAC + EQK(167)=EG(2)*EG(29)/EG(3)/EG(24) + EQK(170)=EG(13)/EG(1)/EG(10)/PFAC + EQK(172)=EG(3)*EG(18)/EG(4)/EG(11) + EQK(175)=EG(3)*EG(29)/EG(4)/EG(23) + EQK(176)=EG(7)*EG(22)/EG(4)/EG(23) + EQK(177)=EG(29)/EG(2)/EG(28)/PFAC + EQK(181)=EG(13)*EG(17)/EG(2)/EG(29) + EQK(182)=EG(1)*EG(28)/EG(2)/EG(29) + EQK(183)=EG(6)*EG(28)/EG(5)/EG(29) + EQK(184)=EG(17)*EG(19)/EG(5)/EG(29) +! +! +! ! Compute reverse reaction rates +! +! PARAMETER (SMALL = 1.D-200) +! + RB(1) = RF(1) / MAX(EQK(1),SMALL) + RB(2) = RF(2) / MAX(EQK(2),SMALL) + RB(3) = RF(3) / MAX(EQK(3),SMALL) + RB(4) = RF(4) / MAX(EQK(4),SMALL) + RB(5) = RF(5) / MAX(EQK(5),SMALL) + RB(6) = RF(6) / MAX(EQK(6),SMALL) + RB(7) = RF(7) / MAX(EQK(7),SMALL) + RB(8) = RF(8) / MAX(EQK(8),SMALL) + RB(9) = RF(9) / MAX(EQK(9),SMALL) + RB(10) = RF(10) / MAX(EQK(10),SMALL) + RB(11) = RF(11) / MAX(EQK(11),SMALL) + RB(12) = RF(12) / MAX(EQK(12),SMALL) + RB(13) = RF(13) / MAX(EQK(13),SMALL) + RB(14) = RF(14) / MAX(EQK(14),SMALL) + RB(15) = RF(15) / MAX(EQK(15),SMALL) + RB(16) = RF(16) / MAX(EQK(16),SMALL) + RB(17) = RF(17) / MAX(EQK(17),SMALL) + RB(18) = RF(18) / MAX(EQK(18),SMALL) + RB(19) = RF(19) / MAX(EQK(19),SMALL) + RB(20) = RF(20) / MAX(EQK(20),SMALL) + RB(21) = RF(21) / MAX(EQK(21),SMALL) + RB(22) = RF(22) / MAX(EQK(22),SMALL) + RB(23) = RF(23) / MAX(EQK(23),SMALL) + RB(24) = RF(24) / MAX(EQK(24),SMALL) + RB(25) = RF(25) / MAX(EQK(25),SMALL) + RB(26) = RF(26) / MAX(EQK(26),SMALL) + RB(27) = RF(27) / MAX(EQK(27),SMALL) + RB(28) = RF(28) / MAX(EQK(28),SMALL) + RB(29) = RF(29) / MAX(EQK(29),SMALL) + RB(30) = RF(30) / MAX(EQK(30),SMALL) + RB(31) = RF(31) / MAX(EQK(31),SMALL) + RB(32) = RF(32) / MAX(EQK(32),SMALL) + RB(33) = RF(33) / MAX(EQK(33),SMALL) + RB(34) = RF(34) / MAX(EQK(34),SMALL) + RB(35) = RF(35) / MAX(EQK(35),SMALL) + RB(36) = RF(36) / MAX(EQK(36),SMALL) + RB(37) = RF(37) / MAX(EQK(37),SMALL) + + RB(38) = RF(38) / MAX(EQK(38),SMALL) + RB(39) = RF(39) / MAX(EQK(39),SMALL) + RB(40) = RF(40) / MAX(EQK(40),SMALL) + RB(41) = RF(41) / MAX(EQK(41),SMALL) + RB(42) = RF(42) / MAX(EQK(42),SMALL) + RB(43) = RF(43) / MAX(EQK(43),SMALL) + RB(44) = RF(44) / MAX(EQK(44),SMALL) + RB(45) = RF(45) / MAX(EQK(45),SMALL) + RB(46) = RF(46) / MAX(EQK(46),SMALL) + RB(47) = RF(47) / MAX(EQK(47),SMALL) + RB(48) = RF(48) / MAX(EQK(48),SMALL) + RB(49) = RF(49) / MAX(EQK(49),SMALL) + RB(50) = RF(50) / MAX(EQK(50),SMALL) + RB(51) = RF(51) / MAX(EQK(51),SMALL) + RB(52) = RF(52) / MAX(EQK(52),SMALL) + RB(53) = RF(53) / MAX(EQK(53),SMALL) + RB(54) = RF(54) / MAX(EQK(54),SMALL) + RB(55) = RF(55) / MAX(EQK(55),SMALL) + RB(56) = RF(56) / MAX(EQK(56),SMALL) + RB(57) = RF(57) / MAX(EQK(57),SMALL) + RB(58) = RF(58) / MAX(EQK(58),SMALL) + RB(59) = RF(59) / MAX(EQK(59),SMALL) + RB(60) = RF(60) / MAX(EQK(60),SMALL) + RB(61) = RF(61) / MAX(EQK(61),SMALL) + RB(62) = RF(62) / MAX(EQK(62),SMALL) + RB(63) = RF(63) / MAX(EQK(63),SMALL) + RB(64) = RF(64) / MAX(EQK(64),SMALL) + RB(65) = RF(65) / MAX(EQK(65),SMALL) + RB(66) = RF(66) / MAX(EQK(66),SMALL) + RB(67) = RF(67) / MAX(EQK(67),SMALL) + RB(68) = RF(68) / MAX(EQK(68),SMALL) + RB(69) = RF(69) / MAX(EQK(69),SMALL) + RB(70) = RF(70) / MAX(EQK(70),SMALL) + RB(71) = RF(71) / MAX(EQK(71),SMALL) + RB(72) = RF(72) / MAX(EQK(72),SMALL) + RB(73) = RF(73) / MAX(EQK(73),SMALL) + RB(74) = RF(74) / MAX(EQK(74),SMALL) + RB(75) = RF(75) / MAX(EQK(75),SMALL) + RB(76) = RF(76) / MAX(EQK(76),SMALL) + RB(77) = RF(77) / MAX(EQK(77),SMALL) + RB(78) = RF(78) / MAX(EQK(78),SMALL) + RB(79) = RF(79) / MAX(EQK(79),SMALL) + RB(80) = RF(80) / MAX(EQK(80),SMALL) + RB(81) = RF(81) / MAX(EQK(81),SMALL) + RB(82) = RF(82) / MAX(EQK(82),SMALL) + RB(83) = RF(83) / MAX(EQK(83),SMALL) + RB(84) = RF(84) / MAX(EQK(84),SMALL) + RB(85) = RF(85) / MAX(EQK(85),SMALL) + RB(86) = RF(86) / MAX(EQK(86),SMALL) + RB(87) = RF(87) / MAX(EQK(87),SMALL) + RB(88) = RF(88) / MAX(EQK(88),SMALL) + RB(89) = RF(89) / MAX(EQK(89),SMALL) + RB(90) = RF(90) / MAX(EQK(90),SMALL) + RB(91) = RF(91) / MAX(EQK(91),SMALL) + RB(92) = RF(92) / MAX(EQK(92),SMALL) + RB(93) = RF(93) / MAX(EQK(93),SMALL) + RB(94) = RF(94) / MAX(EQK(94),SMALL) + RB(95) = RF(95) / MAX(EQK(95),SMALL) + RB(96) = RF(96) / MAX(EQK(96),SMALL) + RB(97) = RF(97) / MAX(EQK(97),SMALL) + RB(98) = RF(98) / MAX(EQK(98),SMALL) + RB(99) = RF(99) / MAX(EQK(99),SMALL) + RB(100) = RF(100) / MAX(EQK(100),SMALL) + RB(101) = RF(101) / MAX(EQK(101),SMALL) + RB(102) = RF(102) / MAX(EQK(102),SMALL) + RB(103) = RF(103) / MAX(EQK(103),SMALL) + RB(104) = RF(104) / MAX(EQK(104),SMALL) + RB(105) = RF(105) / MAX(EQK(105),SMALL) + RB(106) = RF(106) / MAX(EQK(106),SMALL) + RB(107) = RF(107) / MAX(EQK(107),SMALL) + RB(108) = RF(108) / MAX(EQK(108),SMALL) + RB(109) = RF(109) / MAX(EQK(109),SMALL) + RB(110) = RF(110) / MAX(EQK(110),SMALL) + RB(111) = RF(111) / MAX(EQK(111),SMALL) + RB(112) = RF(112) / MAX(EQK(112),SMALL) + RB(113) = RF(113) / MAX(EQK(113),SMALL) + RB(114) = RF(114) / MAX(EQK(114),SMALL) + RB(115) = RF(115) / MAX(EQK(115),SMALL) + RB(116) = RF(116) / MAX(EQK(116),SMALL) + RB(117) = RF(117) / MAX(EQK(117),SMALL) + RB(118) = RF(118) / MAX(EQK(118),SMALL) + RB(119) = RF(119) / MAX(EQK(119),SMALL) + RB(120) = RF(120) / MAX(EQK(120),SMALL) + RB(121) = RF(121) / MAX(EQK(121),SMALL) + RB(122) = RF(122) / MAX(EQK(122),SMALL) + RB(123) = RF(123) / MAX(EQK(123),SMALL) + RB(124) = RF(124) / MAX(EQK(124),SMALL) + RB(125) = RF(125) / MAX(EQK(125),SMALL) + RB(126) = 0.0 + RB(127) = RF(127) / MAX(EQK(127),SMALL) + RB(128) = RF(128) / MAX(EQK(128),SMALL) + RB(129) = RF(129) / MAX(EQK(129),SMALL) + RB(130) = RF(130) / MAX(EQK(130),SMALL) + RB(131) = RF(131) / MAX(EQK(131),SMALL) + RB(132) = RF(132) / MAX(EQK(132),SMALL) + RB(133) = RF(133) / MAX(EQK(133),SMALL) + RB(134) = RF(134) / MAX(EQK(134),SMALL) + RB(135) = RF(135) / MAX(EQK(135),SMALL) + RB(136) = RF(136) / MAX(EQK(136),SMALL) + RB(137) = RF(137) / MAX(EQK(137),SMALL) + RB(138) = RF(138) / MAX(EQK(138),SMALL) + RB(139) = RF(139) / MAX(EQK(139),SMALL) + RB(140) = RF(140) / MAX(EQK(140),SMALL) + RB(141) = RF(141) / MAX(EQK(141),SMALL) + RB(142) = RF(142) / MAX(EQK(142),SMALL) + RB(143) = RF(143) / MAX(EQK(143),SMALL) + RB(144) = RF(144) / MAX(EQK(144),SMALL) + RB(145) = RF(145) / MAX(EQK(145),SMALL) + RB(146) = RF(146) / MAX(EQK(146),SMALL) + RB(147) = RF(147) / MAX(EQK(147),SMALL) + RB(148) = RF(148) / MAX(EQK(148),SMALL) + RB(149) = RF(149) / MAX(EQK(149),SMALL) + RB(150) = RF(150) / MAX(EQK(150),SMALL) + RB(151) = RF(151) / MAX(EQK(151),SMALL) + RB(152) = RF(152) / MAX(EQK(152),SMALL) + RB(153) = RF(153) / MAX(EQK(153),SMALL) + RB(154) = RF(154) / MAX(EQK(154),SMALL) + RB(155) = RF(155) / MAX(EQK(155),SMALL) + RB(156) = RF(156) / MAX(EQK(156),SMALL) + RB(157) = RF(157) / MAX(EQK(157),SMALL) + RB(158) = RF(158) / MAX(EQK(158),SMALL) + RB(159) = RF(159) / MAX(EQK(159),SMALL) + RB(160) = RF(160) / MAX(EQK(160),SMALL) + RB(161) = RF(161) / MAX(EQK(161),SMALL) + RB(162) = RF(162) / MAX(EQK(162),SMALL) + RB(163) = RF(163) / MAX(EQK(163),SMALL) + RB(164) = RF(164) / MAX(EQK(164),SMALL) + RB(165) = RF(165) / MAX(EQK(165),SMALL) + RB(166) = 0.0 + RB(167) = RF(167) / MAX(EQK(167),SMALL) + RB(168) = RF(168) / MAX(EQK(168),SMALL) + RB(169) = 0.0 + RB(170) = RF(170) / MAX(EQK(170),SMALL) + RB(171) = 0.0 + RB(172) = RF(172) / MAX(EQK(172),SMALL) + RB(173) = 0.0 + RB(174) = 0.0 + RB(175) = RF(175) / MAX(EQK(175),SMALL) + RB(176) = RF(176) / MAX(EQK(176),SMALL) + RB(177) = RF(177) / MAX(EQK(177),SMALL) + RB(178) = 0.0 + RB(179) = 0.0 + RB(180) = 0.0 + RB(181) = RF(181) / MAX(EQK(181),SMALL) + RB(182) = RF(182) / MAX(EQK(182),SMALL) + RB(183) = RF(183) / MAX(EQK(183),SMALL) + RB(184) = RF(184) / MAX(EQK(184),SMALL) +! +! +! rates at low pressure limit +! + RKLOW(1) = EXP(3.40312786D1 -1.50965D3/T) + RKLOW(2) = EXP(5.99064331D1 -2.76D0*ALOGT -8.05146668D2/T) + RKLOW(3) = EXP(7.69484824D1 -4.76D0*ALOGT -1.22784867D3/T) + RKLOW(4) = EXP(5.61662604D1 -2.57D0*ALOGT -2.13867084D2/T) + RKLOW(5) = EXP(7.39217399D1 -4.82D0*ALOGT -3.28600484D3/T) + RKLOW(6) = EXP(6.98660102D1 -4.8D0*ALOGT -2.79788467D3/T) + RKLOW(7) = EXP(7.28526099D1 -4.65D0*ALOGT -2.55634067D3/T) + RKLOW(8) = EXP(9.59450043D1 -7.44D0*ALOGT -7.08529068D3/T) + RKLOW(9) = EXP(9.34384048D1 -7.27D0*ALOGT -3.63322434D3/T) + RKLOW(10) = EXP(6.9414025D1 -3.86D0*ALOGT -1.67067934D3/T) + RKLOW(11) = EXP(9.61977483D1 -7.62D0*ALOGT -3.50742017D3/T) + RKLOW(12) = EXP(9.50941235D1 -7.08D0*ALOGT -3.36400342D3/T) + RKLOW(13) = EXP(6.37931383D1 -3.42D0*ALOGT -4.24463259D4/T) + RKLOW(14) = EXP(4.22794408D1 -9.D-1*ALOGT +8.55468335D2/T) + RKLOW(15) = EXP(8.42793577D1 -5.92D0*ALOGT -1.58010034D3/T) + RKLOW(16) = EXP(6.54619238D1 -3.74D0*ALOGT -9.74227469D2/T) + RKLOW(17) = EXP(7.69748493D1 -5.11D0*ALOGT -3.57032226D3/T) + RKLOW(18) = EXP(8.81295053D1 -6.36D0*ALOGT -2.536212D3/T) + RKLOW(19) = EXP(9.56297642D1 -7.03D0*ALOGT -1.38988444D3/T) + RKLOW(20) = EXP(1.17889265D2 -9.3D0*ALOGT -4.92145901D4/T) + RKLOW(21) = EXP(5.91374013D1 -2.8D0*ALOGT -2.96897834D2/T) + RKLOW(22) = EXP(9.67205025D1 -7.63D0*ALOGT -1.93939704D3/T) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! third-body concentrations +! ! +! SUBROUTINE RATX (T, C, RF, RB, RKLOW) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! PARAMETER (SMALL = 1.D-200) +! DIMENSION C(*), RF(*), RB(*), RKLOW(*) +! + ALOGT = LOG(T) + CTOT = 0.0 + DO K = 1, 19 + CTOT = CTOT + C(K) + ENDDO +! + CTB(1) = CTOT + 1.4D0*C(1) + 1.44D1*C(6) + C(10) + 7.5D-1*C(11) & + + 2.6D0*C(12) + 2.D0*C(17) + CTB(2) = CTOT + C(1) + 5.D0*C(6) + C(10) + 5.D-1*C(11) + C(12) & + + 2.D0*C(17) + CTB(47) = CTB(2) + CTB(51) = CTB(2) + CTB(53) = CTB(2) + CTB(54) = CTB(2) + CTB(56) = CTB(2) + CTB(60) = CTB(2) + CTB(67) = CTB(2) + CTB(68) = CTB(2) + CTB(70) = CTB(2) + CTB(72) = CTB(2) + CTB(78) = CTB(2) + CTB(80) = CTB(2) + CTB(90) = CTB(2) + CTB(122) = CTB(2) + CTB(131) = CTB(2) + CTB(137) = CTB(2) + CTB(148) = CTB(2) + CTB(162) = CTB(2) + CTB(170) = CTB(2) + CTB(177) = CTB(2) + CTB(12) = CTOT + C(1) + 5.D0*C(4) + 5.D0*C(6) + C(10) & + + 5.D-1*C(11) + 2.5D0*C(12) + 2.D0*C(17) + CTB(31) = CTOT - C(4) - C(6) - 2.5D-1*C(11) + 5.D-1*C(12) & + + 5.D-1*C(17) - C(19) + CTB(36) = CTOT - C(1) - C(6) + C(10) - C(12) + 2.D0*C(17) + CTB(40) = CTOT - 2.7D-1*C(1) + 2.65D0*C(6) + C(10) + 2.D0*C(17) + CTB(49) = CTOT + C(1) + 5.D0*C(6) + 2.D0*C(10) + 5.D-1*C(11) & + + C(12) + 2.D0*C(17) + CTB(157) = CTOT + C(1) - C(6) + C(10) + 5.D-1*C(11) + C(12) & + + 2.D0*C(17) +! +! +! fall-off reactions +! +! + PR = RKLOW(1) * CTB(12) / RF(12) + PCOR = PR / (1.0 + PR) + RF(12) = RF(12) * PCOR + RB(12) = RB(12) * PCOR +! + PR = RKLOW(2) * CTB(47) / RF(47) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.38D-1*EXP(-T/9.1D1) + 5.62D-1*EXP(-T/5.836D3)& + + EXP(-8.552D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(47) = RF(47) * PCOR + RB(47) = RB(47) * PCOR +! + PR = RKLOW(3) * CTB(49) / RF(49) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.17D-1*EXP(-T/7.4D1) + 7.83D-1*EXP(-T/2.941D3)& + + EXP(-6.964D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(49) = RF(49) * PCOR + RB(49) = RB(49) * PCOR +! + PR = RKLOW(4) * CTB(51) / RF(51) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.176D-1*EXP(-T/2.71D2) + 7.824D-1*EXP(-T/2.755D3)& + + EXP(-6.57D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(51) = RF(51) * PCOR + RB(51) = RB(51) * PCOR + + PR = RKLOW(5) * CTB(53) / RF(53) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.813D-1*EXP(-T/1.03D2) + 7.187D-1*EXP(-T/1.291D3)& + + EXP(-4.16D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(53) = RF(53) * PCOR + RB(53) = RB(53) * PCOR + + PR = RKLOW(6) * CTB(54) / RF(54) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.42D-1*EXP(-T/9.4D1) + 7.58D-1*EXP(-T/1.555D3)& + + EXP(-4.2D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(54) = RF(54) * PCOR + RB(54) = RB(54) * PCOR + + PR = RKLOW(7) * CTB(56) / RF(56) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.D-1*EXP(-T/1.D2) + 6.D-1*EXP(-T/9.D4)& + + EXP(-1.D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(56) = RF(56) * PCOR + RB(56) = RB(56) * PCOR + + PR = RKLOW(8) * CTB(60) / RF(60) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.D-1*EXP(-T/1.D2) + 7.D-1*EXP(-T/9.D4)& + + EXP(-1.D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(60) = RF(60) * PCOR + RB(60) = RB(60) * PCOR + + PR = RKLOW(9) * CTB(67) / RF(67) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.493D-1*EXP(-T/9.85D1) + 7.507D-1*EXP(-T/1.302D3)& + + EXP(-4.167D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(67) = RF(67) * PCOR + RB(67) = RB(67) * PCOR + + PR = RKLOW(10) * CTB(68) / RF(68) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.18D-1*EXP(-T/2.075D2) + 7.82D-1*EXP(-T/2.663D3)& + + EXP(-6.095D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(68) = RF(68) * PCOR + RB(68) = RB(68) * PCOR + + PR = RKLOW(11) * CTB(70) / RF(70) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.47D-2*EXP(-T/2.1D2) + 9.753D-1*EXP(-T/9.84D2)& + + EXP(-4.374D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(70) = RF(70) * PCOR + RB(70) = RB(70) * PCOR + + PR = RKLOW(12) * CTB(72) / RF(72) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 1.578D-1*EXP(-T/1.25D2) + 8.422D-1*EXP(-T/2.219D3)& + + EXP(-6.882D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(72) = RF(72) * PCOR + RB(72) = RB(72) * PCOR + + PR = RKLOW(13) * CTB(78) / RF(78) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 6.8D-2*EXP(-T/1.97D2) + 9.32D-1*EXP(-T/1.54D3)& + + EXP(-1.03D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(78) = RF(78) * PCOR + RB(78) = RB(78) * PCOR + + PR = RKLOW(14) * CTB(80) / RF(80) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.654D-1*EXP(-T/9.4D1) + 7.346D-1*EXP(-T/1.756D3)& + + EXP(-5.182D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(80) = RF(80) * PCOR + RB(80) = RB(80) * PCOR + + PR = RKLOW(15) * CTB(90) / RF(90) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 5.88D-1*EXP(-T/1.95D2) + 4.12D-1*EXP(-T/5.9D3)& + + EXP(-6.394D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(90) = RF(90) * PCOR + RB(90) = RB(90) * PCOR + + PR = RKLOW(16) * CTB(122) / RF(122) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.243D-1*EXP(-T/2.37D2) + 5.757D-1*EXP(-T/1.652D3)& + + EXP(-5.069D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(122) = RF(122) * PCOR + RB(122) = RB(122) * PCOR + + PR = RKLOW(17) * CTB(131) / RF(131) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.093D-1*EXP(-T/2.75D2) + 5.907D-1*EXP(-T/1.226D3)& + + EXP(-5.185D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(131) = RF(131) * PCOR + RB(131) = RB(131) * PCOR + + PR = RKLOW(18) * CTB(137) / RF(137) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.973D-1*EXP(-T/2.08D2) + 6.027D-1*EXP(-T/3.922D3)& + + EXP(-1.018D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(137) = RF(137) * PCOR + RB(137) = RB(137) * PCOR + + PR = RKLOW(19) * CTB(148) / RF(148) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.81D-1*EXP(-T/7.32D1) + 6.19D-1*EXP(-T/1.18D3)& + + EXP(-9.999D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(148) = RF(148) * PCOR + RB(148) = RB(148) * PCOR + + PR = RKLOW(20) * CTB(162) / RF(162) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.655D-1*EXP(-T/1.8D2) + 7.345D-1*EXP(-T/1.035D3)& + + EXP(-5.417D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(162) = RF(162) * PCOR + RB(162) = RB(162) * PCOR + + PR = RKLOW(21) * CTB(170) / RF(170) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.22D-1*EXP(-T/1.22D2) + 5.78D-1*EXP(-T/2.535D3)& + + EXP(-9.365D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(170) = RF(170) * PCOR + RB(170) = RB(170) * PCOR + + PR = RKLOW(22) * CTB(177) / RF(177) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 5.35D-1*EXP(-T/2.01D2) + 4.65D-1*EXP(-T/1.773D3)& + + EXP(-5.333D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(177) = RF(177) * PCOR + RB(177) = RB(177) * PCOR + + RF(1) = RF(1)*CTB(1)*C(3)*C(3) + RF(2) = RF(2)*CTB(2)*C(3)*C(2) + RF(3) = RF(3)*C(3)*C(1) + RF(4) = RF(4)*C(3)*C(7) + RF(5) = RF(5)*C(3)*C(8) + RF(6) = RF(6)*C(3) + RF(7) = RF(7)*C(3) + RF(8) = RF(8)*C(3) + RF(9) = RF(9)*C(3) + RF(10) = RF(10)*C(3)*C(9) + RF(11) = RF(11)*C(3)*C(10) + RF(12) = RF(12)*C(3)*C(11) + RF(13) = RF(13)*C(3) + RF(14) = RF(14)*C(3) + RF(15) = RF(15)*C(3)*C(13) + RF(16) = RF(16)*C(3) + RF(17) = RF(17)*C(3) + RF(18) = RF(18)*C(3)*C(14) + RF(19) = RF(19)*C(3)*C(14) + RF(20) = RF(20)*C(3)*C(15) + RF(21) = RF(21)*C(3)*C(15) + RF(22) = RF(22)*C(3) + RF(23) = RF(23)*C(3)*C(16) + RF(24) = RF(24)*C(3) + RF(25) = RF(25)*C(3)*C(17) + RF(26) = RF(26)*C(3) + RF(27) = RF(27)*C(3)*C(18) + RF(28) = RF(28)*C(3)*C(18) + RF(29) = RF(29)*C(4)*C(11) + RF(30) = RF(30)*C(4)*C(13) + RF(31) = RF(31)*CTB(31)*C(2)*C(4) + RF(32) = RF(32)*C(2)*C(4)*C(4) + RF(33) = RF(33)*C(2)*C(4)*C(6) + RF(34) = RF(34)*C(2)*C(4)*C(19) + RF(35) = RF(35)*C(2)*C(4) + RF(36) = RF(36)*CTB(36)*C(2)*C(2) + RF(37) = RF(37)*C(2)*C(2)*C(1) + RF(38) = RF(38)*C(2)*C(2)*C(6) + RF(39) = RF(39)*C(2)*C(2)*C(12) + RF(40) = RF(40)*CTB(40)*C(2)*C(5) + RF(41) = RF(41)*C(2)*C(7) + RF(42) = RF(42)*C(2)*C(7) + RF(43) = RF(43)*C(2)*C(7) + RF(44) = RF(44)*C(2)*C(8) + RF(45) = RF(45)*C(2)*C(8) + RF(46) = RF(46)*C(2) + RF(47) = RF(47)*C(2) + RF(48) = RF(48)*C(2) + RF(49) = RF(49)*C(2)*C(9) + RF(50) = RF(50)*C(2)*C(10) + RF(51) = RF(51)*C(2) + RF(52) = RF(52)*C(2) + RF(53) = RF(53)*C(2)*C(13) + RF(54) = RF(54)*C(2)*C(13) + RF(55) = RF(55)*C(2)*C(13) + RF(56) = RF(56)*C(2) + RF(57) = RF(57)*C(2) + RF(58) = RF(58)*C(2) + RF(59) = RF(59)*C(2) + RF(60) = RF(60)*C(2) + RF(61) = RF(61)*C(2) + RF(62) = RF(62)*C(2) + RF(63) = RF(63)*C(2) + RF(64) = RF(64)*C(2) + RF(65) = RF(65)*C(2)*C(14) + RF(66) = RF(66)*C(2)*C(14) + RF(67) = RF(67)*C(2)*C(15) + RF(68) = RF(68)*C(2) + RF(69) = RF(69)*C(2) + RF(70) = RF(70)*C(2)*C(16) + RF(71) = RF(71)*C(2)*C(16) + RF(72) = RF(72)*C(2) + RF(73) = RF(73)*C(2) + RF(74) = RF(74)*C(2)*C(17) + RF(75) = RF(75)*C(2) + RF(76) = RF(76)*C(2)*C(18) + RF(77) = RF(77)*C(2)*C(18) + RF(78) = RF(78)*C(1)*C(11) + RF(79) = RF(79)*C(5)*C(1) + RF(80) = RF(80)*C(5)*C(5) + RF(81) = RF(81)*C(5)*C(5) + RF(82) = RF(82)*C(5)*C(7) + RF(83) = RF(83)*C(5)*C(8) + RF(84) = RF(84)*C(5)*C(8) + RF(85) = RF(85)*C(5) + RF(86) = RF(86)*C(5) + RF(87) = RF(87)*C(5) + RF(88) = RF(88)*C(5) + RF(89) = RF(89)*C(5) + RF(90) = RF(90)*C(5)*C(9) + RF(91) = RF(91)*C(5)*C(9) + RF(92) = RF(92)*C(5)*C(9) + RF(93) = RF(93)*C(5)*C(10) + RF(94) = RF(94)*C(5)*C(11) + RF(95) = RF(95)*C(5) + RF(96) = RF(96)*C(5)*C(13) + RF(97) = RF(97)*C(5) + RF(98) = RF(98)*C(5) + RF(99) = RF(99)*C(5)*C(14) + RF(100) = RF(100)*C(5)*C(14) + RF(101) = RF(101)*C(5)*C(15) + RF(102) = RF(102)*C(5)*C(15) + RF(103) = RF(103)*C(5) + RF(104) = RF(104)*C(5)*C(16) + RF(105) = RF(105)*C(5)*C(17) + RF(106) = RF(106)*C(5)*C(18) + RF(107) = RF(107)*C(7)*C(7) + RF(108) = RF(108)*C(7)*C(7) + RF(109) = RF(109)*C(7) + RF(110) = RF(110)*C(7)*C(9) + RF(111) = RF(111)*C(7)*C(9) + RF(112) = RF(112)*C(7)*C(11) + RF(113) = RF(113)*C(7)*C(13) + RF(114) = RF(114)*C(4) + RF(115) = RF(115)*C(9) + RF(116) = RF(116)*C(4) + RF(117) = RF(117)*C(1) + RF(118) = RF(118)*C(6) + RF(120) = RF(120)*C(9) + RF(121) = RF(121)*C(10) + RF(122) = RF(122)*C(11) + RF(123) = RF(123)*C(12) + RF(124) = RF(124)*C(13) + RF(126) = RF(126)*C(4) + RF(127) = RF(127)*C(1) + RF(129) = RF(129)*C(9) + RF(130) = RF(130)*C(10) + RF(131) = RF(131)*C(11) + RF(133) = RF(133)*C(19) + RF(134) = RF(134)*C(4) + RF(135) = RF(135)*C(4) + RF(136) = RF(136)*C(1) + RF(137) = RF(137)*C(6) + RF(138) = RF(138)*C(6) + RF(139) = RF(139)*C(9) + RF(140) = RF(140)*C(10) + RF(141) = RF(141)*C(11) + RF(142) = RF(142)*C(12) + RF(143) = RF(143)*C(12) + RF(144) = RF(144)*C(17) + RF(145) = RF(145)*C(9)*C(4) + RF(146) = RF(146)*C(9)*C(4) + RF(147) = RF(147)*C(9)*C(8) + RF(148) = RF(148)*C(9)*C(9) + RF(149) = RF(149)*C(9)*C(9) + RF(150) = RF(150)*C(9) + RF(151) = RF(151)*C(9)*C(13) + RF(152) = RF(152)*C(9)*C(14) + RF(153) = RF(153)*C(9)*C(14) + RF(154) = RF(154)*C(9)*C(16) + RF(155) = RF(155)*C(9)*C(17) + RF(156) = RF(156)*C(6) + RF(157) = RF(157)*CTB(157) + RF(158) = RF(158)*C(4) + RF(159) = RF(159)*C(4) + RF(160) = RF(160)*C(4) + RF(161) = RF(161)*C(4) + RF(162) = RF(162)*C(16) + RF(163) = RF(163)*C(4) + RF(164) = RF(164)*C(4) + RF(166) = RF(166)*C(3)*C(9) + RF(167) = RF(167)*C(3)*C(16) + RF(168) = RF(168)*C(5)*C(7) + RF(169) = RF(169)*C(5)*C(9) + RF(170) = RF(170)*C(1) + RF(171) = RF(171)*C(4) + RF(172) = RF(172)*C(4) + RF(174) = RF(174)*C(6) + RF(175) = RF(175)*C(4) + RF(176) = RF(176)*C(4) + RF(177) = RF(177)*C(2)*C(18) + RF(178) = RF(178)*C(3) + RF(179) = RF(179)*C(4) + RF(180) = RF(180)*C(4) + RF(181) = RF(181)*C(2) + RF(182) = RF(182)*C(2) + RF(183) = RF(183)*C(5) + RF(184) = RF(184)*C(5) + RB(1) = RB(1)*CTB(1)*C(4) + RB(2) = RB(2)*CTB(2)*C(5) + RB(3) = RB(3)*C(2)*C(5) + RB(4) = RB(4)*C(5)*C(4) + RB(5) = RB(5)*C(5)*C(7) + RB(6) = RB(6)*C(2)*C(11) + RB(7) = RB(7)*C(2) + RB(8) = RB(8)*C(1)*C(11) + RB(9) = RB(9)*C(2) + RB(10) = RB(10)*C(2)*C(13) + RB(11) = RB(11)*C(5)*C(9) + RB(12) = RB(12)*C(12) + RB(13) = RB(13)*C(5)*C(11) + RB(14) = RB(14)*C(2)*C(12) + RB(15) = RB(15)*C(5) + RB(16) = RB(16)*C(5)*C(13) + RB(17) = RB(17)*C(5)*C(13) + RB(18) = RB(18)*C(5) + RB(19) = RB(19)*C(5) + RB(20) = RB(20)*C(2) + RB(21) = RB(21)*C(11) + RB(22) = RB(22)*C(2)*C(18) + RB(23) = RB(23)*C(9) + RB(24) = RB(24)*C(9)*C(13) + RB(25) = RB(25)*C(5) + RB(26) = RB(26)*C(2)*C(11)*C(11) + RB(27) = RB(27)*C(5) + RB(28) = RB(28)*C(12) + RB(29) = RB(29)*C(3)*C(12) + RB(30) = RB(30)*C(7) + RB(31) = RB(31)*CTB(31)*C(7) + RB(32) = RB(32)*C(7)*C(4) + RB(33) = RB(33)*C(7)*C(6) + RB(34) = RB(34)*C(7)*C(19) + RB(35) = RB(35)*C(3)*C(5) + RB(36) = RB(36)*CTB(36)*C(1) + RB(37) = RB(37)*C(1)*C(1) + RB(38) = RB(38)*C(1)*C(6) + RB(39) = RB(39)*C(1)*C(12) + RB(40) = RB(40)*CTB(40)*C(6) + RB(41) = RB(41)*C(3)*C(6) + RB(42) = RB(42)*C(4)*C(1) + RB(43) = RB(43)*C(5)*C(5) + RB(44) = RB(44)*C(7)*C(1) + RB(45) = RB(45)*C(5)*C(6) + RB(46) = RB(46)*C(1) + RB(47) = RB(47)*C(9) + RB(48) = RB(48)*C(1) + RB(49) = RB(49)*C(10) + RB(50) = RB(50)*C(9)*C(1) + RB(51) = RB(51)*C(13) + RB(52) = RB(52)*C(1)*C(11) + RB(55) = RB(55)*C(1) + RB(56) = RB(56)*C(14) + RB(57) = RB(57)*C(1)*C(13) + RB(58) = RB(58)*C(5)*C(9) + RB(59) = RB(59)*C(6) + RB(60) = RB(60)*C(14) + RB(61) = RB(61)*C(2) + RB(62) = RB(62)*C(1)*C(13) + RB(63) = RB(63)*C(5)*C(9) + RB(64) = RB(64)*C(6) + RB(65) = RB(65)*C(1) + RB(66) = RB(66)*C(1) + RB(68) = RB(68)*C(16) + RB(69) = RB(69)*C(1)*C(15) + RB(71) = RB(71)*C(1) + RB(72) = RB(72)*C(17) + RB(73) = RB(73)*C(1)*C(16) + RB(74) = RB(74)*C(1) + RB(75) = RB(75)*C(11) + RB(76) = RB(76)*C(1) + RB(77) = RB(77)*C(9)*C(11) + RB(78) = RB(78)*C(13) + RB(79) = RB(79)*C(2)*C(6) + RB(80) = RB(80)*C(8) + RB(81) = RB(81)*C(3)*C(6) + RB(82) = RB(82)*C(4)*C(6) + RB(83) = RB(83)*C(7)*C(6) + RB(84) = RB(84)*C(7)*C(6) + RB(85) = RB(85)*C(2)*C(11) + RB(86) = RB(86)*C(2) + RB(87) = RB(87)*C(2)*C(13) + RB(88) = RB(88)*C(6) + RB(89) = RB(89)*C(2)*C(13) + RB(90) = RB(90)*C(14) + RB(91) = RB(91)*C(6) + RB(92) = RB(92)*C(6) + RB(93) = RB(93)*C(9)*C(6) + RB(94) = RB(94)*C(2)*C(12) + RB(95) = RB(95)*C(6)*C(11) + RB(96) = RB(96)*C(6) + RB(97) = RB(97)*C(6)*C(13) + RB(98) = RB(98)*C(6)*C(13) + RB(99) = RB(99)*C(6) + RB(100) = RB(100)*C(6) + RB(101) = RB(101)*C(2)*C(18) + RB(102) = RB(102)*C(9)*C(11) + RB(103) = RB(103)*C(6)*C(15) + RB(104) = RB(104)*C(6) + RB(105) = RB(105)*C(6) + RB(106) = RB(106)*C(6) + RB(107) = RB(107)*C(4)*C(8) + RB(108) = RB(108)*C(4)*C(8) + RB(109) = RB(109)*C(5)*C(13) + RB(110) = RB(110)*C(4)*C(10) + RB(111) = RB(111)*C(5) + RB(112) = RB(112)*C(5)*C(12) + RB(113) = RB(113)*C(8) + RB(114) = RB(114)*C(3)*C(11) + RB(115) = RB(115)*C(2)*C(15) + RB(116) = RB(116)*C(3) + RB(117) = RB(117)*C(2) + RB(118) = RB(118)*C(2)*C(13) + RB(119) = RB(119)*C(2)*C(15) + RB(120) = RB(120)*C(2) + RB(121) = RB(121)*C(2)*C(16) + RB(123) = RB(123)*C(11) + RB(124) = RB(124)*C(2)*C(18) + RB(125) = RB(125)*C(11)*C(15) + RB(127) = RB(127)*C(2)*C(9) + RB(128) = RB(128)*C(1)*C(15) + RB(129) = RB(129)*C(2)*C(16) + RB(130) = RB(130)*C(9)*C(9) + RB(131) = RB(131)*C(18) + RB(132) = RB(132)*C(11) + RB(133) = RB(133)*C(19) + RB(134) = RB(134)*C(2)*C(5)*C(11) + RB(135) = RB(135)*C(11)*C(6) + RB(136) = RB(136)*C(9)*C(2) + RB(137) = RB(137)*C(14) + RB(138) = RB(138)*C(6) + RB(139) = RB(139)*C(2)*C(16) + RB(140) = RB(140)*C(9)*C(9) + RB(141) = RB(141)*C(11) + RB(142) = RB(142)*C(12) + RB(143) = RB(143)*C(11)*C(13) + RB(144) = RB(144)*C(9) + RB(145) = RB(145)*C(3) + RB(146) = RB(146)*C(5)*C(13) + RB(147) = RB(147)*C(7)*C(10) + RB(148) = RB(148)*C(17) + RB(149) = RB(149)*C(2) + RB(150) = RB(150)*C(10)*C(11) + RB(151) = RB(151)*C(10) + RB(152) = RB(152)*C(10) + RB(153) = RB(153)*C(10) + RB(154) = RB(154)*C(10) + RB(155) = RB(155)*C(10) + RB(156) = RB(156)*C(2)*C(11)*C(6) + RB(157) = RB(157)*CTB(157)*C(2)*C(11) + RB(158) = RB(158)*C(7)*C(11) + RB(159) = RB(159)*C(7)*C(13) + RB(160) = RB(160)*C(7)*C(13) + RB(161) = RB(161)*C(13) + RB(162) = RB(162)*C(1)*C(15) + RB(163) = RB(163)*C(7)*C(16) + RB(164) = RB(164)*C(5)*C(11)*C(11) + RB(165) = RB(165)*C(11)*C(11)*C(15) + RB(167) = RB(167)*C(2) + RB(168) = RB(168)*C(4)*C(6) + RB(170) = RB(170)*C(9) + RB(172) = RB(172)*C(3)*C(13) + RB(175) = RB(175)*C(3) + RB(176) = RB(176)*C(7)*C(15) + RB(181) = RB(181)*C(9) + RB(182) = RB(182)*C(18)*C(1) + RB(183) = RB(183)*C(6)*C(18) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! solving QSS species concentration +! ------------------------------------------- +! +! SUBROUTINE QSSA(RF, RB, XQ) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! PARAMETER (SMALL = 1.D-200) +! DIMENSION RF(*), RB(*), XQ(*) +! + RF(119) = 0.D0 + RF(125) = 0.D0 + RF(128) = 0.D0 + RF(132) = 0.D0 + RF(165) = 0.D0 + RF(173) = 0.D0 + RB(180) = 0.D0 + RB(184) = 0.D0 + +! C + DEN = +RF( 85) +RF(114) +RF(115) +RB( 46) + A1_0 = ( +RB( 85) +RB(114) +RB(115) )/MAX(DEN, SMALL) + A1_2 = ( +RF( 46) )/MAX(DEN, SMALL) +! CH + DEN = +RF( 6) +RF( 46) +RF( 86) +RF(116) +RF(117) & + +RF(118) +RF(120) +RF(121) +RF(122) +RF(123) +RF(124) & + +RF(170) +RB( 48) +RB( 88) + A2_0 = ( +RB( 6) +RB(118) +RB(119) +RB(121) +RB(124) & + +RB(125) +RB(170) )/MAX(DEN, SMALL) + A2_1 = ( +RB( 46) )/MAX(DEN, SMALL) + A2_3 = ( +RF( 88) +RB(117) )/MAX(DEN, SMALL) + A2_4 = ( +RF( 48) )/MAX(DEN, SMALL) + A2_5 = ( +RB( 86) +RB(116) +RB(123) )/MAX(DEN, SMALL) + A2_8 = ( +RB(120) )/MAX(DEN, SMALL) + + A2_10 = ( +RB(122) )/MAX(DEN, SMALL) +! CH2 + DEN = +RF( 7) +RF( 47) +RF( 87) +RF( 88) +RF(109) & + +RF(126) +RF(127) +RF(129) +RF(130) +RF(131) +RF(171) & + +RF(172) +RB( 21) +RB( 28) +RB( 91) +RB(117) +RB(133) & + +RB(138) +RB(141) +RB(142) +RB(178) + A3_0 = ( +RF( 21) +RF( 28) +RB( 47) +RB( 87) +RF( 91) & + +RB(109) +RB(119) +RB(126) +RB(127) +RB(128) +RB(128) & + +RB(129) +RB(130) +RB(131) +RB(171) +RB(172) +RB(173) & + +RB(173) )/MAX(DEN, SMALL) + A3_2 = ( +RB( 88) +RF(117) )/MAX(DEN, SMALL) + A3_4 = ( +RF(133) +RF(138) +RF(141) +RF(142) )/MAX(DEN, SMALL) + A3_5 = ( +RB( 7) )/MAX(DEN, SMALL) + A3_8 = ( +RB(132) )/MAX(DEN, SMALL) + A3_11 = ( +RF(178) )/MAX(DEN, SMALL) +! CH2(S) + DEN = +RF( 8) +RF( 9) +RF( 48) +RF( 89) +RF(133) & + +RF(134) +RF(135) +RF(136) +RF(137) +RF(138) +RF(139) & + +RF(140) +RF(141) +RF(142) +RF(143) +RF(144) +RF(174) & + +RB( 59) +RB( 64) +RB( 75) +RB( 92) + A4_0 = ( +RB( 8) +RB( 89) +RF( 92) +RB(134) +RB(135) & + +RB(136) +RB(137) +RB(139) +RB(140) +RB(143) +RB(174) )& + /MAX(DEN, SMALL) + A4_2 = ( +RB( 48) )/MAX(DEN, SMALL) + A4_3 = ( +RB(133) +RB(138) +RB(141) +RB(142) )/MAX(DEN, SMALL) + A4_5 = ( +RB( 9) )/MAX(DEN, SMALL) + A4_6 = ( +RF( 59) )/MAX(DEN, SMALL) + A4_7 = ( +RF( 64) )/MAX(DEN, SMALL) + A4_9 = ( +RB(144) )/MAX(DEN, SMALL) + A4_10 = ( +RF( 75) )/MAX(DEN, SMALL) +! HCO + DEN = +RF( 13) +RF( 14) +RF( 51) +RF( 52) +RF( 95) & + +RF(150) +RF(156) +RF(157) +RF(158) +RB( 7) +RB( 9) & + +RB( 15) +RB( 23) +RB( 30) +RB( 55) +RB( 86) +RB( 96) & + +RB(113) +RB(116) +RB(123) +RB(151) +RB(161) +RB(181) + A5_0 = ( +RB( 13) +RB( 14) +RF( 15) +RF( 23) +RF( 30) & + +RB( 51) +RB( 52) +RF( 55) +RB( 95) +RF( 96) +RF(113) & + +RB(150) +RF(151) +RB(156) +RB(157) +RB(158) )/MAX(DEN, SMALL) + A5_2 = ( +RF( 86) +RF(116) +RF(123) )/MAX(DEN, SMALL) + A5_3 = ( +RF( 7) )/MAX(DEN, SMALL) + A5_4 = ( +RF( 9) )/MAX(DEN, SMALL) + A5_8 = ( +RF(161) )/MAX(DEN, SMALL) + A5_11 = ( +RF(180) +RF(180) +RF(181) +RF(184) )/MAX(DEN, SMALL) +! CH2OH + DEN = +RF( 16) +RF( 56) +RF( 57) +RF( 58) +RF( 59) & + +RF( 97) +RF(159) +RB( 18) +RB( 53) +RB( 61) +RB( 65) & + +RB( 99) +RB(152) + A6_0 = ( +RB( 16) +RF( 18) +RF( 53) +RB( 56) +RB( 57) & + +RB( 58) +RF( 65) +RB( 97) +RF( 99) +RF(152) +RB(159) )& + /MAX(DEN, SMALL) + A6_4 = ( +RB( 59) )/MAX(DEN, SMALL) + A6_7 = ( +RF( 61) )/MAX(DEN, SMALL) + A6_11 = ( +RF(184) )/MAX(DEN, SMALL) +! CH3O + DEN = +RF( 17) +RF( 60) +RF( 61) +RF( 62) +RF( 63) & + +RF( 64) +RF( 98) +RF(160) +RB( 19) +RB( 54) +RB( 66) & + +RB(100) +RB(111) +RB(145) +RB(153) + A7_0 = ( +RB( 17) +RF( 19) +RF( 54) +RB( 60) +RB( 62) & + +RB( 63) +RF( 66) +RB( 98) +RF(100) +RF(111) +RF(145) & + +RF(153) +RB(160) )/MAX(DEN, SMALL) + A7_4 = ( +RB( 64) )/MAX(DEN, SMALL) + A7_6 = ( +RB( 61) )/MAX(DEN, SMALL) +! C2H3 + DEN = +RF( 22) +RF( 68) +RF( 69) +RF(103) +RF(161) & + +RF(175) +RF(176) +RB( 67) +RB( 71) +RB(104) +RB(120) & + +RB(132) +RB(154) + A8_0 = ( +RB( 22) +RF( 67) +RB( 68) +RB( 69) +RF( 71) & + +RB(103) +RF(104) +RF(154) +RB(176) )/MAX(DEN, SMALL) + A8_2 = ( +RF(120) )/MAX(DEN, SMALL) + A8_5 = ( +RB(161) )/MAX(DEN, SMALL) + A8_11 = ( +RB(175) )/MAX(DEN, SMALL) +! C2H5 + DEN = +RF( 24) +RF( 72) +RF( 73) +RF(163) +RB( 25) & + +RB( 70) +RB( 74) +RB(105) +RB(144) +RB(149) +RB(155) + A9_0 = ( +RB( 24) +RF( 25) +RF( 70) +RB( 72) +RB( 73) & + +RF( 74) +RF(105) +RF(149) +RF(155) +RB(163) )/MAX(DEN, SMALL) + A9_4 = ( +RF(144) )/MAX(DEN, SMALL) +! HCCO + DEN = +RF( 26) +RF( 75) +RF(164) +RB( 20) +RB( 27) & + +RB( 76) +RB(106) +RB(122) + A10_0 = ( +RF( 20) +RB( 26) +RF( 27) +RF( 76) +RF(106) & + +RB(125) +RB(164) +RB(165) +RB(165) )/MAX(DEN, SMALL) + A10_2 = ( +RF(122) )/MAX(DEN, SMALL) + A10_4 = ( +RB( 75) )/MAX(DEN, SMALL) + A10_8 = ( +RB(132) )/MAX(DEN, SMALL) +! CH2CHO + DEN = +RF(178) +RF(179) +RF(180) +RF(181) +RF(182) & + +RF(183) +RF(184) +RB(167) +RB(175) +RB(177) + A11_0 = ( +RF(167) +RF(177) +RB(179) +RB(182) +RB(183) )& + /MAX(DEN, SMALL) + A11_5 = ( +RB(181) )/MAX(DEN, SMALL) + A11_8 = ( +RF(175) )/MAX(DEN, SMALL) +! + A2_0 = A2_0 + A2_1*A1_0 + DEN = 1 -A2_1*A1_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A2_10 = A2_10/MAX(DEN, SMALL) + A2_8 = A2_8/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_9*A9_0 + DEN = 1 -A4_9*A9_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A4_10 = A4_10/MAX(DEN, SMALL) + A4_7 = A4_7/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_11*A11_0 + A5_8 = A5_8 + A5_11*A11_8 + DEN = 1 -A5_11*A11_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A5_3 = A5_3/MAX(DEN, SMALL) + A5_8 = A5_8/MAX(DEN, SMALL) + A3_0 = A3_0 + A3_11*A11_0 + A3_5 = A3_5 + A3_11*A11_5 + A3_8 = A3_8 + A3_11*A11_8 + A6_0 = A6_0 + A6_11*A11_0 + A6_5 = A6_11*A11_5 + A6_8 = A6_11*A11_8 + A8_0 = A8_0 + A8_11*A11_0 + A8_5 = A8_5 + A8_11*A11_5 + DEN = 1 -A8_11*A11_8 + A8_0 = A8_0/MAX(DEN, SMALL) + A8_2 = A8_2/MAX(DEN, SMALL) + A8_5 = A8_5/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_8*A8_0 + A2_5 = A2_5 + A2_8*A8_5 + DEN = 1 -A2_8*A8_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A2_10 = A2_10/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_8*A8_0 + A5_2 = A5_2 + A5_8*A8_2 + DEN = 1 -A5_8*A8_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A5_3 = A5_3/MAX(DEN, SMALL) + A3_0 = A3_0 + A3_8*A8_0 + A3_2 = A3_2 + A3_8*A8_2 + A3_5 = A3_5 + A3_8*A8_5 + A6_0 = A6_0 + A6_8*A8_0 + A6_2 = A6_8*A8_2 + A6_5 = A6_5 + A6_8*A8_5 + A10_0 = A10_0 + A10_8*A8_0 + A10_2 = A10_2 + A10_8*A8_2 + A10_5 = A10_8*A8_5 + A4_0 = A4_0 + A4_7*A7_0 + A4_6 = A4_6 + A4_7*A7_6 + DEN = 1 -A4_7*A7_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A4_10 = A4_10/MAX(DEN, SMALL) + A6_0 = A6_0 + A6_7*A7_0 + A6_4 = A6_4 + A6_7*A7_4 + DEN = 1 -A6_7*A7_6 + A6_0 = A6_0/MAX(DEN, SMALL) + A6_4 = A6_4/MAX(DEN, SMALL) + A6_2 = A6_2/MAX(DEN, SMALL) + A6_5 = A6_5/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_10*A10_0 + A4_2 = A4_2 + A4_10*A10_2 + A4_5 = A4_5 + A4_10*A10_5 + DEN = 1 -A4_10*A10_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_10*A10_0 + A2_4 = A2_4 + A2_10*A10_4 + A2_5 = A2_5 + A2_10*A10_5 + DEN = 1 -A2_10*A10_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_6*A6_0 + A4_2 = A4_2 + A4_6*A6_2 + A4_5 = A4_5 + A4_6*A6_5 + DEN = 1 -A4_6*A6_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_3*A3_0 + A4_2 = A4_2 + A4_3*A3_2 + A4_5 = A4_5 + A4_3*A3_5 + DEN = 1 -A4_3*A3_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_3*A3_0 + A2_4 = A2_4 + A2_3*A3_4 + A2_5 = A2_5 + A2_3*A3_5 + DEN = 1 -A2_3*A3_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_3*A3_0 + A5_4 = A5_4 + A5_3*A3_4 + A5_2 = A5_2 + A5_3*A3_2 + DEN = 1 -A5_3*A3_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_5*A5_0 + A4_2 = A4_2 + A4_5*A5_2 + DEN = 1 -A4_5*A5_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_5*A5_0 + A2_4 = A2_4 + A2_5*A5_4 + DEN = 1 -A2_5*A5_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_2*A2_0 + DEN = 1 -A4_2*A2_4 + A4_0 = A4_0/MAX(DEN, SMALL) + XQ(4) = A4_0 + XQ(2) = A2_0 +A2_4*XQ(4) + XQ(5) = A5_0 +A5_4*XQ(4) +A5_2*XQ(2) + XQ(3) = A3_0 +A3_4*XQ(4) +A3_2*XQ(2) +A3_5*XQ(5) + XQ(6) = A6_0 +A6_4*XQ(4) +A6_2*XQ(2) +A6_5*XQ(5) + XQ(10) = A10_0 +A10_4*XQ(4) +A10_2*XQ(2) +A10_5*XQ(5) + XQ(7) = A7_0 +A7_4*XQ(4) +A7_6*XQ(6) + XQ(8) = A8_0 +A8_2*XQ(2) +A8_5*XQ(5) + XQ(11) = A11_0 +A11_5*XQ(5) +A11_8*XQ(8) + XQ(9) = A9_0 +A9_4*XQ(4) + XQ(1) = A1_0 +A1_2*XQ(2) +! +! +! --------------------------------------------- +! +! update rates of reactions involving QSS species +! + RF( 6) = RF( 6)*XQ( 2) + RF( 7) = RF( 7)*XQ( 3) + RB( 7) = RB( 7)*XQ( 5) + RF( 8) = RF( 8)*XQ( 4) + RF( 9) = RF( 9)*XQ( 4) + RB( 9) = RB( 9)*XQ( 5) + RF( 13) = RF( 13)*XQ( 5) + RF( 14) = RF( 14)*XQ( 5) + RB( 15) = RB( 15)*XQ( 5) + RF( 16) = RF( 16)*XQ( 6) + RF( 17) = RF( 17)*XQ( 7) + RB( 18) = RB( 18)*XQ( 6) + RB( 19) = RB( 19)*XQ( 7) + RB( 20) = RB( 20)*XQ(10) + RB( 21) = RB( 21)*XQ( 3) + RF( 22) = RF( 22)*XQ( 8) + RB( 23) = RB( 23)*XQ( 5) + RF( 24) = RF( 24)*XQ( 9) + RB( 25) = RB( 25)*XQ( 9) + RF( 26) = RF( 26)*XQ(10) + RB( 27) = RB( 27)*XQ(10) + RB( 28) = RB( 28)*XQ( 3) + RB( 30) = RB( 30)*XQ( 5) + RF( 46) = RF( 46)*XQ( 2) + RB( 46) = RB( 46)*XQ( 1) + RF( 47) = RF( 47)*XQ( 3) + RF( 48) = RF( 48)*XQ( 4) + RB( 48) = RB( 48)*XQ( 2) + RF( 51) = RF( 51)*XQ( 5) + RF( 52) = RF( 52)*XQ( 5) + RB( 53) = RB( 53)*XQ( 6) + RB( 54) = RB( 54)*XQ( 7) + RB( 55) = RB( 55)*XQ( 5) + RF( 56) = RF( 56)*XQ( 6) + RF( 57) = RF( 57)*XQ( 6) + RF( 58) = RF( 58)*XQ( 6) + RF( 59) = RF( 59)*XQ( 6) + RB( 59) = RB( 59)*XQ( 4) + RF( 60) = RF( 60)*XQ( 7) + RF( 61) = RF( 61)*XQ( 7) + RB( 61) = RB( 61)*XQ( 6) + RF( 62) = RF( 62)*XQ( 7) + RF( 63) = RF( 63)*XQ( 7) + RF( 64) = RF( 64)*XQ( 7) + RB( 64) = RB( 64)*XQ( 4) + RB( 65) = RB( 65)*XQ( 6) + RB( 66) = RB( 66)*XQ( 7) + RB( 67) = RB( 67)*XQ( 8) + RF( 68) = RF( 68)*XQ( 8) + RF( 69) = RF( 69)*XQ( 8) + RB( 70) = RB( 70)*XQ( 9) + RB( 71) = RB( 71)*XQ( 8) + RF( 72) = RF( 72)*XQ( 9) + RF( 73) = RF( 73)*XQ( 9) + RB( 74) = RB( 74)*XQ( 9) + RF( 75) = RF( 75)*XQ(10) + RB( 75) = RB( 75)*XQ( 4) + RB( 76) = RB( 76)*XQ(10) + RF( 85) = RF( 85)*XQ( 1) + RF( 86) = RF( 86)*XQ( 2) + RB( 86) = RB( 86)*XQ( 5) + RF( 87) = RF( 87)*XQ( 3) + RF( 88) = RF( 88)*XQ( 3) + RB( 88) = RB( 88)*XQ( 2) + RF( 89) = RF( 89)*XQ( 4) + RB( 91) = RB( 91)*XQ( 3) + RB( 92) = RB( 92)*XQ( 4) + RF( 95) = RF( 95)*XQ( 5) + RB( 96) = RB( 96)*XQ( 5) + RF( 97) = RF( 97)*XQ( 6) + RF( 98) = RF( 98)*XQ( 7) + RB( 99) = RB( 99)*XQ( 6) + RB(100) = RB(100)*XQ( 7) + RF(103) = RF(103)*XQ( 8) + RB(104) = RB(104)*XQ( 8) + RB(105) = RB(105)*XQ( 9) + RB(106) = RB(106)*XQ(10) + RF(109) = RF(109)*XQ( 3) + RB(111) = RB(111)*XQ( 7) + RB(113) = RB(113)*XQ( 5) + RF(114) = RF(114)*XQ( 1) + RF(115) = RF(115)*XQ( 1) + RF(116) = RF(116)*XQ( 2) + RB(116) = RB(116)*XQ( 5) + RF(117) = RF(117)*XQ( 2) + RB(117) = RB(117)*XQ( 3) + RF(118) = RF(118)*XQ( 2) + RF(120) = RF(120)*XQ( 2) + RB(120) = RB(120)*XQ( 8) + RF(121) = RF(121)*XQ( 2) + RF(122) = RF(122)*XQ( 2) + RB(122) = RB(122)*XQ(10) + RF(123) = RF(123)*XQ( 2) + RB(123) = RB(123)*XQ( 5) + RF(124) = RF(124)*XQ( 2) + RF(126) = RF(126)*XQ( 3) + RF(127) = RF(127)*XQ( 3) + RF(129) = RF(129)*XQ( 3) + RF(130) = RF(130)*XQ( 3) + RF(131) = RF(131)*XQ( 3) + RB(132) = RB(132)*XQ( 8) + RF(133) = RF(133)*XQ( 4) + RB(133) = RB(133)*XQ( 3) + RF(134) = RF(134)*XQ( 4) + RF(135) = RF(135)*XQ( 4) + RF(136) = RF(136)*XQ( 4) + RF(137) = RF(137)*XQ( 4) + RF(138) = RF(138)*XQ( 4) + RB(138) = RB(138)*XQ( 3) + RF(139) = RF(139)*XQ( 4) + RF(140) = RF(140)*XQ( 4) + RF(141) = RF(141)*XQ( 4) + RB(141) = RB(141)*XQ( 3) + RF(142) = RF(142)*XQ( 4) + RB(142) = RB(142)*XQ( 3) + RF(143) = RF(143)*XQ( 4) + RF(144) = RF(144)*XQ( 4) + RB(144) = RB(144)*XQ( 9) + RB(145) = RB(145)*XQ( 7) + RB(149) = RB(149)*XQ( 9) + RF(150) = RF(150)*XQ( 5) + RB(151) = RB(151)*XQ( 5) + RB(152) = RB(152)*XQ( 6) + RB(153) = RB(153)*XQ( 7) + RB(154) = RB(154)*XQ( 8) + RB(155) = RB(155)*XQ( 9) + RF(156) = RF(156)*XQ( 5) + RF(157) = RF(157)*XQ( 5) + RF(158) = RF(158)*XQ( 5) + RF(159) = RF(159)*XQ( 6) + RF(160) = RF(160)*XQ( 7) + RF(161) = RF(161)*XQ( 8) + RB(161) = RB(161)*XQ( 5) + RF(163) = RF(163)*XQ( 9) + RF(164) = RF(164)*XQ(10) + RB(167) = RB(167)*XQ(11) + RF(170) = RF(170)*XQ( 2) + RF(171) = RF(171)*XQ( 3) + RF(172) = RF(172)*XQ( 3) + RF(174) = RF(174)*XQ( 4) + RF(175) = RF(175)*XQ( 8) + RB(175) = RB(175)*XQ(11) + RF(176) = RF(176)*XQ( 8) + RB(177) = RB(177)*XQ(11) + RF(178) = RF(178)*XQ(11) + RB(178) = RB(178)*XQ( 3) + RF(179) = RF(179)*XQ(11) + RF(180) = RF(180)*XQ(11) + RF(181) = RF(181)*XQ(11) + RB(181) = RB(181)*XQ( 5) + RF(182) = RF(182)*XQ(11) + RF(183) = RF(183)*XQ(11) + RF(184) = RF(184)*XQ(11) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! ! ompute WDOT +! +! SUBROUTINE RDOT(RF, RB, WDOT) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION RF(*), RB(*), WDOT(*), ROP(184) +! + DO I = 1, 184 + ROP(I) = RF(I) - RB(I) + ENDDO +! +! H2 + WDOT( 1) = -ROP( 3) +ROP( 8) +ROP( 36) +ROP( 37) & + +ROP( 38) +ROP( 39) +ROP( 42) +ROP( 44) & + +ROP( 46) +ROP( 48) +ROP( 50) +ROP( 52) & + +ROP( 55) +ROP( 57) +ROP( 62) +ROP( 65) & + +ROP( 66) +ROP( 69) +ROP( 71) +ROP( 73) & + +ROP( 74) +ROP( 76) -ROP( 78) -ROP( 79) & + -ROP(117) -ROP(127) +ROP(128) -ROP(136) & + +ROP(162) +ROP(166) +ROP(169) -ROP(170) & + +ROP(174) +ROP(182) +! H + WDOT( 2) = -ROP( 2) +ROP( 3) +ROP( 6) -ROP( 7) & + -2*ROP( 8) -ROP( 9) +ROP( 10) +ROP( 14) & + -ROP( 17) +ROP( 19) +ROP( 20) +2*ROP( 21) & + -ROP( 24) +ROP( 25) +ROP( 26) +2*ROP( 28) & + -ROP( 31) -ROP( 32) -ROP( 33) -ROP( 34) & + -ROP( 35) -2*ROP( 36) -2*ROP( 37) -2*ROP( 38) & + -2*ROP( 39) -ROP( 40) -ROP( 41) -ROP( 42) & + -ROP( 43) -ROP( 44) -ROP( 45) -ROP( 46) & + -3*ROP( 47) -3*ROP( 48) -ROP( 49) -ROP( 50) & + -ROP( 51) -ROP( 52) -ROP( 53) -ROP( 55) & + -ROP( 56) -ROP( 57) -ROP( 58) +ROP( 59) & + -2*ROP( 60) -ROP( 61) -2*ROP( 62) -2*ROP( 63) & + -ROP( 65) -2*ROP( 68) -2*ROP( 69) -2*ROP( 72) & + -2*ROP( 73) +ROP( 75) -ROP( 76) -ROP( 77) & + +ROP( 79) +ROP( 85) +ROP( 86) -ROP( 87) & + -2*ROP( 88) -ROP( 89) +2*ROP( 91) +2*ROP( 92) & + +ROP( 94) -ROP( 98) +ROP(100) +ROP(101) & + -ROP(103) +ROP(104) +ROP(105) -2*ROP(109) & + +ROP(111) +ROP(115) +3*ROP(117) +ROP(118) & + -ROP(119) +2*ROP(120) +ROP(121) +ROP(124) & + -ROP(126) -ROP(127) -4*ROP(128) -ROP(129) & + -2*ROP(130) -2*ROP(131) -ROP(132) -ROP(134) & + -2*ROP(135) -ROP(136) -2*ROP(137) -ROP(139) & + -2*ROP(140) -2*ROP(143) -ROP(144) +ROP(145) & + +2*ROP(149) +ROP(153) +ROP(154) +ROP(155) & + +ROP(156) +ROP(157) -ROP(160) -ROP(161) & + -ROP(163) +ROP(166) +2*ROP(167) -2*ROP(172) & + -2*ROP(173) -2*ROP(174) -ROP(176) +2*ROP(178) & + -ROP(179) -ROP(180) -2*ROP(181) -2*ROP(182) & + -ROP(183) -ROP(184) +! O + WDOT( 3) = -2*ROP( 1) -ROP( 2) -ROP( 3) -ROP( 4) & + -ROP( 5) -2*ROP( 6) -ROP( 7) -ROP( 8) & + -ROP( 9) -ROP( 10) -ROP( 11) -ROP( 12) & + -ROP( 13) -ROP( 14) -ROP( 15) -ROP( 16) & + -ROP( 17) -ROP( 18) -ROP( 19) -ROP( 20) & + -ROP( 21) -2*ROP( 22) -ROP( 23) -ROP( 24) & + -ROP( 25) -ROP( 26) -ROP( 27) -ROP( 28) & + +ROP( 29) +ROP( 35) +ROP( 41) +ROP( 48) & + +ROP( 67) -ROP( 68) -ROP( 69) +ROP( 71) & + +ROP( 81) -ROP( 85) -ROP( 86) +ROP( 88) & + -ROP(103) +ROP(104) -ROP(115) -ROP(117) & + -ROP(118) -ROP(119) -ROP(121) -ROP(122) & + -ROP(123) -ROP(124) -ROP(125) +ROP(132) & + +ROP(145) +ROP(154) -ROP(161) -ROP(166) & + -ROP(167) -ROP(170) +ROP(172) -ROP(176) & + -ROP(178) +! O2 + WDOT( 4) = +ROP( 1) +ROP( 4) +2*ROP( 6) +ROP( 8) & + +ROP( 13) +ROP( 14) -ROP( 15) +ROP( 16) & + -ROP( 18) -ROP( 20) -ROP( 21) +ROP( 22) & + -ROP( 23) +ROP( 26) -ROP( 27) -ROP( 28) & + -ROP( 29) -2*ROP( 30) -ROP( 31) -ROP( 32) & + -ROP( 33) -ROP( 34) -ROP( 35) +ROP( 42) & + +ROP( 46) +ROP( 47) -ROP( 48) +ROP( 51) & + +ROP( 52) -ROP( 53) -ROP( 55) +ROP( 56) & + +ROP( 57) +ROP( 58) -ROP( 61) -ROP( 64) & + -ROP( 65) -ROP( 67) +ROP( 68) +ROP( 69) & + -ROP( 71) -ROP( 76) +ROP( 82) +ROP( 85) & + +ROP( 86) +ROP( 87) -ROP( 88) +ROP( 89) & + -ROP( 91) -ROP( 92) +ROP( 95) -ROP( 96) & + +ROP( 97) -ROP( 99) +ROP(103) -ROP(104) & + -ROP(106) +ROP(107) +ROP(108) +ROP(109) & + +ROP(110) -ROP(113) +ROP(115) +ROP(117) & + +2*ROP(118) +3*ROP(119) +ROP(120) +2*ROP(121) & + +ROP(122) +ROP(123) +2*ROP(124) +3*ROP(125) & + +ROP(127) +2*ROP(128) +ROP(129) +ROP(130) & + +ROP(131) +ROP(132) +ROP(136) +ROP(137) & + +ROP(139) +ROP(140) +ROP(143) +ROP(144) & + -ROP(145) -ROP(146) +ROP(150) -ROP(151) & + -ROP(152) -ROP(154) +ROP(156) +ROP(157) & + -ROP(160) -ROP(161) -ROP(163) +2*ROP(165) & + +ROP(168) +2*ROP(170) +2*ROP(173) +ROP(174) & + -ROP(178) -ROP(179) -3*ROP(180) -ROP(181) & + -2*ROP(184) +! OH + WDOT( 5) = +ROP( 2) +ROP( 3) +ROP( 4) +ROP( 5) & + +ROP( 11) +ROP( 13) +ROP( 15) +ROP( 16) & + +ROP( 17) +ROP( 18) +ROP( 19) +ROP( 20) & + +ROP( 25) -ROP( 26) +2*ROP( 27) +ROP( 35) & + -ROP( 40) +2*ROP( 43) +ROP( 45) +ROP( 58) & + +ROP( 63) -ROP( 75) +ROP( 76) -ROP( 79) & + -2*ROP( 80) -2*ROP( 81) -ROP( 82) -ROP( 83) & + -ROP( 84) -ROP( 85) -ROP( 86) -ROP( 87) & + -ROP( 88) -ROP( 89) -ROP( 90) -ROP( 91) & + -ROP( 92) -ROP( 93) -ROP( 94) -ROP( 95) & + -ROP( 96) -ROP( 97) -ROP( 98) -ROP( 99) & + -ROP(100) -ROP(101) -ROP(102) -ROP(103) & + -ROP(104) -ROP(105) +ROP(109) +ROP(111) & + +ROP(112) +ROP(122) -ROP(125) +ROP(126) & + -ROP(132) +ROP(134) +ROP(146) -2*ROP(165) & + -ROP(168) -ROP(169) +ROP(179) +ROP(180) & + -ROP(183) -ROP(184) +! H2O + WDOT( 6) = +ROP( 40) +ROP( 41) +ROP( 45) +ROP( 59) & + +ROP( 64) +ROP( 79) +ROP( 81) +ROP( 82) & + +ROP( 83) +ROP( 84) +ROP( 88) +ROP( 91) & + +ROP( 92) +ROP( 93) +ROP( 95) +ROP( 96) & + +ROP( 97) +ROP( 98) +ROP( 99) +ROP(100) & + +ROP(103) +ROP(104) +ROP(105) +ROP(106) & + -ROP(118) +ROP(135) -ROP(137) +ROP(168) & + -ROP(174) +ROP(183) +! HO2 + WDOT( 7) = -ROP( 4) +ROP( 5) -ROP( 6) +ROP( 7) & + +ROP( 9) -ROP( 13) -ROP( 14) +ROP( 15) & + -ROP( 16) +ROP( 18) +ROP( 23) +2*ROP( 30) & + +ROP( 31) +ROP( 32) +ROP( 33) +ROP( 34) & + -ROP( 41) -ROP( 42) -ROP( 43) +ROP( 44) & + -ROP( 46) +ROP( 48) -ROP( 51) -ROP( 52) & + +ROP( 53) +ROP( 55) -ROP( 56) -ROP( 57) & + -ROP( 58) -ROP( 59) +ROP( 61) +ROP( 65) & + -ROP( 82) +ROP( 83) +ROP( 84) +ROP( 88) & + -ROP( 95) +ROP( 96) -ROP( 97) +ROP( 99) & + -2*ROP(107) -2*ROP(108) -ROP(109) -ROP(110) & + -ROP(111) -ROP(112) -ROP(117) -ROP(118) & + -ROP(119) -ROP(120) -ROP(121) -ROP(122) & + -ROP(124) -ROP(125) +ROP(147) -ROP(150) & + +ROP(151) +ROP(152) -ROP(156) -ROP(157) & + +ROP(160) +ROP(161) +ROP(163) -ROP(168) & + -ROP(170) +ROP(176) +2*ROP(180) +ROP(181) & + +2*ROP(184) +! H2O2 + WDOT( 8) = -ROP( 5) -ROP( 44) -ROP( 45) +ROP( 80) & + -ROP( 83) -ROP( 84) +ROP(107) +ROP(108) & + +ROP(113) -ROP(147) +! CH3 + WDOT( 9) = -ROP( 10) +ROP( 11) +ROP( 23) +ROP( 24) & + +ROP( 47) -ROP( 49) +ROP( 50) +ROP( 58) & + +ROP( 63) +ROP( 77) -ROP( 90) -ROP( 91) & + -ROP( 92) +ROP( 93) +ROP(102) -ROP(110) & + -ROP(111) -ROP(115) -ROP(120) +ROP(127) & + -ROP(129) +2*ROP(130) +ROP(136) -ROP(139) & + +2*ROP(140) +ROP(144) -ROP(145) -ROP(146) & + -ROP(147) -2*ROP(148) -2*ROP(149) -ROP(150) & + -ROP(151) -ROP(152) -ROP(153) -ROP(154) & + -ROP(155) -ROP(166) -ROP(169) +ROP(170) & + +ROP(181) +! CH4 + WDOT(10) = -ROP( 11) +ROP( 49) -ROP( 50) -ROP( 93) & + +ROP(110) -ROP(121) -ROP(130) -ROP(140) & + +ROP(147) +ROP(150) +ROP(151) +ROP(152) & + +ROP(153) +ROP(154) +ROP(155) +! CO + WDOT(11) = +ROP( 7) +ROP( 8) +ROP( 9) -ROP( 12) & + -ROP( 14) +ROP( 15) +2*ROP( 20) +ROP( 21) & + +ROP( 23) +2*ROP( 27) -ROP( 29) +ROP( 30) & + +ROP( 48) -ROP( 51) +ROP( 55) -ROP( 75) & + +2*ROP( 76) +ROP( 77) -ROP( 78) +ROP( 88) & + -ROP( 94) +ROP( 96) +ROP(102) +2*ROP(106) & + -ROP(112) +ROP(113) -ROP(115) -ROP(117) & + -ROP(118) -ROP(119) -ROP(120) -ROP(121) & + +ROP(123) -ROP(124) -2*ROP(125) +ROP(126) & + -ROP(131) -ROP(132) +ROP(134) +ROP(135) & + +ROP(143) +ROP(151) +ROP(161) -2*ROP(165) & + +ROP(166) -ROP(170) +ROP(179) +2*ROP(180) & + +ROP(181) +ROP(184) +! CO2 + WDOT(12) = -ROP( 7) -ROP( 8) -ROP( 9) +ROP( 12) & + +ROP( 14) +ROP( 21) +2*ROP( 28) +ROP( 29) & + -ROP( 47) -ROP( 48) +ROP( 59) +ROP( 64) & + +ROP( 75) -ROP( 87) -ROP( 88) -ROP( 89) & + +ROP( 91) +ROP( 92) +ROP( 94) -ROP(109) & + +ROP(112) +ROP(117) -ROP(119) -ROP(123) & + -ROP(126) -ROP(127) -2*ROP(128) -ROP(129) & + -ROP(130) -ROP(131) -ROP(132) -ROP(134) & + -ROP(135) -ROP(136) -ROP(137) -ROP(139) & + -ROP(140) -2*ROP(143) -ROP(144) -ROP(172) & + -2*ROP(173) -ROP(174) +2*ROP(178) +! CH2O + WDOT(13) = +ROP( 10) -ROP( 15) +ROP( 18) +ROP( 19) & + +ROP( 24) -ROP( 30) +ROP( 51) -ROP( 55) & + -ROP( 56) -ROP( 58) -ROP( 59) -ROP( 60) & + -ROP( 63) -ROP( 64) +ROP( 65) +ROP( 66) & + +ROP( 78) +ROP( 87) +ROP( 89) -ROP( 96) & + +ROP( 99) +ROP(100) +ROP(109) +ROP(111) & + -ROP(113) +ROP(118) -ROP(124) +ROP(143) & + +ROP(145) +ROP(146) -ROP(151) +ROP(152) & + +ROP(153) +ROP(161) +ROP(169) +ROP(172) & + +ROP(174) +ROP(179) +ROP(184) +! CH3OH + WDOT(14) = -ROP( 18) -ROP( 19) +ROP( 56) +ROP( 60) & + -ROP( 65) -ROP( 66) +ROP( 90) -ROP( 99) & + -ROP(100) +ROP(137) -ROP(152) -ROP(153) +! C2H2 + WDOT(15) = -ROP( 20) -ROP( 21) -ROP( 67) +ROP( 69) & + -ROP(101) -ROP(102) +ROP(103) +ROP(115) & + +ROP(119) +ROP(125) +ROP(128) +ROP(162) & + +ROP(165) +ROP(173) +ROP(176) +! C2H4 + WDOT(16) = -ROP( 23) -ROP( 24) +ROP( 25) +ROP( 68) & + -ROP( 71) -ROP( 72) +ROP( 74) -ROP(104) & + +ROP(105) +ROP(121) +ROP(129) +ROP(139) & + +ROP(144) +ROP(149) -ROP(154) +ROP(155) & + -ROP(162) -ROP(167) +! C2H6 + WDOT(17) = -ROP( 25) +ROP( 72) -ROP( 74) -ROP(105) & + -ROP(144) +ROP(148) -ROP(155) +! CH2CO + WDOT(18) = -ROP( 27) -ROP( 28) +ROP( 67) -ROP( 68) & + -ROP( 69) +ROP( 71) -ROP( 76) -ROP( 77) & + +ROP(101) -ROP(103) +ROP(104) -ROP(106) & + +ROP(120) +ROP(124) +ROP(131) +ROP(132) & + +ROP(154) -ROP(161) +ROP(167) -ROP(176) & + -ROP(178) -ROP(179) -ROP(180) -ROP(181) & + -ROP(184) +! N2 + WDOT(19) = 0.0 + + ! Correction for unit compatibility in Cantera + WDOT(1:19) = WDOT(1:19)*1D6 + + RETURN + END \ No newline at end of file diff --git a/samples/python/AVBP/inputs/Lu_ARC.yaml b/samples/python/AVBP/inputs/Lu_ARC.yaml new file mode 100644 index 00000000000..91213b6c00c --- /dev/null +++ b/samples/python/AVBP/inputs/Lu_ARC.yaml @@ -0,0 +1,2230 @@ +units: {length: cm, quantity: mol, activation-energy: cal/mol} +solution: + generator: Cantera SolutionArray + cantera-version: 3.0.0 + git-commit: "'c4e2732'" + date: Tue Dec 19 21:16:13 2023 + reactants: + size: 1 + type: inlet + points: 1 + mass-flux: 0.3218542195132330 + temperature: 300.0 + pressure: 1.0e+05 + mass-fractions: + O2: 0.2201412376866278 + CH4: 0.05518666598235154 + N2: 0.7246720963310207 + flame: + CH2O: [2.512053803898528e-13, 5.963718667192086e-13, 4.060244108455286e-12, + 5.156316656302329e-11, 3.017932821671933e-10, 2.142704546543387e-09, + 1.568562522811727e-08, 5.473619662708908e-08, 2.178288436068591e-07, + 4.934890277869252e-07, 1.205591763701419e-06, 3.038693103931656e-06, + 5.031627156092249e-06, 8.563759718949816e-06, 1.476765182821246e-05, + 1.961492044427392e-05, 2.622122763716273e-05, 3.515119866218731e-05, + 4.709466611079824e-05, 5.458671776967307e-05, 6.327036179369539e-05, + 7.328761907561809e-05, 8.478338008155919e-05, 9.790155071489928e-05, + 1.127805870938681e-04, 1.295486366101845e-04, 1.483185539490984e-04, + 1.691830664707253e-04, 1.922103173599540e-04, 2.174399264348096e-04, + 2.448796000512884e-04, 2.745022214354262e-04, 3.062432846609130e-04, + 3.399985067070681e-04, 3.756214345279704e-04, 4.129207746025741e-04, + 4.323847811943790e-04, 4.521993972936451e-04, 4.723233214268235e-04, + 4.927110287561689e-04, 5.133125011166184e-04, 5.340729431694315e-04, + 5.549324859102945e-04, 5.758258692590154e-04, 5.966820854850825e-04, + 6.174239584000158e-04, 6.379676315080298e-04, 6.582219419524513e-04, + 6.780876667954507e-04, 6.974566468111822e-04, 7.162108238025886e-04, + 7.342196770134151e-04, 7.513419200445636e-04, 7.674291977936843e-04, + 7.823211015261201e-04, 7.892946052905859e-04, 7.958980892963555e-04, + 8.021076938821166e-04, 8.078989280537642e-04, 8.132467523024792e-04, + 8.181256795617379e-04, 8.225098951616811e-04, 8.263733961509715e-04, + 8.2969014977373e-04, 8.324342702061904e-04, 8.345802118728811e-04, + 8.361029767819781e-04, 8.369783323603977e-04, 8.371830352612549e-04, + 8.366950556054275e-04, 8.354937951696713e-04, 8.335602922292375e-04, + 8.308774052052658e-04, 8.274299670724441e-04, 8.232049027757485e-04, + 8.181913028096732e-04, 8.123804477390855e-04, 8.057657808664194e-04, + 7.983428295060086e-04, 7.901090793752616e-04, 7.810638113298180e-04, + 7.712079148043050e-04, 7.659642234609910e-04, 7.605176213276153e-04, + 7.548686445767433e-04, 7.490178071745198e-04, 7.429657316905899e-04, + 7.367131049895832e-04, 7.302606785328122e-04, 7.236092703438868e-04, + 7.167597692050895e-04, 7.097131411571825e-04, 7.024704384611451e-04, + 6.950328111454101e-04, 6.874015212204334e-04, 6.795779595947497e-04, + 6.715636656736668e-04, 6.633603495636184e-04, 6.549699167436230e-04, + 6.463944950007646e-04, 6.376364633609303e-04, 6.286984826804450e-04, + 6.195835275003e-04, 6.102949187040740e-04, 6.008363564655144e-04, + 5.912119529226917e-04, 5.814262639759097e-04, 5.714843195758585e-04, + 5.613916518498106e-04, 5.511543204069877e-04, 5.407789341708296e-04, + 5.302726691062779e-04, 5.196432812447529e-04, 5.088991144574764e-04, + 4.980491024890689e-04, 4.871027648372130e-04, 4.760701961482420e-04, + 4.649620488926223e-04, 4.537895091848745e-04, 4.425642657183772e-04, + 4.312984718939019e-04, 4.200047013284263e-04, 4.086958974496182e-04, + 3.973853163001656e-04, 3.860861491952930e-04, 3.748123955256286e-04, + 3.524058524845366e-04, 3.302655678924825e-04, 3.085009415350808e-04, + 2.872174732124539e-04, 2.665145251918756e-04, 2.464832733922401e-04, + 2.272049395143667e-04, 2.087493762734469e-04, 1.911740540960056e-04, + 1.745234722678595e-04, 1.588289926825976e-04, 1.441090719129753e-04, + 1.303698487634960e-04, 1.176060307004433e-04, 1.058020139949255e-04, + 9.493316895322364e-05, 8.496722273266425e-05, 7.586567714186971e-05, + 6.758520652776391e-05, 6.007899034033536e-05, 5.3297945279603e-05, + 4.719183223815456e-05, 4.171022290285856e-05, 3.680331940840278e-05, + 3.242262756609342e-05, 2.852148981016463e-05, 2.505548812856142e-05, + 2.198272999023423e-05, 1.926403182309834e-05, 1.686301514490703e-05, + 1.474613022020699e-05, 1.288262131725517e-05, 1.124444645438780e-05, + 9.806163112472248e-06, 8.544789874138437e-06, 6.491685361516127e-06, + 4.920595215427144e-06, 3.7214576397747e-06, 2.807681461655717e-06, + 2.111638540671e-06, 1.215662615565951e-06, 6.990879075994651e-07, + 4.017997463994176e-07, 2.306510178248878e-07, 1.317304021078908e-07, + 7.382178264448285e-08, 2.619514583643850e-08, 9.435383475207747e-09, + 3.485294093839820e-09, 1.351620117142246e-09, 5.774263667449611e-10, + 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composition: + H: 5 + C: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.30646568, -4.18658892e-03, 4.97142807e-05, -5.99126606e-08, + 2.30509004e-11, 1.28416265e+04, 4.70720924] + - [1.95465642, 0.0173972722, -7.98206668e-06, 1.75217689e-09, + -1.49641576e-13, 1.285752e+04, 13.4624343] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L12/92 + - name: C2H6 + composition: + H: 6 + C: 2 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [4.29142492, -5.5015427e-03, 5.99438288e-05, -7.08466285e-08, + 2.68685771e-11, -1.15222055e+04, 2.66682316] + - [1.0718815, 0.0216852677, -1.00256067e-05, 2.21412001e-09, -1.9000289e-13, + -1.14263932e+04, 15.1156107] + transport: + model: gas + geometry: nonlinear + diameter: 4.302 + well-depth: 252.3 + rotational-relaxation: 1.5 + note: L8/88 + - name: HCCO + composition: + H: 1 + C: 2 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 4000.0] + data: + - [2.2517214, 0.017655021, -2.3729101e-05, 1.7275759e-08, -5.0664811e-12, + 2.0059449e+04, 12.490417] + - [5.6282058, 4.0853401e-03, -1.5934547e-06, 2.8626052e-10, -1.9407832e-14, + 1.9327215e+04, -3.9302595] + transport: + model: gas + geometry: nonlinear + diameter: 2.5 + well-depth: 150.0 + rotational-relaxation: 1.0 + note: SRIC91 + - name: CH2CO + composition: + H: 2 + C: 2 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [200.0, 1000.0, 3500.0] + data: + - [2.1358363, 0.0181188721, -1.73947474e-05, 9.34397568e-09, + -2.01457615e-12, -7042.91804, 12.215648] + - [4.51129732, 9.00359745e-03, -4.16939635e-06, 9.23345882e-10, + -7.94838201e-14, -7551.05311, 0.632247205] + transport: + model: gas + geometry: nonlinear + diameter: 3.97 + well-depth: 436.0 + rotational-relaxation: 2.0 + note: L5/90 + - name: CH2CHO + composition: + H: 3 + C: 2 + O: 1 + thermo: + model: NASA7 + temperature-ranges: [300.0, 1000.0, 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-c customkinetics.f90 -g -fPIC -o customkinetics.o + gfortran -shared -o customkinetics.so customkinetics.o + \ No newline at end of file diff --git a/samples/python/AVBP/mech_lib/customkinetics.f90 b/samples/python/AVBP/mech_lib/customkinetics.f90 new file mode 100755 index 00000000000..355e516069d --- /dev/null +++ b/samples/python/AVBP/mech_lib/customkinetics.f90 @@ -0,0 +1,2317 @@ +! +! A 15-step reduced mechanism based on GRI3.0 +! +! by Tianfeng Lu +! Email: tlu@engr.uconn.edu +! +! Reference: +! Tianfeng Lu and Chung K. Law, +! "A criterion based on computational singular perturbation +! for the identification of quasi steady state species: +! A reduced mechanism for methane oxidation with NO chemistry," +! Combustion and Flame, Vol.154 No.4 pp.761�774, 2008. +! +! SUBROUTINE CKWYP (P, T, Y, ICKWRK, RCKWRK, WDOT) + SUBROUTINE customkinetics(P, T, Y, WDOT) + IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! +! DIMENSION ICKWRK(*), RCKWRK(*), WDOT(*), Y(*) + PARAMETER (RU=8.314510D7, PATM=1.01325D6, SMALL = 1.D-200) + DIMENSION WDOT(19), Y(19) + DIMENSION TN(5), ROP(184), CTB(184) + DIMENSION RF(184), RB(184), RKLOW(22), XQ(11), C(19) + DIMENSION EQK(184), SMH(30), EG(30) + + ! Correction for units compatibility in Cantera + P = P*10.D0 +! +! CALL YTCP(P, T, Y, C) +! CALL RATT(T, RF, RB, RKLOW) +! CALL RATX(T, C, RF, RB, RKLOW) +! CALL QSSA(RF, RB, XQ) +! CALL RDOT(RF, RB, WDOT) +! END +! +! ----------------------------------------------------------------------! +! +! SUBROUTINE YTCP (P, T, Y, C) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION Y(*), C(*) +! +! +! convert Y to ! + + C(1) = Y(1)*4.96046521D-1 + C(2) = Y(2)*9.92093043D-1 + C(3) = Y(3)*6.25023433D-2 + C(4) = Y(4)*3.12511716D-2 + C(5) = Y(5)*5.87980383D-2 + C(6) = Y(6)*5.55082499D-2 + C(7) = Y(7)*3.02968146D-2 + C(8) = Y(8)*2.93990192D-2 + C(9) = Y(9)*6.65112065D-2 + C(10) = Y(10)*6.23323639D-2 + C(11) = Y(11)*3.57008335D-2 + C(12) = Y(12)*2.27221341D-2 + C(13) = Y(13)*3.33039255D-2 + C(14) = Y(14)*3.12086189D-2 + C(15) = Y(15)*3.84050525D-2 + C(16) = Y(16)*3.56453112D-2 + C(17) = Y(17)*3.32556033D-2 + C(18) = Y(18)*2.37882046D-2 + C(19) = Y(19)*3.56972032D-2 +! + SUM = 0.0 + DO K = 1, 19 + SUM = SUM + C(K) + ENDDO + SUM = P/(SUM*T*8.314510D7) +! + DO K = 1, 19 + C(K) = MAX(C(K),SMALL) * SUM + ENDDO +! END +! +! ----------------------------------------------------------------------! +! +! +! forward reaction rates +! +! SUBROUTINE RATT (T, RF, RB, RKLOW) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION RF(*), RB(*), RKLOW(*), EQK(184), SMH(30), EG(30) +! + ALOGT = LOG(T) + TI = 1.0D0/T + TI2 = TI*TI +! + RF(1) = 1.2D17*TI + RF(2) = 5.D17*TI + RF(3) = EXP(1.05635949D1 +2.7D0*ALOGT -3.15013634D3*TI) + RF(4) = 2.D13 + RF(5) = EXP(1.60803938D1 +2.D0*ALOGT -2.01286667D3*TI) + RF(6) = 5.7D13 + RF(7) = 8.D13 + RF(8) = 1.5D13 + RF(9) = 1.5D13 + RF(10) = 5.06D13 + RF(11) = EXP(2.07430685D1 +1.5D0*ALOGT -4.32766334D3*TI) + RF(12) = EXP(2.36136376D1 -1.20017175D3*TI) + RF(13) = 3.D13 + RF(14) = 3.D13 + RF(15) = EXP(3.12945828D1 -1.781387D3*TI) + RF(16) = 1.D13 + RF(17) = 1.D13 + RF(18) = EXP(1.28687606D1 +2.5D0*ALOGT -1.55997167D3*TI) + RF(19) = EXP(1.17752897D1 +2.5D0*ALOGT -2.51608334D3*TI) + TMP = EXP(2.D0*ALOGT -9.56111669D2*TI ) + RF(20) = 1.35D7 * TMP + RF(21) = 6.94D6 * TMP + RF(22) = 3.D13 + TMP = EXP(1.83D0*ALOGT -1.10707667D2*TI ) + RF(23) = 1.25D7 * TMP + RF(167) = 6.7D6 * TMP + RF(24) = 2.24D13 + RF(25) = EXP(1.83130955D1 +1.92D0*ALOGT -2.86330284D3*TI) + RF(26) = 1.D14 + TMP = EXP(-4.02573334D3*TI) + RF(27) = 1.D13 * TMP + RF(76) = 5.D13 * TMP + RF(28) = EXP(2.81906369D1 -6.79342501D2*TI) + RF(29) = EXP(2.85473118D1 -2.40537567D4*TI) + RF(30) = EXP(3.22361913D1 -2.01286667D4*TI) + RF(31) = EXP(4.24761511D1 -8.6D-1*ALOGT) + TMP = EXP(-1.24D0*ALOGT) + RF(32) = 2.08D19 * TMP + RF(34) = 2.6D19 * TMP + RF(33) = EXP(4.38677883D1 -7.6D-1*ALOGT) + RF(35) = EXP(3.78159211D1 -6.707D-1*ALOGT -8.57531523D3*TI) + RF(36) = 1.D18*TI + RF(37) = EXP(3.90385861D1 -6.D-1*ALOGT) + RF(38) = EXP(4.55408762D1 -1.25D0*ALOGT) + RF(39) = 5.5D20*TI2 + RF(40) = 2.2D22*TI2 + RF(41) = EXP(2.90097872D1 -3.37658384D2*TI) + RF(42) = EXP(3.14332293D1 -5.37435401D2*TI) + RF(43) = EXP(3.20618379D1 -3.19542584D2*TI) + RF(44) = EXP(1.6308716D1 +2.D0*ALOGT -2.61672667D3*TI) + RF(45) = EXP(2.99336062D1 -1.81158D3*TI) + RF(46) = 1.65D14 + RF(47) = 6.D14 + RF(48) = 3.D13 + RF(49) = EXP(3.71706652D1 -5.34D-1*ALOGT -2.69724134D2*TI) + RF(50) = EXP(2.03077504D1 +1.62D0*ALOGT -5.45486868D3*TI) + RF(51) = EXP(2.77171988D1 +4.8D-1*ALOGT +1.30836334D2*TI) + RF(52) = 7.34D13 + RF(53) = EXP(2.7014835D1 +4.54D-1*ALOGT -1.81158D3*TI) + RF(54) = EXP(2.7014835D1 +4.54D-1*ALOGT -1.30836334D3*TI) + RF(55) = EXP(1.78655549D1 +1.9D0*ALOGT -1.3798201D3*TI) + RF(56) = EXP(2.76845619D1 +5.D-1*ALOGT -4.32766334D1*TI) + RF(57) = 2.D13 + RF(58) = EXP(2.58292113D1 +6.5D-1*ALOGT +1.42913534D2*TI) + RF(59) = EXP(3.11214496D1 -9.D-2*ALOGT -3.06962167D2*TI) + RF(60) = EXP(2.85189124D1 +5.15D-1*ALOGT -2.51608334D1*TI) + RF(61) = EXP(1.7541204D1 +1.63D0*ALOGT -9.68188869D2*TI) + RF(62) = 2.D13 + RF(63) = EXP(2.80364862D1 +5.D-1*ALOGT +5.53538334D1*TI) + RF(64) = EXP(3.31993656D1 -2.3D-1*ALOGT -5.38441834D2*TI) + TMP = EXP(2.1D0*ALOGT -2.45066517D3*TI ) + RF(65) = 1.7D7 * TMP + RF(66) = 4.2D6 * TMP + RF(67) = EXP(2.93537877D1 -1.20772D3*TI) + RF(68) = EXP(2.94360258D1 +2.7D-1*ALOGT -1.40900667D2*TI) + RF(69) = 3.D13 + RF(70) = EXP(2.7014835D1 +4.54D-1*ALOGT -9.15854335D2*TI) + RF(71) = EXP(1.4096923D1 +2.53D0*ALOGT -6.15937201D3*TI) + RF(72) = EXP(4.07945264D1 -9.9D-1*ALOGT -7.95082335D2*TI) + RF(73) = 2.D12 + RF(74) = EXP(1.85604427D1 +1.9D0*ALOGT -3.78922151D3*TI) + RF(75) = 1.D14 + RF(77) = EXP(3.00558238D1 -1.72502674D3*TI) + RF(78) = EXP(1.75767107D1 +1.5D0*ALOGT -4.00560467D4*TI) + RF(79) = EXP(1.9190789D1 +1.51D0*ALOGT -1.72603317D3*TI) + RF(80) = EXP(3.19350862D1 -3.7D-1*ALOGT) + RF(81) = EXP(1.0482906D1 +2.4D0*ALOGT +1.06178717D3*TI) + RF(82) = EXP(3.03051698D1 +2.51608334D2*TI) + RF(83) = EXP(2.83241683D1 -2.14873517D2*TI) + RF(84) = EXP(4.19771599D1 -1.47996022D4*TI) + RF(85) = 5.D13 + RF(86) = 3.D13 + RF(87) = 2.D13 + RF(88) = EXP(1.62403133D1 +2.D0*ALOGT -1.50965D3*TI) + RF(89) = 3.D13 + RF(90) = EXP(4.24725733D1 -1.43D0*ALOGT -6.69278168D2*TI) + RF(91) = EXP(1.78408622D1 +1.6D0*ALOGT -2.72743434D3*TI) + RF(92) = EXP(4.10064751D1 -1.34D0*ALOGT -7.13058018D2*TI) + RF(93) = EXP(1.84206807D1 +1.6D0*ALOGT -1.570036D3*TI) + RF(94) = EXP(1.76783433D1 +1.228D0*ALOGT -3.52251667D1*TI) + RF(95) = 5.D13 + RF(96) = EXP(2.19558261D1 +1.18D0*ALOGT +2.2493785D2*TI) + RF(97) = 5.D12 + RF(98) = 5.D12 + RF(99) = EXP(1.41801537D1 +2.D0*ALOGT +4.22702001D2*TI) + RF(100) = EXP(1.56560602D1 +2.D0*ALOGT -7.54825001D2*TI) + RF(101) = EXP(-8.4310155D0 +4.5D0*ALOGT +5.03216668D2*TI) + RF(102) = EXP(-7.6354939D0 +4.D0*ALOGT +1.00643334D3*TI) + RF(103) = 5.D12 + RF(104) = EXP(1.50964444D1 +2.D0*ALOGT -1.25804167D3*TI) + RF(105) = EXP(1.50796373D1 +2.12D0*ALOGT -4.37798501D2*TI) + RF(106) = EXP(2.96459241D1 -1.00643334D3*TI) + RF(107) = EXP(2.55908003D1 +8.20243168D2*TI) + RF(108) = EXP(3.36712758D1 -6.03860001D3*TI) + RF(109) = 2.D13 + RF(110) = 1.D12 + RF(111) = 3.78D13 + RF(112) = EXP(3.26416564D1 -1.18759134D4*TI) + RF(113) = EXP(1.55382772D1 +2.D0*ALOGT -6.03860001D3*TI) + RF(114) = EXP(3.16914641D1 -2.89852801D2*TI) + RF(115) = 5.D13 + RF(116) = 6.71D13 + RF(117) = EXP(3.23131523D1 -1.56500384D3*TI) + RF(118) = EXP(2.93732401D1 +3.79928584D2*TI) + RF(119) = 4.D13 + RF(120) = 3.D13 + RF(121) = 6.D13 + RF(122) = 5.D13 + RF(123) = EXP(3.28780452D1 -7.94679762D3*TI) + RF(124) = EXP(3.21806786D1 +2.59156584D2*TI) + RF(125) = 5.D13 + TMP = EXP(-7.54825001D2*TI) + RF(126) = 5.D12 * TMP + RF(171) = 5.8D12 * TMP + RF(172) = 2.4D12 * TMP + RF(127) = EXP(1.31223634D1 +2.D0*ALOGT -3.63825651D3*TI) + RF(128) = EXP(3.500878D1 -6.01041988D3*TI) + RF(129) = 4.D13 + RF(130) = EXP(1.47156719D1 +2.D0*ALOGT -4.16160184D3*TI) + RF(131) = EXP(2.74203001D1 +5.D-1*ALOGT -2.26950717D3*TI) + RF(132) = 3.D13 + RF(133) = EXP(3.03390713D1 -3.01930001D2*TI) + RF(134) = 2.8D13 + RF(135) = 1.2D13 + RF(136) = 7.D13 + RF(137) = EXP(4.07167205D1 -1.16D0*ALOGT -5.76183084D2*TI) + RF(138) = 3.D13 + TMP = EXP(2.86833501D2*TI) + RF(139) = 1.2D13 * TMP + RF(140) = 1.6D13 * TMP + RF(141) = 9.D12 + RF(142) = 7.D12 + RF(143) = 1.4D13 + RF(144) = EXP(3.13199006D1 +2.76769167D2*TI) + RF(145) = EXP(3.12033668D1 -1.5338044D4*TI) + RF(146) = EXP(2.84682686D1 -1.02228466D4*TI) + RF(147) = EXP(1.01064284D1 +2.47D0*ALOGT -2.60666234D3*TI) + RF(148) = EXP(3.87538626D1 -1.18D0*ALOGT -3.29103701D2*TI) + RF(149) = EXP(2.95538088D1 +1.D-1*ALOGT -5.33409668D3*TI) + RF(150) = 2.648D13 + RF(151) = EXP(8.10772006D0 +2.81D0*ALOGT -2.94884967D3*TI) + TMP = EXP(1.5D0*ALOGT -5.00197368D3*TI) + RF(152) = 3.D7 * TMP + RF(153) = 1.D7 * TMP + RF(154) = EXP(1.23327053D1 +2.D0*ALOGT -4.62959334D3*TI) + RF(155) = EXP(1.56303353D1 +1.74D0*ALOGT -5.25861418D3*TI) + TMP = EXP(-1.D0*ALOGT -8.55468335D3*TI) + RF(156) = 1.5D18 * TMP + RF(157) = 1.87D17 * TMP + RF(158) = EXP(3.02300002D1 -2.01286667D2*TI) + RF(159) = EXP(3.05213929D1 -4.52895001D2*TI) + RF(160) = EXP(-2.84796532D1 +7.6D0*ALOGT +1.77635484D3*TI) + RF(161) = EXP(3.83630605D1 -1.39D0*ALOGT -5.10764918D2*TI) + RF(162) = EXP(2.97104627D1 +4.4D-1*ALOGT -4.36641103D4*TI) + RF(163) = EXP(2.74566677D1 -1.94996459D3*TI) + RF(164) = EXP(2.87941719D1 -4.29747034D2*TI) + RF(165) = 1.D13 + RF(166) = 3.37D13 + RF(168) = EXP(3.61482143D1 -8.72074485D3*TI) + RF(169) = EXP(2.28027074D1 +5.D-1*ALOGT +8.83145252D2*TI) + RF(170) = EXP(2.83090547D1 +4.3D-1*ALOGT +1.86190167D2*TI) + RF(173) = EXP(3.29293385D1 -5.52984796D3*TI) + RF(174) = EXP(2.49457104D1 +2.5D-1*ALOGT +4.70507584D2*TI) + RF(175) = EXP(2.64369986D1 +2.9D-1*ALOGT -5.53538334D0*TI) + RF(176) = EXP(1.41059389D1 +1.61D0*ALOGT +1.932352D2*TI) + RF(177) = EXP(2.69105027D1 +4.22D-1*ALOGT +8.83145252D2*TI) + RF(178) = 1.5D14 + RF(179) = 1.81D10 + RF(180) = 2.35D10 + RF(181) = 2.2D13 + RF(182) = 1.1D13 + RF(183) = 1.2D13 + RF(184) = 3.01D13 +! +! +! thermal data +! +! + TLOG = LOG(T) + TI = 1.0D0/T + TN(1) = TLOG - 1.0 + TN(2) = T + TN(3) = TN(2)*T + TN(4) = TN(3)*T + TN(5) = TN(4)*T +! + IF (T .GT. 1.D3) THEN +! + SMH(1) = -3.20502331D+00 + 9.50158922D+02*TI & + + 3.33727920D+00*TN(1) - 2.47012365D-05*TN(2) & + + 8.32427963D-08*TN(3) - 1.49638662D-11*TN(4) & + + 1.00127688D-15*TN(5) + SMH(2) = -4.46682914D-01 - 2.54736599D+04*TI & + + 2.50000001D+00*TN(1) - 1.15421486D-11*TN(2) & + + 2.69269913D-15*TN(3) - 3.94596029D-19*TN(4) & + + 2.49098679D-23*TN(5) + SMH(3) = 4.78433864D+00 - 2.92175791D+04*TI & + + 2.56942078D+00*TN(1) - 4.29870569D-05*TN(2) & + + 6.99140982D-09*TN(3) - 8.34814992D-13*TN(4) & + + 6.14168455D-17*TN(5) + SMH(4) = 5.45323129D+00 + 1.08845772D+03*TI & + + 3.28253784D+00*TN(1) + 7.41543770D-04*TN(2) & + - 1.26327778D-07*TN(3) + 1.74558796D-11*TN(4) & + - 1.08358897D-15*TN(5) + SMH(5) = 4.47669610D+00 - 3.85865700D+03*TI & + + 3.09288767D+00*TN(1) + 2.74214858D-04*TN(2) & + + 2.10842047D-08*TN(3) - 7.32884630D-12*TN(4) & + + 5.87061880D-16*TN(5) + SMH(6) = 4.96677010D+00 + 3.00042971D+04*TI & + + 3.03399249D+00*TN(1) + 1.08845902D-03*TN(2) & + - 2.73454197D-08*TN(3) - 8.08683225D-12*TN(4) & + + 8.41004960D-16*TN(5) + SMH(7) = 3.78510215D+00 - 1.11856713D+02*TI & + + 4.01721090D+00*TN(1) + 1.11991007D-03*TN(2) & + - 1.05609692D-07*TN(3) + 9.52053083D-12*TN(4) & + - 5.39542675D-16*TN(5) + SMH(8) = 2.91615662D+00 + 1.78617877D+04*TI & + + 4.16500285D+00*TN(1) + 2.45415847D-03*TN(2) & + - 3.16898708D-07*TN(3) + 3.09321655D-11*TN(4) & + - 1.43954153D-15*TN(5) + SMH(9) = 4.80150373D+00 - 8.54512953D+04*TI & + + 2.49266888D+00*TN(1) + 2.39944642D-05*TN(2) & + - 1.20722503D-08*TN(3) + 3.11909191D-12*TN(4) & + - 2.43638946D-16*TN(5) + SMH(10) = 5.48497999D+00 - 7.10124364D+04*TI & + + 2.87846473D+00*TN(1) + 4.85456841D-04*TN(2) & + + 2.40742758D-08*TN(3) - 1.08906541D-11*TN(4) & + + 8.80396915D-16*TN(5) + SMH(11) = 6.17119324D+00 - 4.62636040D+04*TI & + + 2.87410113D+00*TN(1) + 1.82819646D-03*TN(2) & + - 2.34824328D-07*TN(3) + 2.16816291D-11*TN(4) & + - 9.38637835D-16*TN(5) + SMH(12) = 8.62650169D+00 - 5.09259997D+04*TI & + + 2.29203842D+00*TN(1) + 2.32794319D-03*TN(2) & + - 3.35319912D-07*TN(3) + 3.48255000D-11*TN(4) & + - 1.69858183D-15*TN(5) + SMH(13) = 8.48007179D+00 - 1.67755843D+04*TI & + + 2.28571772D+00*TN(1) + 3.61995018D-03*TN(2) & + - 4.97857247D-07*TN(3) + 4.96403870D-11*TN(4) & + - 2.33577197D-15*TN(5) + SMH(14) = 1.84373180D+01 + 9.46834459D+03*TI & + + 7.48514950D-02*TN(1) + 6.69547335D-03*TN(2) & + - 9.55476348D-07*TN(3) + 1.01910446D-10*TN(4) & + - 5.09076150D-15*TN(5) + SMH(15) = 7.81868772D+00 + 1.41518724D+04*TI & + + 2.71518561D+00*TN(1) + 1.03126372D-03*TN(2) & + - 1.66470962D-07*TN(3) + 1.91710840D-11*TN(4) & + - 1.01823858D-15*TN(5) + SMH(16) = 2.27163806D+00 + 4.87591660D+04*TI & + + 3.85746029D+00*TN(1) + 2.20718513D-03*TN(2) & + - 3.69135673D-07*TN(3) + 4.36241823D-11*TN(4) & + - 2.36042082D-15*TN(5) + SMH(17) = 9.79834492D+00 - 4.01191815D+03*TI & + + 2.77217438D+00*TN(1) + 2.47847763D-03*TN(2) & + - 4.14076022D-07*TN(3) + 4.90968148D-11*TN(4) & + - 2.66754356D-15*TN(5) + SMH(18) = 1.36563230D+01 + 1.39958323D+04*TI & + + 1.76069008D+00*TN(1) + 4.60000041D-03*TN(2) & + - 7.37098022D-07*TN(3) + 8.38676767D-11*TN(4) & + - 4.41927820D-15*TN(5) + SMH(19) = 5.81043215D+00 + 3.24250627D+03*TI & + + 3.69266569D+00*TN(1) + 4.32288399D-03*TN(2) & + - 6.25168533D-07*TN(3) + 6.56028863D-11*TN(4) & + - 3.24277101D-15*TN(5) + SMH(20) = 2.92957500D+00 - 1.27832520D+02*TI & + + 3.77079900D+00*TN(1) + 3.93574850D-03*TN(2) & + - 4.42730667D-07*TN(3) + 3.28702583D-11*TN(4) & + - 1.05630800D-15*TN(5) + + SMH(21) = 1.45023623D+01 + 2.53748747D+04*TI & + + 1.78970791D+00*TN(1) + 7.04691460D-03*TN(2) & + - 1.06083472D-06*TN(3) + 1.15142571D-10*TN(4) & + - 5.85301100D-15*TN(5) + SMH(22) = -1.23028121D+00 - 2.59359992D+04*TI & + + 4.14756964D+00*TN(1) + 2.98083332D-03*TN(2) & + - 3.95491420D-07*TN(3) + 3.89510143D-11*TN(4) & + - 1.80617607D-15*TN(5) + SMH(23) = 7.78732378D+00 - 3.46128739D+04*TI & + + 3.01672400D+00*TN(1) + 5.16511460D-03*TN(2) & + - 7.80137248D-07*TN(3) + 8.48027400D-11*TN(4) & + - 4.31303520D-15*TN(5) + SMH(24) = 1.03053693D+01 - 4.93988614D+03*TI & + + 2.03611116D+00*TN(1) + 7.32270755D-03*TN(2) & + - 1.11846319D-06*TN(3) + 1.22685769D-10*TN(4) & + - 6.28530305D-15*TN(5) + SMH(25) = 1.34624343D+01 - 1.28575200D+04*TI & + + 1.95465642D+00*TN(1) + 8.69863610D-03*TN(2) & + - 1.33034445D-06*TN(3) + 1.46014741D-10*TN(4) & + - 7.48207880D-15*TN(5) + SMH(26) = 1.51156107D+01 + 1.14263932D+04*TI & + + 1.07188150D+00*TN(1) + 1.08426339D-02*TN(2) & + - 1.67093445D-06*TN(3) + 1.84510001D-10*TN(4) & + - 9.50014450D-15*TN(5) + SMH(27) = -3.93025950D+00 - 1.93272150D+04*TI & + + 5.62820580D+00*TN(1) + 2.04267005D-03*TN(2) & + - 2.65575783D-07*TN(3) + 2.38550433D-11*TN(4) & + - 9.70391600D-16*TN(5) + SMH(28) = 6.32247205D-01 + 7.55105311D+03*TI & + + 4.51129732D+00*TN(1) + 4.50179872D-03*TN(2) & + - 6.94899392D-07*TN(3) + 7.69454902D-11*TN(4) & + - 3.97419100D-15*TN(5) + SMH(29) = -5.04525100D+00 - 4.90321800D+02*TI & + + 5.97567000D+00*TN(1) + 4.06529550D-03*TN(2) & + - 4.57270667D-07*TN(3) + 3.39192000D-11*TN(4) & + - 1.08800850D-15*TN(5) +! + ELSE +! + SMH(1) = 6.83010238D-01 + 9.17935173D+02*TI & + + 2.34433112D+00*TN(1) + 3.99026037D-03*TN(2) & + - 3.24635850D-06*TN(3) + 1.67976745D-09*TN(4) & + - 3.68805881D-13*TN(5) + SMH(2) = -4.46682853D-01 - 2.54736599D+04*TI & + + 2.50000000D+00*TN(1) + 3.52666409D-13*TN(2) & + - 3.32653273D-16*TN(3) + 1.91734693D-19*TN(4) & + - 4.63866166D-23*TN(5) + SMH(3) = 2.05193346D+00 - 2.91222592D+04*TI & + + 3.16826710D+00*TN(1) - 1.63965942D-03*TN(2) & + + 1.10717733D-06*TN(3) - 5.10672187D-10*TN(4) & + + 1.05632986D-13*TN(5) + SMH(4) = 3.65767573D+00 + 1.06394356D+03*TI & + + 3.78245636D+00*TN(1) - 1.49836708D-03*TN(2) & + + 1.64121700D-06*TN(3) - 8.06774591D-10*TN(4) & + + 1.62186419D-13*TN(5) + SMH(5) = -1.03925458D-01 - 3.61508056D+03*TI & + + 3.99201543D+00*TN(1) - 1.20065876D-03*TN(2) & + + 7.69656402D-07*TN(3) - 3.23427778D-10*TN(4) & + + 6.82057350D-14*TN(5) + SMH(6) = -8.49032208D-01 + 3.02937267D+04*TI & + + 4.19864056D+00*TN(1) - 1.01821705D-03*TN(2) & + + 1.08673369D-06*TN(3) - 4.57330885D-10*TN(4) & + + 8.85989085D-14*TN(5) + SMH(7) = 3.71666245D+00 - 2.94808040D+02*TI & + + 4.30179801D+00*TN(1) - 2.37456025D-03*TN(2) & + + 3.52638152D-06*TN(3) - 2.02303245D-09*TN(4) & + + 4.64612562D-13*TN(5) + SMH(8) = 3.43505074D+00 + 1.77025821D+04*TI & + + 4.27611269D+00*TN(1) - 2.71411208D-04*TN(2) & + + 2.78892835D-06*TN(3) - 1.79809011D-09*TN(4) & + + 4.31227182D-13*TN(5) + SMH(9) = 4.53130848D+00 - 8.54438832D+04*TI & + + 2.55423955D+00*TN(1) - 1.60768862D-04*TN(2) & + + 1.22298708D-07*TN(3) - 6.10195741D-11*TN(4) & + + 1.33260723D-14*TN(5) + SMH(10) = 2.08401108D+00 - 7.07972934D+04*TI & + + 3.48981665D+00*TN(1) + 1.61917771D-04*TN(2) & + - 2.81498442D-07*TN(3) + 2.63514439D-10*TN(4) & + - 7.03045335D-14*TN(5) + SMH(11) = 1.56253185D+00 - 4.60040401D+04*TI & + + 3.76267867D+00*TN(1) + 4.84436072D-04*TN(2) & + + 4.65816402D-07*TN(3) - 3.20909294D-10*TN(4) & + + 8.43708595D-14*TN(5) + SMH(12) = -7.69118967D-01 - 5.04968163D+04*TI & + + 4.19860411D+00*TN(1) - 1.18330710D-03*TN(2) & + + 1.37216037D-06*TN(3) - 5.57346651D-10*TN(4) & + + 9.71573685D-14*TN(5) + SMH(13) = 1.60456433D+00 - 1.64449988D+04*TI & + + 3.67359040D+00*TN(1) + 1.00547588D-03*TN(2) & + + 9.55036427D-07*TN(3) - 5.72597854D-10*TN(4) & + + 1.27192867D-13*TN(5) + SMH(14) = -4.64130376D+00 + 1.02466476D+04*TI & + + 5.14987613D+00*TN(1) - 6.83548940D-03*TN(2) & + + 8.19667665D-06*TN(3) - 4.03952522D-09*TN(4) & + + 8.33469780D-13*TN(5) + SMH(15) = 3.50840928D+00 + 1.43440860D+04*TI & + + 3.57953347D+00*TN(1) - 3.05176840D-04*TN(2) & + + 1.69469055D-07*TN(3) + 7.55838237D-11*TN(4) & + - 4.52212249D-14*TN(5) + SMH(16) = 9.90105222D+00 + 4.83719697D+04*TI & + + 2.35677352D+00*TN(1) + 4.49229839D-03*TN(2) & + - 1.18726045D-06*TN(3) + 2.04932518D-10*TN(4) & + - 7.18497740D-15*TN(5) + SMH(17) = 3.39437243D+00 - 3.83956496D+03*TI & + + 4.22118584D+00*TN(1) - 1.62196266D-03*TN(2) & + + 2.29665743D-06*TN(3) - 1.10953411D-09*TN(4) & + + 2.16884433D-13*TN(5) + SMH(18) = 6.02812900D-01 + 1.43089567D+04*TI & + + 4.79372315D+00*TN(1) - 4.95416685D-03*TN(2) & + + 6.22033347D-06*TN(3) - 3.16071051D-09*TN(4) & + + 6.58863260D-13*TN(5) + SMH(19) = 5.47302243D+00 + 3.19391367D+03*TI & + + 3.86388918D+00*TN(1) + 2.79836152D-03*TN(2) & + + 9.88786318D-07*TN(3) - 8.71100100D-10*TN(4) & + + 2.18483639D-13*TN(5) + SMH(20) = 1.31521770D+01 - 9.78601100D+02*TI & + + 2.10620400D+00*TN(1) + 3.60829750D-03*TN(2) & + + 8.89745333D-07*TN(3) - 6.14803000D-10*TN(4) & + + 1.03780500D-13*TN(5) + SMH(21) = -1.50409823D+00 + 2.56427656D+04*TI & + + 5.71539582D+00*TN(1) - 7.61545645D-03*TN(2) & + + 1.08740193D-05*TN(3) - 5.92339074D-09*TN(4) & + + 1.30676349D-12*TN(5) + SMH(22) = 1.39397051D+01 - 2.64289807D+04*TI & + + 8.08681094D-01*TN(1) + 1.16807815D-02*TN(2) & + - 5.91953025D-06*TN(3) + 2.33460364D-09*TN(4) & + - 4.25036487D-13*TN(5) + SMH(23) = 8.51054025D+00 - 3.48598468D+04*TI & + + 3.21246645D+00*TN(1) + 7.57395810D-04*TN(2) & + + 4.32015687D-06*TN(3) - 2.98048206D-09*TN(4) & + + 7.35754365D-13*TN(5) + SMH(24) = 4.09733096D+00 - 5.08977593D+03*TI & + + 3.95920148D+00*TN(1) - 3.78526124D-03*TN(2) & + + 9.51650487D-06*TN(3) - 5.76323961D-09*TN(4) & + + 1.34942187D-12*TN(5) + SMH(25) = 4.70720924D+00 - 1.28416265D+04*TI & + + 4.30646568D+00*TN(1) - 2.09329446D-03*TN(2) & + + 8.28571345D-06*TN(3) - 4.99272172D-09*TN(4) & + + 1.15254502D-12*TN(5) + SMH(26) = 2.66682316D+00 + 1.15222055D+04*TI & + + 4.29142492D+00*TN(1) - 2.75077135D-03*TN(2) & + + 9.99063813D-06*TN(3) - 5.90388571D-09*TN(4) & + + 1.34342886D-12*TN(5) + SMH(27) = 1.24904170D+01 - 2.00594490D+04*TI & + + 2.25172140D+00*TN(1) + 8.82751050D-03*TN(2) & + - 3.95485017D-06*TN(3) + 1.43964658D-09*TN(4) & + - 2.53324055D-13*TN(5) + SMH(28) = 1.22156480D+01 + 7.04291804D+03*TI & + + 2.13583630D+00*TN(1) + 9.05943605D-03*TN(2) & + - 2.89912457D-06*TN(3) + 7.78664640D-10*TN(4) & + - 1.00728807D-13*TN(5) + SMH(29) = 9.55829000D+00 - 1.52147660D+03*TI & + + 3.40906200D+00*TN(1) + 5.36928700D-03*TN(2) & + + 3.15248667D-07*TN(3) - 5.96548583D-10*TN(4) & + + 1.43369250D-13*TN(5) + ENDIF +! CALL RDSMH (T, SMH) +! +! equilibrium constants +! + DO N = 1, 29 + EG(N) = EXP(SMH(N)) + ENDDO +! + PFAC = PATM / (RU*T) + PFAC2 = PFAC*PFAC + PFAC3 = PFAC2*PFAC +! + EQK(1)=EG(4)/EG(3)/EG(3)/PFAC + EQK(2)=EG(5)/EG(2)/EG(3)/PFAC + EQK(3)=EG(2)*EG(5)/EG(1)/EG(3) + EQK(4)=EG(4)*EG(5)/EG(3)/EG(7) + EQK(5)=EG(5)*EG(7)/EG(3)/EG(8) + EQK(6)=EG(2)*EG(15)/EG(3)/EG(10) + EQK(7)=EG(2)*EG(17)/EG(3)/EG(11) + EQK(8)=EG(1)*EG(15)/EG(3)/EG(12) + EQK(9)=EG(2)*EG(17)/EG(3)/EG(12) + EQK(10)=EG(2)*EG(18)/EG(3)/EG(13) + EQK(11)=EG(5)*EG(13)/EG(3)/EG(14) + EQK(12)=EG(16)/EG(3)/EG(15)/PFAC + EQK(13)=EG(5)*EG(15)/EG(3)/EG(17) + EQK(14)=EG(2)*EG(16)/EG(3)/EG(17) + EQK(15)=EG(5)*EG(17)/EG(3)/EG(18) + EQK(16)=EG(5)*EG(18)/EG(3)/EG(19) + EQK(17)=EG(5)*EG(18)/EG(3)/EG(20) + EQK(18)=EG(5)*EG(19)/EG(3)/EG(21) + EQK(19)=EG(5)*EG(20)/EG(3)/EG(21) + EQK(20)=EG(2)*EG(27)/EG(3)/EG(22) + EQK(21)=EG(11)*EG(15)/EG(3)/EG(22) + EQK(22)=EG(2)*EG(28)/EG(3)/EG(23) + EQK(23)=EG(13)*EG(17)/EG(3)/EG(24) + EQK(24)=EG(13)*EG(18)/EG(3)/EG(25) + EQK(25)=EG(5)*EG(25)/EG(3)/EG(26) + EQK(26)=EG(2)*EG(15)*EG(15)/EG(3)/EG(27)*PFAC + EQK(27)=EG(5)*EG(27)/EG(3)/EG(28) + EQK(28)=EG(11)*EG(16)/EG(3)/EG(28) + EQK(29)=EG(3)*EG(16)/EG(4)/EG(15) + EQK(30)=EG(7)*EG(17)/EG(4)/EG(18) + EQK(31)=EG(7)/EG(2)/EG(4)/PFAC + EQK(32)=EQK(31) + EQK(33)=EQK(31) + EQK(34)=EQK(31) + EQK(35)=EG(3)*EG(5)/EG(2)/EG(4) + EQK(36)=EG(1)/EG(2)/EG(2)/PFAC + EQK(37)=EQK(36) + EQK(38)=EQK(36) + EQK(39)=EQK(36) + EQK(40)=EG(6)/EG(2)/EG(5)/PFAC + EQK(41)=EG(3)*EG(6)/EG(2)/EG(7) + EQK(42)=EG(1)*EG(4)/EG(2)/EG(7) + EQK(43)=EG(5)*EG(5)/EG(2)/EG(7) + EQK(44)=EG(1)*EG(7)/EG(2)/EG(8) + EQK(45)=EG(5)*EG(6)/EG(2)/EG(8) + EQK(46)=EG(1)*EG(9)/EG(2)/EG(10) + EQK(47)=EG(13)/EG(2)/EG(11)/PFAC + EQK(48)=EG(1)*EG(10)/EG(2)/EG(12) + EQK(49)=EG(14)/EG(2)/EG(13)/PFAC + EQK(50)=EG(1)*EG(13)/EG(2)/EG(14) + EQK(51)=EG(18)/EG(2)/EG(17)/PFAC + EQK(52)=EG(1)*EG(15)/EG(2)/EG(17) + EQK(53)=EG(19)/EG(2)/EG(18)/PFAC + EQK(54)=EG(20)/EG(2)/EG(18)/PFAC + EQK(55)=EG(1)*EG(17)/EG(2)/EG(18) + EQK(56)=EG(21)/EG(2)/EG(19)/PFAC + EQK(57)=EG(1)*EG(18)/EG(2)/EG(19) + EQK(58)=EG(5)*EG(13)/EG(2)/EG(19) + EQK(59)=EG(6)*EG(12)/EG(2)/EG(19) + EQK(60)=EG(21)/EG(2)/EG(20)/PFAC + EQK(61)=EG(19)/EG(20) + EQK(62)=EG(1)*EG(18)/EG(2)/EG(20) + EQK(63)=EG(5)*EG(13)/EG(2)/EG(20) + EQK(64)=EG(6)*EG(12)/EG(2)/EG(20) + EQK(65)=EG(1)*EG(19)/EG(2)/EG(21) + EQK(66)=EG(1)*EG(20)/EG(2)/EG(21) + EQK(67)=EG(23)/EG(2)/EG(22)/PFAC + EQK(68)=EG(24)/EG(2)/EG(23)/PFAC + EQK(69)=EG(1)*EG(22)/EG(2)/EG(23) + EQK(70)=EG(25)/EG(2)/EG(24)/PFAC + EQK(71)=EG(1)*EG(23)/EG(2)/EG(24) + EQK(72)=EG(26)/EG(2)/EG(25)/PFAC + EQK(73)=EG(1)*EG(24)/EG(2)/EG(25) + EQK(74)=EG(1)*EG(25)/EG(2)/EG(26) + EQK(75)=EG(12)*EG(15)/EG(2)/EG(27) + EQK(76)=EG(1)*EG(27)/EG(2)/EG(28) + EQK(77)=EG(13)*EG(15)/EG(2)/EG(28) + EQK(78)=EG(18)/EG(1)/EG(15)/PFAC + EQK(79)=EG(2)*EG(6)/EG(1)/EG(5) + EQK(80)=EG(8)/EG(5)/EG(5)/PFAC + EQK(81)=EG(3)*EG(6)/EG(5)/EG(5) + EQK(82)=EG(4)*EG(6)/EG(5)/EG(7) + EQK(168)=EQK(82) + EQK(83)=EG(6)*EG(7)/EG(5)/EG(8) + EQK(84)=EQK(83) + EQK(85)=EG(2)*EG(15)/EG(5)/EG(9) + EQK(86)=EG(2)*EG(17)/EG(5)/EG(10) + EQK(87)=EG(2)*EG(18)/EG(5)/EG(11) + EQK(88)=EG(6)*EG(10)/EG(5)/EG(11) + EQK(89)=EG(2)*EG(18)/EG(5)/EG(12) + EQK(90)=EG(21)/EG(5)/EG(13)/PFAC + EQK(91)=EG(6)*EG(11)/EG(5)/EG(13) + EQK(92)=EG(6)*EG(12)/EG(5)/EG(13) + EQK(93)=EG(6)*EG(13)/EG(5)/EG(14) + EQK(94)=EG(2)*EG(16)/EG(5)/EG(15) + EQK(95)=EG(6)*EG(15)/EG(5)/EG(17) + EQK(96)=EG(6)*EG(17)/EG(5)/EG(18) + EQK(97)=EG(6)*EG(18)/EG(5)/EG(19) + EQK(98)=EG(6)*EG(18)/EG(5)/EG(20) + EQK(99)=EG(6)*EG(19)/EG(5)/EG(21) + EQK(100)=EG(6)*EG(20)/EG(5)/EG(21) + EQK(101)=EG(2)*EG(28)/EG(5)/EG(22) + EQK(102)=EG(13)*EG(15)/EG(5)/EG(22) + EQK(103)=EG(6)*EG(22)/EG(5)/EG(23) + EQK(104)=EG(6)*EG(23)/EG(5)/EG(24) + EQK(105)=EG(6)*EG(25)/EG(5)/EG(26) + EQK(106)=EG(6)*EG(27)/EG(5)/EG(28) + EQK(107)=EG(4)*EG(8)/EG(7)/EG(7) + EQK(108)=EQK(107) + EQK(109)=EG(5)*EG(18)/EG(7)/EG(11) + EQK(110)=EG(4)*EG(14)/EG(7)/EG(13) + EQK(111)=EG(5)*EG(20)/EG(7)/EG(13) + EQK(112)=EG(5)*EG(16)/EG(7)/EG(15) + EQK(113)=EG(8)*EG(17)/EG(7)/EG(18) + EQK(114)=EG(3)*EG(15)/EG(4)/EG(9) + EQK(115)=EG(2)*EG(22)/EG(9)/EG(13) + EQK(116)=EG(3)*EG(17)/EG(4)/EG(10) + EQK(117)=EG(2)*EG(11)/EG(1)/EG(10) + EQK(118)=EG(2)*EG(18)/EG(6)/EG(10) + EQK(119)=EG(2)*EG(22)/EG(10)/EG(11) + EQK(120)=EG(2)*EG(23)/EG(10)/EG(13) + EQK(121)=EG(2)*EG(24)/EG(10)/EG(14) + EQK(122)=EG(27)/EG(10)/EG(15)/PFAC + EQK(123)=EG(15)*EG(17)/EG(10)/EG(16) + EQK(124)=EG(2)*EG(28)/EG(10)/EG(18) + EQK(125)=EG(15)*EG(22)/EG(10)/EG(27) + EQK(127)=EG(2)*EG(13)/EG(1)/EG(11) + EQK(128)=EG(1)*EG(22)/EG(11)/EG(11) + EQK(129)=EG(2)*EG(24)/EG(11)/EG(13) + EQK(130)=EG(13)*EG(13)/EG(11)/EG(14) + EQK(131)=EG(28)/EG(11)/EG(15)/PFAC + EQK(132)=EG(15)*EG(23)/EG(11)/EG(27) + EQK(133)=EG(11)/EG(12) + EQK(138)=EQK(133) + EQK(141)=EQK(133) + EQK(142)=EQK(133) + EQK(134)=EG(2)*EG(5)*EG(15)/EG(4)/EG(12)*PFAC + EQK(135)=EG(6)*EG(15)/EG(4)/EG(12) + EQK(136)=EG(2)*EG(13)/EG(1)/EG(12) + EQK(137)=EG(21)/EG(6)/EG(12)/PFAC + EQK(139)=EG(2)*EG(24)/EG(12)/EG(13) + EQK(140)=EG(13)*EG(13)/EG(12)/EG(14) + EQK(143)=EG(15)*EG(18)/EG(12)/EG(16) + EQK(144)=EG(13)*EG(25)/EG(12)/EG(26) + EQK(145)=EG(3)*EG(20)/EG(4)/EG(13) + EQK(146)=EG(5)*EG(18)/EG(4)/EG(13) + EQK(147)=EG(7)*EG(14)/EG(8)/EG(13) + EQK(148)=EG(26)/EG(13)/EG(13)/PFAC + EQK(149)=EG(2)*EG(25)/EG(13)/EG(13) + EQK(150)=EG(14)*EG(15)/EG(13)/EG(17) + EQK(151)=EG(14)*EG(17)/EG(13)/EG(18) + EQK(152)=EG(14)*EG(19)/EG(13)/EG(21) + EQK(153)=EG(14)*EG(20)/EG(13)/EG(21) + EQK(154)=EG(14)*EG(23)/EG(13)/EG(24) + EQK(155)=EG(14)*EG(25)/EG(13)/EG(26) + EQK(156)=EG(2)*EG(15)/EG(17)*PFAC + EQK(157)=EQK(156) + EQK(158)=EG(7)*EG(15)/EG(4)/EG(17) + EQK(159)=EG(7)*EG(18)/EG(4)/EG(19) + EQK(160)=EG(7)*EG(18)/EG(4)/EG(20) + EQK(161)=EG(17)*EG(18)/EG(4)/EG(23) + EQK(162)=EG(1)*EG(22)/EG(24)*PFAC + EQK(163)=EG(7)*EG(24)/EG(4)/EG(25) + EQK(164)=EG(5)*EG(15)*EG(15)/EG(4)/EG(27)*PFAC + EQK(165)=EG(15)*EG(15)*EG(22)/EG(27)/EG(27)*PFAC + EQK(167)=EG(2)*EG(29)/EG(3)/EG(24) + EQK(170)=EG(13)/EG(1)/EG(10)/PFAC + EQK(172)=EG(3)*EG(18)/EG(4)/EG(11) + EQK(175)=EG(3)*EG(29)/EG(4)/EG(23) + EQK(176)=EG(7)*EG(22)/EG(4)/EG(23) + EQK(177)=EG(29)/EG(2)/EG(28)/PFAC + EQK(181)=EG(13)*EG(17)/EG(2)/EG(29) + EQK(182)=EG(1)*EG(28)/EG(2)/EG(29) + EQK(183)=EG(6)*EG(28)/EG(5)/EG(29) + EQK(184)=EG(17)*EG(19)/EG(5)/EG(29) +! +! +! ! Compute reverse reaction rates +! +! PARAMETER (SMALL = 1.D-200) +! + RB(1) = RF(1) / MAX(EQK(1),SMALL) + RB(2) = RF(2) / MAX(EQK(2),SMALL) + RB(3) = RF(3) / MAX(EQK(3),SMALL) + RB(4) = RF(4) / MAX(EQK(4),SMALL) + RB(5) = RF(5) / MAX(EQK(5),SMALL) + RB(6) = RF(6) / MAX(EQK(6),SMALL) + RB(7) = RF(7) / MAX(EQK(7),SMALL) + RB(8) = RF(8) / MAX(EQK(8),SMALL) + RB(9) = RF(9) / MAX(EQK(9),SMALL) + RB(10) = RF(10) / MAX(EQK(10),SMALL) + RB(11) = RF(11) / MAX(EQK(11),SMALL) + RB(12) = RF(12) / MAX(EQK(12),SMALL) + RB(13) = RF(13) / MAX(EQK(13),SMALL) + RB(14) = RF(14) / MAX(EQK(14),SMALL) + RB(15) = RF(15) / MAX(EQK(15),SMALL) + RB(16) = RF(16) / MAX(EQK(16),SMALL) + RB(17) = RF(17) / MAX(EQK(17),SMALL) + RB(18) = RF(18) / MAX(EQK(18),SMALL) + RB(19) = RF(19) / MAX(EQK(19),SMALL) + RB(20) = RF(20) / MAX(EQK(20),SMALL) + RB(21) = RF(21) / MAX(EQK(21),SMALL) + RB(22) = RF(22) / MAX(EQK(22),SMALL) + RB(23) = RF(23) / MAX(EQK(23),SMALL) + RB(24) = RF(24) / MAX(EQK(24),SMALL) + RB(25) = RF(25) / MAX(EQK(25),SMALL) + RB(26) = RF(26) / MAX(EQK(26),SMALL) + RB(27) = RF(27) / MAX(EQK(27),SMALL) + RB(28) = RF(28) / MAX(EQK(28),SMALL) + RB(29) = RF(29) / MAX(EQK(29),SMALL) + RB(30) = RF(30) / MAX(EQK(30),SMALL) + RB(31) = RF(31) / MAX(EQK(31),SMALL) + RB(32) = RF(32) / MAX(EQK(32),SMALL) + RB(33) = RF(33) / MAX(EQK(33),SMALL) + RB(34) = RF(34) / MAX(EQK(34),SMALL) + RB(35) = RF(35) / MAX(EQK(35),SMALL) + RB(36) = RF(36) / MAX(EQK(36),SMALL) + RB(37) = RF(37) / MAX(EQK(37),SMALL) + + RB(38) = RF(38) / MAX(EQK(38),SMALL) + RB(39) = RF(39) / MAX(EQK(39),SMALL) + RB(40) = RF(40) / MAX(EQK(40),SMALL) + RB(41) = RF(41) / MAX(EQK(41),SMALL) + RB(42) = RF(42) / MAX(EQK(42),SMALL) + RB(43) = RF(43) / MAX(EQK(43),SMALL) + RB(44) = RF(44) / MAX(EQK(44),SMALL) + RB(45) = RF(45) / MAX(EQK(45),SMALL) + RB(46) = RF(46) / MAX(EQK(46),SMALL) + RB(47) = RF(47) / MAX(EQK(47),SMALL) + RB(48) = RF(48) / MAX(EQK(48),SMALL) + RB(49) = RF(49) / MAX(EQK(49),SMALL) + RB(50) = RF(50) / MAX(EQK(50),SMALL) + RB(51) = RF(51) / MAX(EQK(51),SMALL) + RB(52) = RF(52) / MAX(EQK(52),SMALL) + RB(53) = RF(53) / MAX(EQK(53),SMALL) + RB(54) = RF(54) / MAX(EQK(54),SMALL) + RB(55) = RF(55) / MAX(EQK(55),SMALL) + RB(56) = RF(56) / MAX(EQK(56),SMALL) + RB(57) = RF(57) / MAX(EQK(57),SMALL) + RB(58) = RF(58) / MAX(EQK(58),SMALL) + RB(59) = RF(59) / MAX(EQK(59),SMALL) + RB(60) = RF(60) / MAX(EQK(60),SMALL) + RB(61) = RF(61) / MAX(EQK(61),SMALL) + RB(62) = RF(62) / MAX(EQK(62),SMALL) + RB(63) = RF(63) / MAX(EQK(63),SMALL) + RB(64) = RF(64) / MAX(EQK(64),SMALL) + RB(65) = RF(65) / MAX(EQK(65),SMALL) + RB(66) = RF(66) / MAX(EQK(66),SMALL) + RB(67) = RF(67) / MAX(EQK(67),SMALL) + RB(68) = RF(68) / MAX(EQK(68),SMALL) + RB(69) = RF(69) / MAX(EQK(69),SMALL) + RB(70) = RF(70) / MAX(EQK(70),SMALL) + RB(71) = RF(71) / MAX(EQK(71),SMALL) + RB(72) = RF(72) / MAX(EQK(72),SMALL) + RB(73) = RF(73) / MAX(EQK(73),SMALL) + RB(74) = RF(74) / MAX(EQK(74),SMALL) + RB(75) = RF(75) / MAX(EQK(75),SMALL) + RB(76) = RF(76) / MAX(EQK(76),SMALL) + RB(77) = RF(77) / MAX(EQK(77),SMALL) + RB(78) = RF(78) / MAX(EQK(78),SMALL) + RB(79) = RF(79) / MAX(EQK(79),SMALL) + RB(80) = RF(80) / MAX(EQK(80),SMALL) + RB(81) = RF(81) / MAX(EQK(81),SMALL) + RB(82) = RF(82) / MAX(EQK(82),SMALL) + RB(83) = RF(83) / MAX(EQK(83),SMALL) + RB(84) = RF(84) / MAX(EQK(84),SMALL) + RB(85) = RF(85) / MAX(EQK(85),SMALL) + RB(86) = RF(86) / MAX(EQK(86),SMALL) + RB(87) = RF(87) / MAX(EQK(87),SMALL) + RB(88) = RF(88) / MAX(EQK(88),SMALL) + RB(89) = RF(89) / MAX(EQK(89),SMALL) + RB(90) = RF(90) / MAX(EQK(90),SMALL) + RB(91) = RF(91) / MAX(EQK(91),SMALL) + RB(92) = RF(92) / MAX(EQK(92),SMALL) + RB(93) = RF(93) / MAX(EQK(93),SMALL) + RB(94) = RF(94) / MAX(EQK(94),SMALL) + RB(95) = RF(95) / MAX(EQK(95),SMALL) + RB(96) = RF(96) / MAX(EQK(96),SMALL) + RB(97) = RF(97) / MAX(EQK(97),SMALL) + RB(98) = RF(98) / MAX(EQK(98),SMALL) + RB(99) = RF(99) / MAX(EQK(99),SMALL) + RB(100) = RF(100) / MAX(EQK(100),SMALL) + RB(101) = RF(101) / MAX(EQK(101),SMALL) + RB(102) = RF(102) / MAX(EQK(102),SMALL) + RB(103) = RF(103) / MAX(EQK(103),SMALL) + RB(104) = RF(104) / MAX(EQK(104),SMALL) + RB(105) = RF(105) / MAX(EQK(105),SMALL) + RB(106) = RF(106) / MAX(EQK(106),SMALL) + RB(107) = RF(107) / MAX(EQK(107),SMALL) + RB(108) = RF(108) / MAX(EQK(108),SMALL) + RB(109) = RF(109) / MAX(EQK(109),SMALL) + RB(110) = RF(110) / MAX(EQK(110),SMALL) + RB(111) = RF(111) / MAX(EQK(111),SMALL) + RB(112) = RF(112) / MAX(EQK(112),SMALL) + RB(113) = RF(113) / MAX(EQK(113),SMALL) + RB(114) = RF(114) / MAX(EQK(114),SMALL) + RB(115) = RF(115) / MAX(EQK(115),SMALL) + RB(116) = RF(116) / MAX(EQK(116),SMALL) + RB(117) = RF(117) / MAX(EQK(117),SMALL) + RB(118) = RF(118) / MAX(EQK(118),SMALL) + RB(119) = RF(119) / MAX(EQK(119),SMALL) + RB(120) = RF(120) / MAX(EQK(120),SMALL) + RB(121) = RF(121) / MAX(EQK(121),SMALL) + RB(122) = RF(122) / MAX(EQK(122),SMALL) + RB(123) = RF(123) / MAX(EQK(123),SMALL) + RB(124) = RF(124) / MAX(EQK(124),SMALL) + RB(125) = RF(125) / MAX(EQK(125),SMALL) + RB(126) = 0.0 + RB(127) = RF(127) / MAX(EQK(127),SMALL) + RB(128) = RF(128) / MAX(EQK(128),SMALL) + RB(129) = RF(129) / MAX(EQK(129),SMALL) + RB(130) = RF(130) / MAX(EQK(130),SMALL) + RB(131) = RF(131) / MAX(EQK(131),SMALL) + RB(132) = RF(132) / MAX(EQK(132),SMALL) + RB(133) = RF(133) / MAX(EQK(133),SMALL) + RB(134) = RF(134) / MAX(EQK(134),SMALL) + RB(135) = RF(135) / MAX(EQK(135),SMALL) + RB(136) = RF(136) / MAX(EQK(136),SMALL) + RB(137) = RF(137) / MAX(EQK(137),SMALL) + RB(138) = RF(138) / MAX(EQK(138),SMALL) + RB(139) = RF(139) / MAX(EQK(139),SMALL) + RB(140) = RF(140) / MAX(EQK(140),SMALL) + RB(141) = RF(141) / MAX(EQK(141),SMALL) + RB(142) = RF(142) / MAX(EQK(142),SMALL) + RB(143) = RF(143) / MAX(EQK(143),SMALL) + RB(144) = RF(144) / MAX(EQK(144),SMALL) + RB(145) = RF(145) / MAX(EQK(145),SMALL) + RB(146) = RF(146) / MAX(EQK(146),SMALL) + RB(147) = RF(147) / MAX(EQK(147),SMALL) + RB(148) = RF(148) / MAX(EQK(148),SMALL) + RB(149) = RF(149) / MAX(EQK(149),SMALL) + RB(150) = RF(150) / MAX(EQK(150),SMALL) + RB(151) = RF(151) / MAX(EQK(151),SMALL) + RB(152) = RF(152) / MAX(EQK(152),SMALL) + RB(153) = RF(153) / MAX(EQK(153),SMALL) + RB(154) = RF(154) / MAX(EQK(154),SMALL) + RB(155) = RF(155) / MAX(EQK(155),SMALL) + RB(156) = RF(156) / MAX(EQK(156),SMALL) + RB(157) = RF(157) / MAX(EQK(157),SMALL) + RB(158) = RF(158) / MAX(EQK(158),SMALL) + RB(159) = RF(159) / MAX(EQK(159),SMALL) + RB(160) = RF(160) / MAX(EQK(160),SMALL) + RB(161) = RF(161) / MAX(EQK(161),SMALL) + RB(162) = RF(162) / MAX(EQK(162),SMALL) + RB(163) = RF(163) / MAX(EQK(163),SMALL) + RB(164) = RF(164) / MAX(EQK(164),SMALL) + RB(165) = RF(165) / MAX(EQK(165),SMALL) + RB(166) = 0.0 + RB(167) = RF(167) / MAX(EQK(167),SMALL) + RB(168) = RF(168) / MAX(EQK(168),SMALL) + RB(169) = 0.0 + RB(170) = RF(170) / MAX(EQK(170),SMALL) + RB(171) = 0.0 + RB(172) = RF(172) / MAX(EQK(172),SMALL) + RB(173) = 0.0 + RB(174) = 0.0 + RB(175) = RF(175) / MAX(EQK(175),SMALL) + RB(176) = RF(176) / MAX(EQK(176),SMALL) + RB(177) = RF(177) / MAX(EQK(177),SMALL) + RB(178) = 0.0 + RB(179) = 0.0 + RB(180) = 0.0 + RB(181) = RF(181) / MAX(EQK(181),SMALL) + RB(182) = RF(182) / MAX(EQK(182),SMALL) + RB(183) = RF(183) / MAX(EQK(183),SMALL) + RB(184) = RF(184) / MAX(EQK(184),SMALL) +! +! +! rates at low pressure limit +! + RKLOW(1) = EXP(3.40312786D1 -1.50965D3/T) + RKLOW(2) = EXP(5.99064331D1 -2.76D0*ALOGT -8.05146668D2/T) + RKLOW(3) = EXP(7.69484824D1 -4.76D0*ALOGT -1.22784867D3/T) + RKLOW(4) = EXP(5.61662604D1 -2.57D0*ALOGT -2.13867084D2/T) + RKLOW(5) = EXP(7.39217399D1 -4.82D0*ALOGT -3.28600484D3/T) + RKLOW(6) = EXP(6.98660102D1 -4.8D0*ALOGT -2.79788467D3/T) + RKLOW(7) = EXP(7.28526099D1 -4.65D0*ALOGT -2.55634067D3/T) + RKLOW(8) = EXP(9.59450043D1 -7.44D0*ALOGT -7.08529068D3/T) + RKLOW(9) = EXP(9.34384048D1 -7.27D0*ALOGT -3.63322434D3/T) + RKLOW(10) = EXP(6.9414025D1 -3.86D0*ALOGT -1.67067934D3/T) + RKLOW(11) = EXP(9.61977483D1 -7.62D0*ALOGT -3.50742017D3/T) + RKLOW(12) = EXP(9.50941235D1 -7.08D0*ALOGT -3.36400342D3/T) + RKLOW(13) = EXP(6.37931383D1 -3.42D0*ALOGT -4.24463259D4/T) + RKLOW(14) = EXP(4.22794408D1 -9.D-1*ALOGT +8.55468335D2/T) + RKLOW(15) = EXP(8.42793577D1 -5.92D0*ALOGT -1.58010034D3/T) + RKLOW(16) = EXP(6.54619238D1 -3.74D0*ALOGT -9.74227469D2/T) + RKLOW(17) = EXP(7.69748493D1 -5.11D0*ALOGT -3.57032226D3/T) + RKLOW(18) = EXP(8.81295053D1 -6.36D0*ALOGT -2.536212D3/T) + RKLOW(19) = EXP(9.56297642D1 -7.03D0*ALOGT -1.38988444D3/T) + RKLOW(20) = EXP(1.17889265D2 -9.3D0*ALOGT -4.92145901D4/T) + RKLOW(21) = EXP(5.91374013D1 -2.8D0*ALOGT -2.96897834D2/T) + RKLOW(22) = EXP(9.67205025D1 -7.63D0*ALOGT -1.93939704D3/T) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! third-body concentrations +! ! +! SUBROUTINE RATX (T, C, RF, RB, RKLOW) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! PARAMETER (SMALL = 1.D-200) +! DIMENSION C(*), RF(*), RB(*), RKLOW(*) +! + ALOGT = LOG(T) + CTOT = 0.0 + DO K = 1, 19 + CTOT = CTOT + C(K) + ENDDO +! + CTB(1) = CTOT + 1.4D0*C(1) + 1.44D1*C(6) + C(10) + 7.5D-1*C(11) & + + 2.6D0*C(12) + 2.D0*C(17) + CTB(2) = CTOT + C(1) + 5.D0*C(6) + C(10) + 5.D-1*C(11) + C(12) & + + 2.D0*C(17) + CTB(47) = CTB(2) + CTB(51) = CTB(2) + CTB(53) = CTB(2) + CTB(54) = CTB(2) + CTB(56) = CTB(2) + CTB(60) = CTB(2) + CTB(67) = CTB(2) + CTB(68) = CTB(2) + CTB(70) = CTB(2) + CTB(72) = CTB(2) + CTB(78) = CTB(2) + CTB(80) = CTB(2) + CTB(90) = CTB(2) + CTB(122) = CTB(2) + CTB(131) = CTB(2) + CTB(137) = CTB(2) + CTB(148) = CTB(2) + CTB(162) = CTB(2) + CTB(170) = CTB(2) + CTB(177) = CTB(2) + CTB(12) = CTOT + C(1) + 5.D0*C(4) + 5.D0*C(6) + C(10) & + + 5.D-1*C(11) + 2.5D0*C(12) + 2.D0*C(17) + CTB(31) = CTOT - C(4) - C(6) - 2.5D-1*C(11) + 5.D-1*C(12) & + + 5.D-1*C(17) - C(19) + CTB(36) = CTOT - C(1) - C(6) + C(10) - C(12) + 2.D0*C(17) + CTB(40) = CTOT - 2.7D-1*C(1) + 2.65D0*C(6) + C(10) + 2.D0*C(17) + CTB(49) = CTOT + C(1) + 5.D0*C(6) + 2.D0*C(10) + 5.D-1*C(11) & + + C(12) + 2.D0*C(17) + CTB(157) = CTOT + C(1) - C(6) + C(10) + 5.D-1*C(11) + C(12) & + + 2.D0*C(17) +! +! +! fall-off reactions +! +! + PR = RKLOW(1) * CTB(12) / RF(12) + PCOR = PR / (1.0 + PR) + RF(12) = RF(12) * PCOR + RB(12) = RB(12) * PCOR +! + PR = RKLOW(2) * CTB(47) / RF(47) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.38D-1*EXP(-T/9.1D1) + 5.62D-1*EXP(-T/5.836D3)& + + EXP(-8.552D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(47) = RF(47) * PCOR + RB(47) = RB(47) * PCOR +! + PR = RKLOW(3) * CTB(49) / RF(49) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.17D-1*EXP(-T/7.4D1) + 7.83D-1*EXP(-T/2.941D3)& + + EXP(-6.964D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(49) = RF(49) * PCOR + RB(49) = RB(49) * PCOR +! + PR = RKLOW(4) * CTB(51) / RF(51) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.176D-1*EXP(-T/2.71D2) + 7.824D-1*EXP(-T/2.755D3)& + + EXP(-6.57D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(51) = RF(51) * PCOR + RB(51) = RB(51) * PCOR + + PR = RKLOW(5) * CTB(53) / RF(53) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.813D-1*EXP(-T/1.03D2) + 7.187D-1*EXP(-T/1.291D3)& + + EXP(-4.16D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(53) = RF(53) * PCOR + RB(53) = RB(53) * PCOR + + PR = RKLOW(6) * CTB(54) / RF(54) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.42D-1*EXP(-T/9.4D1) + 7.58D-1*EXP(-T/1.555D3)& + + EXP(-4.2D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(54) = RF(54) * PCOR + RB(54) = RB(54) * PCOR + + PR = RKLOW(7) * CTB(56) / RF(56) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.D-1*EXP(-T/1.D2) + 6.D-1*EXP(-T/9.D4)& + + EXP(-1.D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(56) = RF(56) * PCOR + RB(56) = RB(56) * PCOR + + PR = RKLOW(8) * CTB(60) / RF(60) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.D-1*EXP(-T/1.D2) + 7.D-1*EXP(-T/9.D4)& + + EXP(-1.D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(60) = RF(60) * PCOR + RB(60) = RB(60) * PCOR + + PR = RKLOW(9) * CTB(67) / RF(67) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.493D-1*EXP(-T/9.85D1) + 7.507D-1*EXP(-T/1.302D3)& + + EXP(-4.167D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(67) = RF(67) * PCOR + RB(67) = RB(67) * PCOR + + PR = RKLOW(10) * CTB(68) / RF(68) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.18D-1*EXP(-T/2.075D2) + 7.82D-1*EXP(-T/2.663D3)& + + EXP(-6.095D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(68) = RF(68) * PCOR + RB(68) = RB(68) * PCOR + + PR = RKLOW(11) * CTB(70) / RF(70) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.47D-2*EXP(-T/2.1D2) + 9.753D-1*EXP(-T/9.84D2)& + + EXP(-4.374D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(70) = RF(70) * PCOR + RB(70) = RB(70) * PCOR + + PR = RKLOW(12) * CTB(72) / RF(72) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 1.578D-1*EXP(-T/1.25D2) + 8.422D-1*EXP(-T/2.219D3)& + + EXP(-6.882D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(72) = RF(72) * PCOR + RB(72) = RB(72) * PCOR + + PR = RKLOW(13) * CTB(78) / RF(78) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 6.8D-2*EXP(-T/1.97D2) + 9.32D-1*EXP(-T/1.54D3)& + + EXP(-1.03D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(78) = RF(78) * PCOR + RB(78) = RB(78) * PCOR + + PR = RKLOW(14) * CTB(80) / RF(80) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.654D-1*EXP(-T/9.4D1) + 7.346D-1*EXP(-T/1.756D3)& + + EXP(-5.182D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(80) = RF(80) * PCOR + RB(80) = RB(80) * PCOR + + PR = RKLOW(15) * CTB(90) / RF(90) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 5.88D-1*EXP(-T/1.95D2) + 4.12D-1*EXP(-T/5.9D3)& + + EXP(-6.394D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(90) = RF(90) * PCOR + RB(90) = RB(90) * PCOR + + PR = RKLOW(16) * CTB(122) / RF(122) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.243D-1*EXP(-T/2.37D2) + 5.757D-1*EXP(-T/1.652D3)& + + EXP(-5.069D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(122) = RF(122) * PCOR + RB(122) = RB(122) * PCOR + + PR = RKLOW(17) * CTB(131) / RF(131) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.093D-1*EXP(-T/2.75D2) + 5.907D-1*EXP(-T/1.226D3)& + + EXP(-5.185D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(131) = RF(131) * PCOR + RB(131) = RB(131) * PCOR + + PR = RKLOW(18) * CTB(137) / RF(137) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.973D-1*EXP(-T/2.08D2) + 6.027D-1*EXP(-T/3.922D3)& + + EXP(-1.018D4/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(137) = RF(137) * PCOR + RB(137) = RB(137) * PCOR + + PR = RKLOW(19) * CTB(148) / RF(148) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 3.81D-1*EXP(-T/7.32D1) + 6.19D-1*EXP(-T/1.18D3)& + + EXP(-9.999D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(148) = RF(148) * PCOR + RB(148) = RB(148) * PCOR + + PR = RKLOW(20) * CTB(162) / RF(162) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 2.655D-1*EXP(-T/1.8D2) + 7.345D-1*EXP(-T/1.035D3)& + + EXP(-5.417D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(162) = RF(162) * PCOR + RB(162) = RB(162) * PCOR + + PR = RKLOW(21) * CTB(170) / RF(170) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 4.22D-1*EXP(-T/1.22D2) + 5.78D-1*EXP(-T/2.535D3)& + + EXP(-9.365D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(170) = RF(170) * PCOR + RB(170) = RB(170) * PCOR + + PR = RKLOW(22) * CTB(177) / RF(177) + PCOR = PR / (1.0 + PR) + PRLOG = LOG10(MAX(PR,SMALL)) + FCENT = 5.35D-1*EXP(-T/2.01D2) + 4.65D-1*EXP(-T/1.773D3)& + + EXP(-5.333D3/T) + FCLOG = LOG10(MAX(FCENT,SMALL)) + XN = 0.75 - 1.27*FCLOG + CPRLOG= PRLOG - (0.4 + 0.67*FCLOG) + FLOG = FCLOG/(1.0 + (CPRLOG/(XN-0.14*CPRLOG))**2) + FC = 10.0**FLOG + PCOR = FC * PCOR + RF(177) = RF(177) * PCOR + RB(177) = RB(177) * PCOR + + RF(1) = RF(1)*CTB(1)*C(3)*C(3) + RF(2) = RF(2)*CTB(2)*C(3)*C(2) + RF(3) = RF(3)*C(3)*C(1) + RF(4) = RF(4)*C(3)*C(7) + RF(5) = RF(5)*C(3)*C(8) + RF(6) = RF(6)*C(3) + RF(7) = RF(7)*C(3) + RF(8) = RF(8)*C(3) + RF(9) = RF(9)*C(3) + RF(10) = RF(10)*C(3)*C(9) + RF(11) = RF(11)*C(3)*C(10) + RF(12) = RF(12)*C(3)*C(11) + RF(13) = RF(13)*C(3) + RF(14) = RF(14)*C(3) + RF(15) = RF(15)*C(3)*C(13) + RF(16) = RF(16)*C(3) + RF(17) = RF(17)*C(3) + RF(18) = RF(18)*C(3)*C(14) + RF(19) = RF(19)*C(3)*C(14) + RF(20) = RF(20)*C(3)*C(15) + RF(21) = RF(21)*C(3)*C(15) + RF(22) = RF(22)*C(3) + RF(23) = RF(23)*C(3)*C(16) + RF(24) = RF(24)*C(3) + RF(25) = RF(25)*C(3)*C(17) + RF(26) = RF(26)*C(3) + RF(27) = RF(27)*C(3)*C(18) + RF(28) = RF(28)*C(3)*C(18) + RF(29) = RF(29)*C(4)*C(11) + RF(30) = RF(30)*C(4)*C(13) + RF(31) = RF(31)*CTB(31)*C(2)*C(4) + RF(32) = RF(32)*C(2)*C(4)*C(4) + RF(33) = RF(33)*C(2)*C(4)*C(6) + RF(34) = RF(34)*C(2)*C(4)*C(19) + RF(35) = RF(35)*C(2)*C(4) + RF(36) = RF(36)*CTB(36)*C(2)*C(2) + RF(37) = RF(37)*C(2)*C(2)*C(1) + RF(38) = RF(38)*C(2)*C(2)*C(6) + RF(39) = RF(39)*C(2)*C(2)*C(12) + RF(40) = RF(40)*CTB(40)*C(2)*C(5) + RF(41) = RF(41)*C(2)*C(7) + RF(42) = RF(42)*C(2)*C(7) + RF(43) = RF(43)*C(2)*C(7) + RF(44) = RF(44)*C(2)*C(8) + RF(45) = RF(45)*C(2)*C(8) + RF(46) = RF(46)*C(2) + RF(47) = RF(47)*C(2) + RF(48) = RF(48)*C(2) + RF(49) = RF(49)*C(2)*C(9) + RF(50) = RF(50)*C(2)*C(10) + RF(51) = RF(51)*C(2) + RF(52) = RF(52)*C(2) + RF(53) = RF(53)*C(2)*C(13) + RF(54) = RF(54)*C(2)*C(13) + RF(55) = RF(55)*C(2)*C(13) + RF(56) = RF(56)*C(2) + RF(57) = RF(57)*C(2) + RF(58) = RF(58)*C(2) + RF(59) = RF(59)*C(2) + RF(60) = RF(60)*C(2) + RF(61) = RF(61)*C(2) + RF(62) = RF(62)*C(2) + RF(63) = RF(63)*C(2) + RF(64) = RF(64)*C(2) + RF(65) = RF(65)*C(2)*C(14) + RF(66) = RF(66)*C(2)*C(14) + RF(67) = RF(67)*C(2)*C(15) + RF(68) = RF(68)*C(2) + RF(69) = RF(69)*C(2) + RF(70) = RF(70)*C(2)*C(16) + RF(71) = RF(71)*C(2)*C(16) + RF(72) = RF(72)*C(2) + RF(73) = RF(73)*C(2) + RF(74) = RF(74)*C(2)*C(17) + RF(75) = RF(75)*C(2) + RF(76) = RF(76)*C(2)*C(18) + RF(77) = RF(77)*C(2)*C(18) + RF(78) = RF(78)*C(1)*C(11) + RF(79) = RF(79)*C(5)*C(1) + RF(80) = RF(80)*C(5)*C(5) + RF(81) = RF(81)*C(5)*C(5) + RF(82) = RF(82)*C(5)*C(7) + RF(83) = RF(83)*C(5)*C(8) + RF(84) = RF(84)*C(5)*C(8) + RF(85) = RF(85)*C(5) + RF(86) = RF(86)*C(5) + RF(87) = RF(87)*C(5) + RF(88) = RF(88)*C(5) + RF(89) = RF(89)*C(5) + RF(90) = RF(90)*C(5)*C(9) + RF(91) = RF(91)*C(5)*C(9) + RF(92) = RF(92)*C(5)*C(9) + RF(93) = RF(93)*C(5)*C(10) + RF(94) = RF(94)*C(5)*C(11) + RF(95) = RF(95)*C(5) + RF(96) = RF(96)*C(5)*C(13) + RF(97) = RF(97)*C(5) + RF(98) = RF(98)*C(5) + RF(99) = RF(99)*C(5)*C(14) + RF(100) = RF(100)*C(5)*C(14) + RF(101) = RF(101)*C(5)*C(15) + RF(102) = RF(102)*C(5)*C(15) + RF(103) = RF(103)*C(5) + RF(104) = RF(104)*C(5)*C(16) + RF(105) = RF(105)*C(5)*C(17) + RF(106) = RF(106)*C(5)*C(18) + RF(107) = RF(107)*C(7)*C(7) + RF(108) = RF(108)*C(7)*C(7) + RF(109) = RF(109)*C(7) + RF(110) = RF(110)*C(7)*C(9) + RF(111) = RF(111)*C(7)*C(9) + RF(112) = RF(112)*C(7)*C(11) + RF(113) = RF(113)*C(7)*C(13) + RF(114) = RF(114)*C(4) + RF(115) = RF(115)*C(9) + RF(116) = RF(116)*C(4) + RF(117) = RF(117)*C(1) + RF(118) = RF(118)*C(6) + RF(120) = RF(120)*C(9) + RF(121) = RF(121)*C(10) + RF(122) = RF(122)*C(11) + RF(123) = RF(123)*C(12) + RF(124) = RF(124)*C(13) + RF(126) = RF(126)*C(4) + RF(127) = RF(127)*C(1) + RF(129) = RF(129)*C(9) + RF(130) = RF(130)*C(10) + RF(131) = RF(131)*C(11) + RF(133) = RF(133)*C(19) + RF(134) = RF(134)*C(4) + RF(135) = RF(135)*C(4) + RF(136) = RF(136)*C(1) + RF(137) = RF(137)*C(6) + RF(138) = RF(138)*C(6) + RF(139) = RF(139)*C(9) + RF(140) = RF(140)*C(10) + RF(141) = RF(141)*C(11) + RF(142) = RF(142)*C(12) + RF(143) = RF(143)*C(12) + RF(144) = RF(144)*C(17) + RF(145) = RF(145)*C(9)*C(4) + RF(146) = RF(146)*C(9)*C(4) + RF(147) = RF(147)*C(9)*C(8) + RF(148) = RF(148)*C(9)*C(9) + RF(149) = RF(149)*C(9)*C(9) + RF(150) = RF(150)*C(9) + RF(151) = RF(151)*C(9)*C(13) + RF(152) = RF(152)*C(9)*C(14) + RF(153) = RF(153)*C(9)*C(14) + RF(154) = RF(154)*C(9)*C(16) + RF(155) = RF(155)*C(9)*C(17) + RF(156) = RF(156)*C(6) + RF(157) = RF(157)*CTB(157) + RF(158) = RF(158)*C(4) + RF(159) = RF(159)*C(4) + RF(160) = RF(160)*C(4) + RF(161) = RF(161)*C(4) + RF(162) = RF(162)*C(16) + RF(163) = RF(163)*C(4) + RF(164) = RF(164)*C(4) + RF(166) = RF(166)*C(3)*C(9) + RF(167) = RF(167)*C(3)*C(16) + RF(168) = RF(168)*C(5)*C(7) + RF(169) = RF(169)*C(5)*C(9) + RF(170) = RF(170)*C(1) + RF(171) = RF(171)*C(4) + RF(172) = RF(172)*C(4) + RF(174) = RF(174)*C(6) + RF(175) = RF(175)*C(4) + RF(176) = RF(176)*C(4) + RF(177) = RF(177)*C(2)*C(18) + RF(178) = RF(178)*C(3) + RF(179) = RF(179)*C(4) + RF(180) = RF(180)*C(4) + RF(181) = RF(181)*C(2) + RF(182) = RF(182)*C(2) + RF(183) = RF(183)*C(5) + RF(184) = RF(184)*C(5) + RB(1) = RB(1)*CTB(1)*C(4) + RB(2) = RB(2)*CTB(2)*C(5) + RB(3) = RB(3)*C(2)*C(5) + RB(4) = RB(4)*C(5)*C(4) + RB(5) = RB(5)*C(5)*C(7) + RB(6) = RB(6)*C(2)*C(11) + RB(7) = RB(7)*C(2) + RB(8) = RB(8)*C(1)*C(11) + RB(9) = RB(9)*C(2) + RB(10) = RB(10)*C(2)*C(13) + RB(11) = RB(11)*C(5)*C(9) + RB(12) = RB(12)*C(12) + RB(13) = RB(13)*C(5)*C(11) + RB(14) = RB(14)*C(2)*C(12) + RB(15) = RB(15)*C(5) + RB(16) = RB(16)*C(5)*C(13) + RB(17) = RB(17)*C(5)*C(13) + RB(18) = RB(18)*C(5) + RB(19) = RB(19)*C(5) + RB(20) = RB(20)*C(2) + RB(21) = RB(21)*C(11) + RB(22) = RB(22)*C(2)*C(18) + RB(23) = RB(23)*C(9) + RB(24) = RB(24)*C(9)*C(13) + RB(25) = RB(25)*C(5) + RB(26) = RB(26)*C(2)*C(11)*C(11) + RB(27) = RB(27)*C(5) + RB(28) = RB(28)*C(12) + RB(29) = RB(29)*C(3)*C(12) + RB(30) = RB(30)*C(7) + RB(31) = RB(31)*CTB(31)*C(7) + RB(32) = RB(32)*C(7)*C(4) + RB(33) = RB(33)*C(7)*C(6) + RB(34) = RB(34)*C(7)*C(19) + RB(35) = RB(35)*C(3)*C(5) + RB(36) = RB(36)*CTB(36)*C(1) + RB(37) = RB(37)*C(1)*C(1) + RB(38) = RB(38)*C(1)*C(6) + RB(39) = RB(39)*C(1)*C(12) + RB(40) = RB(40)*CTB(40)*C(6) + RB(41) = RB(41)*C(3)*C(6) + RB(42) = RB(42)*C(4)*C(1) + RB(43) = RB(43)*C(5)*C(5) + RB(44) = RB(44)*C(7)*C(1) + RB(45) = RB(45)*C(5)*C(6) + RB(46) = RB(46)*C(1) + RB(47) = RB(47)*C(9) + RB(48) = RB(48)*C(1) + RB(49) = RB(49)*C(10) + RB(50) = RB(50)*C(9)*C(1) + RB(51) = RB(51)*C(13) + RB(52) = RB(52)*C(1)*C(11) + RB(55) = RB(55)*C(1) + RB(56) = RB(56)*C(14) + RB(57) = RB(57)*C(1)*C(13) + RB(58) = RB(58)*C(5)*C(9) + RB(59) = RB(59)*C(6) + RB(60) = RB(60)*C(14) + RB(61) = RB(61)*C(2) + RB(62) = RB(62)*C(1)*C(13) + RB(63) = RB(63)*C(5)*C(9) + RB(64) = RB(64)*C(6) + RB(65) = RB(65)*C(1) + RB(66) = RB(66)*C(1) + RB(68) = RB(68)*C(16) + RB(69) = RB(69)*C(1)*C(15) + RB(71) = RB(71)*C(1) + RB(72) = RB(72)*C(17) + RB(73) = RB(73)*C(1)*C(16) + RB(74) = RB(74)*C(1) + RB(75) = RB(75)*C(11) + RB(76) = RB(76)*C(1) + RB(77) = RB(77)*C(9)*C(11) + RB(78) = RB(78)*C(13) + RB(79) = RB(79)*C(2)*C(6) + RB(80) = RB(80)*C(8) + RB(81) = RB(81)*C(3)*C(6) + RB(82) = RB(82)*C(4)*C(6) + RB(83) = RB(83)*C(7)*C(6) + RB(84) = RB(84)*C(7)*C(6) + RB(85) = RB(85)*C(2)*C(11) + RB(86) = RB(86)*C(2) + RB(87) = RB(87)*C(2)*C(13) + RB(88) = RB(88)*C(6) + RB(89) = RB(89)*C(2)*C(13) + RB(90) = RB(90)*C(14) + RB(91) = RB(91)*C(6) + RB(92) = RB(92)*C(6) + RB(93) = RB(93)*C(9)*C(6) + RB(94) = RB(94)*C(2)*C(12) + RB(95) = RB(95)*C(6)*C(11) + RB(96) = RB(96)*C(6) + RB(97) = RB(97)*C(6)*C(13) + RB(98) = RB(98)*C(6)*C(13) + RB(99) = RB(99)*C(6) + RB(100) = RB(100)*C(6) + RB(101) = RB(101)*C(2)*C(18) + RB(102) = RB(102)*C(9)*C(11) + RB(103) = RB(103)*C(6)*C(15) + RB(104) = RB(104)*C(6) + RB(105) = RB(105)*C(6) + RB(106) = RB(106)*C(6) + RB(107) = RB(107)*C(4)*C(8) + RB(108) = RB(108)*C(4)*C(8) + RB(109) = RB(109)*C(5)*C(13) + RB(110) = RB(110)*C(4)*C(10) + RB(111) = RB(111)*C(5) + RB(112) = RB(112)*C(5)*C(12) + RB(113) = RB(113)*C(8) + RB(114) = RB(114)*C(3)*C(11) + RB(115) = RB(115)*C(2)*C(15) + RB(116) = RB(116)*C(3) + RB(117) = RB(117)*C(2) + RB(118) = RB(118)*C(2)*C(13) + RB(119) = RB(119)*C(2)*C(15) + RB(120) = RB(120)*C(2) + RB(121) = RB(121)*C(2)*C(16) + RB(123) = RB(123)*C(11) + RB(124) = RB(124)*C(2)*C(18) + RB(125) = RB(125)*C(11)*C(15) + RB(127) = RB(127)*C(2)*C(9) + RB(128) = RB(128)*C(1)*C(15) + RB(129) = RB(129)*C(2)*C(16) + RB(130) = RB(130)*C(9)*C(9) + RB(131) = RB(131)*C(18) + RB(132) = RB(132)*C(11) + RB(133) = RB(133)*C(19) + RB(134) = RB(134)*C(2)*C(5)*C(11) + RB(135) = RB(135)*C(11)*C(6) + RB(136) = RB(136)*C(9)*C(2) + RB(137) = RB(137)*C(14) + RB(138) = RB(138)*C(6) + RB(139) = RB(139)*C(2)*C(16) + RB(140) = RB(140)*C(9)*C(9) + RB(141) = RB(141)*C(11) + RB(142) = RB(142)*C(12) + RB(143) = RB(143)*C(11)*C(13) + RB(144) = RB(144)*C(9) + RB(145) = RB(145)*C(3) + RB(146) = RB(146)*C(5)*C(13) + RB(147) = RB(147)*C(7)*C(10) + RB(148) = RB(148)*C(17) + RB(149) = RB(149)*C(2) + RB(150) = RB(150)*C(10)*C(11) + RB(151) = RB(151)*C(10) + RB(152) = RB(152)*C(10) + RB(153) = RB(153)*C(10) + RB(154) = RB(154)*C(10) + RB(155) = RB(155)*C(10) + RB(156) = RB(156)*C(2)*C(11)*C(6) + RB(157) = RB(157)*CTB(157)*C(2)*C(11) + RB(158) = RB(158)*C(7)*C(11) + RB(159) = RB(159)*C(7)*C(13) + RB(160) = RB(160)*C(7)*C(13) + RB(161) = RB(161)*C(13) + RB(162) = RB(162)*C(1)*C(15) + RB(163) = RB(163)*C(7)*C(16) + RB(164) = RB(164)*C(5)*C(11)*C(11) + RB(165) = RB(165)*C(11)*C(11)*C(15) + RB(167) = RB(167)*C(2) + RB(168) = RB(168)*C(4)*C(6) + RB(170) = RB(170)*C(9) + RB(172) = RB(172)*C(3)*C(13) + RB(175) = RB(175)*C(3) + RB(176) = RB(176)*C(7)*C(15) + RB(181) = RB(181)*C(9) + RB(182) = RB(182)*C(18)*C(1) + RB(183) = RB(183)*C(6)*C(18) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! solving QSS species concentration +! ------------------------------------------- +! +! SUBROUTINE QSSA(RF, RB, XQ) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! PARAMETER (SMALL = 1.D-200) +! DIMENSION RF(*), RB(*), XQ(*) +! + RF(119) = 0.D0 + RF(125) = 0.D0 + RF(128) = 0.D0 + RF(132) = 0.D0 + RF(165) = 0.D0 + RF(173) = 0.D0 + RB(180) = 0.D0 + RB(184) = 0.D0 + +! C + DEN = +RF( 85) +RF(114) +RF(115) +RB( 46) + A1_0 = ( +RB( 85) +RB(114) +RB(115) )/MAX(DEN, SMALL) + A1_2 = ( +RF( 46) )/MAX(DEN, SMALL) +! CH + DEN = +RF( 6) +RF( 46) +RF( 86) +RF(116) +RF(117) & + +RF(118) +RF(120) +RF(121) +RF(122) +RF(123) +RF(124) & + +RF(170) +RB( 48) +RB( 88) + A2_0 = ( +RB( 6) +RB(118) +RB(119) +RB(121) +RB(124) & + +RB(125) +RB(170) )/MAX(DEN, SMALL) + A2_1 = ( +RB( 46) )/MAX(DEN, SMALL) + A2_3 = ( +RF( 88) +RB(117) )/MAX(DEN, SMALL) + A2_4 = ( +RF( 48) )/MAX(DEN, SMALL) + A2_5 = ( +RB( 86) +RB(116) +RB(123) )/MAX(DEN, SMALL) + A2_8 = ( +RB(120) )/MAX(DEN, SMALL) + + A2_10 = ( +RB(122) )/MAX(DEN, SMALL) +! CH2 + DEN = +RF( 7) +RF( 47) +RF( 87) +RF( 88) +RF(109) & + +RF(126) +RF(127) +RF(129) +RF(130) +RF(131) +RF(171) & + +RF(172) +RB( 21) +RB( 28) +RB( 91) +RB(117) +RB(133) & + +RB(138) +RB(141) +RB(142) +RB(178) + A3_0 = ( +RF( 21) +RF( 28) +RB( 47) +RB( 87) +RF( 91) & + +RB(109) +RB(119) +RB(126) +RB(127) +RB(128) +RB(128) & + +RB(129) +RB(130) +RB(131) +RB(171) +RB(172) +RB(173) & + +RB(173) )/MAX(DEN, SMALL) + A3_2 = ( +RB( 88) +RF(117) )/MAX(DEN, SMALL) + A3_4 = ( +RF(133) +RF(138) +RF(141) +RF(142) )/MAX(DEN, SMALL) + A3_5 = ( +RB( 7) )/MAX(DEN, SMALL) + A3_8 = ( +RB(132) )/MAX(DEN, SMALL) + A3_11 = ( +RF(178) )/MAX(DEN, SMALL) +! CH2(S) + DEN = +RF( 8) +RF( 9) +RF( 48) +RF( 89) +RF(133) & + +RF(134) +RF(135) +RF(136) +RF(137) +RF(138) +RF(139) & + +RF(140) +RF(141) +RF(142) +RF(143) +RF(144) +RF(174) & + +RB( 59) +RB( 64) +RB( 75) +RB( 92) + A4_0 = ( +RB( 8) +RB( 89) +RF( 92) +RB(134) +RB(135) & + +RB(136) +RB(137) +RB(139) +RB(140) +RB(143) +RB(174) )& + /MAX(DEN, SMALL) + A4_2 = ( +RB( 48) )/MAX(DEN, SMALL) + A4_3 = ( +RB(133) +RB(138) +RB(141) +RB(142) )/MAX(DEN, SMALL) + A4_5 = ( +RB( 9) )/MAX(DEN, SMALL) + A4_6 = ( +RF( 59) )/MAX(DEN, SMALL) + A4_7 = ( +RF( 64) )/MAX(DEN, SMALL) + A4_9 = ( +RB(144) )/MAX(DEN, SMALL) + A4_10 = ( +RF( 75) )/MAX(DEN, SMALL) +! HCO + DEN = +RF( 13) +RF( 14) +RF( 51) +RF( 52) +RF( 95) & + +RF(150) +RF(156) +RF(157) +RF(158) +RB( 7) +RB( 9) & + +RB( 15) +RB( 23) +RB( 30) +RB( 55) +RB( 86) +RB( 96) & + +RB(113) +RB(116) +RB(123) +RB(151) +RB(161) +RB(181) + A5_0 = ( +RB( 13) +RB( 14) +RF( 15) +RF( 23) +RF( 30) & + +RB( 51) +RB( 52) +RF( 55) +RB( 95) +RF( 96) +RF(113) & + +RB(150) +RF(151) +RB(156) +RB(157) +RB(158) )/MAX(DEN, SMALL) + A5_2 = ( +RF( 86) +RF(116) +RF(123) )/MAX(DEN, SMALL) + A5_3 = ( +RF( 7) )/MAX(DEN, SMALL) + A5_4 = ( +RF( 9) )/MAX(DEN, SMALL) + A5_8 = ( +RF(161) )/MAX(DEN, SMALL) + A5_11 = ( +RF(180) +RF(180) +RF(181) +RF(184) )/MAX(DEN, SMALL) +! CH2OH + DEN = +RF( 16) +RF( 56) +RF( 57) +RF( 58) +RF( 59) & + +RF( 97) +RF(159) +RB( 18) +RB( 53) +RB( 61) +RB( 65) & + +RB( 99) +RB(152) + A6_0 = ( +RB( 16) +RF( 18) +RF( 53) +RB( 56) +RB( 57) & + +RB( 58) +RF( 65) +RB( 97) +RF( 99) +RF(152) +RB(159) )& + /MAX(DEN, SMALL) + A6_4 = ( +RB( 59) )/MAX(DEN, SMALL) + A6_7 = ( +RF( 61) )/MAX(DEN, SMALL) + A6_11 = ( +RF(184) )/MAX(DEN, SMALL) +! CH3O + DEN = +RF( 17) +RF( 60) +RF( 61) +RF( 62) +RF( 63) & + +RF( 64) +RF( 98) +RF(160) +RB( 19) +RB( 54) +RB( 66) & + +RB(100) +RB(111) +RB(145) +RB(153) + A7_0 = ( +RB( 17) +RF( 19) +RF( 54) +RB( 60) +RB( 62) & + +RB( 63) +RF( 66) +RB( 98) +RF(100) +RF(111) +RF(145) & + +RF(153) +RB(160) )/MAX(DEN, SMALL) + A7_4 = ( +RB( 64) )/MAX(DEN, SMALL) + A7_6 = ( +RB( 61) )/MAX(DEN, SMALL) +! C2H3 + DEN = +RF( 22) +RF( 68) +RF( 69) +RF(103) +RF(161) & + +RF(175) +RF(176) +RB( 67) +RB( 71) +RB(104) +RB(120) & + +RB(132) +RB(154) + A8_0 = ( +RB( 22) +RF( 67) +RB( 68) +RB( 69) +RF( 71) & + +RB(103) +RF(104) +RF(154) +RB(176) )/MAX(DEN, SMALL) + A8_2 = ( +RF(120) )/MAX(DEN, SMALL) + A8_5 = ( +RB(161) )/MAX(DEN, SMALL) + A8_11 = ( +RB(175) )/MAX(DEN, SMALL) +! C2H5 + DEN = +RF( 24) +RF( 72) +RF( 73) +RF(163) +RB( 25) & + +RB( 70) +RB( 74) +RB(105) +RB(144) +RB(149) +RB(155) + A9_0 = ( +RB( 24) +RF( 25) +RF( 70) +RB( 72) +RB( 73) & + +RF( 74) +RF(105) +RF(149) +RF(155) +RB(163) )/MAX(DEN, SMALL) + A9_4 = ( +RF(144) )/MAX(DEN, SMALL) +! HCCO + DEN = +RF( 26) +RF( 75) +RF(164) +RB( 20) +RB( 27) & + +RB( 76) +RB(106) +RB(122) + A10_0 = ( +RF( 20) +RB( 26) +RF( 27) +RF( 76) +RF(106) & + +RB(125) +RB(164) +RB(165) +RB(165) )/MAX(DEN, SMALL) + A10_2 = ( +RF(122) )/MAX(DEN, SMALL) + A10_4 = ( +RB( 75) )/MAX(DEN, SMALL) + A10_8 = ( +RB(132) )/MAX(DEN, SMALL) +! CH2CHO + DEN = +RF(178) +RF(179) +RF(180) +RF(181) +RF(182) & + +RF(183) +RF(184) +RB(167) +RB(175) +RB(177) + A11_0 = ( +RF(167) +RF(177) +RB(179) +RB(182) +RB(183) )& + /MAX(DEN, SMALL) + A11_5 = ( +RB(181) )/MAX(DEN, SMALL) + A11_8 = ( +RF(175) )/MAX(DEN, SMALL) +! + A2_0 = A2_0 + A2_1*A1_0 + DEN = 1 -A2_1*A1_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A2_10 = A2_10/MAX(DEN, SMALL) + A2_8 = A2_8/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_9*A9_0 + DEN = 1 -A4_9*A9_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A4_10 = A4_10/MAX(DEN, SMALL) + A4_7 = A4_7/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_11*A11_0 + A5_8 = A5_8 + A5_11*A11_8 + DEN = 1 -A5_11*A11_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A5_3 = A5_3/MAX(DEN, SMALL) + A5_8 = A5_8/MAX(DEN, SMALL) + A3_0 = A3_0 + A3_11*A11_0 + A3_5 = A3_5 + A3_11*A11_5 + A3_8 = A3_8 + A3_11*A11_8 + A6_0 = A6_0 + A6_11*A11_0 + A6_5 = A6_11*A11_5 + A6_8 = A6_11*A11_8 + A8_0 = A8_0 + A8_11*A11_0 + A8_5 = A8_5 + A8_11*A11_5 + DEN = 1 -A8_11*A11_8 + A8_0 = A8_0/MAX(DEN, SMALL) + A8_2 = A8_2/MAX(DEN, SMALL) + A8_5 = A8_5/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_8*A8_0 + A2_5 = A2_5 + A2_8*A8_5 + DEN = 1 -A2_8*A8_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A2_10 = A2_10/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_8*A8_0 + A5_2 = A5_2 + A5_8*A8_2 + DEN = 1 -A5_8*A8_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A5_3 = A5_3/MAX(DEN, SMALL) + A3_0 = A3_0 + A3_8*A8_0 + A3_2 = A3_2 + A3_8*A8_2 + A3_5 = A3_5 + A3_8*A8_5 + A6_0 = A6_0 + A6_8*A8_0 + A6_2 = A6_8*A8_2 + A6_5 = A6_5 + A6_8*A8_5 + A10_0 = A10_0 + A10_8*A8_0 + A10_2 = A10_2 + A10_8*A8_2 + A10_5 = A10_8*A8_5 + A4_0 = A4_0 + A4_7*A7_0 + A4_6 = A4_6 + A4_7*A7_6 + DEN = 1 -A4_7*A7_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A4_10 = A4_10/MAX(DEN, SMALL) + A6_0 = A6_0 + A6_7*A7_0 + A6_4 = A6_4 + A6_7*A7_4 + DEN = 1 -A6_7*A7_6 + A6_0 = A6_0/MAX(DEN, SMALL) + A6_4 = A6_4/MAX(DEN, SMALL) + A6_2 = A6_2/MAX(DEN, SMALL) + A6_5 = A6_5/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_10*A10_0 + A4_2 = A4_2 + A4_10*A10_2 + A4_5 = A4_5 + A4_10*A10_5 + DEN = 1 -A4_10*A10_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_6 = A4_6/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_10*A10_0 + A2_4 = A2_4 + A2_10*A10_4 + A2_5 = A2_5 + A2_10*A10_5 + DEN = 1 -A2_10*A10_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A2_3 = A2_3/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_6*A6_0 + A4_2 = A4_2 + A4_6*A6_2 + A4_5 = A4_5 + A4_6*A6_5 + DEN = 1 -A4_6*A6_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A4_3 = A4_3/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_3*A3_0 + A4_2 = A4_2 + A4_3*A3_2 + A4_5 = A4_5 + A4_3*A3_5 + DEN = 1 -A4_3*A3_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A4_5 = A4_5/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_3*A3_0 + A2_4 = A2_4 + A2_3*A3_4 + A2_5 = A2_5 + A2_3*A3_5 + DEN = 1 -A2_3*A3_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A2_5 = A2_5/MAX(DEN, SMALL) + A5_0 = A5_0 + A5_3*A3_0 + A5_4 = A5_4 + A5_3*A3_4 + A5_2 = A5_2 + A5_3*A3_2 + DEN = 1 -A5_3*A3_5 + A5_0 = A5_0/MAX(DEN, SMALL) + A5_4 = A5_4/MAX(DEN, SMALL) + A5_2 = A5_2/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_5*A5_0 + A4_2 = A4_2 + A4_5*A5_2 + DEN = 1 -A4_5*A5_4 + A4_0 = A4_0/MAX(DEN, SMALL) + A4_2 = A4_2/MAX(DEN, SMALL) + A2_0 = A2_0 + A2_5*A5_0 + A2_4 = A2_4 + A2_5*A5_4 + DEN = 1 -A2_5*A5_2 + A2_0 = A2_0/MAX(DEN, SMALL) + A2_4 = A2_4/MAX(DEN, SMALL) + A4_0 = A4_0 + A4_2*A2_0 + DEN = 1 -A4_2*A2_4 + A4_0 = A4_0/MAX(DEN, SMALL) + XQ(4) = A4_0 + XQ(2) = A2_0 +A2_4*XQ(4) + XQ(5) = A5_0 +A5_4*XQ(4) +A5_2*XQ(2) + XQ(3) = A3_0 +A3_4*XQ(4) +A3_2*XQ(2) +A3_5*XQ(5) + XQ(6) = A6_0 +A6_4*XQ(4) +A6_2*XQ(2) +A6_5*XQ(5) + XQ(10) = A10_0 +A10_4*XQ(4) +A10_2*XQ(2) +A10_5*XQ(5) + XQ(7) = A7_0 +A7_4*XQ(4) +A7_6*XQ(6) + XQ(8) = A8_0 +A8_2*XQ(2) +A8_5*XQ(5) + XQ(11) = A11_0 +A11_5*XQ(5) +A11_8*XQ(8) + XQ(9) = A9_0 +A9_4*XQ(4) + XQ(1) = A1_0 +A1_2*XQ(2) +! +! +! --------------------------------------------- +! +! update rates of reactions involving QSS species +! + RF( 6) = RF( 6)*XQ( 2) + RF( 7) = RF( 7)*XQ( 3) + RB( 7) = RB( 7)*XQ( 5) + RF( 8) = RF( 8)*XQ( 4) + RF( 9) = RF( 9)*XQ( 4) + RB( 9) = RB( 9)*XQ( 5) + RF( 13) = RF( 13)*XQ( 5) + RF( 14) = RF( 14)*XQ( 5) + RB( 15) = RB( 15)*XQ( 5) + RF( 16) = RF( 16)*XQ( 6) + RF( 17) = RF( 17)*XQ( 7) + RB( 18) = RB( 18)*XQ( 6) + RB( 19) = RB( 19)*XQ( 7) + RB( 20) = RB( 20)*XQ(10) + RB( 21) = RB( 21)*XQ( 3) + RF( 22) = RF( 22)*XQ( 8) + RB( 23) = RB( 23)*XQ( 5) + RF( 24) = RF( 24)*XQ( 9) + RB( 25) = RB( 25)*XQ( 9) + RF( 26) = RF( 26)*XQ(10) + RB( 27) = RB( 27)*XQ(10) + RB( 28) = RB( 28)*XQ( 3) + RB( 30) = RB( 30)*XQ( 5) + RF( 46) = RF( 46)*XQ( 2) + RB( 46) = RB( 46)*XQ( 1) + RF( 47) = RF( 47)*XQ( 3) + RF( 48) = RF( 48)*XQ( 4) + RB( 48) = RB( 48)*XQ( 2) + RF( 51) = RF( 51)*XQ( 5) + RF( 52) = RF( 52)*XQ( 5) + RB( 53) = RB( 53)*XQ( 6) + RB( 54) = RB( 54)*XQ( 7) + RB( 55) = RB( 55)*XQ( 5) + RF( 56) = RF( 56)*XQ( 6) + RF( 57) = RF( 57)*XQ( 6) + RF( 58) = RF( 58)*XQ( 6) + RF( 59) = RF( 59)*XQ( 6) + RB( 59) = RB( 59)*XQ( 4) + RF( 60) = RF( 60)*XQ( 7) + RF( 61) = RF( 61)*XQ( 7) + RB( 61) = RB( 61)*XQ( 6) + RF( 62) = RF( 62)*XQ( 7) + RF( 63) = RF( 63)*XQ( 7) + RF( 64) = RF( 64)*XQ( 7) + RB( 64) = RB( 64)*XQ( 4) + RB( 65) = RB( 65)*XQ( 6) + RB( 66) = RB( 66)*XQ( 7) + RB( 67) = RB( 67)*XQ( 8) + RF( 68) = RF( 68)*XQ( 8) + RF( 69) = RF( 69)*XQ( 8) + RB( 70) = RB( 70)*XQ( 9) + RB( 71) = RB( 71)*XQ( 8) + RF( 72) = RF( 72)*XQ( 9) + RF( 73) = RF( 73)*XQ( 9) + RB( 74) = RB( 74)*XQ( 9) + RF( 75) = RF( 75)*XQ(10) + RB( 75) = RB( 75)*XQ( 4) + RB( 76) = RB( 76)*XQ(10) + RF( 85) = RF( 85)*XQ( 1) + RF( 86) = RF( 86)*XQ( 2) + RB( 86) = RB( 86)*XQ( 5) + RF( 87) = RF( 87)*XQ( 3) + RF( 88) = RF( 88)*XQ( 3) + RB( 88) = RB( 88)*XQ( 2) + RF( 89) = RF( 89)*XQ( 4) + RB( 91) = RB( 91)*XQ( 3) + RB( 92) = RB( 92)*XQ( 4) + RF( 95) = RF( 95)*XQ( 5) + RB( 96) = RB( 96)*XQ( 5) + RF( 97) = RF( 97)*XQ( 6) + RF( 98) = RF( 98)*XQ( 7) + RB( 99) = RB( 99)*XQ( 6) + RB(100) = RB(100)*XQ( 7) + RF(103) = RF(103)*XQ( 8) + RB(104) = RB(104)*XQ( 8) + RB(105) = RB(105)*XQ( 9) + RB(106) = RB(106)*XQ(10) + RF(109) = RF(109)*XQ( 3) + RB(111) = RB(111)*XQ( 7) + RB(113) = RB(113)*XQ( 5) + RF(114) = RF(114)*XQ( 1) + RF(115) = RF(115)*XQ( 1) + RF(116) = RF(116)*XQ( 2) + RB(116) = RB(116)*XQ( 5) + RF(117) = RF(117)*XQ( 2) + RB(117) = RB(117)*XQ( 3) + RF(118) = RF(118)*XQ( 2) + RF(120) = RF(120)*XQ( 2) + RB(120) = RB(120)*XQ( 8) + RF(121) = RF(121)*XQ( 2) + RF(122) = RF(122)*XQ( 2) + RB(122) = RB(122)*XQ(10) + RF(123) = RF(123)*XQ( 2) + RB(123) = RB(123)*XQ( 5) + RF(124) = RF(124)*XQ( 2) + RF(126) = RF(126)*XQ( 3) + RF(127) = RF(127)*XQ( 3) + RF(129) = RF(129)*XQ( 3) + RF(130) = RF(130)*XQ( 3) + RF(131) = RF(131)*XQ( 3) + RB(132) = RB(132)*XQ( 8) + RF(133) = RF(133)*XQ( 4) + RB(133) = RB(133)*XQ( 3) + RF(134) = RF(134)*XQ( 4) + RF(135) = RF(135)*XQ( 4) + RF(136) = RF(136)*XQ( 4) + RF(137) = RF(137)*XQ( 4) + RF(138) = RF(138)*XQ( 4) + RB(138) = RB(138)*XQ( 3) + RF(139) = RF(139)*XQ( 4) + RF(140) = RF(140)*XQ( 4) + RF(141) = RF(141)*XQ( 4) + RB(141) = RB(141)*XQ( 3) + RF(142) = RF(142)*XQ( 4) + RB(142) = RB(142)*XQ( 3) + RF(143) = RF(143)*XQ( 4) + RF(144) = RF(144)*XQ( 4) + RB(144) = RB(144)*XQ( 9) + RB(145) = RB(145)*XQ( 7) + RB(149) = RB(149)*XQ( 9) + RF(150) = RF(150)*XQ( 5) + RB(151) = RB(151)*XQ( 5) + RB(152) = RB(152)*XQ( 6) + RB(153) = RB(153)*XQ( 7) + RB(154) = RB(154)*XQ( 8) + RB(155) = RB(155)*XQ( 9) + RF(156) = RF(156)*XQ( 5) + RF(157) = RF(157)*XQ( 5) + RF(158) = RF(158)*XQ( 5) + RF(159) = RF(159)*XQ( 6) + RF(160) = RF(160)*XQ( 7) + RF(161) = RF(161)*XQ( 8) + RB(161) = RB(161)*XQ( 5) + RF(163) = RF(163)*XQ( 9) + RF(164) = RF(164)*XQ(10) + RB(167) = RB(167)*XQ(11) + RF(170) = RF(170)*XQ( 2) + RF(171) = RF(171)*XQ( 3) + RF(172) = RF(172)*XQ( 3) + RF(174) = RF(174)*XQ( 4) + RF(175) = RF(175)*XQ( 8) + RB(175) = RB(175)*XQ(11) + RF(176) = RF(176)*XQ( 8) + RB(177) = RB(177)*XQ(11) + RF(178) = RF(178)*XQ(11) + RB(178) = RB(178)*XQ( 3) + RF(179) = RF(179)*XQ(11) + RF(180) = RF(180)*XQ(11) + RF(181) = RF(181)*XQ(11) + RB(181) = RB(181)*XQ( 5) + RF(182) = RF(182)*XQ(11) + RF(183) = RF(183)*XQ(11) + RF(184) = RF(184)*XQ(11) +! +! END +! ! +! ----------------------------------------------------------------------! +! ! +! +! ! ompute WDOT +! +! SUBROUTINE RDOT(RF, RB, WDOT) +! IMPLICIT DOUBLE PRECISION (A-H, O-Z), INTEGER (I-N) +! DIMENSION RF(*), RB(*), WDOT(*), ROP(184) +! + DO I = 1, 184 + ROP(I) = RF(I) - RB(I) + ENDDO +! +! H2 + WDOT( 1) = -ROP( 3) +ROP( 8) +ROP( 36) +ROP( 37) & + +ROP( 38) +ROP( 39) +ROP( 42) +ROP( 44) & + +ROP( 46) +ROP( 48) +ROP( 50) +ROP( 52) & + +ROP( 55) +ROP( 57) +ROP( 62) +ROP( 65) & + +ROP( 66) +ROP( 69) +ROP( 71) +ROP( 73) & + +ROP( 74) +ROP( 76) -ROP( 78) -ROP( 79) & + -ROP(117) -ROP(127) +ROP(128) -ROP(136) & + +ROP(162) +ROP(166) +ROP(169) -ROP(170) & + +ROP(174) +ROP(182) +! H + WDOT( 2) = -ROP( 2) +ROP( 3) +ROP( 6) -ROP( 7) & + -2*ROP( 8) -ROP( 9) +ROP( 10) +ROP( 14) & + -ROP( 17) +ROP( 19) +ROP( 20) +2*ROP( 21) & + -ROP( 24) +ROP( 25) +ROP( 26) +2*ROP( 28) & + -ROP( 31) -ROP( 32) -ROP( 33) -ROP( 34) & + -ROP( 35) -2*ROP( 36) -2*ROP( 37) -2*ROP( 38) & + -2*ROP( 39) -ROP( 40) -ROP( 41) -ROP( 42) & + -ROP( 43) -ROP( 44) -ROP( 45) -ROP( 46) & + -3*ROP( 47) -3*ROP( 48) -ROP( 49) -ROP( 50) & + -ROP( 51) -ROP( 52) -ROP( 53) -ROP( 55) & + -ROP( 56) -ROP( 57) -ROP( 58) +ROP( 59) & + -2*ROP( 60) -ROP( 61) -2*ROP( 62) -2*ROP( 63) & + -ROP( 65) -2*ROP( 68) -2*ROP( 69) -2*ROP( 72) & + -2*ROP( 73) +ROP( 75) -ROP( 76) -ROP( 77) & + +ROP( 79) +ROP( 85) +ROP( 86) -ROP( 87) & + -2*ROP( 88) -ROP( 89) +2*ROP( 91) +2*ROP( 92) & + +ROP( 94) -ROP( 98) +ROP(100) +ROP(101) & + -ROP(103) +ROP(104) +ROP(105) -2*ROP(109) & + +ROP(111) +ROP(115) +3*ROP(117) +ROP(118) & + -ROP(119) +2*ROP(120) +ROP(121) +ROP(124) & + -ROP(126) -ROP(127) -4*ROP(128) -ROP(129) & + -2*ROP(130) -2*ROP(131) -ROP(132) -ROP(134) & + -2*ROP(135) -ROP(136) -2*ROP(137) -ROP(139) & + -2*ROP(140) -2*ROP(143) -ROP(144) +ROP(145) & + +2*ROP(149) +ROP(153) +ROP(154) +ROP(155) & + +ROP(156) +ROP(157) -ROP(160) -ROP(161) & + -ROP(163) +ROP(166) +2*ROP(167) -2*ROP(172) & + -2*ROP(173) -2*ROP(174) -ROP(176) +2*ROP(178) & + -ROP(179) -ROP(180) -2*ROP(181) -2*ROP(182) & + -ROP(183) -ROP(184) +! O + WDOT( 3) = -2*ROP( 1) -ROP( 2) -ROP( 3) -ROP( 4) & + -ROP( 5) -2*ROP( 6) -ROP( 7) -ROP( 8) & + -ROP( 9) -ROP( 10) -ROP( 11) -ROP( 12) & + -ROP( 13) -ROP( 14) -ROP( 15) -ROP( 16) & + -ROP( 17) -ROP( 18) -ROP( 19) -ROP( 20) & + -ROP( 21) -2*ROP( 22) -ROP( 23) -ROP( 24) & + -ROP( 25) -ROP( 26) -ROP( 27) -ROP( 28) & + +ROP( 29) +ROP( 35) +ROP( 41) +ROP( 48) & + +ROP( 67) -ROP( 68) -ROP( 69) +ROP( 71) & + +ROP( 81) -ROP( 85) -ROP( 86) +ROP( 88) & + -ROP(103) +ROP(104) -ROP(115) -ROP(117) & + -ROP(118) -ROP(119) -ROP(121) -ROP(122) & + -ROP(123) -ROP(124) -ROP(125) +ROP(132) & + +ROP(145) +ROP(154) -ROP(161) -ROP(166) & + -ROP(167) -ROP(170) +ROP(172) -ROP(176) & + -ROP(178) +! O2 + WDOT( 4) = +ROP( 1) +ROP( 4) +2*ROP( 6) +ROP( 8) & + +ROP( 13) +ROP( 14) -ROP( 15) +ROP( 16) & + -ROP( 18) -ROP( 20) -ROP( 21) +ROP( 22) & + -ROP( 23) +ROP( 26) -ROP( 27) -ROP( 28) & + -ROP( 29) -2*ROP( 30) -ROP( 31) -ROP( 32) & + -ROP( 33) -ROP( 34) -ROP( 35) +ROP( 42) & + +ROP( 46) +ROP( 47) -ROP( 48) +ROP( 51) & + +ROP( 52) -ROP( 53) -ROP( 55) +ROP( 56) & + +ROP( 57) +ROP( 58) -ROP( 61) -ROP( 64) & + -ROP( 65) -ROP( 67) +ROP( 68) +ROP( 69) & + -ROP( 71) -ROP( 76) +ROP( 82) +ROP( 85) & + +ROP( 86) +ROP( 87) -ROP( 88) +ROP( 89) & + -ROP( 91) -ROP( 92) +ROP( 95) -ROP( 96) & + +ROP( 97) -ROP( 99) +ROP(103) -ROP(104) & + -ROP(106) +ROP(107) +ROP(108) +ROP(109) & + +ROP(110) -ROP(113) +ROP(115) +ROP(117) & + +2*ROP(118) +3*ROP(119) +ROP(120) +2*ROP(121) & + +ROP(122) +ROP(123) +2*ROP(124) +3*ROP(125) & + +ROP(127) +2*ROP(128) +ROP(129) +ROP(130) & + +ROP(131) +ROP(132) +ROP(136) +ROP(137) & + +ROP(139) +ROP(140) +ROP(143) +ROP(144) & + -ROP(145) -ROP(146) +ROP(150) -ROP(151) & + -ROP(152) -ROP(154) +ROP(156) +ROP(157) & + -ROP(160) -ROP(161) -ROP(163) +2*ROP(165) & + +ROP(168) +2*ROP(170) +2*ROP(173) +ROP(174) & + -ROP(178) -ROP(179) -3*ROP(180) -ROP(181) & + -2*ROP(184) +! OH + WDOT( 5) = +ROP( 2) +ROP( 3) +ROP( 4) +ROP( 5) & + +ROP( 11) +ROP( 13) +ROP( 15) +ROP( 16) & + +ROP( 17) +ROP( 18) +ROP( 19) +ROP( 20) & + +ROP( 25) -ROP( 26) +2*ROP( 27) +ROP( 35) & + -ROP( 40) +2*ROP( 43) +ROP( 45) +ROP( 58) & + +ROP( 63) -ROP( 75) +ROP( 76) -ROP( 79) & + -2*ROP( 80) -2*ROP( 81) -ROP( 82) -ROP( 83) & + -ROP( 84) -ROP( 85) -ROP( 86) -ROP( 87) & + -ROP( 88) -ROP( 89) -ROP( 90) -ROP( 91) & + -ROP( 92) -ROP( 93) -ROP( 94) -ROP( 95) & + -ROP( 96) -ROP( 97) -ROP( 98) -ROP( 99) & + -ROP(100) -ROP(101) -ROP(102) -ROP(103) & + -ROP(104) -ROP(105) +ROP(109) +ROP(111) & + +ROP(112) +ROP(122) -ROP(125) +ROP(126) & + -ROP(132) +ROP(134) +ROP(146) -2*ROP(165) & + -ROP(168) -ROP(169) +ROP(179) +ROP(180) & + -ROP(183) -ROP(184) +! H2O + WDOT( 6) = +ROP( 40) +ROP( 41) +ROP( 45) +ROP( 59) & + +ROP( 64) +ROP( 79) +ROP( 81) +ROP( 82) & + +ROP( 83) +ROP( 84) +ROP( 88) +ROP( 91) & + +ROP( 92) +ROP( 93) +ROP( 95) +ROP( 96) & + +ROP( 97) +ROP( 98) +ROP( 99) +ROP(100) & + +ROP(103) +ROP(104) +ROP(105) +ROP(106) & + -ROP(118) +ROP(135) -ROP(137) +ROP(168) & + -ROP(174) +ROP(183) +! HO2 + WDOT( 7) = -ROP( 4) +ROP( 5) -ROP( 6) +ROP( 7) & + +ROP( 9) -ROP( 13) -ROP( 14) +ROP( 15) & + -ROP( 16) +ROP( 18) +ROP( 23) +2*ROP( 30) & + +ROP( 31) +ROP( 32) +ROP( 33) +ROP( 34) & + -ROP( 41) -ROP( 42) -ROP( 43) +ROP( 44) & + -ROP( 46) +ROP( 48) -ROP( 51) -ROP( 52) & + +ROP( 53) +ROP( 55) -ROP( 56) -ROP( 57) & + -ROP( 58) -ROP( 59) +ROP( 61) +ROP( 65) & + -ROP( 82) +ROP( 83) +ROP( 84) +ROP( 88) & + -ROP( 95) +ROP( 96) -ROP( 97) +ROP( 99) & + -2*ROP(107) -2*ROP(108) -ROP(109) -ROP(110) & + -ROP(111) -ROP(112) -ROP(117) -ROP(118) & + -ROP(119) -ROP(120) -ROP(121) -ROP(122) & + -ROP(124) -ROP(125) +ROP(147) -ROP(150) & + +ROP(151) +ROP(152) -ROP(156) -ROP(157) & + +ROP(160) +ROP(161) +ROP(163) -ROP(168) & + -ROP(170) +ROP(176) +2*ROP(180) +ROP(181) & + +2*ROP(184) +! H2O2 + WDOT( 8) = -ROP( 5) -ROP( 44) -ROP( 45) +ROP( 80) & + -ROP( 83) -ROP( 84) +ROP(107) +ROP(108) & + +ROP(113) -ROP(147) +! CH3 + WDOT( 9) = -ROP( 10) +ROP( 11) +ROP( 23) +ROP( 24) & + +ROP( 47) -ROP( 49) +ROP( 50) +ROP( 58) & + +ROP( 63) +ROP( 77) -ROP( 90) -ROP( 91) & + -ROP( 92) +ROP( 93) +ROP(102) -ROP(110) & + -ROP(111) -ROP(115) -ROP(120) +ROP(127) & + -ROP(129) +2*ROP(130) +ROP(136) -ROP(139) & + +2*ROP(140) +ROP(144) -ROP(145) -ROP(146) & + -ROP(147) -2*ROP(148) -2*ROP(149) -ROP(150) & + -ROP(151) -ROP(152) -ROP(153) -ROP(154) & + -ROP(155) -ROP(166) -ROP(169) +ROP(170) & + +ROP(181) +! CH4 + WDOT(10) = -ROP( 11) +ROP( 49) -ROP( 50) -ROP( 93) & + +ROP(110) -ROP(121) -ROP(130) -ROP(140) & + +ROP(147) +ROP(150) +ROP(151) +ROP(152) & + +ROP(153) +ROP(154) +ROP(155) +! CO + WDOT(11) = +ROP( 7) +ROP( 8) +ROP( 9) -ROP( 12) & + -ROP( 14) +ROP( 15) +2*ROP( 20) +ROP( 21) & + +ROP( 23) +2*ROP( 27) -ROP( 29) +ROP( 30) & + +ROP( 48) -ROP( 51) +ROP( 55) -ROP( 75) & + +2*ROP( 76) +ROP( 77) -ROP( 78) +ROP( 88) & + -ROP( 94) +ROP( 96) +ROP(102) +2*ROP(106) & + -ROP(112) +ROP(113) -ROP(115) -ROP(117) & + -ROP(118) -ROP(119) -ROP(120) -ROP(121) & + +ROP(123) -ROP(124) -2*ROP(125) +ROP(126) & + -ROP(131) -ROP(132) +ROP(134) +ROP(135) & + +ROP(143) +ROP(151) +ROP(161) -2*ROP(165) & + +ROP(166) -ROP(170) +ROP(179) +2*ROP(180) & + +ROP(181) +ROP(184) +! CO2 + WDOT(12) = -ROP( 7) -ROP( 8) -ROP( 9) +ROP( 12) & + +ROP( 14) +ROP( 21) +2*ROP( 28) +ROP( 29) & + -ROP( 47) -ROP( 48) +ROP( 59) +ROP( 64) & + +ROP( 75) -ROP( 87) -ROP( 88) -ROP( 89) & + +ROP( 91) +ROP( 92) +ROP( 94) -ROP(109) & + +ROP(112) +ROP(117) -ROP(119) -ROP(123) & + -ROP(126) -ROP(127) -2*ROP(128) -ROP(129) & + -ROP(130) -ROP(131) -ROP(132) -ROP(134) & + -ROP(135) -ROP(136) -ROP(137) -ROP(139) & + -ROP(140) -2*ROP(143) -ROP(144) -ROP(172) & + -2*ROP(173) -ROP(174) +2*ROP(178) +! CH2O + WDOT(13) = +ROP( 10) -ROP( 15) +ROP( 18) +ROP( 19) & + +ROP( 24) -ROP( 30) +ROP( 51) -ROP( 55) & + -ROP( 56) -ROP( 58) -ROP( 59) -ROP( 60) & + -ROP( 63) -ROP( 64) +ROP( 65) +ROP( 66) & + +ROP( 78) +ROP( 87) +ROP( 89) -ROP( 96) & + +ROP( 99) +ROP(100) +ROP(109) +ROP(111) & + -ROP(113) +ROP(118) -ROP(124) +ROP(143) & + +ROP(145) +ROP(146) -ROP(151) +ROP(152) & + +ROP(153) +ROP(161) +ROP(169) +ROP(172) & + +ROP(174) +ROP(179) +ROP(184) +! CH3OH + WDOT(14) = -ROP( 18) -ROP( 19) +ROP( 56) +ROP( 60) & + -ROP( 65) -ROP( 66) +ROP( 90) -ROP( 99) & + -ROP(100) +ROP(137) -ROP(152) -ROP(153) +! C2H2 + WDOT(15) = -ROP( 20) -ROP( 21) -ROP( 67) +ROP( 69) & + -ROP(101) -ROP(102) +ROP(103) +ROP(115) & + +ROP(119) +ROP(125) +ROP(128) +ROP(162) & + +ROP(165) +ROP(173) +ROP(176) +! C2H4 + WDOT(16) = -ROP( 23) -ROP( 24) +ROP( 25) +ROP( 68) & + -ROP( 71) -ROP( 72) +ROP( 74) -ROP(104) & + +ROP(105) +ROP(121) +ROP(129) +ROP(139) & + +ROP(144) +ROP(149) -ROP(154) +ROP(155) & + -ROP(162) -ROP(167) +! C2H6 + WDOT(17) = -ROP( 25) +ROP( 72) -ROP( 74) -ROP(105) & + -ROP(144) +ROP(148) -ROP(155) +! CH2CO + WDOT(18) = -ROP( 27) -ROP( 28) +ROP( 67) -ROP( 68) & + -ROP( 69) +ROP( 71) -ROP( 76) -ROP( 77) & + +ROP(101) -ROP(103) +ROP(104) -ROP(106) & + +ROP(120) +ROP(124) +ROP(131) +ROP(132) & + +ROP(154) -ROP(161) +ROP(167) -ROP(176) & + -ROP(178) -ROP(179) -ROP(180) -ROP(181) & + -ROP(184) +! N2 + WDOT(19) = 0.0 + + ! Correction for unit compatibility in Cantera + WDOT(1:19) = WDOT(1:19)*1D6 + + RETURN + END \ No newline at end of file diff --git a/samples/python/AVBP/mixture_database.dat b/samples/python/AVBP/mixture_database.dat new file mode 100755 index 00000000000..17db30799c2 --- /dev/null +++ b/samples/python/AVBP/mixture_database.dat @@ -0,0 +1,102 @@ +$MIXTURE + +!--------------------------------------------------------------------------------------------------------------------- +! Reactive mixture CH4/AIR. Reduced chemistry with PEA formalism, 2S-BFER scheme. +!--------------------------------------------------------------------------------------------------------------------- + mixture_name = BFER_nopea + validity_info = 300-700K/1-12atm + transport = computed + combustion_chemistry = reduced_pea + species_name = CH4 CO2 CO O2 H2O N2 + species_Schmidt_number = 0.7d0 0.7d0 0.7d0 0.7d0 0.7d0 0.7d0 + viscosity_law = power + mu_ref = 1.8405d-5 + T_ref = 300.d0 + viscosity_law_coeff = 0.6759d0 + prandtl_number = 0.7d0 + atom_for_z_calculation = C + fuel_tank_composition = 1.d0 0.d0 0.d0 0.d0 0.d0 0.d0 + oxydizer_tank_composition = 0.d0 0.d0 0.d0 0.233d0 0.d0 0.767d0 + + ! 2S-BFER Reaction #1 : CH4 + 1.5 O2 => CO + 2 H2O + !----------------------------------------- + reac_name = CH4-AIR-2S-BFER-1 + reac_species_number = 4 + reac_species_name = CH4 O2 CO H2O + reac_stoich_coeff = -1.d0 -1.5d0 1.d0 2.d0 + reac_Arrh_fwd_coeff = 0.5d0 0.65d0 0.d0 0.d0 + reac_Arrh_bwd_coeff = 0.d0 0.d0 0.d0 0.d0 + reac_preexp = 4.9d9 + reac_act_energ = 35500.0d0 + reac_temp_exp = 0.d0 + reac_third_body_number = 0 + reac_third_body_name = no + reac_third_body_eff = 0.d0 + + ! 2S-BFER Reaction #2 : CO + 0.5 O2 <=> CO2 + !---------------------------------- + reac_name = CH4-AIR-2S-BFER-2 + reac_species_number = 3 + reac_species_name = CO O2 CO2 + reac_stoich_coeff = -1.d0 -0.5d0 1.d0 + reac_Arrh_fwd_coeff = 1.d0 0.5d0 0.d0 + reac_Arrh_bwd_coeff = 0.d0 0.d0 1.d0 + reac_preexp = -2.0d8 + reac_act_energ = 12000.0d0 + reac_temp_exp = 0.7d0 + reac_third_body_number = 0 + reac_third_body_name = no + reac_third_body_eff = 0.d0 + +!--------------------------------------------------------------------------------------------------------------------- +! Reactive mixture CH4/AIR. Reduced chemistry with PEA formalism, 2S-BFER scheme. +!--------------------------------------------------------------------------------------------------------------------- + mixture_name = BFER_pea + validity_info = 300-700K/1-12atm + transport = computed + combustion_chemistry = reduced_pea + species_name = CH4 CO2 CO O2 H2O N2 + species_Schmidt_number = 0.7d0 0.7d0 0.7d0 0.7d0 0.7d0 0.7d0 + viscosity_law = power + mu_ref = 1.8405d-5 + T_ref = 300.d0 + viscosity_law_coeff = 0.6759d0 + prandtl_number = 0.7d0 + pea_method = pea2 + pea_coeff = 1.10d0 0.09d0 0.37d0 1.13d0 0.03d0 6.7d0 1.6d0 0.22d0 + pea_coeff = 0.95d0 0.08d0 2.5d-5 1.3d0 0.04d0 0.0087d0 1.2d0 0.04d0 1.2d0 0.05d0 + atom_for_z_calculation = C + fuel_tank_composition = 1.d0 0.d0 0.d0 0.d0 0.d0 0.d0 + oxydizer_tank_composition = 0.d0 0.d0 0.d0 0.233d0 0.d0 0.767d0 + + ! 2S-BFER Reaction #1 : CH4 + 1.5 O2 => CO + 2 H2O + !----------------------------------------- + reac_name = CH4-AIR-2S-BFER-1 + reac_species_number = 4 + reac_species_name = CH4 O2 CO H2O + reac_stoich_coeff = -1.d0 -1.5d0 1.d0 2.d0 + reac_Arrh_fwd_coeff = 0.5d0 0.65d0 0.d0 0.d0 + reac_Arrh_bwd_coeff = 0.d0 0.d0 0.d0 0.d0 + reac_preexp = 4.9d9 + reac_act_energ = 35500.0d0 + reac_temp_exp = 0.d0 + reac_third_body_number = 0 + reac_third_body_name = no + reac_third_body_eff = 0.d0 + + ! 2S-BFER Reaction #2 : CO + 0.5 O2 <=> CO2 + !---------------------------------- + reac_name = CH4-AIR-2S-BFER-2 + reac_species_number = 3 + reac_species_name = CO O2 CO2 + reac_stoich_coeff = -1.d0 -0.5d0 1.d0 + reac_Arrh_fwd_coeff = 1.d0 0.5d0 0.d0 + reac_Arrh_bwd_coeff = 0.d0 0.d0 1.d0 + reac_preexp = -2.0d8 + reac_act_energ = 12000.0d0 + reac_temp_exp = 0.7d0 + reac_third_body_number = 0 + reac_third_body_name = no + reac_third_body_eff = 0.d0 + +$end_MIXTURE \ No newline at end of file diff --git a/samples/python/AVBP/postproc.py b/samples/python/AVBP/postproc.py new file mode 100644 index 00000000000..6bea2f1c5e9 --- /dev/null +++ b/samples/python/AVBP/postproc.py @@ -0,0 +1,79 @@ +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Parameters of the solver +loglevel = 1 +refine_grid = 'refine' + +# Setting up the gas object (operating conditions) +if ct.__version__ >= '2.5.0': + gas = ct.Solution('gri30.yaml') +else: + gas = ct.Solution('gri30.cti') + +p = 1e5 +tin = 300.0 +phi = 1.0 +fuel = {'CH4':1} +oxidizer = {'O2': 1, 'N2': 3.76} +gas.TP = tin, p +gas.set_equivalence_ratio(phi, fuel, oxidizer) + +# Setting up the flame object +f = ct.FreeFlame(gas, width=0.02) +f.inlet.X = gas.X +f.inlet.T = gas.T + +f.energy_enabled = True +f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05, prune=0.01) +f.set_max_jac_age(10, 10) +f.set_time_step(1e-8, [10, 20, 40, 80, 100, 100, 150]) +f.max_time_step_count = 500 + +f.solve(loglevel, refine_grid) + +# Compute thermal flame thickness +z = f.flame.grid +T = f.T +grad = np.gradient(T,z) +thickness = (max(T) -min(T)) / max(grad) +print(' ') +print('laminar thermal flame thickness (delta_T) = ', thickness) +print(' ') + +# Compute HRR flame thickness +# Remark : slight difference when using np.gradient (5% in relative) +# Therefore manual computation of gradient is used +HRR = f.heat_release_rate +gradHRR = (HRR[2:]-HRR[0:-2])/(z[2:]-z[0:-2]) +HRR = HRR[1:-1] +x = z[1:-1] +gradHRR2 = (gradHRR[2:]-gradHRR[0:-2])/(x[2:]-x[0:-2]) +x = x[1:-1] +gradHRR = gradHRR[1:-1] +HRR = HRR[1:-1] +delta_HRR = -2.0*(-2.0*HRR*gradHRR2)**0.5/gradHRR2 +where = np.where(HRR > 1e3) +delta_HRR = np.nanmin(delta_HRR[where]) + +print(' ') +print('laminar HRR flame thickness (delta_HRR) = ', delta_HRR) +print(' ') +print('delta_T / delta_HRR = ', thickness / delta_HRR) +print(' ') + +# Compute schmidt numbers +print('SCHMIDT NUMBERS (in burnt gases):') +f.set_gas_state(f.flame.n_points-1) +list_species = f.gas.species_names +for species in list_species: + print (species,gas.viscosity/gas.mix_diff_coeffs[gas.species_index(species)]/gas.density) +print(' ') + +print('PRANDTL NUMBER (in fresh gases):') +f.set_gas_state(f.flame.n_points-f.flame.n_points) +Pr = gas.cp_mass * gas.viscosity / gas.thermal_conductivity +print('Prandtl = '+str(Pr)) \ No newline at end of file diff --git a/samples/python/AVBP/write_csv.py b/samples/python/AVBP/write_csv.py new file mode 100644 index 00000000000..e41ae5bac68 --- /dev/null +++ b/samples/python/AVBP/write_csv.py @@ -0,0 +1,37 @@ +import cantera as ct +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +# Parameters of the solver +loglevel = 1 +refine_grid = 'refine' + +# Setting up the gas object (operating conditions) +if ct.__version__ >= '2.5.0': + gas = ct.Solution('gri30.yaml') +else: + gas = ct.Solution('gri30.cti') +p = 1e5 +tin = 300.0 +phi = 1.0 +fuel = {'CH4':1} +oxidizer = {'O2': 1, 'N2': 3.76} +gas.TP = tin, p +gas.set_equivalence_ratio(phi, fuel, oxidizer) + +# Setting up the flame object +f = ct.FreeFlame(gas, width=0.02) +f.inlet.X = gas.X +f.inlet.T = gas.T + +f.energy_enabled = True +f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05, prune=0.01) +f.set_max_jac_age(10, 10) +f.set_time_step(1e-8, [10, 20, 40, 80, 100, 100, 150]) +f.max_time_step_count = 500 + +f.solve(loglevel, refine_grid) + +# Write AVBP solution for can2av +f.write_AVBP("./RESULTS/AVBP-Solution.csv") \ No newline at end of file diff --git a/samples/python/multiphase/README.rst b/samples/python/multiphase/README.rst new file mode 100644 index 00000000000..b6b2d91eff3 --- /dev/null +++ b/samples/python/multiphase/README.rst @@ -0,0 +1,2 @@ +Multiphase +---------- diff --git a/samples/python/onedim/adiabatic_flame.csv b/samples/python/onedim/adiabatic_flame.csv new file mode 100644 index 00000000000..42bb921593b --- /dev/null +++ b/samples/python/onedim/adiabatic_flame.csv @@ -0,0 +1,141 @@ 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[0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, + 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] + points: 140 + tolerances: + steady-abstol: 1.0e-09 + transient-reltol: 1.0e-04 + transient-abstol: 1.0e-11 + steady-reltol: 1.0e-04 + transport-model: mixture-averaged + phase: + name: ohmech + source: /Users/theot/Documents/INSTALL_DIR/lib/python3.9/site-packages/cantera/data/h2o2.yaml + radiation-enabled: false + energy-enabled: true + Soret-enabled: false + species-enabled: true + refine-criteria: + ratio: 3.0 + slope: 0.06 + curve: 0.12 + prune: 0.0 + grid-min: 1.0e-10 + max-points: 1000 + fixed-point: + location: 0.021 + temperature: 698.1678485027371 + basis: mass + components: [grid, velocity, T, D, H2, H, O, O2, OH, H2O, HO2, H2O2, AR, N2] + products: + size: 0 + type: outlet + points: 1 diff --git a/samples/python/surface_chemistry/README.rst b/samples/python/surface_chemistry/README.rst new file mode 100644 index 00000000000..baaa67d5443 --- /dev/null +++ b/samples/python/surface_chemistry/README.rst @@ -0,0 +1,2 @@ +Surface chemistry +----------------- From b3e371b8d684ee2f1c8382db19dd299545377046 Mon Sep 17 00:00:00 2001 From: pestre Date: Thu, 30 Jan 2025 12:05:19 +0100 Subject: [PATCH 21/98] Merge differences in src directory Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: new file: src/base/Parser.cpp modified: src/base/application.h modified: src/clib/ctonedim.cpp modified: src/extensions/pythonShim.cpp new file: src/kinetics/CustomKinetics.cpp modified: src/kinetics/Kinetics.cpp modified: src/kinetics/KineticsFactory.cpp modified: src/oneD/Boundary1D.cpp modified: src/oneD/Domain1D.cpp modified: src/oneD/DomainFactory.cpp new file: src/oneD/Flamelet.cpp modified: src/oneD/IonFlow.cpp modified: src/oneD/Sim1D.cpp modified: src/oneD/StFlow.cpp modified: src/oneD/refine.cpp new file: src/transport/AVBPTransport.cpp modified: src/transport/TransportFactory.cpp Conflicts: src/extensions/pythonShim.cpp Author: pestre Date: Thu Jan 30 12:05:19 2025 +0100 On branch WIP/merge_CERFACS_devs You are currently cherry-picking commit 22c89db5c. Changes to be committed: new file: src/base/Parser.cpp modified: src/clib/ctonedim.cpp modified: src/extensions/pythonShim.cpp new file: src/kinetics/CustomKinetics.cpp modified: src/kinetics/Kinetics.cpp modified: src/kinetics/KineticsFactory.cpp modified: src/oneD/Boundary1D.cpp modified: src/oneD/Domain1D.cpp modified: src/oneD/DomainFactory.cpp new file: src/oneD/Flamelet.cpp modified: src/oneD/IonFlow.cpp modified: src/oneD/Sim1D.cpp modified: src/oneD/StFlow.cpp modified: src/oneD/refine.cpp new file: src/transport/AVBPTransport.cpp modified: src/transport/TransportFactory.cpp Author: pestre interactive rebase in progress; onto 7aec821a8 Last commands done (6 commands done): pick 925ed423a Merge differences in samples directory pick 68a09c47e Merge differences in src directory Next commands to do (8 remaining commands): pick f298a7d4e Merge differences in test directory pick e118cf6c4 Merge differences for other files You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. Changes to be committed: new file: src/base/Parser.cpp modified: src/clib/ctonedim.cpp modified: src/extensions/pythonShim.cpp new file: src/kinetics/CustomKinetics.cpp modified: src/kinetics/Kinetics.cpp modified: src/kinetics/KineticsFactory.cpp modified: src/oneD/Boundary1D.cpp modified: src/oneD/Domain1D.cpp modified: src/oneD/DomainFactory.cpp new file: src/oneD/Flamelet.cpp modified: src/oneD/IonFlow.cpp modified: src/oneD/Sim1D.cpp modified: src/oneD/StFlow.cpp modified: src/oneD/refine.cpp new file: src/transport/AVBPTransport.cpp modified: src/transport/TransportFactory.cpp --- src/base/Parser.cpp | 275 ++++ src/clib/ctonedim.cpp | 5 +- src/extensions/pythonShim.cpp | 2 +- src/kinetics/CustomKinetics.cpp | 58 + src/kinetics/Kinetics.cpp | 2 + src/kinetics/KineticsFactory.cpp | 3 + src/oneD/Boundary1D.cpp | 159 ++- src/oneD/Domain1D.cpp | 4 +- src/oneD/DomainFactory.cpp | 43 +- src/oneD/Flamelet.cpp | 471 +++++++ src/oneD/IonFlow.cpp | 2 +- src/oneD/Sim1D.cpp | 332 ++++- src/oneD/StFlow.cpp | 2011 +++++++++++++++++++++++++++- src/oneD/refine.cpp | 417 ++++++ src/transport/AVBPTransport.cpp | 278 ++++ src/transport/TransportFactory.cpp | 7 + 16 files changed, 3984 insertions(+), 85 deletions(-) create mode 100644 src/base/Parser.cpp create mode 100644 src/kinetics/CustomKinetics.cpp create mode 100644 src/oneD/Flamelet.cpp create mode 100644 src/transport/AVBPTransport.cpp diff --git a/src/base/Parser.cpp b/src/base/Parser.cpp new file mode 100644 index 00000000000..bbee10b6160 --- /dev/null +++ b/src/base/Parser.cpp @@ -0,0 +1,275 @@ +#include "cantera/base/Parser.h" + +#include +#include +#include +#include +#include + +void Param::print() { + cout << m_name; + for (int i = 0; i < m_args.size(); ++i) + cout << " " << m_args[i]; + cout << endl; +} + +double Param::readDouble(const int i) { + double value; + std::string value_str; + if ( i >= m_args.size() ) { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: no argument " << i << " of param " << m_name << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } else { + //std::stringstream stream(m_args[i]); + value_str = Param::readString(i); + std::replace( value_str.begin(), value_str.end(), 'd', 'e'); + std::stringstream stream(value_str); + if ( stream >> value ) { + return(value); + } else { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: argument " << i << " of param " << m_name << " in not a double" << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } + } +} + +int Param::readInteger(const int i) { + int value; + if ( i >= m_args.size() ) { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: no argument " << i << " of param " << m_name << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } else { + std::stringstream stream(m_args[i]); + if ( stream >> value ) { + return(value); + } else { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: argument " << i << " of param " << m_name << " in not an integer" << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } + } +} + +string Param::readString(const int i) { + if ( i >= m_args.size() ) { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: no argument " << i << " of param " << m_name << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } else { + return(m_args[i]); + } +} + +bool Param::readBool(const int i) { + if ( i >= m_args.size() ) { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: no argument " << i << " of param " << m_name << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } else { + if ((m_args[i]=="true")||(m_args[i]=="TRUE")) + return(true); + else if ((m_args[i]=="false")||(m_args[i]=="FALSE")) + return(false); + else { + cout << "---------------------------------------------------------" << endl; + cout << " Parser error: argument " << i << " of param " << m_name << " in not a boolean" << endl; + cout << "---------------------------------------------------------" << endl; + exit(1); + } + } +} + +Param * Parser::getParam(const string& name) { + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if ( p->Name() == name ) { + p->incrCount(); + return(&(*p)); + } + } + cout << " Param " << name << " is required ! " << endl; + exit(1); +} + +Param * Parser::getParam(const string& name, const size_t n) { + size_t count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if (p->Name() == name) { + if (count == n ) { + p->incrCount(); + return(&(*p)); + } else { + ++count; + } + } + } + cout << n <<"th param " << name << " does not exist ! " << endl; + exit(1); +} + +Param * Parser::getParam(const string& name, const size_t n, const size_t m) { + size_t global_count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if (p->Name() == name && global_count >= n && global_count <= m) { + p->incrCount(); + return(&(*p)); + } + global_count = global_count + 1; + } + cout << " param " << name << " does not exist for selected mixture ! " << endl; + exit(1); +} + +// Non-existing method in cantera version +Param * Parser::getParam(const string& name, const size_t n, const size_t m, const size_t l) { + size_t global_count = 0; + size_t count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if (p->Name() == name && global_count >=n && global_count <=m) { + if (count == l ) { + p->incrCount(); + return(&(*p)); + } else { + ++count; + } + } + global_count = global_count + 1; + } + cout << n <<"th param " << name << " does not exist ! " << endl; + exit(1); +} + + +size_t Parser::getParamNumber(const string& name, const size_t n) { + size_t global_count = 0; + size_t param_count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if (p->Name() == name) { + if (param_count == n) { + return(global_count); + } + param_count = param_count + 1; + } + global_count = global_count + 1; + } + return(string::npos); +} + +bool Parser::checkParam(const string& name) { + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if ( p->Name() == name ) { + p->incrCount(); + return(true); + } + } + return(false); +} + +// Non-existing method in cantera version +bool Parser::checkParam(const string& name, const size_t n, const size_t m) { + size_t global_count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if ( p->Name() == name && global_count >= n && global_count <= m) { + p->incrCount(); + return(true); + } + global_count = global_count + 1; + } + return(false); +} + + +size_t Parser::nbParamOccurence(const string& name) { + size_t count = 0; + for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) { + if ( p->Name() == name ) { + ++count; + } + } + return(count); +} + +void Parser::parseFile(const string& file) { + +// Disclaimer + //cout << "--------------------------------------------" << endl; + //cout << " Parsing input file "+ file<< endl; + //cout << "--------------------------------------------" << endl; + +// File exist ? + ifstream inputfile(file); + if (!inputfile.good()) { + cout << "------------------------------------------------------" << endl; + cout << " Parser error: input file "+file+" does not exist !" << endl; + cout << "------------------------------------------------------" << endl; + exit(1); + } + +// Loop on lines + bool goodParam; + while (inputfile.good()) { + string line; + Param buffer_param; + goodParam = false; + getline(inputfile,line); + if (addParamFromLine(buffer_param,line)) { + m_params.push_back(buffer_param); + m_count += 1; + //i_count.push_back(m_count); + } + } + +// Print params +// for (std::list::iterator p = m_params.begin(); p != m_params.end(); ++p) +// p->print(); + +} + +bool Parser::addParamFromLine(Param& param,const string& line) { + // look for a hash (Comment operator) and trim + size_t hashPos = line.find_first_of("!",0); + string trimmed_line = line.substr(0,hashPos); + + // look for first character /= of "=" + string delimiters = " \t="; + size_t beg = trimmed_line.find_first_not_of(delimiters,0); + + // Empty line + if (beg == string::npos) return(false); + + // look for "=" and store Param name + size_t delpos = trimmed_line.find_first_of(delimiters,beg); + param.setName(trimmed_line.substr(beg,delpos-beg)); + + // look for parameter arguments, separated by space + trimmed_line = trimmed_line.substr(delpos+2,trimmed_line.size()); + + // Remove initial spaces + beg = trimmed_line.find_first_not_of(" ",0); + size_t end = trimmed_line.find_last_not_of(" \t"); + trimmed_line = trimmed_line.substr(beg,end); + + // Loop on arguments + while (!(beg == string::npos)) { + beg = trimmed_line.find_first_of(" ",0); + if (!(beg == string::npos)) { + param.addArgs(trimmed_line.substr(0,beg)); + trimmed_line = trimmed_line.substr(beg,trimmed_line.size()); + size_t space = trimmed_line.find_first_not_of(" ",0); + if (!(space == string::npos)) { + trimmed_line = trimmed_line.substr(space,trimmed_line.size()); + } + } else { + param.addArgs(trimmed_line.substr(0,trimmed_line.size())); + } + } + return(true); +} diff --git a/src/clib/ctonedim.cpp b/src/clib/ctonedim.cpp index ee55c77408d..48376fe6043 100644 --- a/src/clib/ctonedim.cpp +++ b/src/clib/ctonedim.cpp @@ -664,10 +664,11 @@ extern "C" { } } - int sim1D_solve(int i, int loglevel, int refine_grid) + int sim1D_solve(int i, int loglevel, const char* refine_grid) { try { - bool r = (refine_grid == 0 ? false : true); + // bool r = (refine_grid == 0 ? false : true); + string r = (std::strcmp(refine_grid, "remesh") ? "disabled" : "refine"); SimCabinet::item(i).solve(loglevel, r); return 0; } catch (...) { diff --git a/src/extensions/pythonShim.cpp b/src/extensions/pythonShim.cpp index e5c1f0d5f67..d8f70ff2275 100644 --- a/src/extensions/pythonShim.cpp +++ b/src/extensions/pythonShim.cpp @@ -72,7 +72,7 @@ void loadCanteraPython() const char* venv_path = getenv("VIRTUAL_ENV"); if (venv_path != nullptr) { PyConfig pyconf; - pyconf.buffered_stdio = 0; + // pyconf.buffered_stdio = 0; PyConfig_InitPythonConfig(&pyconf); #ifdef _WIN32 diff --git a/src/kinetics/CustomKinetics.cpp b/src/kinetics/CustomKinetics.cpp new file mode 100644 index 00000000000..cc4b08c6449 --- /dev/null +++ b/src/kinetics/CustomKinetics.cpp @@ -0,0 +1,58 @@ +/** + * @file CustomKinetics.cpp + * + * @ingroup chemkinetics + */ + +// +// Author: Q. Cazeres, A. Felden, P. Pepiot +// +// +#include "cantera/kinetics/CustomKinetics.h" +// #include "cantera/kinetics/Kinetics.h" +#include "cantera/thermo/ThermoPhase.h" + +#include +#include + +using namespace std; + +namespace Cantera +{ + CustomKinetics::CustomKinetics() : GasKinetics() + { + printf("WARNING: Using customized kinetics from f90 file.\n"); + handle = dlopen("customkinetics.so", RTLD_LAZY); + + // load symbol + ck = (ck_t) dlsym(handle, "customkinetics_"); + + } + + void CustomKinetics::get_wdot_reduced(double* wdot) + { + + double P = thermo().pressure(); + double T = thermo().temperature(); + // New yarc2 format + //double rho = thermo().density(); + const double* m_y = thermo().massFractions(); + + ck(&P,&T,&m_y[0],&wdot[0]); + + // New yarc2 format + //ck(&P,&T,&rho,&m_y[0],&wdot[0]); + + // Old yarc format + //mol/kmol conversion cantera is in kmol + for (size_t i=0;i namespace Cantera @@ -35,6 +37,7 @@ KineticsFactory::KineticsFactory() { addDeprecatedAlias("surface", "surf"); reg("edge", []() { return new EdgeKinetics(); }); addDeprecatedAlias("edge", "Edge"); + reg("custom", []() { return new CustomKinetics(); }); } KineticsFactory* KineticsFactory::factory() { diff --git a/src/oneD/Boundary1D.cpp b/src/oneD/Boundary1D.cpp index 9b5909a3838..bf70d14737d 100644 --- a/src/oneD/Boundary1D.cpp +++ b/src/oneD/Boundary1D.cpp @@ -35,11 +35,21 @@ void Boundary1D::_init(size_t n) Domain1D& r = container().domain(m_index-1); if (!r.isConnector()) { // multi-point domain m_left_nv = r.nComponents(); - if (m_left_nv > c_offset_Y) { - m_left_nsp = m_left_nv - c_offset_Y; - } else { - m_left_nsp = 0; + + if (m_type == cFlameletFlow) { + if (m_left_nv > c_offset_Yflamelet) { + m_left_nsp = m_left_nv - c_offset_Yflamelet; + } else { + m_left_nsp = 0; + } + }else{ + if (m_left_nv > c_offset_Y) { + m_left_nsp = m_left_nv - c_offset_Y; + } else { + m_left_nsp = 0; + } } + m_left_loc = container().start(m_index-1); m_left_points = r.nPoints(); m_flow_left = dynamic_cast(&r); @@ -58,10 +68,19 @@ void Boundary1D::_init(size_t n) Domain1D& r = container().domain(m_index+1); if (!r.isConnector()) { // multi-point domain m_right_nv = r.nComponents(); - if (m_right_nv > c_offset_Y) { - m_right_nsp = m_right_nv - c_offset_Y; - } else { - m_right_nsp = 0; + + if (m_type == cFlameletFlow) { + if (m_right_nv > c_offset_Yflamelet) { + m_right_nsp = m_right_nv - c_offset_Yflamelet; + } else { + m_right_nsp = 0; + } + }else{ + if (m_right_nv > c_offset_Y) { + m_right_nsp = m_right_nv - c_offset_Y; + } else { + m_right_nsp = 0; + } } m_right_loc = container().start(m_index+1); m_flow_right = dynamic_cast(&r); @@ -146,6 +165,25 @@ void Inlet1D::setMoleFractions(const double* xin) } } +void Inlet1D::setMassFractions(const std::string& xin) +{ + m_xstr = xin; + if (m_flow) { + m_flow->phase().setMassFractionsByName(xin); + m_flow->phase().getMassFractions(m_yin.data()); + needJacUpdate(); + } +} + +void Inlet1D::setMassFractions(const double* xin) +{ + if (m_flow) { + m_flow->phase().setMassFractions(xin); + m_flow->phase().getMassFractions(m_yin.data()); + needJacUpdate(); + } +} + void Inlet1D::init() { _init(0); @@ -191,17 +229,31 @@ void Inlet1D::eval(size_t jg, double* xg, double* rg, double* xb = xg + m_flow->loc(); double* rb = rg + m_flow->loc(); - // The first flow residual is for u. This, however, is not modified by - // the inlet, since this is set within the flow domain from the - // continuity equation. - - if (m_flow->doEnergy(0)) { - // The third flow residual is for T, where it is set to T(0). Subtract - // the local temperature to hold the flow T to the inlet T. - rb[c_offset_T] -= m_temp; - } else { - rb[c_offset_T] -= m_flow->T_fixed(0); - } + if ( m_flow->nEq() == 1 ) { // Solving in mixture fraction space + if (m_flow->doEnergy(0)) { + // The third flow residual is for T, where it is set to T(0). Subtract + // the local temperature to hold the flow T to the inlet T. + rb[c_offset_Tflamelet] -= m_temp; + } else { + rb[c_offset_Tflamelet] -= m_flow->T_fixed(0); + } + for (size_t k = 0; k < m_nsp; k++) { + if (k != m_flow_right->leftExcessSpecies()) { + rb[c_offset_Yflamelet+k] -= m_yin[k]; + } + } + } else { // Phisical space + // The first flow residual is for u. This, however, is not modified by + // the inlet, since this is set within the flow domain from the + // continuity equation. + + if (m_flow->doEnergy(0)) { + // The third flow residual is for T, where it is set to T(0). Subtract + // the local temperature to hold the flow T to the inlet T. + rb[c_offset_T] -= m_temp; + } else { + rb[c_offset_T] -= m_flow->T_fixed(0); + } if (m_flow->isFree()) { // if the flow is a freely-propagating flame, mdot is not specified. @@ -229,39 +281,54 @@ void Inlet1D::eval(size_t jg, double* xg, double* rg, rb[c_offset_U] = m_flow->density(0) * xb[c_offset_U] - m_mdot; } - // add the convective term to the species residual equations - for (size_t k = 0; k < m_nsp; k++) { - if (k != m_flow_right->leftExcessSpecies()) { - rb[c_offset_Y+k] += m_mdot*m_yin[k]; + // add the convective term to the species residual equations + for (size_t k = 0; k < m_nsp; k++) { + if (k != m_flow_right->leftExcessSpecies()) { + rb[c_offset_Y+k] += m_mdot*m_yin[k]; + } } } } else { // right inlet (should only be used for counter-flow flames) // Array elements corresponding to the last point in the flow domain + double* rb = rg + loc() - m_flow->nComponents(); double* xb = xg + loc() - m_flow->nComponents(); size_t last_index = m_flow->nPoints() - 1; + if (m_flow->nEq() == 1 ) { // mixture fraction space + if (m_flow->doEnergy(m_flow->nPoints() - 1)) { + rb[c_offset_Tflamelet] -= m_temp; // T + } else { + rb[c_offset_Tflamelet] -= m_flow->T_fixed(m_flow->nPoints() - 1); + } + for (size_t k = 0; k < m_nsp; k++) { + if (k != m_flow_left->rightExcessSpecies()) { + rb[c_offset_Yflamelet+k] -= m_yin[k]; + } + } + } else { // physical space rb[c_offset_V] -= m_V0; - if (m_flow->doEnergy(m_flow->nPoints() - 1)) { - rb[c_offset_T] -= m_temp; // T - } else { - rb[c_offset_T] -= m_flow->T_fixed(m_flow->nPoints() - 1); - } + if (m_flow->doEnergy(m_flow->nPoints() - 1)) { + rb[c_offset_T] -= m_temp; // T + } else { + rb[c_offset_T] -= m_flow->T_fixed(m_flow->nPoints() - 1); + } - if (m_flow->twoPointControlEnabled()) { // For point control adjustments - // At the right boundary, the mdot is dictated by the velocity at the right - // boundary, which comes from the Uo variable. The variable Uo is the - // left-moving velocity and has a negative value, so the mass flow has to be - // negated to give a positive value when using Uo. - m_mdot = -m_flow->density(last_index) * xb[c_offset_Uo]; - } - rb[c_offset_U] += m_mdot; + if (m_flow->twoPointControlEnabled()) { // For point control adjustments + // At the right boundary, the mdot is dictated by the velocity at the right + // boundary, which comes from the Uo variable. The variable Uo is the + // left-moving velocity and has a negative value, so the mass flow has to be + // negated to give a positive value when using Uo. + m_mdot = -m_flow->density(last_index) * xb[c_offset_Uo]; + } + rb[c_offset_U] += m_mdot; - for (size_t k = 0; k < m_nsp; k++) { - if (k != m_flow_left->rightExcessSpecies()) { - rb[c_offset_Y+k] += m_mdot * m_yin[k]; + for (size_t k = 0; k < m_nsp; k++) { + if (k != m_flow_left->rightExcessSpecies()) { + rb[c_offset_Y+k] += m_mdot * m_yin[k]; + } } } } @@ -418,10 +485,18 @@ void Outlet1D::eval(size_t jg, double* xg, double* rg, integer* diagg, int* db = diag - nc; size_t last = m_flow_left->nPoints() - 1; - if (m_flow_left->doEnergy(last)) { - rb[c_offset_T] = xb[c_offset_T] - xb[c_offset_T - nc]; // zero T gradient + if (m_flow_left->nEq() == 1) { // mixture fraction space + if (m_flow_left->doEnergy(last)) { + rb[c_offset_Tflamelet] = xb[c_offset_Tflamelet] - xb[c_offset_Tflamelet - nc]; // zero T gradient + } else { + rb[c_offset_Tflamelet] = xb[c_offset_Tflamelet] - m_flow_left->T_fixed(last); + } } else { - rb[c_offset_T] = xb[c_offset_T] - m_flow_left->T_fixed(last); + if (m_flow_left->doEnergy(last)) { + rb[c_offset_T] = xb[c_offset_T] - xb[c_offset_T - nc]; // zero T gradient + } else { + rb[c_offset_T] = xb[c_offset_T] - m_flow_left->T_fixed(last); + } } size_t kSkip = c_offset_Y + m_flow_left->rightExcessSpecies(); for (size_t k = c_offset_Y; k < nc; k++) { diff --git a/src/oneD/Domain1D.cpp b/src/oneD/Domain1D.cpp index c5c2790d4f8..f0a87500bab 100644 --- a/src/oneD/Domain1D.cpp +++ b/src/oneD/Domain1D.cpp @@ -16,9 +16,9 @@ namespace Cantera { -Domain1D::Domain1D(size_t nv, size_t points, double time) +Domain1D::Domain1D(size_t nv, size_t points, double time, size_t nsoot, size_t neq) { - resize(nv, points); + resize(nv+nsoot+neq, points); } Domain1D::~Domain1D() diff --git a/src/oneD/DomainFactory.cpp b/src/oneD/DomainFactory.cpp index de164e3a32b..4760701df96 100644 --- a/src/oneD/DomainFactory.cpp +++ b/src/oneD/DomainFactory.cpp @@ -6,6 +6,7 @@ #include "cantera/oneD/DomainFactory.h" #include "cantera/oneD/Boundary1D.h" #include "cantera/oneD/Flow1D.h" +#include "cantera/oneD/Flamelet.h" #include "cantera/oneD/IonFlow.h" #include "cantera/oneD/StFlow.h" #include "cantera/transport/Transport.h" @@ -18,66 +19,76 @@ std::mutex DomainFactory::domain_mutex; DomainFactory::DomainFactory() { - reg("inlet", [](shared_ptr solution, const string& id) { + reg("inlet", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Inlet1D(solution, id); }); - reg("empty", [](shared_ptr solution, const string& id) { + reg("empty", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Empty1D(solution, id); }); - reg("symmetry-plane", [](shared_ptr solution, const string& id) { + reg("symmetry-plane", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Symm1D(solution, id); }); - reg("outlet", [](shared_ptr solution, const string& id) { + reg("outlet", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Outlet1D(solution, id); }); - reg("outlet-reservoir", [](shared_ptr solution, const string& id) { + reg("outlet-reservoir", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new OutletRes1D(solution, id); }); - reg("surface", [](shared_ptr solution, const string& id) { + reg("surface", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new Surf1D(solution, id); }); - reg("reacting-surface", [](shared_ptr solution, const string& id) { + reg("reacting-surface", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new ReactingSurf1D(solution, id); }); reg("gas-flow", [](shared_ptr solution, const string& id) { return new Flow1D(solution, id); }); - reg("legacy-flow", [](shared_ptr solution, const string& id) { - return new StFlow(solution, id); + reg("legacy-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + return new StFlow(solution, id, sections); }); - reg("ion-flow", [](shared_ptr solution, const string& id) { + reg("ion-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new IonFlow(solution, id); }); - reg("free-flow", [](shared_ptr solution, const string& id) { + reg("free-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { Flow1D* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new Flow1D(solution, id); + ret = new StFlow(solution, id, sections); } ret->setFreeFlow(); return ret; }); - reg("axisymmetric-flow", [](shared_ptr solution, const string& id) { + reg("axisymmetric-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { Flow1D* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new Flow1D(solution, id); + ret = new Flow1D(solution, id, sections); } ret->setAxisymmetricFlow(); return ret; }); - reg("unstrained-flow", [](shared_ptr solution, const string& id) { + reg("unstrained-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { Flow1D* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new Flow1D(solution, id); + ret = new StFlow(solution, id, sections); } ret->setUnstrainedFlow(); return ret; }); + reg("flamelet-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + StFlow* ret; + if (solution->transport()->transportModel() == "ionized-gas") { + ret = new IonFlow(solution, id); + } else { + ret = new Flamelet(solution, id, sections); // neq = 1 for flamelet + } + ret->setFlameletFlow(); + return ret; + }); } DomainFactory* DomainFactory::factory() diff --git a/src/oneD/Flamelet.cpp b/src/oneD/Flamelet.cpp new file mode 100644 index 00000000000..96efc38633d --- /dev/null +++ b/src/oneD/Flamelet.cpp @@ -0,0 +1,471 @@ +// ! Flamelet definitions +// + +#include "cantera/transport/TransportBase.h" +#include "cantera/numerics/funcs.h" + + +#include "cantera/base/SolutionArray.h" +#include "cantera/oneD/StFlow.h" +#include "cantera/oneD/refine.h" +#include "cantera/transport/Transport.h" +#include "cantera/transport/TransportFactory.h" +#include "cantera/numerics/funcs.h" +#include "cantera/base/global.h" +#include "cantera/base/Parser.h" + +#include + +#include "cantera/oneD/Flamelet.h" +// import erf function +using namespace std; + +namespace Cantera +{ + +Flamelet::Flamelet(IdealGasPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : + StFlow(ph, nsp, nsoot, neq, points) { + m_dovisc = true; + m_updateChi = true; + m_do_unityLewisNumber = true; + } + +Flamelet::Flamelet(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) + : StFlow(th.get(), nsp, nsoot, neq, points) { + m_solution = Solution::create(); + m_solution->setThermo(th); + } + +Flamelet::Flamelet(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) + : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) { + m_solution = sol; + m_id = id; + m_kin = m_solution->kinetics().get(); + m_trans = m_solution->transport().get(); + + m_solution->registerChangedCallback(this, [this]() { + setKinetics(m_solution->kinetics()); + setTransport(m_solution->transport()); + }); + + if (m_trans->transportModel() == "none") { + // @deprecated + warn_deprecated("StFlow", + "An appropriate transport model\nshould be set when instantiating the " + "Solution ('gas') object.\nImplicit setting of the transport model " + "is deprecated and\nwill be removed after Cantera 3.0."); + setTransportModel("mixture-averaged"); + } + } + +Flamelet::~Flamelet() {} + +void Flamelet::resize(size_t ncomponents, size_t points) +{ + Domain1D::resize(ncomponents, points); + m_rho.resize(m_points, 0.0); + m_wtm.resize(m_points, 0.0); + m_cp.resize(m_points, 0.0); + m_hr.resize(m_points, 0.0); + m_h.resize(m_points, 0.0); + m_tcon.resize(m_points, 0.0); + m_visc.resize(m_points, 0.0); + h_RT.resize(m_nsp, 0.0); + cp_R.resize(m_nsp, 0.0); + m_hk.resize(m_nsp, m_points, 0.0); + m_Lek.resize(m_nsp*m_points); + + m_diff.resize(m_nsp*m_points); + if (m_do_multicomponent) { + m_multidiff.resize(m_nsp*m_nsp*m_points); + m_dthermal.resize(m_nsp, m_points, 0.0); + } + + m_wdot.resize(m_nsp,m_points, 0.0); + m_do_energy.resize(m_points,false); + m_qdotRadiation.resize(m_points, 0.0); + m_fixedtemp.resize(m_points); + + m_dz.resize(m_points-1); + m_z.resize(m_points); + m_chi.resize(m_points); + m_updateChi = true; +} + +void Flamelet::eval(size_t jg, double* xg, + double* rg, integer* diagg, double rdt) +{ + // if evaluating a Jacobian, and the global point is outside + // the domain of influence for this domain, then skip + // evaluating the residual + if (jg != npos && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) { + return; + } + + // if evaluating a Jacobian, compute the steady-state residual + if (jg != npos) { + rdt = 0.0; + } + + // start of local part of global arrays + double* x = xg + loc(); + double* rsd = rg + loc(); + integer* diag = diagg + loc(); + + size_t jmin, jmax; + + if (jg == npos) { // evaluate all points + jmin = 0; + jmax = m_points - 1; + } else { // evaluate points for Jacobian + size_t jpt = (jg == 0) ? 0 : jg - firstPoint(); + jmin = std::max(jpt, 1) - 1; + jmax = std::min(jpt+1,m_points-1); + } + + // properties are computed for grid points from j0 to j1 + size_t j0 = std::max(jmin, 1) - 1; + size_t j1 = std::min(jmax+1,m_points-1); + + //----------------------------------------------------- + // update properties + //----------------------------------------------------- + // update thermodynamic properties + updateThermo(x, j0, j1); + + // update transport properties + if (jg == npos) { + updateTransport(x, j0, j1); + } + + //--------------------------------------------------- + // evaluate the chi profile + //--------------------------------------------------- + if ( m_updateChi ) setChi(); + + //---------------------------------------------------- + // evaluate the residual equations at all required + // grid points + //---------------------------------------------------- + + for (size_t j = jmin; j <= jmax; j++) { + //---------------------------------------------- + // left boundary + //---------------------------------------------- + + if (j == 0) { + + // these may be modified by a boundary object + rsd[index(c_offset_Tflamelet, j)] = T(x,j); + + // The default boundary condition for species is zero + // flux. However, the boundary object may modify this. + double sum = 0.0; + for ( size_t k = 0; k < m_nsp; k++) { + sum += Y(x,k,0); + rsd[index(c_offset_Yflamelet + k, j)] = Y(x,k,j); + } + rsd[index(c_offset_Yflamelet + leftExcessSpecies(), 0)] = 1.0 - sum; + } + + //---------------------------------------------- + // right boundary + //---------------------------------------------- + + else if (j == m_points - 1) { + + // the boundary object connected to the right of this + // one may modify or replace these equations. The + // default boundary conditions are zero u, V, and T, + // and zero diffusive flux for all species. + rsd[index(c_offset_Tflamelet,j)] = T(x,j); + + double sum = 0.0; + for (size_t k = 0; k < m_nsp; k++) { + sum += Y(x,k,j); + rsd[index(c_offset_Yflamelet + k ,j)] = Y(x,k,j); + } + rsd[index(c_offset_Yflamelet + rightExcessSpecies(), j)] = 1.0 - sum; + diag[index(c_offset_Yflamelet + rightExcessSpecies(), j)] = 0; + } + + //------------------------------------------ + // interior points + //------------------------------------------ + + else { + + //------------------------------------------------- + // Species equations + // + // rho * dY/dt = 1/2 * 1/Le_k * \rho * \chi * d^2Y/dz^2 + // + 1/4 * (1/Le_k - 1 ) * ( d\rho\chi/dz + \rho * \chi * Cp * 1/\lambda * d(\lambda * 1/Cp)/dz ) + // + M_k * \omega_k + // + // Temperature equation + // + // rho * dT/dt = 1/2 * \rho * \chi * d^2T/dz^2 + 1/2 * \rho * \chi 1/Cp * dCp/dz * dT/dz + HR + // + 1/2 * \rho * \chi 1/Cp * dT/dz * ∑_k Cp_k dYk/dz + //------------------------------------------------- + getWdot(x,j); + + double drhoChidZ = (m_rho[j+1]*chi(j+1) - m_rho[j-1]*chi(j-1))/(z(j+1) - z(j-1)); + double dlambdaoverCpdZ = (m_tcon[j+1]/m_cp[j+1] - m_tcon[j-1]/m_cp[j-1])/(z(j+1) - z(j-1)); + + for (size_t k = 0; k < m_nsp; k++) { + rsd[index(c_offset_Yflamelet + k, j)] = + m_wt[k]*wdot(k,j)/m_rho[j] + + 0.5*chi(j)/Lek(k,j)*d2Ydz2(x,k,j) + + 0.25 / m_rho[j] * (1.0/Lek(k,j) - 1.0) + * ( drhoChidZ + m_rho[j] * chi(j) * m_cp[j] / m_tcon[j] * dlambdaoverCpdZ ) + * cdif1(x,c_offset_Yflamelet+k,j) + - rdt*(Y(x,k,j) - Y_prev(k,j)); + diag[index(c_offset_Yflamelet + k, j)] = 1; + } + + // heat release term + setGas(x,j); + + m_thermo->getEnthalpy_RT_ref(&h_RT[0]); + m_thermo->getCp_R_ref(&cp_R[0]); + + double dCpdZ; + double sum = 0.0; + double sum2 = 0.0; + for (size_t k = 0; k < m_nsp; k++) { + sum += wdot(k,j) * h_RT[k]; + sum2 += cp_R[k] / m_wt[k] * GasConstant / Lek(k,j) + * cdif1(x,c_offset_Yflamelet+k,j); + } + sum *= -T(x,j) * GasConstant / m_cp[j]; // consistent units + m_hr[j] = sum*m_cp[j]; + dCpdZ = (m_cp[j+1] - m_cp[j-1])/(z(j+1) - z(j-1)); + + rsd[index(c_offset_Tflamelet, j)] = + sum/m_rho[j] + + 0.5*chi(j)*d2Tdz2(x,j) + + 0.5*chi(j)/m_cp[j]*dCpdZ*cdif1(x,c_offset_Tflamelet,j) + + 0.5*chi(j)/m_cp[j]*sum2*cdif1(x,c_offset_Tflamelet,j) + - rdt*(T(x,j) - T_prev(j)); + diag[index(c_offset_Tflamelet, j)] = 1; + } + } +} + +string Flamelet::componentName(size_t n) const +{ + switch (n) { + case c_offset_Tflamelet: + return "T"; + default: + if (n >= c_offset_Yflamelet && n < (c_offset_Yflamelet + m_nsp)) { + return m_thermo->speciesName(n - c_offset_Yflamelet); + } else { + return ""; + } + } +} + +size_t Flamelet::componentIndex(const string &name) const +{ + if (name=="T") { + return c_offset_Tflamelet; + } else { + for (size_t n=m_neq; nsetTemperature(T(x,j)); + const double* yy = x + m_nv*j + c_offset_Yflamelet; + m_thermo->setMassFractions_NoNorm(yy); + m_thermo->setPressure(m_press); +} + +void Flamelet::resetBadValues(double* xg) +{ + double* x = xg + loc(); + for (size_t j = 0; j < m_points; j++) { + double* Y = x + m_nv*j + c_offset_Yflamelet; + m_thermo->setMassFractions(Y); + m_thermo->getMassFractions(Y); + } +} + +vector Flamelet::dCpdT(const Array2D sol) +{ + vector dCpdT; + double delta_T = 1.0; + double cp_l, cp_u; + double * yspec = new double[m_nsp]; + m_thermo->setPressure(m_press); + for (size_t n = 0; n < m_points; n++) { + for (size_t k = 0; k < m_nsp; k++) { + yspec[k] = sol(k+1,n); + } + m_thermo->setMassFractions_NoNorm(yspec); + m_thermo->setTemperature(sol(0,n)-delta_T); + cp_l = m_thermo->cp_mass(); + m_thermo->setTemperature(sol(0,n)+delta_T); + cp_u = m_thermo->cp_mass(); + dCpdT.push_back( ( cp_u - cp_l ) / ( 2.0 * delta_T )); + } + return dCpdT; + delete[] yspec; +} + +vector Flamelet::d2CpdT2(const Array2D sol) +{ + vector d2CpdT2; + double delta_T = 1.0; + double cp_l, cp_c, cp_u; + double * yspec = new double[m_nsp]; + m_thermo->setPressure(m_press); + for (size_t n = 0; n < m_points; n++) { + for (size_t k = 0; k < m_nsp; k++) { + yspec[k] = sol(k+1,n); + } + m_thermo->setMassFractions_NoNorm(yspec); + m_thermo->setTemperature(sol(0,n)); + cp_c = m_thermo->cp_mass(); + m_thermo->setTemperature(sol(0,n)-2.0*delta_T); + cp_l = m_thermo->cp_mass(); + m_thermo->setTemperature(sol(0,n)+2.0*delta_T); + cp_u = m_thermo->cp_mass(); + d2CpdT2.push_back( ( cp_u + cp_l - 2.0*cp_c ) / ( 4.0 * std::pow(delta_T,2.0) )); + } + return d2CpdT2; + delete[] yspec; +} + +/** + * Set the gas state to be consistent with the solution at the + * midpoint between j and j + 1. + */ +void Flamelet::setGasAtMidpoint(const double* x, size_t j) +{ + m_thermo->setTemperature(0.5*(T(x,j)+T(x,j+1))); + const double* yyj = x + m_nv*j + c_offset_Yflamelet; + const double* yyjp = x + m_nv*(j+1) + c_offset_Yflamelet; + for (size_t k = 0; k < m_nsp; k++) { + m_ybar[k] = 0.5*(yyj[k] + yyjp[k]); + } + + m_thermo->setMassFractions_NoNorm(m_ybar.data()); + m_thermo->setPressure(m_press); +} + +void Flamelet::updateTransport(double* x, size_t j0, size_t j1) +{ + for (size_t j = j0; j < j1; j++) { + setGasAtMidpoint(x,j); + m_visc[j] = m_trans->viscosity(); + m_tcon[j] = m_trans->thermalConductivity(); + m_trans->getMixDiffCoeffs(&m_diff[j*m_nsp]); + for (size_t k = 0; k < m_nsp; k++) { + if ( m_do_unityLewisNumber ) { + m_Lek[m_nsp*j+k] = 1.0; + } else { + m_Lek[m_nsp*j+k] = m_tcon[j] / ( m_rho[j] * m_cp[j] * m_diff[j*m_nsp+k] ); + } + } + } +} + +void Flamelet::setChi() +{ + m_chi[0]=0.0; + m_chi[m_points-1]=0.0; + for (size_t j = 1; j < m_points-1; j++) { + m_chi[j] = m_chiSt * exactChi(z(j)) / exactChi(m_zSt); + } + m_updateChi = false; +} + +double Flamelet::exactChi(double zz) +{ + double p1 = fabs(2.0*zz - 1.0); + double q1 = 1.0 - p1; + return exp(-2.0 * erfinv(p1,q1) * erfinv(p1,q1)); +} + +double Flamelet::erfinv(double p1,double q1) +{ + double X,S,T,LNQ,F; + T = 0.0; + S = 0.0; + const double C = 0.5625; + const double C1 = 0.87890625; + const double C2 =-0.2302585092994045684017991454684364e3; + const double R = 0.8862269254527580136490837416705726; + const double A[7] = {0.841467547194693616e-01,0.160499904248262200e1,0.809451641478547505e1,0.164273396973002581e2,0.154297507839223692e2,0.669584134660994039e1,0.108455979679682472e1}; + const double B[7] = {.352281538790042405e-2,0.293409069065309557,0.326709873508963100e1,0.123611641257633210e2,0.207984023857547070e2,0.170791197367677668e2,0.669253523595376683e1}; + const double A1[7] = {0.552755110179178015e2,0.657347545992519152e3,0.124276851197202733e4,0.818859792456464820e3,0.234425632359410093e3,0.299942187305427917e2,0.140496035731853946e1}; + const double B1[6] = {0.179209835890172156e3,0.991315839349539886e3,0.138271033653003487e4,0.764020340925985926e3,0.194354053300991923e3,0.228139510050586581e2}; + + const double A2[7] ={0.500926197430588206e1,0.111349802614499199e3,0.353872732756132161e3,0.356000407341490731e3,0.143264457509959760e3,0.240823237485307567e2,0.140496035273226366e1}; + const double B2[6]= {0.209004294324106981e2,0.198607335199741185e3,0.439311287748524270e3,0.355415991280861051e3,0.123303672628828521e3,0.186060775181898848e2}; + const double A3[11]={0.237121026548776092e4,0.732899958728969905e6,0.182063754893444775e7,0.269191299062422172e7,0.304817224671614253e7,0.130643103351072345e7,0.296799076241952125e6,0.457006532030955554e5,0.373449801680687213e4,0.118062255483596543e3,0.100000329157954960e1}; + const double B3[10]={0.851911109952055378e6,0.194746720192729966e7,0.373640079258593694e7,0.397271370110424145e7,0.339457682064283712e7,0.136888294898155938e7,0.303357770911491406e6,0.459721480357533823e5,0.373762573565814355e4,0.118064334590001264e3}; + const double A4[9]={0.154269429680540807e12,0.430207405012067454e12,0.182623446525965017e12,0.248740194409838713e11,0.133506080294978121e10,0.302446226073105850e08,0.285909602878724425e6,0.101789226017835707e04,0.100000004821118676e1}; + const double B4[9]={0.220533001293836387e12,0.347822938010402687e12,0.468373326975152250e12,0.185251723580351631e12,0.249464490520921771e11,0.133587491840784926e10,0.302480682561295591e08,0.285913799407861384e6,0.101789250893050230e04}; + + if (p1 <= 0.0 || q1 <= 0.0) { + return 0.0; + } + if (p1 <= 0.75) { + X = C - p1*p1; + S = (((((A[0]*X + A[1])*X + A[2])*X + A[3])*X + A[4])*X + A[5])*X + A[6]; + T = ((((((B[0]*X + B[1])*X + B[2])*X + B[3])*X + B[4])*X + B[5])*X + B[6])*X+1.0; + X=p1*(S/T); + F=erf(X)-p1; + return X-R*exp(X*X)*F; + } + // p = [0,0.75] + else if (p1 >0.75 && p1 <= 0.9375) { + X = C1 - p1*p1; + if (X < 0.1) { + S = ((((((A1[0]*X + A1[1])*X + A1[2])*X + A1[3])*X+ A1[4])*X + A1[5])*X + A1[6]); + T = ((((((B1[0]*X + B1[1])*X + B1[2])*X + B1[3])*X+ B1[4])*X + B1[5])*X +1.0); + } + else if (X>0.1) { + S = ((((((A2[0]*X + A2[1])*X + A2[2])*X + A2[3])*X+ A2[4])*X + A2[5])*X + A2[6]); + T = ((((((B2[0]*X + B2[1])*X + B2[2])*X + B2[3])*X+ B2[4])*X + B2[5])*X + 1.0); + } + X = p1*(S/T); + T = exp(X*X)*erfc(X)-exp(X*X)*q1; + return X + R*T; + } + else if (p1 > 0.9375) { + LNQ = log(q1); + X= 1.0 / pow(-LNQ,0.5); + if (LNQ > C2) { + S = (((((((((A3[0]*X + A3[1])*X + A3[2])*X + A3[3])*X + A3[4])*X+ A3[5])*X + A3[6])*X + A3[7])*X + A3[8])*X+ A3[9])*X + A3[10]; + T = (((((((((B3[0]*X + B3[1])*X + B3[2])*X + B3[3])*X + B3[4])*X+ B3[5])*X + B3[6])*X + B3[7])*X + B3[8])*X + B3[9])*X + 1.0; + } + else if (LNQ < C2) { + S = (((((((A4[0]*X + A4[1])*X + A4[2])*X + A4[3])*X + A4[4])*X+ A4[5])*X + A4[6])*X + A4[7])*X + A4[8]; + T = ((((((((B4[0]*X + B4[1])*X + B4[2])*X + B4[3])*X + B4[4])*X+ B4[5])*X + B4[6])*X + B4[7])*X + B4[8])*X + 1.0; + } + X=S/(X*T); + T = exp(X*X)*erfc(X); + F = log(T) - LNQ - X*X; + return X + R*T*F; + } + else { + return -2.0; + } + +} + +} \ No newline at end of file diff --git a/src/oneD/IonFlow.cpp b/src/oneD/IonFlow.cpp index 9630bd6f19c..2c13c406b55 100644 --- a/src/oneD/IonFlow.cpp +++ b/src/oneD/IonFlow.cpp @@ -16,7 +16,7 @@ namespace Cantera { IonFlow::IonFlow(ThermoPhase* ph, size_t nsp, size_t points) : - Flow1D(ph, nsp, points) + StFlow(ph, nsp, 0, c_offset_Y, points) { // make a local copy of species charge for (size_t k = 0; k < m_nsp; k++) { diff --git a/src/oneD/Sim1D.cpp b/src/oneD/Sim1D.cpp index 6d1a053c5a5..fa7476cd724 100644 --- a/src/oneD/Sim1D.cpp +++ b/src/oneD/Sim1D.cpp @@ -408,7 +408,7 @@ int Sim1D::newtonSolve(int loglevel) } } -void Sim1D::solve(int loglevel, bool refine_grid) +void Sim1D::solve(int loglevel, const string& refine_grid) { int new_points = 1; double dt = m_tstep; @@ -421,6 +421,23 @@ void Sim1D::solve(int loglevel, bool refine_grid) if (loglevel > 6) { clearDebugFile(); } + double domain_size = 0.0; + for (size_t n = 0; n < nDomains(); n++) + { + Domain1D& d = domain(n); + size_t length = d.grid().size(); + + domain_size += d.grid(length-1); + } + domain_size = domain_size/2.0; + + const double& criterion=1.0e-4; + + double mesh_distance; + // maximum number of remeshes (problem sometimes encountered, eternal loop) + int MAX_REMESHES = 20; + int n_remeshes = 0; + while (new_points > 0) { size_t istep = 0; @@ -493,18 +510,77 @@ void Sim1D::solve(int loglevel, bool refine_grid) if (loglevel > 3) { show(); } +/////////////////////////////////////////////////// + + //if (std::strcmp(refine_grid, "remesh") == 0) + if (refine_grid == "remesh") + { + // print new line + if (loglevel>=0) + { + cout<=0) + { + cout<<"old mesh = ["< 6) { + save("debug_sim1d.yaml", "debug", "After regridding"); + } + if (new_points && loglevel > 7) { + saveResidual("debug_sim1d.yaml", "residual", + "After regridding"); + } + } else if (refine_grid == "disabled"){ debuglog("grid refinement disabled.\n", loglevel); new_points = 0; + + } else { + debuglog("WARNING: wrong keyword for refine_grid\nonly acceptable values being: disabled, refine (default value) or remesh \ngrid refinement disabled.\n", loglevel); + new_points = 0; } } } @@ -597,6 +673,256 @@ int Sim1D::refine(int loglevel) finalize(); return np; } +/** +* Remesh the grid in all domains. +*/ +double Sim1D::remesh(int loglevel, double dist_min, double domain_size) //from MUTAGEN +{ + vector znew, xnew; + std::vector dsize; + + double distance=0.0; + for (size_t n = 0; n < nDomains(); n++) + { + Domain1D& d = domain(n); + Refiner& r = d.refiner(); + + // proceed with the remeshing + // double this_distance = r.remeshFromSolution( d.grid().size(), + // d.grid().data(), &m_state[start(n)], + // dist_min, domain_size ); + double this_distance = r.remeshFromSolution( d.grid().size(), + d.grid().data(), m_state->data() + start(n), + dist_min, domain_size ); + distance += this_distance; + + // interpolate the solution on the new grid points + int np_old = d.nPoints(); // old domain grid points + int np_new = r.z_new_size(); // new domain grid points + // loop over points in the new grid + for (size_t m = 0; m < np_new; m++) + { + // new position + double znew_curr = r.z_new(m); + // add it to the global array + znew.push_back(znew_curr); + // interpolation + if (np_new>1) + { + int m_old = r.indxtp(np_old,znew_curr,d.grid().data()); + double z0_old = d.grid(m_old ); + double z1_old = d.grid(m_old+1); + for (size_t i = 0; i < d.nComponents(); i++) + { + double x0_old = value(n,i,m_old ); + double x1_old = value(n,i,m_old+1); + double slope = (x1_old-x0_old)/(z1_old-z0_old); + double val = x0_old + slope * (znew_curr-z0_old); + xnew.push_back(val); + } + } + else + { + for (size_t i = 0; i < d.nComponents(); i++) + { + xnew.push_back(value(n,i,0)); + } + } + } + dsize.push_back(np_new); + } + + // At this point, the new grid znew and the new solution + // vector xnew have been constructed, but the domains + // themselves have not yet been modified. Now update each + // domain with the new grid. + + size_t gridstart = 0, gridsize; + for (size_t n = 0; n < nDomains(); n++) { + Domain1D& d = domain(n); + gridsize = dsize[n]; + d.setupGrid(gridsize, &znew[gridstart]); + gridstart += gridsize; + } + + // Replace the current solution vector with the new one + *m_state = xnew; + resize(); + finalize(); + return distance; +} + + +void Sim1D::getRatio() //from MUTAGEN +{ + for (size_t n = 0; n < nDomains(); n++) + { + Domain1D& d = domain(n); + Refiner& r = d.refiner(); + // r.getRatio(d.grid().size(), d.grid().data(), &m_state[start(n)]); + r.getRatio(d.grid().size(), d.grid().data(), m_state->data() + start(n)); + } +} + +/** +* Add a point in a domain +*/ +void Sim1D::addPoint(size_t ndomain, double zpoint, vector xpoint, int loglevel, bool newjac) //from MUTAGEN +{ + vector znew, xnew; + vector dsize; + + // check the domain number + if ((ndomain<0)||(ndomain>=nDomains())) + { + cout<<"wrong ndomain"<(xpoint.size())!=ncomp) + { + cout<<"wrong number of components in xpoint"<0) + { + if (zpoint(xnew.begin(), xnew.end())); + + // resize the work array + m_xnew.resize(xnew.size()); + // copy(xnew.begin(), xnew.end(), m_xnew.begin()); + + resize(); + finalize(); +} void Sim1D::clearDebugFile() { diff --git a/src/oneD/StFlow.cpp b/src/oneD/StFlow.cpp index f6b0eabc4f3..f1dc1e70128 100644 --- a/src/oneD/StFlow.cpp +++ b/src/oneD/StFlow.cpp @@ -5,31 +5,435 @@ #include "cantera/oneD/StFlow.h" #include "cantera/base/global.h" +#include "cantera/base/Parser.h" +#include using namespace std; namespace Cantera { -StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t points) : - Flow1D(ph, nsp, points) +StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : + Domain1D(nsp, points, 0.0, nsoot, neq), + m_nsp(nsp), + m_neq(neq), + m_nsoot(nsoot) { - warn_deprecated("StFlow::StFlow", - "To be removed after Cantera 3.1. Class replaced by Flow1D."); + m_type = cFlowType; + m_points = points; + + if (ph == 0) { + return; // used to create a dummy object + } + m_thermo = ph; + + size_t nsp2 = m_thermo->nSpecies(); + // the species mass fractions are the last components in the solution + // vector, so the total number of components is the number of species + // plus the offset of the first mass fraction. + + + m_nv = m_neq + m_nsp + m_nsoot; + if (nsp2 + m_nsoot != m_nsp) { + m_nsp = nsp2; + Domain1D::resize(m_nv, points); + } + + // make a local copy of the species molecular weight vector + m_wt = m_thermo->molecularWeights(); + + // set pressure based on associated thermo object + setPressure(m_thermo->pressure()); + + // the species mass fractions are the last components in the solution + // vector, so the total number of components is the number of species + // plus the offset of the first mass fraction. + // m_nv = c_offset_Y + m_nsp; + + // enable all species equations by default + m_do_species.resize(m_nsp, true); + + // but turn off the energy equation at all points + m_do_energy.resize(m_points,false); + + m_diff.resize(m_nsp*m_points); + m_multidiff.resize(m_nsp*m_nsp*m_points); + m_flux.resize(m_nsp,m_points); + m_wdot.resize(m_nsp,m_points, 0.0); + m_hk.resize(m_nsp, m_points, 0.0); + m_dhk_dz.resize(m_nsp, m_points - 1, 0.0); + m_ybar.resize(m_nsp); + m_qdotRadiation.resize(m_points, 0.0); + + //-------------- default solution bounds -------------------- + if (m_neq == 1) { + setBounds(c_offset_Tflamelet, 200.0, 2*m_thermo->maxTemp()); // temperature bounds + } else { + setBounds(c_offset_U, -1e20, 1e20); // no bounds on u + setBounds(c_offset_V, -1e20, 1e20); // V + setBounds(c_offset_T, 200.0, 2*m_thermo->maxTemp()); // temperature bounds + setBounds(c_offset_L, -1e20, 1e20); // lambda should be negative + setBounds(c_offset_E, -1e20, 1e20); // no bounds for inactive component + } + // mass fraction bounds + for (size_t k = 0; k < m_nsp; k++) { + setBounds(m_neq+k, -1.0e-7, 1.0e5); + } + + //-------------------- grid refinement ------------------------- + if (m_neq == 1) { + m_refiner->setActive(c_offset_Tflamelet, false); + } else { + m_refiner->setActive(c_offset_U, false); + m_refiner->setActive(c_offset_V, false); + m_refiner->setActive(c_offset_T, false); + m_refiner->setActive(c_offset_L, false); + } + + vector gr; + for (size_t ng = 0; ng < m_points; ng++) { + gr.push_back(1.0*ng/m_points); + } + setupGrid(m_points, gr.data()); + + // Find indices for radiating species + m_kRadiating.resize(2, npos); + m_kRadiating[0] = m_thermo->speciesIndex("CO2"); + m_kRadiating[1] = m_thermo->speciesIndex("H2O"); + + // P. Wolf + //---------------------AVBP PEA initialization------------------- + AVBPReadInputPea(); + + // B. Franzelli + //---------------------AVBP thickening initialisation------------ + AVBPReadInputChem(); + + // E. Lameloise + //---------------------Soot computation initialisation----------- + if (m_nsoot > 0){ + initSoot(); + } } -StFlow::StFlow(shared_ptr th, size_t nsp, size_t points) - : Flow1D(th, nsp, points) +StFlow::StFlow(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) + : StFlow(th.get(), nsp, nsoot, neq, points) { warn_deprecated("StFlow::StFlow", "To be removed after Cantera 3.1. Class replaced by Flow1D."); } -StFlow::StFlow(shared_ptr sol, const string& id, size_t points) - : Flow1D(sol, id, points) +StFlow::StFlow(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) + : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) { - warn_deprecated("StFlow::StFlow", - "To be removed after Cantera 3.1. Class replaced by Flow1D."); + m_solution = sol; + m_id = id; + m_kin = m_solution->kinetics().get(); + m_trans = m_solution->transport().get(); + if (m_trans->transportModel() == "none") { + // @deprecated + warn_deprecated("StFlow", + "An appropriate transport model\nshould be set when instantiating the " + "Solution ('gas') object.\nImplicit setting of the transport model " + "is deprecated and\nwill be removed after Cantera 3.0."); + setTransportModel("mixture-averaged"); + } + m_solution->registerChangedCallback(this, [this]() { + setKinetics(m_solution->kinetics()); + setTransport(m_solution->transport()); + }); +} + +StFlow::~StFlow() +{ + if (m_solution) { + m_solution->removeChangedCallback(this); + } +} + +string StFlow::type() const { + if (m_isFree) { + return "free-flow"; + } + if (m_usesLambda) { + return "axisymmetric-flow"; + } + return "unstrained-flow"; +} + +void StFlow::setThermo(ThermoPhase& th) { + warn_deprecated("StFlow::setThermo", "To be removed after Cantera 3.0."); + m_thermo = &th; +} + +void StFlow::setKinetics(shared_ptr kin) +{ + if (!m_solution) { + // @todo remove after Cantera 3.0 + throw CanteraError("StFlow::setKinetics", + "Unable to update object that was not constructed from smart pointers."); + } + m_kin = kin.get(); + m_solution->setKinetics(kin); +} + +void StFlow::setKinetics(Kinetics& kin) +{ + warn_deprecated("StFlow::setKinetics(Kinetics&)", "To be removed after Cantera 3.0." + " Replaced by setKinetics(shared_ptr)."); + m_kin = &kin; +} + +void StFlow::setTransport(shared_ptr trans) +{ + if (!m_solution) { + // @todo remove after Cantera 3.0 + throw CanteraError("StFlow::setTransport", + "Unable to update object that was not constructed from smart pointers."); + } + if (!trans) { + throw CanteraError("StFlow::setTransport", "Unable to set empty transport."); + } + m_trans = trans.get(); + if (m_trans->transportModel() == "none") { + throw CanteraError("StFlow::setTransport", "Invalid Transport model 'none'."); + } + m_do_multicomponent = (m_trans->transportModel() == "multicomponent" || + m_trans->transportModel() == "multicomponent-CK"); + + m_diff.resize(m_nsp * m_points); + if (m_do_multicomponent) { + m_multidiff.resize(m_nsp * m_nsp*m_points); + m_dthermal.resize(m_nsp, m_points, 0.0); + } + m_solution->setTransport(trans); +} + +void StFlow::resize(size_t ncomponents, size_t points) +{ + Domain1D::resize(ncomponents, points); + m_rho.resize(m_points, 0.0); + m_wtm.resize(m_points, 0.0); + m_cp.resize(m_points, 0.0); + m_h.resize(m_points, 0.0); + m_hr.resize(m_points, 0.0); + m_visc.resize(m_points, 0.0); + m_tcon.resize(m_points, 0.0); + avbp_thick.resize(m_points,0.0); + + m_diff.resize(m_nsp*m_points); + if (m_do_multicomponent) { + m_multidiff.resize(m_nsp*m_nsp*m_points); + m_dthermal.resize(m_nsp, m_points, 0.0); + } + m_flux.resize(m_nsp,m_points); + m_wdot.resize(m_nsp,m_points, 0.0); + m_hk.resize(m_nsp, m_points, 0.0); + m_dhk_dz.resize(m_nsp, m_points - 1, 0.0); + m_do_energy.resize(m_points,false); + m_qdotRadiation.resize(m_points, 0.0); + m_fixedtemp.resize(m_points); + + m_dz.resize(m_points-1); + m_z.resize(m_points); + + // P. Wolf + m_zmixfrac.resize(m_points); + // Soot + if (m_nsoot > 0){ + sootConsumption.resize(m_nsp, 0.0); + m_soot_diff.resize(m_nsoot, m_points, 0.0); + m_soot_soret.resize(m_nsoot, m_points, 0.0); + m_qdotNucleation.resize(m_points, 0.0); + m_qdotCondensation.resize(m_nsoot, m_points, 0.0); + m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); + m_qdotSg.resize(m_nsoot, m_points, 0.0); + m_qdotOxidation.resize(m_nsoot, m_points, 0.0); + } +} + +void StFlow::setupGrid(size_t n, const double* z) +{ + resize(m_nv, n); + + m_z[0] = z[0]; + for (size_t j = 1; j < m_points; j++) { + if (z[j] <= z[j-1]) { + throw CanteraError("StFlow::setupGrid", + "grid points must be monotonically increasing"); + } + m_z[j] = z[j]; + m_dz[j-1] = m_z[j] - m_z[j-1]; + } +} + +void StFlow::setupGrid(size_t n) +{ + resize(m_nv, n); + + m_z[0] = 0.0; + for (size_t j = 1; j < m_points; j++) { + m_z[j] = (double) j / ( (double) (n-1) ); + m_dz[j-1] = m_z[j] - m_z[j-1]; + } +} + +void StFlow::resetBadValues(double* xg) +{ + double* x = xg + loc(); + for (size_t j = 0; j < m_points; j++) { + double* Y = x + m_nv*j + c_offset_Y; + m_thermo->setMassFractions(Y); + m_thermo->getMassFractions(Y); + } +} + +void StFlow::setTransportModel(const string& trans) +{ + if (!m_solution) { + // @todo remove after Cantera 3.0 + throw CanteraError("StFlow::setTransportModel", + "Unable to set Transport manager by name as object was not initialized\n" + "from a Solution manager: set Transport object directly instead."); + } + m_solution->setTransportModel(trans); +} + +string StFlow::transportModel() const { + return m_trans->transportModel(); +} + +void StFlow::setTransport(Transport& trans) +{ + warn_deprecated("StFlow::setTransport(Transport&)", "To be removed after" + " Cantera 3.0. Replaced by setTransport(shared_ptr)."); + m_trans = &trans; + if (m_trans->transportModel() == "none") { + throw CanteraError("StFlow::setTransport", + "Invalid Transport model 'none'."); + } + m_do_multicomponent = (m_trans->transportModel() == "multicomponent" || + m_trans->transportModel() == "multicomponent-CK"); + + m_diff.resize(m_nsp*m_points); + if (m_do_multicomponent) { + m_multidiff.resize(m_nsp*m_nsp*m_points); + m_dthermal.resize(m_nsp, m_points, 0.0); + } +} + +void StFlow::_getInitialSoln(double* x) +{ + for (size_t j = 0; j < m_points; j++) { + T(x,j) = m_thermo->temperature(); + m_thermo->getMassFractions(&Y(x, 0, j)); + m_rho[j] = m_thermo->density(); + } +} + +void StFlow::setGas(const double* x, size_t j) +{ + m_thermo->setTemperature(T(x,j)); + const double* yy = x + m_nv*j + c_offset_Y; + m_thermo->setMassFractions_NoNorm(yy); + m_thermo->setPressure(m_press); + // P. Wolf + if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ + calcMixFrac(x,j); + } +} + +void StFlow::setGasAtMidpoint(const double* x, size_t j) +{ + m_thermo->setTemperature(0.5*(T(x,j)+T(x,j+1))); + const double* yyj = x + m_nv*j + c_offset_Y; + const double* yyjp = x + m_nv*(j+1) + c_offset_Y; + for (size_t k = 0; k < m_nsp; k++) { + m_ybar[k] = 0.5*(yyj[k] + yyjp[k]); + } + m_thermo->setMassFractions_NoNorm(m_ybar.data()); + m_thermo->setPressure(m_press); + // P. Wolf + if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ + calcMixFrac(x,j); + } +} + + /// Calculates and updates the mixture fraction at point j + /// WARNING: Only correct if no Carbon atoms in the oxidizer line + /// and pure fuel in the fuel line + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + +void StFlow::calcMixFrac(const double* x, size_t j) { + size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom + size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel + double Z_C = 0.0; // passive scalar for C atom + double Z_C_F; // value of the passive scalar in fuel line + double W_C = this->m_thermo->atomicWeight(id_C); // Molecular weight of C atom + double W_fuel = this->m_thermo->molecularWeight(id_fuel); + double n_C; // Number of C atoms in each species + + for (size_t k=0; km_nsp; k++) { + n_C = this->m_thermo->nAtoms(k,id_C); + Z_C += n_C*x[index(c_offset_Y + k, j)]/this->m_thermo->molecularWeight(k); + } + Z_C = Z_C*W_C; + Z_C_F = W_C*this->m_thermo->nAtoms(id_fuel,id_C)/W_fuel; + m_zmixfrac[j] = Z_C/Z_C_F; // ie Z_C=0 in oxidizer line +} + +bool StFlow::fixed_mdot() { + warn_deprecated("StFlow::fixed_mdot", "To be removed after" + " Cantera 3.0. Replaced by isFree()."); + return !m_isFree; +} + +void StFlow::_finalize(const double* x) +{ + if (!m_do_multicomponent && m_do_soret) { + throw CanteraError("StFlow::_finalize", + "Thermal diffusion (the Soret effect) is enabled, and requires " + "using a multicomponent transport model."); + } + + size_t nz = m_zfix.size(); + bool e = m_do_energy[0]; + for (size_t j = 0; j < m_points; j++) { + if (e || nz == 0) { + m_fixedtemp[j] = T(x, j); + } else { + double zz = (z(j) - z(0))/(z(m_points - 1) - z(0)); + double tt = linearInterp(zz, m_zfix, m_tfix); + m_fixedtemp[j] = tt; + } + } + if (e) { + solveEnergyEqn(); + } + + if (m_isFree) { + // If the domain contains the temperature fixed point, make sure that it + // is correctly set. This may be necessary when the grid has been modified + // externally. + if (m_tfixed != Undef) { + for (size_t j = 0; j < m_points; j++) { + if (z(j) == m_zfixed) { + return; // fixed point is already set correctly + } + } + + for (size_t j = 0; j < m_points - 1; j++) { + // Find where the temperature profile crosses the current + // fixed temperature. + if ((T(x, j) - m_tfixed) * (T(x, j+1) - m_tfixed) <= 0.0) { + m_tfixed = T(x, j+1); + m_zfixed = z(j+1); + return; + } + } + } + } } void StFlow::eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) @@ -57,7 +461,33 @@ void StFlow::eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) updateProperties(jg, x, jmin, jmax); evalResidual(x, rsd, diag, rdt, jmin, jmax); - evalUo(x, rsd, diag, rdt, jmin, jmax); +} + +void StFlow::updateProperties(size_t jg, double* x, size_t jmin, size_t jmax) +{ + // properties are computed for grid points from j0 to j1 + size_t j0 = std::max(jmin, 1) - 1; + size_t j1 = std::min(jmax+1,m_points-1); + + updateThermo(x, j0, j1); + if (jg == npos || m_force_full_update) { + // update transport properties only if a Jacobian is not being + // evaluated, or if specifically requested + updateTransport(x, j0, j1); + } + if (jg == npos) { + double* Yleft = x + index(c_offset_Y, jmin); + m_kExcessLeft = distance(Yleft, max_element(Yleft, Yleft + m_nsp)); + double* Yright = x + index(c_offset_Y, jmax); + m_kExcessRight = distance(Yright, max_element(Yright, Yright + m_nsp)); + } + + // update the species diffusive mass fluxes whether or not a + // Jacobian is being evaluated + updateDiffFluxes(x, j0, j1); + if (m_nsoot > 0){ + updateSootDiffFluxes(x, j0, j1); + } } void StFlow::evalResidual(double* x, double* rsd, int* diag, @@ -109,6 +539,12 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, k_P_CO2 /= k_P_ref; k_P += m_press * X(x, m_kRadiating[0], j) * k_P_CO2; } + // absorption coefficient for soot + if (m_nsoot != 0 && m_do_soot_radiation) { + double k_P_soot = 0.0; + k_P_soot = 3.83 * CRad0 * fv(x,j) * T(x,j) / CRad2; + k_P += k_P_soot; + } // calculation of the radiative heat loss term radiative_heat_loss = 2 * k_P *(2 * StefanBoltz * pow(T(x, j), 4) @@ -123,6 +559,12 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, //---------------------------------------------- // left boundary //---------------------------------------------- + if (m_nsoot > 0){ + getDistributionOrdre0(x,j); + } + //avbp_thick.resize(m_points,avbp_fthick); ///////////////////////////// NEW to handle pytest + AVBPcompute_local_thick(x,j); + double thick_j = avbp_thick[j]; if (j == 0) { // these may be modified by a boundary object @@ -153,9 +595,16 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, for (size_t k = 0; k < m_nsp; k++) { sum += Y(x,k,0); rsd[index(c_offset_Y + k, 0)] = - -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); +// no thick -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); + -(m_flux(k,0) * thick_j + rho_u(x,0)* Y(x,k,0)); } rsd[index(c_offset_Y + leftExcessSpecies(), 0)] = 1.0 - sum; + if (m_nsoot > 0){ + for (size_t k = 0; k < m_nsoot; k++){ + rsd[index(c_offset_S + k, 0)] = - (m_soot_diff(k,0) + + rho_u(x,0)* Ys(x,k,0)); + } + } // set residual of poisson's equ to zero rsd[index(c_offset_E, 0)] = x[index(c_offset_E, j)]; @@ -172,6 +621,11 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, // \rho dV/dt + \rho u dV/dz + \rho V^2 // = d(\mu dV/dz)/dz - lambda //------------------------------------------------- + AVBPcompute_local_thick(x,j); + double thick_j = avbp_thick[j]; + double inv_thick = 1.0 / thick_j; + double thick_prev = avbp_thick[j-1]; + if (m_usesLambda) { rsd[index(c_offset_V,j)] = (shear(x, j) - lambda(x, j) - rho_u(x, j) * dVdz(x, j) @@ -183,6 +637,42 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, diag[index(c_offset_V, j)] = 0; } + //------------------------------------------------- + // Soot equation + // + // \rho u dYs/dz + d(-0.554 \mu 1/T dT/dx Ys)/dz + // = d(\rho Ds dYs/dz)/dz + \rhos \rho qdots + // + // convection - Thermophoresis = Diffusion + Source + //------------------------------------------------- + if (m_nsoot > 0) { + sootSource(x,j); + for (size_t k = 0; k < m_nsoot; k++){ + // Convection + double soot_convec = rho_u(x,j)*dYsdz(x,k,j); + // Diffusion + double soot_diffus = 2.0 * (m_soot_diff(k,j) - m_soot_diff(k,j-1)) + / (z(j+1) - z(j-1)); + // Thermophoresis + double soot_soret = 2.0 * (m_soot_soret(k,j) - m_soot_soret(k,j-1)) + / (z(j+1) - z(j-1)); + // Source terms [m3/kg/s] + double soot_source = 0; + soot_source += (k == 0 ? m_qdotNucleation[j] : 0.0); + soot_source += (m_do_condensation ? m_qdotCondensation(k,j) : 0.0); + soot_source += (m_do_coagulation ? m_qdotCoagulation(k,j) : 0.0); + soot_source += (m_do_sg ? m_qdotSg(k,j) : 0.0); + soot_source += (m_do_oxidation ? m_qdotOxidation(k,j) : 0.0); + // kg/s/m^3 + soot_source *= (rho_soot * m_rho[j]); + if(k == m_nsoot - 1 && m_trash_section){soot_source = 0.0;} + // Residual + rsd[index(c_offset_S + k, j)] = + (soot_source - soot_convec + soot_diffus + soot_soret) / m_rho[j] + - rdt * (Ys(x,k,j) - Ys_prev(k,j)); + diag[index(c_offset_S + k, j)] = 1; + } + } //------------------------------------------------- // Species equations // @@ -190,12 +680,20 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, // = M_k\omega_k //------------------------------------------------- getWdot(x,j); + if (m_nsoot > 0 && m_do_retroaction){ + for (size_t k=0; k < m_nsp; k++){ + // (kmol.m^(-3).s^(-1)) + m_wdot(k,j) -= sootConsumption[k]; + } + } for (size_t k = 0; k < m_nsp; k++) { double convec = rho_u(x,j)*dYdz(x,k,j); - double diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) +// no thick double diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) + double diffus = 2.0*(m_flux(k,j)*thick_j - m_flux(k,j-1)*thick_prev) / (z(j+1) - z(j-1)); rsd[index(c_offset_Y + k, j)] - = (m_wt[k]*(wdot(k,j)) + = (m_wt[k]*(wdot(k,j)*inv_thick) +// no thick = (m_wt[k]*(wdot(k,j)) - convec - diffus)/m_rho[j] - rdt*(Y(x,k,j) - Y_prev(k,j)); diag[index(c_offset_Y + k, j)] = 1; @@ -214,16 +712,20 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, setGas(x,j); double dtdzj = dTdz(x,j); double sum = 0.0; + double sum2 = 0.0; grad_hk(x, j); for (size_t k = 0; k < m_nsp; k++) { - double flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); +// no thick double flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); + double flxk = 0.5*(m_flux(k,j-1)*thick_prev + m_flux(k,j)*thick_j); sum += wdot(k,j)*m_hk(k,j); - sum += flxk * m_dhk_dz(k,j) / m_wt[k]; + sum2 += flxk * m_dhk_dz(k,j) / m_wt[k]; } rsd[index(c_offset_T, j)] = - m_cp[j]*rho_u(x,j)*dtdzj - - conduction(x,j) - sum; +// no thick //- divHeatFlux(x,j) - sum; + - AVBPdivHeatFlux(x,j) - sum*inv_thick - sum2; + rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); rsd[index(c_offset_T, j)] -= rdt*(T(x,j) - T_prev(j)); rsd[index(c_offset_T, j)] -= (m_qdotRadiation[j] / (m_rho[j] * m_cp[j])); @@ -244,9 +746,1474 @@ void StFlow::evalResidual(double* x, double* rsd, int* diag, } } +void StFlow::updateTransport(double* x, size_t j0, size_t j1) +{ + if (m_do_multicomponent) { + for (size_t j = j0; j < j1; j++) { + setGasAtMidpoint(x,j); + double wtm = m_thermo->meanMolecularWeight(); + double rho = m_thermo->density(); + m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0); + m_trans->getMultiDiffCoeffs(m_nsp, &m_multidiff[mindex(0,0,j)]); + + // Use m_diff as storage for the factor outside the summation + for (size_t k = 0; k < m_nsp; k++) { + m_diff[k+j*m_nsp] = m_wt[k] * rho / (wtm*wtm); + } + + m_tcon[j] = m_trans->thermalConductivity(); + if (m_do_soret) { + m_trans->getThermalDiffCoeffs(m_dthermal.ptrColumn(0) + j*m_nsp); + } + } + } else { // mixture averaged transport + for (size_t j = j0; j < j1; j++) { + setGasAtMidpoint(x,j); + m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0); + m_trans->getMixDiffCoeffs(&m_diff[j*m_nsp]); + m_tcon[j] = m_trans->thermalConductivity(); + } + } +} + +void StFlow::show(const double* x) +{ + writelog(" Pressure: {:10.4g} Pa\n", m_press); + + Domain1D::show(x); + + if (m_do_radiation) { + writeline('-', 79, false, true); + writelog("\n z radiative heat loss"); + writeline('-', 79, false, true); + for (size_t j = 0; j < m_points; j++) { + writelog("\n {:10.4g} {:10.4g}", m_z[j], m_qdotRadiation[j]); + } + writelog("\n"); + } +} + +void StFlow::updateDiffFluxes(const double* x, size_t j0, size_t j1) +{ + if (m_do_multicomponent) { + for (size_t j = j0; j < j1; j++) { + double dz = z(j+1) - z(j); + for (size_t k = 0; k < m_nsp; k++) { + double sum = 0.0; + for (size_t m = 0; m < m_nsp; m++) { + sum += m_wt[m] * m_multidiff[mindex(k,m,j)] * (X(x,m,j+1)-X(x,m,j)); + } + m_flux(k,j) = sum * m_diff[k+j*m_nsp] / dz; + } + } + } else { + for (size_t j = j0; j < j1; j++) { + double sum = 0.0; + double wtm = m_wtm[j]; + double rho = density(j); + double dz = z(j+1) - z(j); + for (size_t k = 0; k < m_nsp; k++) { + m_flux(k,j) = m_wt[k]*(rho*m_diff[k+m_nsp*j]/wtm); + m_flux(k,j) *= (X(x,k,j) - X(x,k,j+1))/dz; + sum -= m_flux(k,j); + } + // correction flux to insure that \sum_k Y_k V_k = 0. + for (size_t k = 0; k < m_nsp; k++) { + m_flux(k,j) += sum*Y(x,k,j); + } + } + } + + if (m_do_soret) { + for (size_t m = j0; m < j1; m++) { + double gradlogT = 2.0 * (T(x,m+1) - T(x,m)) / + ((T(x,m+1) + T(x,m)) * (z(m+1) - z(m))); + for (size_t k = 0; k < m_nsp; k++) { + m_flux(k,m) -= m_dthermal(k,m)*gradlogT; + } + } + } +} + +string StFlow::componentName(size_t n) const +{ + switch (n) { + case c_offset_U: + return "velocity"; + case c_offset_V: + return "spread_rate"; + case c_offset_T: + return "T"; + case c_offset_L: + return "lambda"; + case c_offset_E: + return "eField"; + default: + if (n >= c_offset_Y && n < (c_offset_Y + m_nsp)) { + return m_thermo->speciesName(n - c_offset_Y); + } else if (n >= c_offset_S && n < (c_offset_S + m_nsoot)) { + return sectionName(n-c_offset_S); + } else { + return ""; + } + } +} + +size_t StFlow::componentIndex(const string& name) const +{ + if (name=="velocity") { + return c_offset_U; + } else if (name=="spread_rate") { + return c_offset_V; + } else if (name=="T") { + return c_offset_T; + } else if (name=="lambda") { + return c_offset_L; + } else if (name == "eField") { + return c_offset_E; + } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()) { + return stoi(name.substr(2))+c_offset_S; // offset not required in previous version, why? + } else { + for (size_t n=c_offset_Y; ntransportModel(); + + state["phase"]["name"] = m_thermo->name(); + AnyValue source = m_thermo->input().getMetadata("filename"); + state["phase"]["source"] = source.empty() ? "" : source.asString(); + + state["radiation-enabled"] = m_do_radiation; + if (m_do_radiation) { + state["emissivity-left"] = m_epsilon_left; + state["emissivity-right"] = m_epsilon_right; + } + + set energy_flags(m_do_energy.begin(), m_do_energy.end()); + if (energy_flags.size() == 1) { + state["energy-enabled"] = m_do_energy[0]; + } else { + state["energy-enabled"] = m_do_energy; + } + + state["Soret-enabled"] = m_do_soret; + + set species_flags(m_do_species.begin(), m_do_species.end()); + if (species_flags.size() == 1) { + state["species-enabled"] = m_do_species[0]; + } else { + for (size_t k = 0; k < m_nsp; k++) { + state["species-enabled"][m_thermo->speciesName(k)] = m_do_species[k]; + } + } + + state["refine-criteria"]["ratio"] = m_refiner->maxRatio(); + state["refine-criteria"]["slope"] = m_refiner->maxDelta(); + state["refine-criteria"]["curve"] = m_refiner->maxSlope(); + state["refine-criteria"]["prune"] = m_refiner->prune(); + state["refine-criteria"]["grid-min"] = m_refiner->gridMin(); + state["refine-criteria"]["max-points"] = + static_cast(m_refiner->maxPoints()); + + if (m_zfixed != Undef) { + state["fixed-point"]["location"] = m_zfixed; + state["fixed-point"]["temperature"] = m_tfixed; + } + + return state; +} + +shared_ptr StFlow::asArray(const double* soln) const +{ + auto arr = SolutionArray::create( + m_solution, static_cast(nPoints()), getMeta()); + arr->addExtra("grid", false); // leading entry + AnyValue value; + value = m_z; + arr->setComponent("grid", value); + vector data(nPoints()); + for (size_t i = 0; i < nComponents(); i++) { + if (componentActive(i)) { + auto name = componentName(i); + for (size_t j = 0; j < nPoints(); j++) { + data[j] = soln[index(i, j)]; + } + if (!arr->hasComponent(name)) { + arr->addExtra(name, componentIndex(name) > c_offset_Y); + } + value = data; + arr->setComponent(name, value); + } + } + value = m_rho; + arr->setComponent("D", value); // use density rather than pressure + + if (m_do_radiation) { + arr->addExtra("radiative-heat-loss", true); // add at end + value = m_qdotRadiation; + arr->setComponent("radiative-heat-loss", value); + } + + return arr; +} + +void StFlow::fromArray(SolutionArray& arr, double* soln) +{ + Domain1D::setMeta(arr.meta()); + arr.setLoc(0); + auto phase = arr.thermo(); + m_press = phase->pressure(); + vector did_section(m_nsoot,false); + bool wrote_header = false; + + const auto grid = arr.getComponent("grid").as>(); + setupGrid(nPoints(), &grid[0]); + + for (size_t i = 0; i < nComponents(); i++) { + if (!componentActive(i)) { + continue; + } + string name = componentName(i); + if (arr.hasComponent(name)) { + const vector data = arr.getComponent(name).as>(); + if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ + size_t n = stoi(name.substr(2)); + did_section[n]=true; + writelog("Adding soot section to soln "+name+"\n"); + } + for (size_t j = 0; j < nPoints(); j++) { + soln[index(i,j)] = data[j]; + } + } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ + size_t n = stoi(name.substr(2)); + did_section[n]=true; + writelog("Creating soot section in soln "+name+"\n"); + for (size_t j = 0; j < nPoints(); j++) { + soln[index(n+c_offset_S,j)] = 0.0; + } + } else { + warn_user("StFlow::fromArray", "Saved state does not contain values for " + "component '{}' in domain '{}'.", name, id()); + } + } + + if (soot_loglevel >= 1 && m_nsoot != 0) { + wrote_header = false; + for (size_t ks = 0; ks < m_nsoot; ks++) { + if (did_section[ks] == false) { + if (!wrote_header) { + writelog("\n\n"); + writelog("Missing data for soot sections:\n"); + wrote_header = true; + } + writelog(m_section_name[ks]+" "); + } + } + } + + updateProperties(npos, soln + loc(), 0, m_points - 1); + setMeta(arr.meta()); +} + +string StFlow::flowType() const { + warn_deprecated("StFlow::flowType", + "To be removed after Cantera 3.0; superseded by 'type'."); + if (m_type == cFreeFlow) { + return "Free Flame"; + } else if (m_type == cAxisymmetricStagnationFlow) { + return "Axisymmetric Stagnation"; + } else if (m_type == cFlameletFlow){ + return "Flamelet"; + } else { + throw CanteraError("StFlow::flowType", "Unknown value for 'm_type'"); + } +} + +void StFlow::setMeta(const AnyMap& state) +{ + if (state.hasKey("energy-enabled")) { + const AnyValue& ee = state["energy-enabled"]; + if (ee.isScalar()) { + m_do_energy.assign(nPoints(), ee.asBool()); + } else { + m_do_energy = ee.asVector(nPoints()); + } + } + + setTransportModel(state.getString("transport-model", "mixture-averaged")); + + if (state.hasKey("Soret-enabled")) { + m_do_soret = state["Soret-enabled"].asBool(); + } + + if (state.hasKey("species-enabled")) { + const AnyValue& se = state["species-enabled"]; + if (se.isScalar()) { + m_do_species.assign(m_thermo->nSpecies(), se.asBool()); + } else { + m_do_species = se.asVector(m_thermo->nSpecies()); + } + } + + if (state.hasKey("radiation-enabled")) { + m_do_radiation = state["radiation-enabled"].asBool(); + if (m_do_radiation) { + m_epsilon_left = state["emissivity-left"].asDouble(); + m_epsilon_right = state["emissivity-right"].asDouble(); + } + } + + if (state.hasKey("refine-criteria")) { + const AnyMap& criteria = state["refine-criteria"].as(); + double ratio = criteria.getDouble("ratio", m_refiner->maxRatio()); + double slope = criteria.getDouble("slope", m_refiner->maxDelta()); + double curve = criteria.getDouble("curve", m_refiner->maxSlope()); + double prune = criteria.getDouble("prune", m_refiner->prune()); + m_refiner->setCriteria(ratio, slope, curve, prune); + + if (criteria.hasKey("grid-min")) { + m_refiner->setGridMin(criteria["grid-min"].asDouble()); + } + if (criteria.hasKey("max-points")) { + m_refiner->setMaxPoints(criteria["max-points"].asInt()); + } + } + + if (state.hasKey("fixed-point")) { + m_zfixed = state["fixed-point"]["location"].asDouble(); + m_tfixed = state["fixed-point"]["temperature"].asDouble(); + } +} + +void StFlow::solveEnergyEqn(size_t j) +{ + bool changed = false; + if (j == npos) { + for (size_t i = 0; i < m_points; i++) { + if (!m_do_energy[i]) { + changed = true; + } + m_do_energy[i] = true; + } + } else { + if (!m_do_energy[j]) { + changed = true; + } + m_do_energy[j] = true; + } + m_refiner->setActive(c_offset_U, true); + m_refiner->setActive(c_offset_V, true); + m_refiner->setActive(c_offset_T, true); + if (changed) { + needJacUpdate(); + } +} + +size_t StFlow::getSolvingStage() const +{ + throw NotImplementedError("StFlow::getSolvingStage", + "Not used by '{}' objects.", type()); +} + +void StFlow::setSolvingStage(const size_t stage) +{ + throw NotImplementedError("StFlow::setSolvingStage", + "Not used by '{}' objects.", type()); +} + +void StFlow::solveElectricField(size_t j) +{ + throw NotImplementedError("StFlow::solveElectricField", + "Not used by '{}' objects.", type()); +} + +void StFlow::fixElectricField(size_t j) +{ + throw NotImplementedError("StFlow::fixElectricField", + "Not used by '{}' objects.", type()); +} + +bool StFlow::doElectricField(size_t j) const +{ + throw NotImplementedError("StFlow::doElectricField", + "Not used by '{}' objects.", type()); +} + +void StFlow::setBoundaryEmissivities(double e_left, double e_right) +{ + if (e_left < 0 || e_left > 1) { + throw CanteraError("StFlow::setBoundaryEmissivities", + "The left boundary emissivity must be between 0.0 and 1.0!"); + } else if (e_right < 0 || e_right > 1) { + throw CanteraError("StFlow::setBoundaryEmissivities", + "The right boundary emissivity must be between 0.0 and 1.0!"); + } else { + m_epsilon_left = e_left; + m_epsilon_right = e_right; + } +} + +void StFlow::fixTemperature(size_t j) +{ + bool changed = false; + if (j == npos) { + for (size_t i = 0; i < m_points; i++) { + if (m_do_energy[i]) { + changed = true; + } + m_do_energy[i] = false; + } + } else { + if (m_do_energy[j]) { + changed = true; + } + m_do_energy[j] = false; + } + m_refiner->setActive(c_offset_U, false); + m_refiner->setActive(c_offset_V, false); + m_refiner->setActive(c_offset_T, false); + if (changed) { + needJacUpdate(); + } +} +/* ------------------------------------------------------------------------ + Reads the mixture_database.dat file and sets accordingly the PEA function(s) + P. Wolf modif by J. Wirtz +--------------------------------------------------------------------------*/ +void StFlow::AVBPReadInputPea() { + Parser parser; + Param* param; + + ifstream avbp_mixturedb("mixture_database.dat"); + if (avbp_mixturedb.good()){ + parser.parseFile("mixture_database.dat"); + // In case of pea, the name of the gas should be the same than the one in the mixture_database. + // Get number of mixtures in database + size_t n_mixtures = parser.nbParamOccurence("mixture_name"); + size_t idx_beg = std::string::npos; + size_t idx_end = std::string::npos; + // Loop through all occurences of keyword "mixture name" + for (size_t i=0; i< n_mixtures; ++i) { + param = parser.getParam("mixture_name",i); + std::string current_str = param->readString(0); + // Check if mixture_name is the one requested in the cti file + if ( current_str == m_thermo->name() ) { + // Store bounding idx to get important info + idx_beg = parser.getParamNumber("mixture_name",i); + idx_end = parser.getParamNumber("mixture_name",i+1); + + // Get the fuel of the 2-step chemistry + param = parser.getParam("species_name", idx_beg, idx_end); + for (size_t i=0; ireadString(i); + if (avbp_species.find('C')!=string::npos && avbp_species.find('H')!=string::npos){ + avbp_fuel = avbp_species; + } + if (avbp_species == "H2"){ + avbp_fuel = avbp_species; + } + + } + + // Check if PEA method and search for the coefficient + if (parser.checkParam("pea_method", idx_beg, idx_end) == true){ + param = parser.getParam("pea_method", idx_beg, idx_end); + std::string avbp_pea = param->readString(0); + if (avbp_pea == "pea1"){ + avbp_ipea = 1; + cout<<"ipea set to 1, PEA_1 will be applied"<readDouble(i); + } + } + else if (avbp_pea == "pea2") { + avbp_ipea = 2; + cout<<"ipea set to 2, PEA_2 will be applied"<readDouble(i); + } + param = parser.getParam("pea_coeff", idx_beg, idx_end, 1); + for (size_t i=0; i<10; i++) { + avbp_pea_coeffs[i+8] = param->readDouble(i); + } + + } + else{ + throw CanteraError("readAvbpInputPEA","ipea is set to a weird value"); + } + } + else { + avbp_ipea = 0; + } + } + else { + // pea not considered as mixture_name (mixture_database.dat) does not correspond to gas name (cti) + avbp_ipea = 0; + } + + // calculate the global equivalence ratio phi_cst + if ((avbp_ipea==1)||(avbp_ipea==2)){ + size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom + size_t id_H = this->m_thermo->elementIndex("H"); // Index of H atom + size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel + size_t id_ox = this->m_thermo->speciesIndex("O2"); // Index of O2 + size_t n_C = this->m_thermo->nAtoms(id_fuel,id_C); + size_t n_H = this->m_thermo->nAtoms(id_fuel,id_H); + //Calculate in mass units phi = s_m*Yf/Yo + phi_cst = (n_C + n_H/4)*this->m_thermo->molecularWeight(id_ox)/this->m_thermo->molecularWeight(id_fuel); + phi_cst = phi_cst*1./0.2333; // WARNING: valid only for Fuel/AIR mixture + } + + if (avbp_ipea!=0){ + break; + } + + } + } + else { + avbp_ipea = 0; + } +} +/********** + Reading the AVBP input_chem.dat + B. Franzelli +*************/ +void StFlow::AVBPReadInputChem() { + avbp_fthick = m_thick; + if (avbp_fthick > 1.0) { + cout << "INFO: Thickening applied with constant value." << endl; + } + else { + avbp_fthick = 1.0; + } +} +void StFlow::AVBPcompute_local_thick(double* x,size_t j){ + avbp_thick[j] = avbp_fthick; +} + +//----------------------// +// SOOT RELATED MTEHODS // +//----------------------// +void StFlow::initSoot(){ + //---------------------------------------------------- + // Initializes soot computation + //---------------------------------------------------- + + // Sets offset of soot sections in solution array + // Resizes necessay arrays + // Sets sections names "YsXX", disables refinement on soot and sets clipping + + // Offset definition + c_offset_S = c_offset_Y + m_nsp; + // Array allocation + m_section_name.resize(m_nsoot); + sootConsumption.resize(m_nsp, 0.0); + q.resize(m_nsoot,0.0); + vSectMin.resize(m_nsoot, 0.0); + vSectMax.resize(m_nsoot, 0.0); + vSectMean.resize(m_nsoot, 0.0); + sSectMean.resize(m_nsoot, 0.0); + dSectMean.resize(m_nsoot, 0.0); + dSectCol.resize(m_nsoot, 0.0); + kfractal.resize(m_nsoot, 1.0); + Dfractal.resize(m_nsoot, 3); + nNucMean.resize(m_nsoot, 0.0); + rNucMean.resize(m_nsoot, 0.0); + rSectCol.resize(m_nsoot, 0.0); + aSectCol.resize(m_nsoot, 0.0); + theta_surf.resize(m_nsoot,2.0); + m_soot_diff.resize(m_nsoot, m_points, 0.0); + m_soot_soret.resize(m_nsoot, m_points, 0.0); + m_qdotNucleation.resize(m_points, 0.0); + m_qdotCondensation.resize(m_nsoot, m_points, 0.0); + m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); + collision_mat.resize(m_nsoot, m_nsoot, 0.0); + m_qdotSg.resize(m_nsoot, m_points, 0.0); + m_qdotOxidation.resize(m_nsoot, m_points, 0.0); + // Sections setup + for (size_t k = 0; k < m_nsoot; k++) { + std::string string_k = std::to_string(k); + m_section_name[k] = "Ys" + string_k; + m_refiner->setActive(c_offset_S+k, false); + setBounds(c_offset_S + k, -1.0e-5, 1e5); + } + +} + +void StFlow::setPrecursors(vector id_precursors){ + //---------------------------------------------------- + // Recovers precursor data for further computation + //---------------------------------------------------- + + if (m_nsoot <= 0){ + writelog("\n--> CANTERA SOOT : no sections :(\n"); + return; + } + size_t id_C = m_thermo->elementIndex("C"); + W_C = m_thermo->atomicWeight(id_C); + n_PAH = id_precursors.size(); + m_precursors.resize(n_PAH); + W_PAH.resize(n_PAH,0.0); + n_C.resize(n_PAH,0.0); + for (size_t k = 0; k != n_PAH; k++){ + m_precursors[k] = id_precursors[k] - c_offset_Y; + W_PAH[k] = m_thermo->molecularWeight(m_precursors[k]); + n_C[k] = m_thermo->nAtoms(m_precursors[k],id_C); + } +} + +void StFlow::finalizeSoot(){ + //---------------------------------------------------- + // Soot setup finalization + //---------------------------------------------------- + // Creates soot volumes + sootCreationVol(); + // Computes collision matrix + sootCollisionInverse(); + // Load surface reactions + if (m_do_sg || m_do_oxidation){ + loadHaca(m_haca_model); + loadSurface();} + + if (soot_loglevel >= 1){showSootInfo();} + if (soot_loglevel >= 2){showSootSections();} +} + +void StFlow::sootCreationVol(){ + // Sections creations + // PAH list boundaries + size_t n_C_min = *min_element(n_C.begin(),n_C.end()); + size_t n_C_max = *max_element(n_C.begin(),n_C.end()); + // First section lower boundary : smallest possible dimer + vSectMin[0] = 2.0 * (double)n_C_min * V_C2; + // First section upper boundary : biggest possible dimer + vSectMax[0] = V_C2 * max(2.0 * n_C_min + n_C_max, 2.0 * n_C_max); + // Following sections : geometrical progression + vSectMin[1] = vSectMax[0]; + if (m_trash_section){ + double vTrashLowLim = Pi * pow(dTrashLowLim,3.0) / 6; + for (size_t k = 1; k < m_nsoot - 2; k++){ + double exponent = double(k) / double(m_nsoot-2); + vSectMax[k] = vSectMin[1] * pow(vTrashLowLim / vSectMin[1],exponent); + vSectMin[k+1] = vSectMax[k]; + } + vSectMax[m_nsoot - 2] = vTrashLowLim; + vSectMin[m_nsoot - 1] = vTrashLowLim; + }else{ + for (size_t k = 1; k < m_nsoot - 1; k++){ + double exponent = double(k) / double(m_nsoot-1); + vSectMax[k] = vSectMin[1] * pow(bigSoot / vSectMin[1],exponent); + vSectMin[k+1] = vSectMax[k]; + } + } + + vSectMax[m_nsoot-1] = bigSoot; + // Building mean values + for (size_t k = 0; k < m_nsoot; k++){ + vSectMean[k] = (vSectMax[k] + vSectMin[k]) / 2.0 ; //(vSectMax[k] - vSectMin[k]) / log (vSectMax[k] / vSectMin[k]); + dSectMean[k] = pow(6 / Pi * vSectMean[k], 1.0 / 3.0); + } + + // Sections morphology + for (size_t k = 0; k < m_nsoot; k++){ + if (vSectMean[k] >= vlim1){ + // Fractal dimension + Dfractal[k] = Df; + // Fractal prefactor + kfractal[k] = 4.46 * pow(Dfractal[k], -2.08); + } + } + + if (m_soot_morphology == "sphere" || m_soot_morphology == "rodrigues"){ + // Soot morphological properties as defined by P. Rodrigues (PhD Thesis, 2018) + // For spheres, theta = 2.0 + for (size_t k = 0; k < m_nsoot; k++){ + if (m_soot_morphology == "rodrigues" && vSectMin[k] >= vlim1){ + theta_surf[k] = (3.0 * (log(vSectMean[k] / vlim1)) + + 2.0 * (log(vlim1 / V_C2))) + / (log(vSectMean[k] / V_C2)); + if (k == m_nsoot-1 && m_trash_section){theta_surf[k] = theta_surf[k-1];} + } + // Collision diameter + dSectCol[k] = 6 / pow(36 * Pi, 1.0 /Dfractal[k]) + * pow(vSectMean[k], (Dfractal[k]-2.0) / Dfractal[k]) + * pow(S_C2 * + pow(vSectMean[k]/V_C2,theta_surf[k] / 3.0),(3.0-Dfractal[k]) / Dfractal[k]); + // Collision radius + rSectCol[k] = dSectCol[k] / 2.0; + // Collision cross-section + aSectCol[k] = Pi * pow(rSectCol[k], 2.0); + // Surface area + sSectMean[k] = S_C2 * pow(vSectMean[k] / V_C2, theta_surf[k] / 3.0); + // Nuclei number + nNucMean[k] = pow(sSectMean[k], 2) / (36. * Pi * pow(vSectMean[k], 2.)); + // Nuclei radius[m] + rNucMean[k] = 3. * vSectMean[k] / sSectMean[k]; + } + // // From P. Rodrigues, trick to help numerical stability (not tested its impact) + // dSectCol[m_nsoot-1] = dSectMean[m_nsoot-1]; + // rSectCol[m_nsoot-1] = dSectCol[m_nsoot-1] / 2.0; + // aSectCol[m_nsoot-1] = Pi * pow(rSectCol[m_nsoot-1], 2.0); + }else if (m_soot_morphology == "thajudeen"){ + // Soot morphological properties as defined by Thajudeen (2012) + for (size_t k = 0; k < m_nsoot; k++){ + // Nuclei number + nNucMean[k] = max(1., vSectMean[k] / vlim1); + // Nuclei radius + rNucMean[k] = min(pow(3.0 * vSectMean[k] / (4.0 * Pi), 1./3.), pow(3.0 * vlim1 / (4.0 * Pi), 1.0/3.0)); + if (vSectMean[k] >= vlim1){ + // Collision radius (Smoluchowski radius) + double alpha1 = 0.253 * pow(Dfractal[k], 2.0) - 1.209 * Dfractal[k] + 1.433; + double alpha2 = -0.218 * pow(Dfractal[k], 2.0) + 0.964 * Dfractal[k] - 0.180; + double phi_r = 1 / (alpha1 * log(nNucMean[k]) + alpha2); + rSectCol[k] = rNucMean[k] * phi_r * pow(nNucMean[k] / kfractal[k], 1/Dfractal[k]); + // Collision cross-section (Projected Area) + double alpha3 = 0.439 * pow(Dfractal[k], 2.0) - 2.221 * Dfractal[k] + 2.787; + double alpha4 = -0.232 * pow(Dfractal[k], 3.0) + 1.273 * pow(Dfractal[k], 2.0) - 2.183 * Dfractal[k] + 1.906; + double phi_p = pow(nNucMean[k], -alpha3) / alpha4; + aSectCol[k] = Pi * pow(rNucMean[k], 2.) * phi_p * pow(nNucMean[k] / kfractal[k], 2.0/Dfractal[k]); + }else{ + rSectCol[k] = dSectMean[k] / 2.; + aSectCol[k] = Pi * pow(rSectCol[k], 2.); + } + //Collision diameter ("Smoluchowski diameter") + dSectCol[k] = 2. * rSectCol[k]; + // Surface area (computed from smoluchowski radius, close to Rodrigues definition) + sSectMean[k] = Pi * pow(dSectCol[k], 2.); + // theta parameter (needed for surface reactions) + theta_surf[k] = 3. * log(sSectMean[k]/S_C2) / log(vSectMean[k]/V_C2); + } + } +} + +void StFlow::sootCollisionInverse(){ + //---------------------------------------------------- + // Computes colision matrix (coagulation) + //---------------------------------------------------- + + for (size_t k = 0; k < m_nsoot; k++){ + for (size_t l = k; l < m_nsoot; l++){ + for (size_t m = l; m < m_nsoot; m++){ + double vol_min = vSectMin[l] + vSectMin[k]; + if(vol_min <= vSectMax[m] && vol_min >= vSectMin[m]){ + collision_mat(k,l) = m; + } + } + } + } +} + +void StFlow::loadSurface(){ + //---------------------------------------------------- + // Resizes and compute surface reactions arrays + //---------------------------------------------------- + + kpower.resize(m_nsoot,0.0); + mpower.resize(m_nsoot,0.0); + vc2power.resize(m_nsoot,0.0); + vc2powerm.resize(m_nsoot,0.0); + vmax_kpower.resize(m_nsoot,0.0); + vmin_kpower.resize(m_nsoot,0.0); + vmax_mpower.resize(m_nsoot,0.0); + vmin_mpower.resize(m_nsoot,0.0); + vmaxmc2_kpower.resize(m_nsoot,0.0); + vminpc2_kpower.resize(m_nsoot,0.0); + vmaxmc2_mpower.resize(m_nsoot,0.0); + vminpc2_mpower.resize(m_nsoot,0.0); + vc2powervect.resize(m_nsoot,0.0); + vc2powermvect.resize(m_nsoot,0.0); + for (size_t k = 0; k < m_nsoot; k++){ + kpower[k] = (theta_surf[k] + 3.0)/3.0; + mpower[k] = theta_surf[k]/3.0; + vc2power[k] = (3.0 - theta_surf[k] )/3.0; + vc2powerm[k] = - mpower[k]; + vmax_kpower[k] = pow(vSectMax[k],kpower[k]); + vmin_kpower[k] = pow(vSectMin[k],kpower[k]); + vmax_mpower[k] = pow(vSectMax[k],mpower[k]); + vmin_mpower[k] = pow(vSectMin[k],mpower[k]); + vmaxmc2_kpower[k] = pow(vSectMax[k] - V_C2,kpower[k]); + vminpc2_kpower[k] = pow(vSectMin[k] + V_C2,kpower[k]); + vmaxmc2_mpower[k] = pow(vSectMax[k] - V_C2,mpower[k]); + vminpc2_mpower[k] = pow(vSectMin[k] + V_C2,mpower[k]); + vc2powervect[k] = pow(V_C2,vc2power[k]); + vc2powermvect[k] = pow(V_C2,vc2powerm[k]); + } +} + +void StFlow::showSootInfo(){ + writelog("\n{:=^47}{:9}{:=^47}", "", "SOOT INFO", ""); + writelog("\n{:21}{:2}{}", "NUMBER OF SECTIONS", ":", m_nsoot); + writelog("\n{:21}{:1}","PRECURSORS", ":"); + for (size_t k = 0; k != n_PAH; k++){ + writelog(" {}", m_thermo->speciesName(m_precursors[k])); + } + if (dTrashLowLim > 0){writelog("\n{:21}{:2}{} m", "MAX DIAMETER", ":", dTrashLowLim);} + writelog("\n{:21}{:2}{}", "AGGREGATES MORPHOLOGY", ":", m_soot_morphology); + writelog("\n{:21}{:2}{}", "RETROACTION", ":", m_do_retroaction); + writelog("\n{:21}{:2}{}", "CONDENSATION", ":", m_do_condensation); + writelog("\n{:21}{:2}{}", "COAGULATION", ":", m_do_coagulation); + writelog("\n{:21}{:2}{}", "SURFACE GROWTH", ":", m_do_sg); + writelog("\n{:21}{:2}{}", "OXIDATION", ":", m_do_oxidation); + if (m_do_sg || m_do_oxidation){ + writelog("\n{:21}{:2}", "HACA MODEL", ":"); + if (m_haca_model == 1){ + writelog("Mauss"); + }else if (m_haca_model == 2){ + writelog("Blanquart"); + }else if (m_haca_model == 3){ + writelog("Kazakov"); + writelog("\n{:21}{:2}{}{:2}", "-> Flame temperature", ":", kazakovTad, " K"); + } + } + writelog("\n{:21}{:2}{}", "RADIATIVE HEAT LOSSES", ":", m_do_soot_radiation); + writelog("\n{:21}{:2}{}", "SORET EFFECT", ":", m_do_soot_soret); + writeline('=', 103, false, true); + writelog("\n"); +} +void StFlow::showSootSections(){ + //---------------------------------------------------- + // Displays section informations + //---------------------------------------------------- + + if (m_nsoot <= 0){ + writelog ("\nSOOT INFO : no sections to show :("); + return; + } + writelog("\n{:=^36}{:30}{:=^37}", "", "SOOT SECTIONS INFO (SI UNITS)", ""); + writelog("\n Section Vol. min. Vol. mean Vol. max. Diam. mean Diam. coll"); + writeline('-', 103, false, true); + for (size_t k = 0; k < m_nsoot; k++) { + writelog("\n {:10d} {:10.4g} {:10.4g} {:10.4g} {:10.4g} {:10.4g}", + k,vSectMin[k],vSectMean[k],vSectMax[k],dSectMean[k],dSectCol[k]); + } + writeline('=', 103, false, true); + writelog("\n"); +} + +void StFlow::sootSource(const double* x, size_t j) { + //---------------------------------------------------- + // Computes soot source terms + //---------------------------------------------------- + // Dimerization + sootDimerization(x,j); + // Nucleation + sootNucleation(x,j); + // Condensation + if (m_do_condensation){sootCondensation(x,j);} + // Coagulation + if (m_do_coagulation){sootCoagulation(x,j);} + // Surface chemistry + if (m_do_sg || m_do_oxidation){sootSurface(x,j);} +} + +void StFlow::sootDimerization(const double* x, size_t j){ + //---------------------------------------------------- + // Computes dimerization source term + //---------------------------------------------------- + double omega = 0, c_dimer = 0; + double V_k, d2_k, omega_k, C_k, gamma_k, k_k; + for (size_t k = 0; k < n_PAH; k++){ + // PAH volume [m3] + V_k = n_C[k] * V_C2 / 2.0; + // Squared PAH diameter [m2] + d2_k = pow(6.0 * V_k / Pi, 2.0/3.0); + // PAH concentraiton [kmol/m3] + C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; + // PAH sticking coefficient [-] + gamma_k = Cn_cst * pow(W_PAH[k], 4.0); + // Reaction rate constant [m3/kmol/s] + k_k = sqrt(4.0 * Pi * Boltzmann * T(x,j) / (W_C * n_C[k] / Avogadro)) * d2_k * Avogadro; + // PAH dimerization reaction rate [kmol/m3/s] + omega_k = gamma_k * k_k * pow(C_k, 2.0); + // PAH consumption [kmol/m3/s] (x2 because 2 mol PAH -> 1 mol dimer) + sootConsumption[m_precursors[k]] = 2 * omega_k; + // Adds PAH contribution to overall local dimerization rate + omega += omega_k; + // Adds PAH contribution to overall dimer carbon atoms + c_dimer += omega_k * n_C[k]; + + } + // Overall dimerization rate [1/kg/s] + r_dimer = omega * Avogadro / m_rho[j]; + // Overall dimer volume [m3] + V_dimer = c_dimer * V_C2 / omega; + + // double K00 = 0, cdimer = 0; + // double V_k, d_k, kdimfwd_k, K00_k, C_k; + // for (size_t k = 0; k < n_PAH; k++){ + // // PAH volume [m3] + // V_k = n_C[k] * V_C2 / 2.0; + // // PAH diameter [m] + // d_k = pow(6.0 * V_k / Pi, 1.0/3.0); + // // PAH concentraiton [mol/m3] + // C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; + // // m6/s/kg/mol2 + // kdimfwd_k = Cn_cst * pow(W_PAH[k], 4.0) / m_rho[j] + // * sqrt((4.0 * Pi * Boltzmann * T(x,j)) / ((W_C / Avogadro) * n_C[k])) + // * pow(d_k, 2.0) * pow(Avogadro, 2.0) ; + // // (mol.g^(-1).s^(-1)) + // K00_k = pow(C_k, 2.0) * kdimfwd_k / Avogadro; + // // (mol.g^(-1).s^(-1)) + // K00 += K00_k; + // cdimer += K00_k * n_C[k]; + // // Precursor consumption (mol/m3/s) + // // (x2 because 2 mol PAH -> 1 mol dimer) + // sootConsumption[m_precursors[k]] = 2 * K00_k * m_rho[j]; + // } + // // Dimerization rate [1/kg/s] + // r_dimer = K00 * Avogadro; + // // Equivalent dimer volume [m3] + // V_dimer = cdimer * V_C2 / K00; +} + +void StFlow::sootNucleation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute nucleation source terms + //---------------------------------------------------- + // [m(11/2)/s/kg] + beta_fm = sqrt(Pi * Boltzmann * T(x,j) + / (rho_soot * 2.0)) / m_rho[j]; + // Dimer collision frequency [m6/s/kg] + beta_dimer = eps_nucl * beta_fm * sqrt(2.0 / V_dimer) + * pow (2.0 * pow(6.0 * V_dimer / Pi, 1.0 / 3.0), 2.0); + // // Dimer particle density [1/m3] + // N_dimer = sqrt((r_dimer / beta_dimer)); + // // Source term for nucleation [m3/kg/s] + // m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer, 2.0); + + // Dimer diameter [m] + double d_dimer = 2.0 * pow(3.0 * V_dimer / (4.0 * Pi), 1.0/3.0); + // Dimer mass [kg] + double m_dimer = V_dimer * rho_soot; + // Reaction rate constant [m3/kmol/s] + // k_nuc = beta_dimer * m_rho[j] * Avogadro / 2 + double k_nuc = eps_nucl * Avogadro * pow(d_dimer, 2.0) + * sqrt(4.0 * Pi * Boltzmann * T(x, j) / m_dimer); + // Dimer concentration (QSS Assumption) [kmol/m3] + double C_dimer = sqrt((r_dimer / Avogadro * m_rho[j]) / (2.0 * k_nuc)); + // Dimer number concentration [1/m3] + N_dimer = C_dimer * Avogadro; + // Nucleation reaction rate [kmol/m3/s] + double omega_nuc = k_nuc * pow(C_dimer, 2.0); + // Nucleation rate [m3/kg/s] + m_qdotNucleation[j] = omega_nuc * Avogadro * V_dimer / m_rho[j] * 2.0; + +} + +void StFlow::sootCondensation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute condensation source term and corrects + // nucleation source term + //---------------------------------------------------- + + double kCond = 0; + double interval, vmoy, term1, term2, term3; + vector beta_cond(m_nsoot,0.0); + for (size_t k = 0; k < m_nsoot; k++){ + // Condensation collision kernel[m6/s/kg] + beta_cond[k] = eps_cond * beta_fm * sqrt(1.0/vSectMean[k]+1.0/V_dimer) + * pow(dSectCol[k] + pow(6.0 / Pi * V_dimer, 1.0/3.0), 2.0); + // Collisional frequency between a dimer and any soot particle [m3/s/kg] + kCond += beta_cond[k] * (q[k] * (vSectMax[k] - vSectMin[k]) / (vSectMean[k])); + } + // Correction of dimer density and nucleation source term + N_dimer = - (kCond / (2.0 * beta_dimer)) + + sqrt((r_dimer / beta_dimer) + + pow(kCond / (2.0 * beta_dimer),2.0)); + // Nucleation source term [m3/kg/1] + m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer,2.0); + + // Condensation source terms + for (size_t k = 0; k < m_nsoot; k++){ + interval = (vSectMax[k] - V_dimer) - vSectMin[k]; + vmoy = ((vSectMax[k] - V_dimer) + vSectMin[k]) / 2; + term1 = N_dimer * beta_cond[k] * q[k] / vmoy * V_dimer * interval; + if ( k==0 ){ + term2 = 0.0; + term3 = 0.0; + }else{ + interval = vSectMax[k-1] - (vSectMax[k-1] - V_dimer); + vmoy = (vSectMax[k-1] + (vSectMax[k-1] - V_dimer)) / 2; + term2 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * V_dimer * interval; + term3 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * vmoy * interval; + } + m_qdotCondensation(k,j) = term1 + term2 + term3; + if ( k>0 ){ + m_qdotCondensation(k-1,j) -= term3; + } + } +} + + +void StFlow::sootCoagulation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute coagulation source terms + //---------------------------------------------------- + + for (size_t k = 0; k < m_nsoot; k++){ + m_qdotCoagulation(k,j) = 0.0; + } + // Viscosity (Cantera) [Pa.s-1] [CLEAN BUT SLOW] + // setGas(x,j); + // double visc = m_trans->viscosity(); + // Viscosity (Sutherland, air) [Pa.s-1] [TRASH BUT QUICK] + double visc = Csut1 * pow(T(x,j),1.5) / (T(x,j) + Csut2); + // Mean free path [m] + double mfp_rod = Boltzmann * T(x,j) / (sqrt(2.0) * Pi * pow(d_gaz,2.0) * m_press); + double mfp_tha = 66.4e-7 * (101325. / m_press) * (T(x,j) / 293.) * (1. + 110./293.) / (1 + 110. / T(x,j)); + double beta_coag_lk = 0.0; + for (size_t k = 0; k < m_nsoot; k++){ + for (size_t l = k; l < m_nsoot; l++){ + if (m_collision_model == "rodrigues" || m_collision_model == "sphere"){ + //Cunnningham numbers [-] + double Cu_k = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[k]; + double Cu_l = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[l]; + // Coagulation rate in continuous regime [m^6.kg^(-1).s-(-1)] + double beta_cont_lk = (2.0 * Boltzmann * T(x,j)) / (3.0 * visc) + * (dSectCol[l] + dSectCol[k]) + * (Cu_l / dSectCol[l] + Cu_k / dSectCol[k]) + / m_rho[j]; + // Coagulation rate in free molecular regime [m^6.kg^(-1).s-(-1)] + double beta_fm_lk = eps_coag * beta_fm + * sqrt(1 / vSectMean[k] + 1 / vSectMean[l]) + * pow(dSectCol[k] + dSectCol[l], 2.0); + // Overall coagulation rate [m^6.kg^(-1).s-(-1)] + beta_coag_lk = (beta_fm_lk * beta_cont_lk) + / (beta_fm_lk + beta_cont_lk); + }else if (m_collision_model == "thajudeen"){ + double reduced_mass = rho_soot * vSectMean[k] * vSectMean[l] / (vSectMean[k] + vSectMean[l]); + double smoluchowski_radius = rNucMean[k] * (1.203 - (0.4315*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])) * pow(rSectCol[k]/rNucMean[k] + rSectCol[l]/rNucMean[k], 0.8806 + (0.3497*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])); + double kn_diff_k = mfp_tha * Pi * rSectCol[k] / aSectCol[k]; + double kn_diff_l = mfp_tha * Pi * rSectCol[l] / aSectCol[l]; + double f_k = (6.0 * Pi * rSectCol[k] * visc) / (1 + kn_diff_k * (1.257 + 0.4 * exp(-1.1/kn_diff_k))); + double f_l = (6.0 * Pi * rSectCol[l] * visc) / (1 + kn_diff_l * (1.257 + 0.4 * exp(-1.1/kn_diff_l))); + double friction_coefficient = f_k * f_l / (f_k + f_l); + double projected_area = pow(smoluchowski_radius, 2.0) * Pi; + double kn_diff = (sqrt(Boltzmann * T(x,j) * reduced_mass) * Pi * smoluchowski_radius) / (friction_coefficient * projected_area); + double H = (4.0 * Pi * pow(kn_diff, 2.0) + 25.836 * pow(kn_diff, 3.0) + eps_coag * sqrt(8.0 * Pi) * 11.211 * pow(kn_diff, 4.0)) / (1 + 3.502 * kn_diff + 7.211 * pow(kn_diff, 2.0) + 11.211 * pow(kn_diff, 3.0)); + beta_coag_lk = (H * friction_coefficient * pow(projected_area, 2.0)) / (reduced_mass * pow(Pi, 2.0) * smoluchowski_radius) / m_rho[j]; + } + // Section of the particle corresponding to the coagulation of (l,k)y + size_t m = collision_mat(k,l); + // Loss of mass in section l due to coagulation with k + double terml = beta_coag_lk * q[l] * q[k] / vSectMean[k] + * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); + // Loss of mass in section k due to coagulation with l + double termk = beta_coag_lk * q[l] * q[k] / vSectMean[l] + * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); + double termm, termmplus; + // Gain in mass in m and m+1 thanks to coagulation of (l,k) + if (vSectMax[l] + vSectMax[k] <= vSectMax[m]){ + termm = terml + termk; + termmplus = 0.0; + }else{ + termm = (terml + termk) + * (vSectMax[m] - (vSectMin[k] + vSectMin[l])) + / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); + termmplus = (terml + termk) + * (vSectMax[k]+vSectMax[l]-vSectMax[m]) + / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); + } + if (m < m_nsoot-1){ + m_qdotCoagulation(m+1,j) += termmplus; + }else{ + termm = terml + termk; + } + m_qdotCoagulation(m,j) += termm; + m_qdotCoagulation(l,j) -= terml; + m_qdotCoagulation(k,j) -= termk; + } + } +} + +void StFlow::updateSootDiffFluxes(const double* x, size_t j0, size_t j1) +{ + //---------------------------------------------------- + // Computes soot molecular and thermal diffusion fluxes + //---------------------------------------------------- + for (size_t j = j0; j < j1; j++) { + // Evaluate gas at midpoints : j->j+1/2 + double Tmid = 0.5 * (T(x,j)+T(x,j+1)); + // [CLEAN BUT SLOW] + // setGasAtMidpoint(x,j); + // double wtm = m_thermo->meanMolecularWeight(); + // double rho = m_thermo->density(); + // double visco = m_trans->viscosity(); + // [TRASH BUT QUICK] + double wtm = 0.5*(m_wtm[j]+m_wtm[j+1]); + double rho = 0.5*(m_rho[j]+m_rho[j+1]); + double visco = Csut1 * pow(Tmid,1.5) / (Tmid + Csut2); + // Evaluate centered differencies at j+1/2 + double dT = T(x,j+1)-T(x,j); + double dz = z(j+1) - z(j); + // Evaluate viscosity + for (size_t k = 0; k < m_nsoot; k++){ + // Evaluate soot mass fraction at j+1/2 + + double Ysmid = 0.5 * (Ys(x,k,j)+Ys(x,k,j+1)); + // Evaluate centered differencies at j+1/2 + double dYs = Ys(x,k,j+1) - Ys(x,k,j); + //Evaluate diffusion coefficient at j+1/2 + double Ds = 3 / (2 * rho_soot * pow(dSectMean[k], 2.0) + * (1 + alphaT * Pi / 8)) + * sqrt ((wtm*Boltzmann*Tmid)/(2*Pi*Avogadro)); + // Evaluate soot mass diffusion flux at j+1/2 + m_soot_diff(k,j) = rho * Ds * dYs/dz; + // Evaluate soot mass soret flux at j+1/2 + if (m_do_soot_soret){ + m_soot_soret(k,j) = C_soot_soret * visco * Ysmid * dT/dz / Tmid; + } + } + } +} + +void StFlow::sootSurface(const double* x, size_t j){ + //---------------------------------------------------- + // Compute surface chemistry source terms + //---------------------------------------------------- + + // Computes reaction rates + sootSurfaceInitialization(x,j); + double term1, term2, term3; + //--------------- + // SURFACE GROWTH + //--------------- + if (m_do_sg){ + for (size_t k = 0; k < m_nsoot; k++){ + term1 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] + * (vmaxmc2_mpower[k] - vmin_mpower[k]); + if (k==0){ + term2 = 0.0; + term3 = 0.0; + }else{ + term2 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k-1] / mpower[k-1] * q[k-1] + * (vmax_mpower[k-1] - vmaxmc2_mpower[k-1]); + term3 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powermvect[k-1] / kpower[k-1] * q[k-1] + * (vmax_kpower[k-1] - vmaxmc2_kpower[k-1]); + } + // Surface growth source term [m3/kg/s] + m_qdotSg(k,j) = term1 + term2 + term3; + if (k > 0){m_qdotSg(k-1,j) -= term3;} + } + } + //---------- + // OXYDATION + //---------- + if (m_do_oxidation){ + for (size_t k=m_nsoot; k --> 0;){ + term1 = alpha_surf * kox / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] + * (vmax_mpower[k] - vminpc2_mpower[k]); + if (k==m_nsoot-1){ + term2 = 0.0; + term3 = 0.0; + }else if (k==m_nsoot-2 && m_trash_section) { + term2 = 0.0; + term3 = 0.0; + }else{ + term2 = alpha_surf * kox / m_rho[j] * vc2powervect[k+1] / mpower[k+1] * q[k+1] + * (vminpc2_mpower[k+1] - vmin_mpower[k+1]); + term3 = alpha_surf * kox / m_rho[j] * vc2powermvect[k+1] / kpower[k+1] * q[k+1] + * (vminpc2_kpower[k+1] - vmin_kpower[k+1]); + } + // Oxidation source term [m3/kg/s] + m_qdotOxidation(k,j) = - (term1 + term2 - term3); + if (k < m_nsoot - 1){ + m_qdotOxidation(k+1,j) -= term3; + } + } + } +} + +void StFlow::sootSurfaceInitialization(const double* x, size_t j){ + // Recover species concentrations [kmol/m3] + double conc_H = 0, conc_H2 = 0, conc_OH = 0, conc_H2O = 0, conc_C2H2 = 0, conc_O2 = 0; + double k01f = 0, k01b = 0, k02f = 0, k02b = 0, k03f = 0, k03b = 0, k04f = 0, k04b = 0; + double k05f = 0, k05b = 0, k06f = 0, k06bisf = 0; + double r01f = 0, r01b = 0, r02f = 0, r02b = 0, r03f = 0, r03b = 0, r04f = 0, r04b = 0; + double r05f = 0, r05b = 0, r06f = 0, r06bisf = 0, r07f = 0; + double ko2, koh, kd, krev, chi, chip, chic, alpha_kazakov; + size_t k; + // Recover molar concentrations + k = m_thermo->speciesIndex("H"); + if (k != npos){conc_H = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("H2"); + if (k != npos){conc_H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){conc_H2O = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){conc_C2H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("O2"); + if (k != npos){conc_O2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("OH"); + if (k != npos){conc_OH = Y(x,k,j) * m_rho[j] / m_wt[k];} + // SI units + double slt = 1.0e3 / GasConstant / T(x,j); // 1e3 because GasConstant in J/kmol/K + double T_log=log(T(x,j)); + if (m_haca_model == 1 || m_haca_model == 11){ //Mauss + // Arrhenius constants + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); // [m3/kmol/s] + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); // [m3/kmol/s] + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); // [m3/kmol/s] + k02b = ak02b * exp(nk02b*T_log - ek02b*slt); // [m3/kmol/s] + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [m3/kmol/s] + k03b = ak03b * exp(nk03b*T_log - ek03b*slt); // [1/s] + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); // [m3/kmol/s] + k04b = ak04b * exp(nk04b*T_log - ek04b*slt); // [1/s] + k05f = ak05f * exp(nk05f*T_log - ek05f*slt); // [1/s] + k05b = ak05b * exp(nk05b*T_log - ek05b*slt); // [m3/kmol/s] + k06f = ak06f * exp(nk06f*T_log - ek06f*slt); // [m3/kmol/s] + k06bisf = k06f; + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_OH; + r02b = k02b * conc_H2O; + r03f = k03f * conc_H; + r03b = k03b; + r04f = k04f * conc_C2H2; + r04b = k04b; + r05f = k05f; + r05b = k05b * conc_H; + r06f = k06f * conc_O2; + r06bisf = k06bisf * conc_O2; + r07f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + double fk10 = r05f / (r04b+r06bisf+r05f); + double A_QSS = (r01f + r02f + r03b + r07f + r05b * (1.0 - fk10)) / (r01b + r02b + r03f + r04f * fk10); + double B_QSS = r04f / ( r04b + r06bisf + r05f); + double D_QSS = r05b / (r04b + r06f + r05f); + + chi = 1.0; + chip = chi * A_QSS; + chic = chi * (A_QSS*B_QSS + D_QSS); + // Partial reaction rates[1/s] + koh = r07f * chi; + kd = r04f * chip; + ko2 = r06f * (chip + chic); + krev = r04b * chic; + // Partial surface growth and oxidation rates [1/s] + ksg = kd - krev; + kox = ko2 + koh; + } else if (m_haca_model == 2){ //Blanquart + // Arrhenius constants [m3/kmol/s] + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); + k02b = ak02b * exp(nk02b*T_log - ek02b*slt); + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [1/s] + k03b = ak03b * exp(nk03b*T_log - ek03b*slt); + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); + k05f = ak05f * exp(nk05f*T_log - ek05f*slt); + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_OH; + r02b = k02b * conc_H2O; + r03f = k03f; + r03b = k03b * conc_H; + r04f = k04f * conc_C2H2; + r05f = k05f * conc_O2; + r06f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + chi = (r01f + r02f + r03f) / (r01b + r02b + r03b + r04f + r05f); // * 1.7e15; + // Oxidation O2 [must be 1/s] + ko2 = chi * r05f; + // Oxidation OH [1/s] + koh = r06f * chi; + // Oxidation + kox = ko2 + koh; + // Surface growth [1/s] + ksg = chi * r04f; + } else if (m_haca_model == 3){ //Kazakov + // Fraction of sites available at the surface of the particle for reaction [-] + alpha_kazakov = (1.0 + tanh(8.168e3/kazakovTad - 4.57)) / 2.0; + // Arrhenius constants [m3/kmol/s] + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_H; + r03f = k03f * conc_C2H2; + r04f = k04f * conc_O2; + r05f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + chi = r01f / (r01b + r02f + r03f + r04f); // * 2.3e14 + // Oxidation O2 [1/s] + ko2 = alpha_kazakov * chi * r04f; + // Oxidation OH [1/s] + koh = r05f * chi; + //Oxidation [1/s] + kox = ko2 + koh; + // Surface growth [1/s] + ksg = alpha_kazakov * chi * r03f; + } + //------------------------- + // RETROACTION ON GAS PHASE + //------------------------- + if (m_do_retroaction){ + double deltaQ = 0.0, soot_surface = 0.0; + for (size_t k = 0; k < m_nsoot; k++){ + deltaQ += vc2powervect[k] / mpower[k] * q[k] * (vmax_mpower[k]-vmin_mpower[k]); + } + //Overall active sites concentration [kmol/m3] + soot_surface = alpha_surf * n_sites * deltaQ / (V_C2 * Avogadro); // n_sites added here + // Surface chemistry reaction rates [kmol/s/m3] + double w01f = 0, w01b = 0, w02f = 0, w02b = 0, w03f = 0, w03b = 0; + double w04f = 0, w04b = 0, w05f = 0, w05b = 0, w06f = 0, w06bisf = 0; + double w07f = 0; + if (m_do_sg || m_do_oxidation){ + // Reaction rates for reactions occuring on both oxidation & surface growth + if (m_haca_model == 1){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chip; + w02f = r02f * soot_surface * chi; + w02b = r02b * soot_surface * chip; + w03f = r03f * soot_surface * chip; + w03b = r03b * soot_surface * chi; + w05f = r05f * soot_surface * chic; + w05b = r05b * soot_surface * chi; + w06bisf = r06bisf * soot_surface * chic; + }else if (m_haca_model == 2){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chi; + w02f = r02f * soot_surface * chi; + w02b = r02b * soot_surface * chi; + w03f = r03f * soot_surface * chi; + w03b = r03b * soot_surface * chi; + }else if (m_haca_model == 3){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chi; + w02f = r02f * soot_surface * chi; + } + } + // Reaction rates for reactions occuring on surfacce growth only + if (m_do_sg){ + if (m_haca_model == 1){ + w04f = r04f * soot_surface * chip; + w04b = r04b * soot_surface * chic; + }else if (m_haca_model == 2){ + w04f = r04f * soot_surface * chi; + }else if (m_haca_model == 3){ + w03f = r03f * soot_surface * chi; + } + } + // Reaction rates for reactions occuring on oxidation only + if (m_do_oxidation){ + if (m_haca_model == 1){ + // Reaction rates [kmol/m3/s] + w06f = r06f * soot_surface * chip; + w07f = r07f * soot_surface * chi; + }else if (m_haca_model == 2){ + w05f = r05f * soot_surface * chi; + w06f = r06f * soot_surface * chi; + }else if (m_haca_model == 3){ + w04f = r04f * soot_surface * chi; + w05f = r05f * soot_surface * chi; + } + } + + // Gaseous species consumption [kmol/s/m3] + if (m_haca_model == 1){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption[k] = - (w01f - w01b) - (w03f - w03b) + (w05f - w05b);} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption[k] = (w04f - w04b);} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption[k] = (w01f - w01b);} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption[k] = - w06f - w06bisf;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption[k] = 2.0 * w06f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption[k] = - (w02f - w02b) - w07f;} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){sootConsumption[k] = + (w02f - w02b);} + k = m_thermo->speciesIndex("HCO"); + if (k != npos){sootConsumption[k] = 2.0 * w06bisf + w07f;} + k = m_thermo->speciesIndex("CH"); + if (k != npos){sootConsumption[k] = w07f;} + }else if (m_haca_model == 2){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption[k] = -(w01f-w01b) + (w03f-w03b) + w04f;} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption[k] = -w04f;} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption[k] = (w01f-w01b) + w05f + w06f;} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption[k] = -w05f;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption[k] = 2.0 * w05f + w06f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption[k] = -(w02f-w02b) - w06f;} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){sootConsumption[k] = (w02f-w02b);} + }else if (m_haca_model == 3){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption[k] = -(w01f-w01b) - w02f + w03f;} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption[k] = -w03f;} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption[k] = (w01f-w01b) + w05f;} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption[k] = -w04f;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption[k] = 2.0 * w04f + w05f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption[k] = - w05f;} + } + } +} + +void StFlow::getDistributionOrdre0(const double* x, size_t j){ + for (size_t k = 0; k < m_nsoot; k++){ + // Soot volume fraction density [1/m3] + q[k] = m_rho[j] * Ys(x,k,j) / (rho_soot * (vSectMax[k] - vSectMin[k])); + } +} +//-----------------------------// +// END OF SOOT RELATED METHODS // +//-----------------------------// + void StFlow::evalRightBoundary(double* x, double* rsd, int* diag, double rdt) { size_t j = m_points - 1; + AVBPcompute_local_thick(x,j); + double thick_prev = avbp_thick[j-1]; // the boundary object connected to the right of this one may modify or // replace these equations. The default boundary conditions are zero u, V, @@ -257,9 +2224,17 @@ void StFlow::evalRightBoundary(double* x, double* rsd, int* diag, double rdt) double sum = 0.0; // set residual of poisson's equ to zero rsd[index(c_offset_E, j)] = x[index(c_offset_E, j)]; + if (m_nsoot > 0){ + for (size_t k = 0; k < m_nsoot; k++){ + if (m_do_retroaction){sum += Ys(x,k,j);} + rsd[index(c_offset_S + k, j)] = + m_soot_diff(k,j-1) + rho_u(x,j)*Ys(x,k,j); + } + } for (size_t k = 0; k < m_nsp; k++) { sum += Y(x,k,j); - rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); + rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1)*thick_prev + rho_u(x,j)*Y(x,k,j); +// no thick rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); } rsd[index(c_offset_Y + rightExcessSpecies(), j)] = 1.0 - sum; diag[index(c_offset_Y + rightExcessSpecies(), j)] = 0; diff --git a/src/oneD/refine.cpp b/src/oneD/refine.cpp index 5364e7e25e3..92bbe552530 100644 --- a/src/oneD/refine.cpp +++ b/src/oneD/refine.cpp @@ -257,4 +257,421 @@ int Refiner::getNewGrid(int n, const double* z, int nn, double* zn) zn[jn] = z[n-1]; return 0; } + + +double Refiner::remeshFromSolution(int np, const doublereal* z, const doublereal* x, const double dist_min, const double domain_size) //from MUTAGEN +// int np; : number of points in the old mesh +// double* z : array of the old mesh points +// double* x : array of variables on the old mesh +{ + + double distance; + + if (m_domain->nPoints() == 1) + { + m_z_new.clear(); + m_z_new.push_back(z[0]); + distance=0.0; + return distance; + } + + if (m_domain->nPoints() <= 0) + { + distance=0.0; + return distance; + } + + // a few defintions + double z_start = z[0]; + double z_end = z[np-1]; + + // compute w_old + // [w_old] = [m^-1] + vector w_old(np-1); + for (int i=0;iz[i+1]-z[i]) + { + dz_min = z[i+1]-z[i]; + z_center = z[i]; + } + } + + // init w1 with a very small (but non-zero) value + // [w1] = [m^-1] + vector w1(np-1); + for (int i=0;i vn(np); + vector gn(np); + vector gc(np-1); + vector cc(np-1); + // loop over active components + for (int icomp=0;icomp m_min_range*vv) + { + // compute w1 for gradient + for (int i=0;i m_min_range*gg) + { + // compute w1 for curvature + for (int i=0;i w2(np-1); + // first, copy w1 in w2 + copy(w1.begin(),w1.end(),w2.begin()); + // parameters + double bndr = m_ratio; + double bndq = 2.0*log10(bndr); + for (int i=0;i w3(np-1); + double rwidth = 5.0; // parameter for the gaussian width + double alpha = 2.5; // the integration interval is [-alpha.sigma;+alpha.sigma] + int nint = 100; // half the number of integration intervals + double w2_max = *max_element(w2.begin(), w2.end()); // max value of w2 + double sigma = rwidth/w2_max; // width of the gaussian [m] + double gintg = sigma*sqrt(Pi); // integral of the gaussian [m] + double dz_int = alpha*sigma/static_cast(nint); // integration step size [m] + for (int i=0;i(j)+0.5)*dz_int; + double zc = 0.5*(z[i+1]+z[i ]); + double zint = zc+c; + double f; + // value at zc+c + if (zint<=z_start) + { + f = 0.0; + } + else if (zint>=z_end) + { + f = 0.0; + } + else + { + int i1=indxtp(np,zint,z); + f = w2[i1]; + } + // convolution product + f = f * exp(-c*c/(sigma*sigma)); + // integration and normalization + w3[i] = w3[i] + f*dz_int/gintg; + } + } + + // compute distance between the two meshes + distance=0.0; + for (int i=0;i w4(np); + w4[0] = 0.0; + for (int i=0;i(1.0+w4_last + 0.5); + + // final remeshing + m_z_new.clear(); + for (int i_new=0;i_new(i_new); + int i = indxtp(np,w,&w4[0]); + double slope = (z[i+1] -z[i])/(w4[i+1]-w4[i]); + double dz = slope*(w-w4[i]); + double z_add = z[i] + dz; + if (z_add<=z_center+domain_size) + { + m_z_new.push_back(z_add); + } + } + + // New size + np_new = m_z_new.size(); + + // Add points if necessary + bool done=false; + if (m_z_new[np_new-1]>=z_center+domain_size) + { + done = true; + } + while(!done) + { + double ratio_last = (m_z_new[np_new-1] - m_z_new[np_new-2])/(m_z_new[np_new-2] - m_z_new[np_new-3]); + double z_add = m_z_new[np_new-1] + ratio_last*(m_z_new[np_new-1] - m_z_new[np_new-2]); + m_z_new.push_back(z_add); + np_new++; + if (m_z_new[np_new-1]>=z_center+domain_size) + { + done = true; + } + } + +/* DO NOTHING... + m_z_new.clear(); + for (int i=0;inPoints() == 1) + { + return; + } + + if (m_domain->nPoints() <= 0) + { + return; + } + + // get gradient and curvature criterions in w1 + vector vn(np); + vector gn(np); + vector gc(np-1); + vector cc(np-1); + vector grad_max(np-1); + vector curve_max(np-1); + // loop over active components + for (int icomp=0;icomp m_min_range*vv) + { + // compute w1 for gradient + for (int i=0;i m_min_range*gg) + { + // compute w1 for curvature + for (int i=0;i +bool has_key(const M& m, int j) { + if (m.find(j) != m.end()) return true; + return false; +} + +static void r_drawline() { + string s(78,'#'); + s += '\n'; + writelog(s.c_str()); +} + +/** + * Return the square root of machine precision. + */ +static doublereal eps() { + doublereal e = 1.0; + while (1.0 + e != 1.0) e *= 0.5; + return sqrt(e); +} + } diff --git a/src/transport/AVBPTransport.cpp b/src/transport/AVBPTransport.cpp new file mode 100644 index 00000000000..509345c859c --- /dev/null +++ b/src/transport/AVBPTransport.cpp @@ -0,0 +1,278 @@ +/** + * @file AVBPTransport.cpp + * Simplified AVBP transport properties for ideal gas mixtures. + */ + +/* $Author: B. Franzelli (v. 1.7) $ + * $Revision: A. Felden (v 2.1-2.3) $ + * $Date: 01/2018 $ + */ + +#include "cantera/transport/AVBPTransport.h" +#include "cantera/thermo/ThermoPhase.h" +#include "cantera/base/stringUtils.h" +#include "cantera/base/utilities.h" +#include "cantera/base/Parser.h" + +#include +#include +#include +#include +#include +#include + +using namespace std; + +namespace Cantera +{ + +// AVBPTransport::AVBPTransport() : +// m_lambda(0.0) +// { +// } + +void AVBPTransport::init(ThermoPhase* thermo, int mode, int log_level) +{ + + GasTransport::init(thermo, mode, log_level); + + ifstream avbp_mixturedb("mixture_database.dat"); + + if (avbp_mixturedb.good()){ + //cout << thermo->name() << thermo->id() << endl; + //std::string mixture_id; + //mixture_id = thermo->name(); + //cout<<"INFO: using simplified transport data for "<< m_thermo->name()<<" from the 'mixture_database.dat' file."<0){ +// cout<<"-Exponent for Second Sutherland Constant: "<cp_mass(); + m_density = m_thermo->density(); + if(avbp_beta<0){ + double avbp_absbeta; + avbp_absbeta = - avbp_beta; + m_viscmix = avbp_mu0 * pow(m_temp/avbp_T0,avbp_absbeta); + } + else if(avbp_beta>0){ + double coeff; + coeff= (avbp_T0 + avbp_beta) / pow(avbp_T0,1.5); + m_viscmix = avbp_mu0 * coeff * pow(m_temp, 1.5) / (m_temp + avbp_beta); + } + else{ + m_viscmix = avbp_mu0; + } + m_lambda = m_viscmix * m_cp / avbp_Prandtl; +} + + +double AVBPTransport::viscosity() +{ + update_T(); + update_C(); + + double vismix = 0.0; + + // AVBP Transport Properties + if(avbp_beta<0){ + double avbp_absbeta; + avbp_absbeta = - avbp_beta; + vismix = avbp_mu0 * pow(m_temp/avbp_T0,avbp_absbeta); + } + else if(avbp_beta>0){ + double coeff; + coeff= (avbp_T0 + avbp_beta) / pow(avbp_T0,1.5); + vismix = avbp_mu0 * coeff * pow(m_temp, 1.5) / (m_temp + avbp_beta); + } + else{ + vismix = avbp_mu0; + } + + m_viscmix = vismix; + return m_viscmix; +} + + +double AVBPTransport::thermalConductivity() +{ + update_T(); + update_C(); + + double m_cp = 0.0; + double m_vismix = 0.0; + m_cp = m_thermo->cp_mass(); + + if(avbp_beta<0){ + double avbp_absbeta; + avbp_absbeta = - avbp_beta; + m_vismix = avbp_mu0 * pow(m_temp/avbp_T0,avbp_absbeta); + }else if(avbp_beta>0){ + double coeff; + coeff = (avbp_T0 + avbp_beta) / pow(avbp_T0,1.5); + m_vismix = avbp_mu0 * coeff * pow (m_temp, 1.5) / (m_temp + avbp_beta); + }else{ + m_vismix = avbp_mu0; + } + + m_lambda = m_vismix * m_cp / avbp_Prandtl; + return m_lambda; +} + + +void AVBPTransport::getMixDiffCoeffs(double* const d) +{ + update_T(); + update_C(); + + double m_cp = 0.0; + double m_density = 0.0; + m_cp = m_thermo->cp_mass(); + m_density = m_thermo->density(); + + double m_vismix = 0.0; + if(avbp_beta<0){ + double avbp_absbeta; + avbp_absbeta = - avbp_beta; + m_vismix = avbp_mu0 * pow(m_temp/avbp_T0,avbp_absbeta); + }else if(avbp_beta>0){ + double coeff; + coeff = (avbp_T0 + avbp_beta) / pow(avbp_T0,1.5); + m_vismix = avbp_mu0 * coeff * pow(m_temp,1.5)/ (m_temp + avbp_beta); + }else{ + m_vismix = avbp_mu0; + } + + for (size_t k=0; ktemperature(); + if (t == m_temp && m_nsp == m_thermo->nSpecies()) { + return; + } + if (t <= 0.0) { + throw CanteraError("AVBPTransport::update_T", + "negative temperature {}", t); + } + + GasTransport::update_T(); + +} + +void AVBPTransport::update_C() +{ + // signal that concentration-dependent quantities will need to + // be recomputed before use, and update the local mole + // fractions. + + m_thermo->getMoleFractions(m_molefracs.data()); + + // add an offset to avoid a pure species condition + for (size_t k = 0; k < m_nsp; k++) { + m_molefracs[k] = std::max(Tiny, m_molefracs[k]); + } +} + + +/** + * Parse the specific mixture_param.dat input file of + * AVBP v7 ++. Use the Parser.cpp located in ../base + */ +void AVBPTransport::read_mixture(std::string inputfile) +{ + Parser parser; + Param* param; + + parser.parseFile(inputfile); + // Get number of mixtures in database + size_t n_mixtures = parser.nbParamOccurence("mixture_name"); + size_t idx_beg = std::string::npos; + size_t idx_end = std::string::npos; + // Loop through all occurences of keyword "mixture name" + for (size_t i=0; i< n_mixtures; ++i) { + param = parser.getParam("mixture_name",i); + std::string current_str = param->readString(0); + // Check if mixture_name is the one requested in the cti file + if ( current_str == m_thermo->name() ) { + // Store bounding idx to get important info + idx_beg = parser.getParamNumber("mixture_name",i); + idx_end = parser.getParamNumber("mixture_name",i+1); + } + } + // Get an error if requested mixture does not match any entry in database + if (idx_beg == idx_end) { + cout<<"FATAL ERROR: cannot find the requested mixture in the 'mixture_database.dat' file.\n \ + Make sure that the name of your gas instance in the Cantera mechanism (.cti/.xml) file matches that provided in the 'mixture_database.dat'."<readDouble(0); + // SCH LE + param = parser.getParam("species_Schmidt_number", idx_beg, idx_end); + avbp_Le.resize(m_nsp); + avbp_Sch.resize(m_nsp); + for (size_t i=0; ireadDouble(i); + avbp_Le[i]= avbp_Sch[i] / avbp_Prandtl; + } + // VISCO + param = parser.getParam("mu_ref", idx_beg, idx_end); + avbp_mu0 = param->readDouble(0); + param = parser.getParam("T_ref", idx_beg, idx_end); + avbp_T0 = param->readDouble(0); + param = parser.getParam("viscosity_law_coeff", idx_beg, idx_end); + avbp_beta = param->readDouble(0); + param = parser.getParam("viscosity_law", idx_beg, idx_end); + avbp_law = param->readString(0); + if (avbp_law == "power") { + avbp_beta = - avbp_beta; + } +} + +double AVBPTransport::pressure_ig() +{ + return (m_thermo->molarDensity() * GasConstant * + m_thermo->temperature()); + +} + +} \ No newline at end of file diff --git a/src/transport/TransportFactory.cpp b/src/transport/TransportFactory.cpp index f721ca08e08..2e47e00beaa 100644 --- a/src/transport/TransportFactory.cpp +++ b/src/transport/TransportFactory.cpp @@ -4,6 +4,7 @@ // at https://cantera.org/license.txt for license and copyright information. // known transport models +#include "cantera/transport/AVBPTransport.h" #include "cantera/transport/MultiTransport.h" #include "cantera/transport/MixTransport.h" #include "cantera/transport/UnityLewisTransport.h" @@ -36,6 +37,11 @@ TransportFactory::TransportFactory() addDeprecatedAlias("mixture-averaged", "Mix"); reg("mixture-averaged-CK", []() { return new MixTransport(); }); addDeprecatedAlias("mixture-averaged-CK", "CK_Mix"); + + reg("AVBP", []() { return new AVBPTransport(); }); + reg("AVBP-CK", []() { return new AVBPTransport(); }); + addDeprecatedAlias("AVBP", "CK_AVBP"); + reg("multicomponent", []() { return new MultiTransport(); }); addDeprecatedAlias("multicomponent", "Multi"); reg("multicomponent-CK", []() { return new MultiTransport(); }); @@ -48,6 +54,7 @@ TransportFactory::TransportFactory() addDeprecatedAlias("high-pressure", "HighP"); m_CK_mode["CK_Mix"] = m_CK_mode["mixture-averaged-CK"] = true; m_CK_mode["CK_Multi"] = m_CK_mode["multicomponent-CK"] = true; + m_CK_mode["CK_AVBP"] = m_CK_mode["AVBP-CK"] = true; } TransportFactory* TransportFactory::factory() { From 399bdcbd669462ef464d60dc3cc7f84f34a954f7 Mon Sep 17 00:00:00 2001 From: pestre Date: Wed, 5 Mar 2025 23:38:58 +0100 Subject: [PATCH 22/98] Merge differences in test directory Committer: pestre On branch WIP/Merge_cantera-avbp Changes to be committed: modified: test/clib/test_ctonedim.cpp new file: test/data/surface2-gas.inp new file: test/data/surface2-thermo.dat new file: test/data/surface2.inp modified: test/oneD/test_oneD.cpp Author: pestre interactive rebase in progress; onto 7aec821a8 Last commands done (7 commands done): pick 68a09c47e Merge differences in src directory pick f298a7d4e Merge differences in test directory Next commands to do (7 remaining commands): pick e118cf6c4 Merge differences for other files pick b0f7cbc5e Add missing part needed for compile_fortran import You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. Changes to be committed: modified: test/clib/test_ctonedim.cpp modified: test/data/surface2.inp modified: test/oneD/test_oneD.cpp --- test/clib/test_ctonedim.cpp | 4 ++-- test/data/surface2.inp | 2 +- test/oneD/test_oneD.cpp | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/test/clib/test_ctonedim.cpp b/test/clib/test_ctonedim.cpp index 24407c6e588..c8969b9df64 100644 --- a/test/clib/test_ctonedim.cpp +++ b/test/clib/test_ctonedim.cpp @@ -232,8 +232,8 @@ TEST(ctonedim, freeflame_from_parts) sim1D_setFixedTemperature(flame, 0.85 * T + .15 * Tad); // solve and save - flow1D_solveEnergyEqn(flow, 1); - bool refine_grid = false; + stflow_solveEnergyEqn(flow, 1); + const char* refine_grid = "disabled"; int loglevel = 0; sim1D_solve(flame, loglevel, refine_grid); ret = sim1D_save(flame, "gtest-freeflame.yaml", "clib", diff --git a/test/data/surface2.inp b/test/data/surface2.inp index 2f86a724ad2..706f24a97a3 100644 --- a/test/data/surface2.inp +++ b/test/data/surface2.inp @@ -1,6 +1,6 @@ SITE/PT_SURFACE/ SDEN/2.72E-9/ _Pt_ H_Pt O2_Pt/3/ H2O_Pt OH_Pt O_Pt - +END REACTIONS JOULES/MOLE MWON H2 + 2_Pt_ => 2H_Pt 4.4579E+10 0.5 0.0 diff --git a/test/oneD/test_oneD.cpp b/test/oneD/test_oneD.cpp index 02194ab6885..df838747e70 100644 --- a/test/oneD/test_oneD.cpp +++ b/test/oneD/test_oneD.cpp @@ -85,7 +85,7 @@ TEST(onedim, freeflame) // solve flow->solveEnergyEqn(); - bool refine_grid = false; + string refine_grid = "disabled"; int loglevel = 0; flame.solve(loglevel, refine_grid); flame.save("gtest-freeflame.yaml", "cpp", "Solution from C++ interface", true); From 3d0dea8d4457c6c69cce2642f95e530da4ba382e Mon Sep 17 00:00:00 2001 From: Antoine Date: Thu, 6 Mar 2025 00:05:33 +0100 Subject: [PATCH 23/98] Merge differences for other files On branch WIP/Merge_cantera-avbp Changes to be committed: modified: .gitignore modified: README.rst modified: SConstruct new file: install_cantera.py new file: main.yaml new file: run_compil new file: run_compil_kraken Author: Antoine interactive rebase in progress; onto 7aec821a8 Last commands done (8 commands done): pick f298a7d4e Merge differences in test directory pick e118cf6c4 Merge differences for other files Next commands to do (6 remaining commands): pick b0f7cbc5e Add missing part needed for compile_fortran import pick 8058ffb5b Add test files to the gitignore You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. Changes to be committed: modified: .gitignore modified: README.rst new file: install_cantera.py new file: main.yaml new file: run_compil new file: run_compil_kraken --- .gitignore | 5 ++ README.rst | 114 +++++++++++++++++++++++++++++---- install_cantera.py | 154 +++++++++++++++++++++++++++++++++++++++++++++ main.yaml | 66 +++++++++++++++++++ run_compil | 5 ++ run_compil_kraken | 9 +++ 6 files changed, 341 insertions(+), 12 deletions(-) create mode 100644 install_cantera.py create mode 100644 main.yaml create mode 100755 run_compil create mode 100755 run_compil_kraken diff --git a/.gitignore b/.gitignore index 0793755a1a4..872f34ff27a 100644 --- a/.gitignore +++ b/.gitignore @@ -49,3 +49,8 @@ environment.y* coverage/ coverage.info .coverage +doc/sphinx/matlab/*.rst +!doc/sphinx/matlab/index.rst +reduced.yaml +INSTALL_DIR/ +*.code-workspace diff --git a/README.rst b/README.rst index 550ee8edb93..db422cfe85d 100644 --- a/README.rst +++ b/README.rst @@ -33,23 +33,113 @@ using the following MyBinder link: Installation ============ -|pip| |anaconda| |conda-forge| +To ensure a smooth installation, we highly recommend setting up Cantera within a virtual environment. +Follow the steps below for a **local** installation: -`Installation instructions for the current release of Cantera -`_ are available from the main `Cantera -documentation site `_. +0. Clone the Cantera repository:: -- The Python module can also be installed using pip on Windows, macOS, and Linux. + cd /Users/$USER/Documents + git clone https://nitrox.cerfacs.fr/cantera/cantera-avbp.git -- Conda packages containing the Cantera Python and Matlab modules are also available - for Windows, macOS, and Linux. +1. Create a virtual environment in your home directory:: -- Additional installation packages are provided for Windows, macOS, Ubuntu, Fedora, - RHEL, Gentoo, and FreeBSD. + cd $HOME + python3 -m venv env_cantera + source ~/env_cantera/bin/activate + +2. (optional) Create an alias to load ``env_cantera``:: + + echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.zshrc + source ~/.zshrc + +3. Navigate to the Cantera directory:: + + cd /Users/$USER/Documents/cantera-avbp + +4. Switch to the right branch and run the installation script:: + + git checkout 3.0 + python3 install_cantera.py + + +5. When prompted about NFS, answer ``no``. +6. Wait for the compilation and installation process to complete successfully. + +If everything goes well, you should see the following message:: + + ******************************************************************************** + To use this newly installed Cantera version, update your environment variables + by adding the following lines to your.bashrc (or equivalent): + + #cantera-avbp-3.0 + export PYTHONPATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH + export PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH + export PYTHON_CMD=/Users/$USER/canavbp3/bin/python3 + + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB=/Users/$USER/cantera-avbp/INSTALL_DIR/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + + #Required for MacOS: + export DYLD_LIBRARY_PATH=$CUSTOM_LIB + + DONT FORGET TO SOURCE YOUR .bashrc! + + ******************************************************************************** + + +Copy and paste the provided lines into your ``.zshrc`` or ``.bashrc`` file and **source it**. + +For **KRAKEN** users, use the following commands to install Cantera: + +1. Load the necessary modules:: + + module purge && module load python/3.9.5 + +2. Install ``ruamel.yaml`` package (not installed by default on KRAKEN):: + + pip3 install --user ruamel.yaml + +3. Create a virtual environment in your home folder and activate it:: + + cd $HOME + python3 -m venv --system-site-packages env_cantera + source ~/env_cantera/bin/activate + +4. (optional) Create an alias to load ``env_cantera``:: + + echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.bashrc + source ~/.bashrc + +5. Clone cantera-avbp repository (e.g. in your ``/scratch``), navigate to it and run the installation script:: + + git clone https://nitrox.cerfacs.fr/cantera/cantera-avbp.git /scratch/cfd/$USER + cd /scratch/cfd/$USER/cantera-avbp + git checkout 3.0 + python3 install_cantera.py + +When prompted about NFS, answer 'yes' and wait for the compilation and installation to finish. + +If everything goes well, you will see a similar message as above, but with an additional question:: + + + We suggest adding the alias 'load_cantera' to purge and load necessary modules in ~/.bashrc + Do you want to add the alias to ~/.bashrc? (yes/no) + + +Answer ``yes`` to this question, then copy and paste the environment variables you need into your ``.bashrc`` file and **source it**. + +Finally, load Cantera with the following command:: + + load_cantera + + +Test if everything works using a sample script, for example:: + + python3 samples/python/AVBP/ARC.py -- For other platforms, or for users wishing to install a development version of - Cantera, `compilation instructions `_ - are also available. Documentation ============= diff --git a/install_cantera.py b/install_cantera.py new file mode 100644 index 00000000000..4245b5d93a8 --- /dev/null +++ b/install_cantera.py @@ -0,0 +1,154 @@ +# Small python script for Cantera CERFACS installation + +import sys +import os +import subprocess + +# Asking about the environment +if sys.version_info[0] < 3: + quit('You should compile cantera with python 3 ! Use module load python/3.9.5') + string_argument = raw_input('Are you installing Cantera on NFS machine ? (yes/no) ') + python_version = 2 +else: + string_argument = input('Are you installing Cantera on NFS machine ? (yes/no) ') + python_version = 3 + +if string_argument in ['yes', 'y']: + argument = 'NFS' +elif string_argument in ['no', 'n']: + argument = 'local' +else: + quit('Invalid answer ! \n Really ?! How could you fail a yes or no question ?') + +dir_path = os.path.dirname(os.path.realpath(__file__)) + +install_dir_path = os.path.dirname(os.path.realpath(__file__)) + "/INSTALL_DIR" + +if not os.path.isdir(install_dir_path): + os.mkdir(install_dir_path) + +#create mech_lib folder in INSTALL_DIR +if not os.path.isdir(install_dir_path + "/mech_lib"): + os.mkdir(install_dir_path + "/mech_lib") + +file_path = dir_path + "/cantera.conf" + +def fill_cantera_conf(file_path, install_dir_path): + f = open(file_path, 'w') + + text = """\ +prefix = '{0}' +""" + + f.write(text.format(install_dir_path)) + + if argument == 'local': + text = """\ +boost_inc_dir = '/opt/homebrew/Cellar/boost/{0}/include' +verbose_tests = True +""" + # use the output of ls /opt/homebrew/Cellar/boost/ to get the version number + f.write(text.format(subprocess.check_output('ls /opt/homebrew/Cellar/boost/', shell=True).decode('utf-8').split('\n')[0])) + else : + text = """\ +boost_inc_dir = '/softs/local/boost/1.78.0_gcc112/include' +""" + f.write(text) + + f.close() + +def execute_with_live_display(command): + process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True) + + while True: + # Read a line from the output + line = process.stdout.readline() + + # Break the loop if there are no more lines + if not line and process.poll() is not None: + break + + # Display the line in real-time + print(line.strip()) + + # Wait for the process to complete + process.wait() + + # Return the exit code of the process + return process.returncode + + +if argument == 'local': + print("""To run cantera, the installation of: \n + - python, boost and gcc with brew command. \n + - numpy, cython, scons, wheel and ruamel.yaml with pip3 command. \n + are required.""") + update_argument = input('Do you want to install/update those libraries ? (yes/no) ') + + if update_argument in ['yes', 'y']: + if subprocess.call('which brew', shell=True) == 1: + subprocess.call('/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"', shell=True) + subprocess.call('brew install boost', shell=True) + subprocess.call('brew install gcc', shell=True) + subprocess.call('pip3 install numpy --no-use-pep517', shell=True) + subprocess.call('pip3 install cython', shell=True) + subprocess.call('pip3 install scons==3.1.2', shell=True) + subprocess.call('pip3 install wheel', shell=True) + subprocess.call('pip3 install ruamel.yaml', shell=True) + elif update_argument in ['no', 'n']: + pass + else: + quit('Invalid answer ! \n Really ?! How could you fail a yes or no question ?') + + fill_cantera_conf(file_path, install_dir_path) + error = subprocess.call('scons build && scons install', shell=True) +else: + fill_cantera_conf(file_path, install_dir_path) + error = execute_with_live_display("./run_compil") + + +#only print the following if the installation was successful +if argument == 'NFS' and not error: + #add an alias to load necessary modules + print("We suggest to add the alias 'load_cantera_mod' to purge and load necessary modules in ~/.bashrc") + #ask user if he wants to add the alias to ~/.bashrc + add_alias = input('Do you want to add the alias to ~/.bashrc ? (yes/no) ') + if add_alias in ['yes', 'y']: + err = subprocess.call("echo 'alias load_cantera_mod=\"module purge && module load compiler/gcc/11.2.0\"' >> ~/.bashrc", shell=True) + if not err : + print("Alias load_cantera_mod added to ~/.bashrc") + else : + print("FAILED to add alias load_cantera_mod to ~/.bashrc, you can do it manually :\ + alias load_cantera_mod='module purge && module load compiler/gcc/11.2.0'") + else : + print("Alias load_cantera_mod NOT added to ~/.bashrc") + +if not error: + print("*" * 80) + print() + print("To use this brandnew Cantera installation, you must update some of your environment variables.") + print("To do so, you can add the following lines to your .bashrc (or equivalent):") + text="""\ +#cantera-avbp-3.0 +export PYTHONPATH={0}/lib/python{1}.{2}/site-packages:$PYTHONPATH +export PKG_CONFIG_PATH={0}/lib/pkgconfig:$PKG_CONFIG_PATH +export LD_LIBRARY_PATH={0}/lib:$LD_LIBRARY_PATH +export PATH={0}/bin:$PATH +export PYTHON_CMD={3} + +#Only if you dont already have a custom lib folder: +export CUSTOM_LIB={0}/mech_lib +export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + +#Required for MacOS: +export DYLD_LIBRARY_PATH=$CUSTOM_LIB + """ + #get the output of which python to get the path to the python executable + pythonpath = subprocess.check_output('which python3', shell=True).decode('utf-8').split('\n')[0] + print() + print(text.format(install_dir_path,str(python_version), str(sys.version_info[1]),pythonpath)) + print() + print("DONT FORGET TO SOURCE YOUR .bashrc !") + print() + print("*" * 80) + diff --git a/main.yaml b/main.yaml new file mode 100644 index 00000000000..603fff34ed1 --- /dev/null +++ b/main.yaml @@ -0,0 +1,66 @@ +name: Tests + +on: + push: + branches: + - '**' + +jobs: + ubuntu-multiple-pythons: + name: ${{ matrix.os }} with Python ${{ matrix.python-version }} + runs-on: ${{ matrix.os }} + timeout-minutes: 60 + strategy: + matrix: + python-version: ['3.9'] + os: ['self-hosted'] + fail-fast: false + env: + HDF5_LIBDIR: /usr/lib/x86_64-linux-gnu/hdf5/serial + HDF5_INCLUDEDIR: /usr/include/hdf5/serial + steps: + - uses: actions/checkout@v3 + name: Checkout the repository + with: + submodules: recursive + - name: Setup Python + uses: actions/setup-python@v4 + with: + python-version: ${{ matrix.python-version }} + architecture: x64 + - name: Install Apt dependencies + run: | + sudo apt -y update + sudo apt -y install libboost-dev gfortran libopenmpi-dev libpython3-dev \ + libblas-dev liblapack-dev libhdf5-dev libfmt-dev + gcc --version + - name: Upgrade pip + run: python3 -m pip install -U pip setuptools wheel + - name: Install Python dependencies + # h5py is optional; some versions don't have binaries (yet) + run: | + python3 -m pip install ruamel.yaml scons==3.1.2 numpy cython pandas pytest \ + pytest-github-actions-annotate-failures pint + python3 -m pip install h5py + - name: Build Cantera + run: | + python3 `which scons` build env_vars=all -j2 debug=n --debug=time \ + system_fmt=y hdf_libdir=$HDF5_LIBDIR hdf_include=$HDF5_INCLUDEDIR \ + cc_flags=-D_GLIBCXX_ASSERTIONS + - name: Upload shared library + uses: actions/upload-artifact@v3 + if: matrix.python-version == '3.10' + with: + path: build/lib/libcantera_shared.so + name: libcantera_shared-${{ matrix.os }}.so + retention-days: 2 + - name: Test Cantera + run: + python3 `which scons` test show_long_tests=yes verbose_tests=yes --debug=time + - name: Save the wheel file to install Cantera + uses: actions/upload-artifact@v3 + with: + path: build/python/dist/Cantera*.whl + retention-days: 2 + name: cantera-wheel-${{ matrix.python-version }}-${{ matrix.os }} + if-no-files-found: error \ No newline at end of file diff --git a/run_compil b/run_compil new file mode 100755 index 00000000000..64c909a8246 --- /dev/null +++ b/run_compil @@ -0,0 +1,5 @@ +module purge +module load python/3.9.5 +module load compiler/gcc/11.2.0 +module list +scons build && scons install diff --git a/run_compil_kraken b/run_compil_kraken new file mode 100755 index 00000000000..2d82c92a262 --- /dev/null +++ b/run_compil_kraken @@ -0,0 +1,9 @@ +#!/bin/bash +module purge +module load python/3.9.5 +module load compiler/gcc/11.2.0 +#require the installation of ruamel.yaml +scons build python2_package=n prefix=/softs/local/cantera-avbp/3.0 blas_lapack_libs=lapack,atlas debug_linker_flags='-L/usr/lib64/atlas' +mv /softs/local/cantera-avbp/3.0 /softs/local/cantera-avbp/3.0-`date +%d%b%Y` +scons install + From 192c2658bdf7f050a9c31c24552589ae01339937 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 4 Apr 2025 21:22:16 +0200 Subject: [PATCH 24/98] Add missing part needed for compile_fortran import On branch WIP/Merge_cantera-avbp Your branch is up to date with 'origin/WIP/Merge_cantera-avbp'. Changes to be committed: modified: ../../../interfaces/cython/cantera/composite.py interactive rebase in progress; onto 7aec821a8 Last commands done (9 commands done): pick e118cf6c4 Merge differences for other files pick b0f7cbc5e Add missing part needed for compile_fortran import Next commands to do (5 remaining commands): pick 8058ffb5b Add test files to the gitignore pick 1c91e26e1 [Bugfix] Segfault if no transport specified in the YAML file You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. Changes to be committed: modified: interfaces/cython/cantera/composite.py --- interfaces/cython/cantera/composite.py | 165 +++++++++++++++++++++++++ 1 file changed, 165 insertions(+) diff --git a/interfaces/cython/cantera/composite.py b/interfaces/cython/cantera/composite.py index 4b5fe32d4fc..a85e7c1135e 100644 --- a/interfaces/cython/cantera/composite.py +++ b/interfaces/cython/cantera/composite.py @@ -392,6 +392,171 @@ def f(self, *args, **kwargs): setattr(Quantity, _attr, _prop(_attr)) +# A pure-Python class to store weakrefs to +class _WeakrefProxy: + pass + + +def compile_fortran(f90_filename, force=False, fortran_format='f90', + mechanism_lib=None, output=False, remote_install=True): + """ Creates dynamic library to compute chemistry source terms for Cantera + + Compile a f90 file (potentially generated through create_mech_f90) containing + all routines necessary to return wdot to Cantera during runs. The output is a + dynamic library, used in Cantera via the custom kinetics keyword. + + :param f90_filename: name of the f90 file to compile + :param force: if True, compiles fortran even if it hasn't been changed + :param fortran_format: string specifying if it's for example in f77 format + :param mechanism_lib: path to the directory where dynamic libraries are to be compiled + :param output: if True displays the output of the make + :param remote_install: if False the compilation will be done automatically in the sources + :return: None + """ + + ## Test to know if subroutine has the right name to do the compiling + line_custom = None + f = open(f90_filename,'r') + for lines in f.readlines(): + if 'subroutine' in lines.lower() and '(p,t,y,wdot)' in lines.replace(" ","").lower(): + line_custom = lines + break + f.close() + + if line_custom == None: + print("The main subroutine of the f90 file should be written : 'subroutine customkinetics (P, T, y, wdot)' to work") + sys.exit() + else: + if 'customkinetics' not in line_custom.lower(): + print("The main subroutine of the f90 file should be written : 'subroutine customkinetics (P, T, y, wdot)' to work") + sys.exit() + + # Check installation path + if not remote_install: + # Finds the path to the cantera module and then copies the f90 file in the correct directory + path_to_init = os.path.realpath(__file__) + + terminator = path_to_init.rfind('/lib') + path = (path_to_init[:terminator]) + + lib_name = '/lib' + + path_to_dir = path + lib_name + + if not os.path.isdir(path_to_dir) and os.path.isdir(path_to_dir + '64'): + lib_name = '/lib64' + path_to_dir = path + lib_name + + elif not os.path.isdir(path_to_dir) and not os.path.isdir(path_to_dir + '64'): + print('There is a problem with your installation, ' + path_to_dir + ' does not exist') + sys.exit() + + elif not os.environ.get('CUSTOM_LIB'): + if mechanism_lib: + path_to_dir = mechanism_lib + else: + # path_to_file = os.path.realpath(__file__) + # terminator = path_to_file.rfind('/') + # path = (path_to_file[:terminator]) + # lib_name = '/mech_lib' + + path_to_dir = './mech_lib' + + path_to_dir = os.path.abspath(path_to_dir) + + if not os.path.isdir(path_to_dir): + try: + os.mkdir(path_to_dir) + except PermissionError: + print("Please specify a mech_lib directory to write in that is accessible " + "with the argument mechanism_lib=the_path_you_want") + quit() + else: + print('The directory ' + path_to_dir + ' has been created') + print('The necessary files for the compilation and customised kinetics run will be stored there') + print("If this location does not suit you, please specify a path as mechanism_lib argument") + + else: + path_to_dir = os.environ['CUSTOM_LIB'] + + # Correct path definitions + + path_to_ext = path_to_dir + '/customkinetics.f90' + path_to_makefile = path_to_dir + '/Makefile' + + make_call = 'make -C ' + path_to_dir + if not output: + make_call += ' &> compilation_output.txt' + + # Copying f90 file to the right place + + if not f90_filename.endswith('.f90'): + f90_filename = f90_filename + '.f90' + + if not os.path.isfile(path_to_ext) or not filecmp.cmp(f90_filename, path_to_ext) or force: + + shutil.copy(f90_filename, path_to_ext) + + # Checks if the Makefile exists, if not creates it + if not os.path.isfile(path_to_makefile): + + f = open(path_to_makefile, 'w') + text = """\ +customkinetics.so: customkinetics.f90 +\tgfortran -ffixed-line-length-0 -c customkinetics.f90 -g -fPIC -o customkinetics.o +\tgfortran -shared -o customkinetics.so customkinetics.o + """ + if fortran_format == 'f77': + text = """\ +customkinetics.so: customkinetics.f90 +\tgfortran -ffixed-line-length-0 -ffixed-form -c customkinetics.f90 -g -fPIC -o customkinetics.o +\tgfortran -shared -o customkinetics.so customkinetics.o + """ + f.write(text) + f.close() + print('The Makefile was missing or wrongly named') + print('The correct Makefile has been created (' + path_to_makefile + ')') + + # In remote installation, sets the correct LD_LIBRARY_PATH for the dynamic library + if not os.environ.get('CUSTOM_LIB'): + custom_env_set = 'export CUSTOM_LIB=' + path_to_dir + environment_set = 'export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH' + + if mechanism_lib: + dir_status = 'you chose' + else: + dir_status = 'automatically created' + + text = ("""\ + +This part is not automated as it would require sneaky modifications of your bashrc and that is privacy violation ! + +Please copy those commands in your bashrc (or execute them in your shell): +{0} +{1} + +It will add the directory {2} to the dynamic library path blab bla bla, informatics stuff ... + +I advise you stick to only one directory for the compilation for 2 reasons: +- 1: it will be boring to add the path again. +- 2: it's absolutely useless to have several.""") + + print(text.format(custom_env_set, environment_set, dir_status)) + sys.exit() + + process = subprocess.call(make_call, shell=True) + + if process != 0: + print('The compilation of the f90 file failed ! There is something wrong ...') + if not output: + print('Check compilation_output.txt for intel') + exit() + else: + + print('Compilation of the f90 successful') + subprocess.call('rm -f compilation_output.txt', shell=True) + time.sleep(0.05) # Necessary for python to understand there was a change + class SolutionArray(SolutionArrayBase): """ A class providing a convenient interface for representing many thermodynamic From bfbe028fb6a94715ab52b7421c5404865ac3eb51 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 22 Apr 2025 14:30:28 +0200 Subject: [PATCH 25/98] Add test files to the gitignore On branch WIP/merge_CERFACS_devs Changes to be committed: modified: .gitignore interactive rebase in progress; onto 7aec821a8 Last commands done (10 commands done): pick b0f7cbc5e Add missing part needed for compile_fortran import pick 8058ffb5b Add test files to the gitignore Next commands to do (4 remaining commands): pick 1c91e26e1 [Bugfix] Segfault if no transport specified in the YAML file pick 5a9cde018 Bugfix : set the transport model in the file Lu_ARC.yaml You are currently rebasing branch 'dev_cantera-avbp' on '7aec821a8'. Changes to be committed: modified: .gitignore --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 872f34ff27a..8f03e74721c 100644 --- a/.gitignore +++ b/.gitignore @@ -54,3 +54,5 @@ doc/sphinx/matlab/*.rst reduced.yaml INSTALL_DIR/ *.code-workspace +samples/python/AVBP/RESULTS/ +test_problems/cxx_samples/flamespeed.yaml From 80273c185eaae6a0226fc4e3ade44212e76f8b38 Mon Sep 17 00:00:00 2001 From: joebarteam11 <85874120+joebarteam11@users.noreply.github.com> Date: Fri, 29 Dec 2023 23:39:56 +0100 Subject: [PATCH 26/98] [Bugfix] Segfault if no transport specified in the YAML file call "registerChangedCallback" before transport setting if transportModel() is "none" --- src/oneD/StFlow.cpp | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/src/oneD/StFlow.cpp b/src/oneD/StFlow.cpp index f1dc1e70128..10e8259bd1e 100644 --- a/src/oneD/StFlow.cpp +++ b/src/oneD/StFlow.cpp @@ -130,6 +130,12 @@ StFlow::StFlow(shared_ptr sol, const string& id, size_t nsoot, size_t m_id = id; m_kin = m_solution->kinetics().get(); m_trans = m_solution->transport().get(); + + m_solution->registerChangedCallback(this, [this]() { + setKinetics(m_solution->kinetics()); + setTransport(m_solution->transport()); + }); + if (m_trans->transportModel() == "none") { // @deprecated warn_deprecated("StFlow", @@ -138,10 +144,7 @@ StFlow::StFlow(shared_ptr sol, const string& id, size_t nsoot, size_t "is deprecated and\nwill be removed after Cantera 3.0."); setTransportModel("mixture-averaged"); } - m_solution->registerChangedCallback(this, [this]() { - setKinetics(m_solution->kinetics()); - setTransport(m_solution->transport()); - }); + } StFlow::~StFlow() From c434656010784a08a438a661d2b1f9655bba967d Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 22 Apr 2025 16:08:43 +0200 Subject: [PATCH 27/98] Bugfix : set the transport model in the file Lu_ARC.yaml On branch WIP/merge_CERFACS_devs Changes to be committed: modified: ARC.py modified: inputs/Lu_ARC.yaml --- samples/python/AVBP/ARC.py | 1 - samples/python/AVBP/inputs/Lu_ARC.yaml | 1 + 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/samples/python/AVBP/ARC.py b/samples/python/AVBP/ARC.py index edc2a530c53..10609e6425e 100644 --- a/samples/python/AVBP/ARC.py +++ b/samples/python/AVBP/ARC.py @@ -18,7 +18,6 @@ gas.TP = tin, p gas.set_equivalence_ratio(phi, fuel, oxidizer) -# gas.transport_model = 'UnityLewis' loglevel = 1 refine_grid = 'refine' diff --git a/samples/python/AVBP/inputs/Lu_ARC.yaml b/samples/python/AVBP/inputs/Lu_ARC.yaml index 91213b6c00c..b759a9f8c64 100644 --- a/samples/python/AVBP/inputs/Lu_ARC.yaml +++ b/samples/python/AVBP/inputs/Lu_ARC.yaml @@ -1649,6 +1649,7 @@ phases: state: T: 300.0 P: 1.01325e+05 + transport: unity-Lewis-number species: - name: H2 composition: From 49d3ee3d2972705839ecec26c99674f5e2c3f84f Mon Sep 17 00:00:00 2001 From: AntoinePestre <101113311+AntoinePestre@users.noreply.github.com> Date: Tue, 29 Apr 2025 11:01:59 +0200 Subject: [PATCH 28/98] Update README.rst for cantera installation --- README.rst | 21 +++++++++++++-------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/README.rst b/README.rst index db422cfe85d..99a75aeb556 100644 --- a/README.rst +++ b/README.rst @@ -39,7 +39,7 @@ Follow the steps below for a **local** installation: 0. Clone the Cantera repository:: cd /Users/$USER/Documents - git clone https://nitrox.cerfacs.fr/cantera/cantera-avbp.git + git clone git@github.com:cerfacs/cantera.git 1. Create a virtual environment in your home directory:: @@ -47,23 +47,28 @@ Follow the steps below for a **local** installation: python3 -m venv env_cantera source ~/env_cantera/bin/activate -2. (optional) Create an alias to load ``env_cantera``:: +2. Install specific python packages:: + + pip install numpy==1.26.4 + pip install scipy==1.13 + +3. (optional) Create an alias to load ``env_cantera``:: echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.zshrc source ~/.zshrc -3. Navigate to the Cantera directory:: +4. Navigate to the Cantera directory:: - cd /Users/$USER/Documents/cantera-avbp + cd /Users/$USER/Documents/cantera -4. Switch to the right branch and run the installation script:: +5. Switch to the right branch and run the installation script:: - git checkout 3.0 + git checkout dev_cantera-avbp python3 install_cantera.py -5. When prompted about NFS, answer ``no``. -6. Wait for the compilation and installation process to complete successfully. +6. When prompted about NFS, answer ``no``. +7. Wait for the compilation and installation process to complete successfully. If everything goes well, you should see the following message:: From 19b3468d610bc2b5decbb52b8a1f731712857cde Mon Sep 17 00:00:00 2001 From: AntoinePestre <101113311+AntoinePestre@users.noreply.github.com> Date: Tue, 29 Apr 2025 11:06:08 +0200 Subject: [PATCH 29/98] Change repository name --- README.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.rst b/README.rst index 99a75aeb556..2b2b3ff5f7a 100644 --- a/README.rst +++ b/README.rst @@ -59,7 +59,7 @@ Follow the steps below for a **local** installation: 4. Navigate to the Cantera directory:: - cd /Users/$USER/Documents/cantera + cd /Users/$USER/Documents/cantera-avbp 5. Switch to the right branch and run the installation script:: From b4cfc512dd4da9c2e0110ac84915bc818396dfae Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Mon, 7 Jul 2025 17:29:10 +0200 Subject: [PATCH 30/98] Several bugfixes after rebase on cantera3.1.0a4 Tests and samples seems to work fine, except for computation On branch dev_cantera-avbp Changes to be committed: modified: include/cantera/kinetics/CustomKinetics.h modified: include/cantera/oneD/Flamelet.h modified: include/cantera/oneD/Flow1D.h deleted: include/cantera/oneD/StFlow.h modified: interfaces/cython/cantera/_onedim.pxd modified: interfaces/cython/cantera/_onedim.pyx modified: samples/python/AVBP/1-runBurner.py modified: samples/python/AVBP/2-restoreBurner.py deleted: samples/python/AVBP/RESULTS/BISETTI.xml deleted: samples/python/AVBP/RESULTS/BISETTI.yaml deleted: samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml deleted: samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.yaml modified: src/kinetics/CustomKinetics.cpp modified: src/oneD/Boundary1D.cpp modified: src/oneD/DomainFactory.cpp modified: src/oneD/Flamelet.cpp modified: src/oneD/Flow1D.cpp modified: src/oneD/IonFlow.cpp deleted: src/oneD/StFlow.cpp modified: test/oneD/test_oneD.cpp --- include/cantera/kinetics/CustomKinetics.h | 4 +- include/cantera/oneD/Flamelet.h | 10 +- include/cantera/oneD/Flow1D.h | 758 +- include/cantera/oneD/StFlow.h | 1232 --- interfaces/cython/cantera/_onedim.pxd | 7 +- interfaces/cython/cantera/_onedim.pyx | 27 - samples/python/AVBP/1-runBurner.py | 4 +- samples/python/AVBP/2-restoreBurner.py | 6 +- samples/python/AVBP/RESULTS/BISETTI.xml | 7624 ----------------- samples/python/AVBP/RESULTS/BISETTI.yaml | 6778 --------------- .../RESULTS/CH4-O2-converged-flamelet-Lu.xml | 1844 ---- .../RESULTS/CH4-O2-converged-flamelet-Lu.yaml | 1565 ---- src/kinetics/CustomKinetics.cpp | 2 +- src/oneD/Boundary1D.cpp | 4 +- src/oneD/DomainFactory.cpp | 13 +- src/oneD/Flamelet.cpp | 14 +- src/oneD/Flow1D.cpp | 1283 ++- src/oneD/IonFlow.cpp | 2 +- src/oneD/StFlow.cpp | 2293 ----- test/oneD/test_oneD.cpp | 93 +- 20 files changed, 2006 insertions(+), 21557 deletions(-) delete mode 100644 include/cantera/oneD/StFlow.h delete mode 100644 samples/python/AVBP/RESULTS/BISETTI.xml delete mode 100644 samples/python/AVBP/RESULTS/BISETTI.yaml delete mode 100644 samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml delete mode 100644 samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.yaml delete mode 100644 src/oneD/StFlow.cpp diff --git a/include/cantera/kinetics/CustomKinetics.h b/include/cantera/kinetics/CustomKinetics.h index 4c720b33800..186f44e8428 100644 --- a/include/cantera/kinetics/CustomKinetics.h +++ b/include/cantera/kinetics/CustomKinetics.h @@ -6,7 +6,7 @@ // Author: Q. Cazeres, A. Felden, P. Pepiot -#include "GasKinetics.h" +#include "BulkKinetics.h" namespace Cantera { @@ -14,7 +14,7 @@ namespace Cantera * Kinetics manager implementing reaction mechanism GRI-Mech 3.0 * @deprecated */ - class CustomKinetics : public GasKinetics + class CustomKinetics : public BulkKinetics { public: /// Default constructor. diff --git a/include/cantera/oneD/Flamelet.h b/include/cantera/oneD/Flamelet.h index a76dfc09edd..be52f1a64cd 100644 --- a/include/cantera/oneD/Flamelet.h +++ b/include/cantera/oneD/Flamelet.h @@ -3,7 +3,7 @@ // #include "Domain1D.h" #include "cantera/base/Array.h" -#include "cantera/oneD/StFlow.h" +#include "cantera/oneD/Flow1D.h" #include "cantera/kinetics/Kinetics.h" #include "cantera/thermo/IdealGasPhase.h" #include "cantera/thermo/ThermoPhase.h" @@ -20,7 +20,7 @@ namespace Cantera { -class Flamelet : public StFlow +class Flamelet : public Flow1D { public: Flamelet(IdealGasPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); @@ -39,14 +39,10 @@ class Flamelet : public StFlow virtual void eval(size_t j, double* x, double* r, integer* mask, double rdt) override; - virtual string type() const override{ + string domainType() const override{ return "flamelet-flow"; } - virtual string flowType() const override{ - return "Flamelet"; - } - virtual void resize(size_t components, size_t points) override; virtual string componentName(size_t n) const override; diff --git a/include/cantera/oneD/Flow1D.h b/include/cantera/oneD/Flow1D.h index c3059c7852a..ca300a36475 100644 --- a/include/cantera/oneD/Flow1D.h +++ b/include/cantera/oneD/Flow1D.h @@ -31,6 +31,13 @@ enum offset , c_offset_Y //! mass fractions }; +//! Offsets of solution components in the 1D solution array for mixture fraction space +enum offset_z +{ + c_offset_Tflamelet, //! Temperature + c_offset_Yflamelet, //! Species mass fractions +}; + class Transport; //! @defgroup flowGroup Flow Domains @@ -54,28 +61,30 @@ class Flow1D : public Domain1D //! to evaluate all thermodynamic, kinetic, and transport properties. //! @param nsp Number of species. //! @param points Initial number of grid points - Flow1D(ThermoPhase* ph = 0, size_t nsp = 1, size_t points = 1); + //! @param n_eq Number of non-species equations (default = 4 for spatial resolution) + Flow1D(ThermoPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); //! Delegating constructor - Flow1D(shared_ptr th, size_t nsp = 1, size_t points = 1); + Flow1D(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); //! Create a new flow domain. //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and //! transport properties //! @param id name of flow domain //! @param points initial number of grid points - Flow1D(shared_ptr sol, const string& id="", size_t points=1); + Flow1D(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Y, size_t points=1); - ~Flow1D(); + virtual ~Flow1D(); // virtual kw required for derived class destructors (flamelet) - string domainType() const override; + virtual string domainType() const override; //! @name Problem Specification //! @{ void setupGrid(size_t n, const double* z) override; + void setupGrid(size_t n); - void resetBadValues(double* xg) override; + virtual void resetBadValues(double* xg) override; ThermoPhase& phase() { return *m_thermo; @@ -85,6 +94,13 @@ class Flow1D : public Domain1D return *m_kin; } + /** + * Set the thermo manager. + * + * @deprecated To be removed after %Cantera 3.0 (unused) + */ + // void setThermo(ThermoPhase& th); + void setKinetics(shared_ptr kin) override; void setTransport(shared_ptr trans) override; @@ -136,6 +152,16 @@ class Flow1D : public Domain1D return m_press; } + //! Set the number of non-species equations + void setNequation(size_t neq){ + m_neq = neq; + } + + //! The current number of non-species equations + size_t nEq(){ + return m_neq; + } + //! Write the initial solution estimate into array x. void _getInitialSoln(double* x) override; @@ -163,6 +189,18 @@ class Flow1D : public Domain1D return m_fixedtemp[j]; } + /// Returns the mixture fraction at point j + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + double getMixFrac(size_t j) { + return m_zmixfrac[j]; + } + + /// Updates the mixture fraction at point j + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + void calcMixFrac(const double* x,size_t j); + //! @} string componentName(size_t n) const override; @@ -172,6 +210,7 @@ class Flow1D : public Domain1D //! Returns true if the specified component is an active part of the solver state virtual bool componentActive(size_t n) const; + //! Print the solution. void show(const double* x) override; shared_ptr asArray(const double* soln) const override; @@ -201,6 +240,23 @@ class Flow1D : public Domain1D m_usesLambda = false; } + void setFlameletFlow() { + // m_type = cFlameletFlow; + m_dovisc = true; + m_isFree = false; + m_usesLambda = true; + } + + //! Return the type of flow domain being represented, either "Free Flame" or + //! "Axisymmetric Stagnation". + //! @see setFreeFlow setAxisymmetricFlow + //! @deprecated To be removed after %Cantera 3.0; replaced by type(). + // virtual string flowType() const; + + virtual void setFuelSpecies(const std::string fuel) { + m_fuel = fuel; + } + void solveEnergyEqn(size_t j=npos); //! Get the solving stage (used by IonFlow specialization) @@ -224,6 +280,18 @@ class Flow1D : public Domain1D virtual bool doElectricField(size_t j) const; //! Turn radiation on / off. + /*! + * The simple radiation model used was established by Liu and Rogg + * @cite liu1991. This model considers the radiation of CO2 and H2O. + * + * This model uses the optically thin limit and the gray-gas approximation to + * simply calculate a volume specified heat flux out of the Planck absorption + * coefficients, the boundary emissivities and the temperature. Polynomial lines + * calculate the species Planck coefficients for H2O and CO2. The data for the + * lines are taken from the RADCAL program @cite RADCAL. + * The coefficients for the polynomials are taken from + * [TNF Workshop](https://tnfworkshop.org/radiation/) material. + */ void enableRadiation(bool doRadiation) { m_do_radiation = doRadiation; } @@ -256,6 +324,341 @@ class Flow1D : public Domain1D return m_epsilon_right; } + // Turn soot formation on / off. + // setSections + const size_t getSections() const{ + return m_nsoot; + } + + void setSections(size_t nSec) { + m_nsoot = nSec; + } + + void setPrecursors(std::vector id_precursors); + + void setSootLoglevel(size_t loglevel){ + soot_loglevel = loglevel; + } + + size_t getSootLoglevel(){ + return soot_loglevel; + } + + void enableCondensation(bool doCondensation) { + m_do_condensation = doCondensation; + } + bool condensationEnabled(){ + return m_do_condensation; + } + + void enableCoagulation(bool doCoagulation) { + m_do_coagulation = doCoagulation; + } + bool coagulationEnabled(){ + return m_do_coagulation; + } + + void setCollisionModel(std::string collisionModel){ + m_collision_model = collisionModel; + } + + std::string getCollisionModel(){ + return m_collision_model; + } + + void setSootMorphology(std::string morphologyModel){ + m_soot_morphology = morphologyModel; + } + + std::string getSootMorphology(){ + return m_soot_morphology; + } + + void enableRetroaction(bool doRetroaction){ + m_do_retroaction = doRetroaction; + } + bool retroactionEnabled(){ + return m_do_retroaction; + } + + void enableSootRadiation(bool do_soot_radiation){ + m_do_soot_radiation = do_soot_radiation; + } + + bool sootRadiationEnabled(){ + return m_do_soot_radiation; + } + + void enableSootSoret(bool do_soot_soret){ + m_do_soot_soret = do_soot_soret; + } + + bool sootSoretEnabled(){ + return m_do_soot_soret; + } + + void enableSurfaceGrowth(bool do_sg){ + m_do_sg = do_sg; + } + bool surfaceGrowthEnabled(){ + return m_do_sg; + } + + void enableOxidation(bool do_oxidation){ + m_do_oxidation = do_oxidation; + } + bool oxidationEnabled(){ + return m_do_oxidation; + } + + void enableTrashSection(double trash_section){ + if (trash_section > 0){ + m_trash_section = true; + dTrashLowLim = trash_section; + }else{ + m_trash_section = false; + dTrashLowLim = 0.0; + } + } + + bool trashSectionEnabled(){ + return m_trash_section; + } + + void setHaca(size_t haca_model){ + m_haca_model = haca_model; + } + + size_t getHaca(){ + return m_haca_model; + } + + double getKazakovTad(){ + return kazakovTad; + } + void setKazakovTad(double kazakov_tad){ + kazakovTad = kazakov_tad; + } + + void loadHaca(size_t m_haca_model){ + if (m_haca_model == 1){ //Mauss + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.0 / S_C2; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Mauss HACA-RC model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; + ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; + // S-H + OH <-> S* + H2O + ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; + ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; + // S* + H <-> S-H + ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; + ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; + // S* + C2H2 <-> S-H + ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; + ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; + // S* <-> S-H + H + ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; + ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; + // S* + O2 -> S-H + 2CO + ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 8.4000e03; + // S* + O2 -> S-H + 2HCO + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + }else if (m_haca_model == 11){ //Mauss tuned (Guo 2016) + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.0 / S_C2; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Mauss HACA-RC model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; + ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; + // S-H + OH <-> S* + H2O + ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; + ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; + // S* + H <-> S-H + ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; + ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; + // S* + C2H2 <-> S-H + ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; + ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; + // S* <-> S-H + H + ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; + ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; + // S* + O2 -> S-H + 2CO + ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 190.000e03; + // S* + O2 -> S-H + 2HCO + // S-H + OH -> S-H + CO + gamma_oh = 0.10; + }else if (m_haca_model == 2){ //Blanquart + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] + double lambda = 1.7e19; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Blanquart HACA model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/kmol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 1.0e8 * 1e-3; nk01f = 1.8; ek01f = 68420.0; + ak01b = 8.68e4 * 1e-3; nk01b = 2.36; ek01b = 25460.0; + // S-H + OH <-> S* + H2O + ak02f = 6.72e1 * 1e-3; nk02f = 3.33; ek02f = 6090.0; + ak02b = 6.44e-1 * 1e-3; nk02b = 3.79; ek02b = 27960.0; + // S-H <-> S* + H + ak03f = 1.13e16; nk03f = -0.06; ek03f = 476050.0; + ak03b = 4.17e13 * 1e-3; nk03b = 0.15; ek03b = 0.0; + // S* + C2H2 -> S-H + ak04f = 2.52e9 * 1e-3; nk04f = 1.77; ek04f = 13540.0; + // S* + O2 -> S + 2CO + ak05f = 2.2e12 * 1e-3; nk05f = 0.0; ek05f = 31380.0; + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + }else if (m_haca_model == 3){ + // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [m-2] + double lambda = 2.3e19; + // Number of sites [-] + // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) + n_sites = lambda * S_C2; + // Kazakov HACA model + //1st order : [1/s] , [-], [J/mol] + //2nd order : [m3/mol/s], [-], [J/mol] + // S-H + H <-> S* + H2 + ak01f = 2.5e14 * 1e-3; nk01f = 0.0; ek01f = 66900.0; + ak01b = 3.9e12 * 1e-3; nk01b = 0.0; ek01b = 39000.0; + // S* + H -> S-H + ak02f = 1.0e14 * 1e-3; nk02f = 0.0; ek02f = 0.0; + // S* + C2H2 -> S-H + H + ak03f = 8.4e11 * 1e-3; nk03f = 0.4; ek03f = 35100.0; + // S* + O2 -> S + 2CO + ak04f = 2.2e12 * 1e-3; nk04f = 0.0; ek04f = 31300.0; + // S-H + OH -> S-H + CO + gamma_oh = 0.13; + } + } + + void finalizeSoot(); + void loadSurface(); + //Initialize soot + void initSoot(); + void showSootInfo(); + // Sections generation and display + void sootCreationVol(); + void showSootSections(); + void sootCollisionModel(); + void getDistributionOrdre0(const double* x, size_t j); + // Soot source terms + void sootSource(const double* x, size_t j); + void sootDimerization(const double* x, size_t j); + void sootNucleation(const double* x, size_t j); + void sootCondensation(const double* x, size_t j); + void sootCoagulation(const double* x, size_t j); + void sootSurface(const double* x, size_t j); + void sootSurfaceInitialization(const double* x, size_t j); + void sootCollisionInverse(); + // Returns section name + std::string sectionName(size_t n) const { + return m_section_name[n]; + } + + const vector& vMin() const { + return vSectMin; + } + + const vector& vMax() const { + return vSectMax; + } + + const vector& vMean() const { + return vSectMean; + } + + const vector& dMean() const { + return dSectMean; + } + + const vector& dCol() const { + return dSectCol; + } + + const vector& aCol() const { + return aSectCol; + } + + const vector& sMean() const { + return sSectMean; + } + + const vector& thetaSoot() const { + return theta_surf; + } + + const vector& fractalPrefactor() const { + return kfractal; + } + + const vector& fractalDimension() const { + return Dfractal; + } + + const double rhoSoot() const { + return rho_soot; + } + + const double getSootInception(size_t j) const { + return m_qdotNucleation[j] * m_rho[j]; + } + + const double getSootCondensation(size_t k, size_t j) const { + return m_qdotCondensation(k,j) * m_rho[j]; + } + + const double getSootCoagulation(size_t k, size_t j) const { + return m_qdotCoagulation(k,j) * m_rho[j]; + } + + const double getSootSg(size_t k, size_t j) const { + return m_qdotSg(k,j) * m_rho[j]; + } + + const double getSootOxidation(size_t k, size_t j) const { + return m_qdotOxidation(k,j) * m_rho[j]; + } + + const double fv(const double* x, size_t j){ + double val = 0.0; + for (size_t k=0; k < m_nsoot; k++){ + val += Ys(x,k,j); + } + val *= m_rho[j] / rho_soot; + return val; + } + + const double sootPrimaryDiam(size_t k) const { + return 2.0 * rNucMean[k]; + } + + const double sootPrimaryPart(size_t k) const { + return nNucMean[k]; + } + + void setThick(double thickness){ + m_thick = thickness; + AVBPReadInputChem(); + } + + double getThick() const { + return m_thick; + } void fixTemperature(size_t j=npos); /** @@ -323,16 +726,33 @@ class Flow1D : public Domain1D void resize(size_t components, size_t points) override; //! Set the gas object state to be consistent with the solution at point j. - void setGas(const double* x, size_t j); + virtual void setGas(const double* x, size_t j); //! Set the gas state to be consistent with the solution at the midpoint //! between j and j + 1. - void setGasAtMidpoint(const double* x, size_t j); + virtual void setGasAtMidpoint(const double* x, size_t j); double density(size_t j) const { return m_rho[j]; } + //! seems unused + double cpBar(size_t j) const { + return m_cpm[j]; + } + + double enthalpy(size_t j) const { + return m_h[j]; + } + + double thCond(size_t j) const { + return m_tcon[j]; + } + + double HR(size_t j) const { + return m_hr[j]; + } + /** * Retrieve flag indicating whether flow is freely propagating. * The flow is unstrained and the axial mass flow rate is not specified. @@ -358,6 +778,19 @@ class Flow1D : public Domain1D m_dovisc = dovisc; } + + // P. Wolf + void AVBPReadInputPea(); + + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + // B. Franzelli modifications to perform thickening + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + void AVBPReadInputChem(); + void AVBPcompute_local_thick(double* x,size_t j); + + double AVBPthick(size_t j) const { + return avbp_thick[j]; + } /** * Evaluate the residual functions for axisymmetric stagnation flow. * If jGlobal == npos, the residual function is evaluated at all grid points. @@ -395,6 +828,138 @@ class Flow1D : public Domain1D AnyMap getMeta() const override; void setMeta(const AnyMap& state) override; + double wdot(size_t k, size_t j) const { + return m_wdot(k,j); + } + +/// write the net production rates at point j into array m_wdot +/// Modified by P. Wolf March 2010 - Thanks to Alireza N. +/// when PEA activated: production rates depends on mixture fraction at point j +/// WARNING: the following is valid only for fuel/AIR right now + void getWdot(double *x, size_t j) + { + double zloc; + double phi; + setGas(x, j); // We'll need to set the gas before retrieving + // std::cout << "after setGas" << std::endl; + zloc = getMixFrac(j); // the Mixture Fraction and calculating wdot + phi = zloc / (1. - zloc) * phi_cst; + + switch (avbp_ipea) + { + case 0: + m_kin->getNetProductionRates(&m_wdot(0, j)); + break; + // ipea = 1, apply the PEA on fuel oxydation reaction only + case 1: + double pea_f; // pea correction function + // Now set the PEA correction function + pea_f = 0.5 * (1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) + + avbp_pea_coeffs[2] / 4. * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) + * (1. + tanh((avbp_pea_coeffs[5] - phi) / avbp_pea_coeffs[6])); + + // Multiply reaction rate of reaction 1 by the pea coeff + m_kin->setMultiplier(1, pea_f); + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + // Restore the original reaction rates (not necessary) + m_kin->setMultiplier(1, 1.0 / pea_f); + break; + // ipea = 2, apply PEA on both reactions + case 2: + // TEST 081014: differencie bien les cas + double pea2_f[2]; // pea correction function + // Now set the PEA correction function + pea2_f[0] = 2. / ((1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) + + avbp_pea_coeffs[2] * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) + + avbp_pea_coeffs[5] * (1. + tanh((phi - avbp_pea_coeffs[6]) / avbp_pea_coeffs[7]))); + + pea2_f[1] = 0.5 * ((1. + tanh((avbp_pea_coeffs[8] - phi) / avbp_pea_coeffs[9])) + + avbp_pea_coeffs[10] * (1. + tanh((phi - avbp_pea_coeffs[11]) / avbp_pea_coeffs[12])) + + avbp_pea_coeffs[13] * (1. + tanh((phi - avbp_pea_coeffs[14]) / avbp_pea_coeffs[15])) + * (1. + tanh((avbp_pea_coeffs[16] - phi) / avbp_pea_coeffs[17]))); + + // Multiply reaction rates by the pea coeff + if (m_kin->nReactions() == 2) + { + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, pea2_f[n]); + } + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + // Restore the original reaction rates (not necessary) + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, 1.0 / pea2_f[n]); + } + } + else + { + throw CanteraError("getWdot", "ipea = 2 but there ain't 2 reactions"); + } + break; + // ipea = 3, apply PEA on both reactions (for CM2 only) + case 3: + double pea3_f[2]; // pea correction function + + // Now set the PEA correction function + if (phi > 1.0) + { + pea3_f[0] = avbp_pea_coeffs[0] * phi * phi + avbp_pea_coeffs[1] * phi + avbp_pea_coeffs[2]; + } + else + { + pea3_f[0] = 1; + } + pea3_f[1] = pea3_f[0]; + + // Multiply reaction rates by the pea coeff + if (m_kin->nReactions() == 2) + { + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, pea2_f[n]); + } + + // Get the net production rates for all species + m_kin->getNetProductionRates(&m_wdot(0, j)); + + // Restore the original reaction rates (not necessary) + for (size_t n = 0; n < m_kin->nReactions(); n++) + { + m_kin->setMultiplier(n, 1.0 / pea2_f[n]); + } + } + else + { + throw CanteraError("getWdot", "ipea = 3 but there ain't 2 reactions"); + } + + break; + + default: + throw CanteraError("getWdot", "ipea is set to a weird value"); + break; + } + } + + //-------------------------------- + // central-differenced derivatives + //-------------------------------- + double cdif1(const double*x, size_t n, size_t j) const { + double c1 = (x[index(n,j+1)] - x[index(n,j-1)]); + return c1/(z(j+1) - z(j-1)); + } + + //! seems unused + double cdif2(const double* x, size_t n, size_t j, + const double* f) const { + double c1 = (f[j] + f[j-1])*(x[index(n,j)] - x[index(n,j-1)]); + double c2 = (f[j+1] + f[j])*(x[index(n,j+1)] - x[index(n,j)]); + return (c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + //! @name Updates of cached properties //! These methods are called by eval() to update cached properties and data that are //! used for the evaluation of the governing equations. @@ -414,7 +979,7 @@ class Flow1D : public Domain1D * * #m_hk (species specific enthalpies) * * #m_wdot (species production rates) */ - void updateThermo(const double* x, size_t j0, size_t j1) { + virtual void updateThermo(const double* x, size_t j0, size_t j1) { for (size_t j = j0; j <= j1; j++) { setGas(x,j); m_rho[j] = m_thermo->density(); @@ -587,13 +1152,11 @@ class Flow1D : public Domain1D virtual void evalElectricField(double* x, double* rsd, int* diag, double rdt, size_t jmin, size_t jmax); - //! @} End of Governing Equations + // Evaluate the species equations' residuals. + virtual void evalSoot(double* x, double* rsd, int* diag, + double rdt, size_t jmin, size_t jmax); - //! Alternate version of evalContinuity with legacy signature. - //! Implemented by StFlow; included here to prevent compiler warnings about shadowed - //! virtual functions. - //! @deprecated To be removed after %Cantera 3.1. - virtual void evalContinuity(size_t j, double* x, double* r, int* diag, double rdt); + //! @} End of Governing Equations /** * Evaluate the oxidizer axial velocity equation residual. @@ -616,13 +1179,13 @@ class Flow1D : public Domain1D //! @name Solution components //! @{ - double T(const double* x, size_t j) const { + virtual double T(const double* x, size_t j) const { return x[index(c_offset_T, j)]; } - double& T(double* x, size_t j) { + virtual double& T(double* x, size_t j) { return x[index(c_offset_T, j)]; } - double T_prev(size_t j) const { + virtual double T_prev(size_t j) const { return prevSoln(c_offset_T, j); } @@ -647,22 +1210,36 @@ class Flow1D : public Domain1D } //! Solution component for oxidizer velocity, @see evalUo - double Uo(const double* x, size_t j) const { + virtual double Uo(const double* x, size_t j) const { return x[index(c_offset_Uo, j)]; } - double Y(const double* x, size_t k, size_t j) const { + virtual double Y(const double* x, size_t k, size_t j) const { return x[index(c_offset_Y + k, j)]; } - double& Y(double* x, size_t k, size_t j) { + virtual double& Y(double* x, size_t k, size_t j) { return x[index(c_offset_Y + k, j)]; } - double Y_prev(size_t k, size_t j) const { + virtual double Y_prev(size_t k, size_t j) const { return prevSoln(c_offset_Y + k, j); } + //Soot + double Ys(const double* x, size_t k, size_t j) const { + return x[index(c_offset_S+k, j)]; + } + + double& Ys(double* x, size_t k, size_t j) { + return x[index(c_offset_S+k, j)]; + } + + double Ys_prev(size_t k, size_t j) const { + return prevSoln(c_offset_S + k, j); + } + //---- + double X(const double* x, size_t k, size_t j) const { return m_wtm[j]*Y(x,k,j)/m_wt[k]; } @@ -720,6 +1297,12 @@ class Flow1D : public Domain1D return (Y(x, k, jloc) - Y(x, k, jloc-1))/m_dz[jloc-1]; } + // Soot + double dYsdz(const double* x, size_t k, size_t j) const { + size_t jloc = (u(x,j) > 0.0 ? j : j + 1); + return (Ys(x,k,jloc) - Ys(x,k,jloc-1))/m_dz[jloc-1]; + } + /** * Calculates the spatial derivative of temperature T with respect to z at point * j using upwind differencing. @@ -778,6 +1361,12 @@ class Flow1D : public Domain1D return -2.0*(A_right - A_left) / (z(j+1) - z(j-1)); } + double AVBPdivHeatFlux(const double* x, size_t j) const { + double c1 = avbp_thick[j-1]*m_tcon[j-1]*(T(x,j) - T(x,j-1)); + double c2 = avbp_thick[j]*m_tcon[j]*(T(x,j+1) - T(x,j)); + return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); + } + /** * Array access mapping for a 3D array stored in a 1D vector. Used for * accessing data in the #m_multidiff member variable. @@ -790,6 +1379,9 @@ class Flow1D : public Domain1D return m*m_nsp*m_nsp + m_nsp*j + k; } + //! Update the soot diffusive mass fluxes. + virtual void updateSootDiffFluxes(const double* x, size_t j0, size_t j1); + /** * Compute the spatial derivative of species specific molar enthalpies using upwind * differencing. Updates all species molar enthalpies for all species at point j. @@ -814,12 +1406,18 @@ class Flow1D : public Domain1D // mixture thermo properties vector m_rho; //!< Vector of size #m_nsp to cache densities vector m_wtm; //!< Vector of size #m_nsp to cache mean molecular weights + // P. Wolf + vector m_zmixfrac; + + vector m_cpm; + vector m_h; // species thermo properties vector m_wt; vector m_cp; //!< Vector of size #m_nsp to cache specific heat capacities // transport properties + vector m_ybar; // CERFACS : Added to the public part to be accessible for Flamelet computations vector m_visc; vector m_tcon; @@ -844,14 +1442,21 @@ class Flow1D : public Domain1D Array2D m_dhk_dz; //! Array of size #m_nsp by #m_points for saving species production rates + vector m_hr; Array2D m_wdot; + size_t m_nsp; //!< Number of species in the mechanism + size_t m_neq; //!< Number of non-species equations + size_t m_nsoot; + std::string m_fuel; ThermoPhase* m_thermo = nullptr; Kinetics* m_kin = nullptr; Transport* m_trans = nullptr; + MultiJac* m_jac = nullptr; + // boundary emissivities for the radiation calculations double m_epsilon_left = 0.0; double m_epsilon_right = 0.0; @@ -860,6 +1465,20 @@ class Flow1D : public Domain1D //! for CO2, second is for H2O. vector m_kRadiating; + // Pierre WOLF: added parameters for input_pea.dat + size_t avbp_ipea = 0; + std::string avbp_fuel; + vector avbp_pea_coeffs; + double phi_cst; + + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + // B. Franzelli modifications to perform thickening + // input_chem parameters + //+++++++++++++++++++++++++++++++++++++++++++++++++++ + double avbp_fthick; + vector avbp_thick; + double m_thick = 1.0; + // flags vector m_do_energy; bool m_do_soret = false; @@ -873,6 +1492,96 @@ class Flow1D : public Domain1D //! radiative heat loss vector vector m_qdotRadiation; + // ---------------------- + // SOOT RELATED VARIABLES + // ---------------------- + bool m_do_soot_soret = true; + bool m_do_condensation = false; + bool m_do_soot_radiation = false; + bool m_do_coagulation = false; + std::string m_soot_morphology; + bool m_do_retroaction = false; + bool m_do_sg = false; + bool m_do_oxidation = false; + bool m_trash_section = false; + std::string m_collision_model = "rodrigues"; + size_t soot_loglevel=1; + size_t c_offset_S = 7; + size_t n_PAH = 0; + size_t m_haca_model; + double Y_PAH; + double C_PAH; + double dTrashLowLim; + vector W_PAH; + double W_C; + vector n_C; + double N_dimer; + double beta_dimer; + double r_dimer; + double V_dimer; + double beta_fm; + double n_sites; + double kazakovTad; + double ksg; + double kox; + Array2D sootConsumption; + vector vSectMin; + vector vSectMax; + vector dSectMean; + vector dSectCol; + vector rSectCol; + vector aSectCol; + vector vSectMean; + vector sSectMean; + vector Dfractal; + vector kfractal; + vector nNucMean; + vector rNucMean; + vector rSmolMean; + vector PAMean; + vector m_qdotNucleation; + Array2D m_qdotCondensation; + Array2D m_qdotCoagulation; + Array2D m_qdotSg; + Array2D m_qdotOxidation; + vector q; + vector theta_surf; + vector jpower; + vector kpower; + vector mpower; + vector vc2power; + vector vc2powerm; + vector vmax_kpower; + vector vmin_kpower; + vector vmax_jpower; + vector vmin_jpower; + vector vmax_mpower; + vector vmin_mpower; + vector vmaxmc2_kpower; + vector vminpc2_kpower; + vector vmaxmc2_jpower; + vector vminpc2_jpower; + vector vmaxmc2_mpower; + vector vminpc2_mpower; + vector vc2powervect; + vector vc2powermvect; + vector m_section_name; + vector m_precursors; + Array2D m_soot_diff ; + Array2D m_soot_soret ; + Array2D collision_mat; + //Surface reactions + double ak00f, nk00f, ek00f, ak01f, nk01f, ek01f, ak02f, nk02f, ek02f, + ak03f, nk03f, ek03f, ak04f, nk04f, ek04f, ak05f, nk05f, ek05f, + ak06f, nk06f, ek06f, ak07f, nk07f, ek07f; + double ak00b, nk00b, ek00b, ak01b, nk01b, ek01b, ak02b, nk02b, ek02b, + ak03b, nk03b, ek03b, ak04b, nk04b, ek04b, ak05b, nk05b, ek05b, + ak06b, nk06b, ek06b, ak07b, nk07b, ek07b; + double gamma_oh; + // ----------------------------- + // END OF SOOT RELATED VARIABLES + // ----------------------------- + // fixed T and Y values vector m_fixedtemp; vector m_zfix; @@ -911,10 +1620,7 @@ class Flow1D : public Domain1D double m_tfixed = -1.0; private: - //! Holds the average of the species mass fractions between grid points j and j+1. - //! Used when building a gas state at the grid midpoints for evaluating transport - //! properties at the midpoints. - vector m_ybar; + }; } diff --git a/include/cantera/oneD/StFlow.h b/include/cantera/oneD/StFlow.h deleted file mode 100644 index 2ddbeb4ebf1..00000000000 --- a/include/cantera/oneD/StFlow.h +++ /dev/null @@ -1,1232 +0,0 @@ -//! @file StFlow.h - -// This file is part of Cantera. See License.txt in the top-level directory or -// at https://cantera.org/license.txt for license and copyright information. -// CERFACS : This file is no more used in CANTERA. CERFACS devs done in this file should be moved somewhere else (Flow1D or in a specific cantera-avbp file) - -#ifndef CT_STFLOW_H -#define CT_STFLOW_H - -#include "Flow1D.h" - -namespace Cantera -{ - -//------------------------------------------ -// constants -//------------------------------------------ - -//! Offsets of solution components in the 1D solution array. -enum offset -{ - c_offset_U //! axial velocity - , c_offset_V //! strain rate - , c_offset_T //! temperature - , c_offset_L //! (1/r)dP/dr - , c_offset_E //! electric poisson's equation - , c_offset_Y //! mass fractions -}; - -//! Offsets of solution components in the 1D solution array for mixture fraction space -enum offset_z -{ - c_offset_Tflamelet, //! Temperature - c_offset_Yflamelet, //! Species mass fractions - // c_offset_Chi not used -}; - -class Transport; - -//! @defgroup flowGroup Flow Domains -//! One-dimensional flow domains. -//! @ingroup onedGroup - -/** - * This class represents 1D flow domains that satisfy the one-dimensional - * similarity solution for chemically-reacting, axisymmetric flows. - * - * @deprecated To be removed after %Cantera 3.1; replaced by Flow1D. - * @ingroup flowGroup - */ -class StFlow : public Flow1D -{ -public: - //! Create a new flow domain. - //! @param ph Object representing the gas phase. This object will be used - //! to evaluate all thermodynamic, kinetic, and transport properties. - //! @param nsp Number of species. - //! @param points Initial number of grid points - //! @param n_eq Number of non-species equations (default = 4 for spatial resolution) - - //StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t points = 1); - StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); - - //! Delegating constructor - StFlow(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); - - //! Create a new flow domain. - //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and - //! transport properties - //! @param id name of flow domain - //! @param points initial number of grid points - StFlow(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Y, size_t points=1); - - virtual ~StFlow(); // virtual kw required for derived class destructors (flamelet) - - virtual string type() const override; - - //! @name Problem Specification - //! @{ - - void setupGrid(size_t n, const double* z) override; - void setupGrid(size_t n); - - virtual void resetBadValues(double* xg) override; - - ThermoPhase& phase() { - return *m_thermo; - } - - Kinetics& kinetics() { - return *m_kin; - } - - /** - * Set the thermo manager. - * - * @deprecated To be removed after %Cantera 3.0 (unused) - */ - void setThermo(ThermoPhase& th); - - void setKinetics(shared_ptr kin) override; - - //! Set the kinetics manager. - //! @deprecated To be removed after %Cantera 3.0; - //! replaced by Domain1D::setKinetics() - void setKinetics(Kinetics& kin); - - void setTransport(shared_ptr trans) override; - - //! Set transport model to existing instance - //! @deprecated To be removed after %Cantera 3.0; - //! replaced by Domain1D::setKinetics() - void setTransport(Transport& trans); - - //! Set the transport model - //! @since New in %Cantera 3.0. - void setTransportModel(const string& trans); - - //! Retrieve transport model - //! @since New in %Cantera 3.0. - string transportModel() const; - - //! Enable thermal diffusion, also known as Soret diffusion. - //! Requires that multicomponent transport properties be - //! enabled to carry out calculations. - void enableSoret(bool withSoret) { - m_do_soret = withSoret; - } - bool withSoret() const { - return m_do_soret; - } - - //! Set the pressure. Since the flow equations are for the limit of small - //! Mach number, the pressure is very nearly constant throughout the flow. - void setPressure(double p) { - m_press = p; - } - - //! The current pressure [Pa]. - double pressure() const { - return m_press; - } - - //! Set the number of non-species equations - void setNequation(size_t neq){ - m_neq = neq; - } - - //! The current number of non-species equations - size_t nEq(){ - return m_neq; - } - - //! Write the initial solution estimate into array x. - void _getInitialSoln(double* x) override; - - void _finalize(const double* x) override; - - //! Sometimes it is desired to carry out the simulation using a specified - //! temperature profile, rather than computing it by solving the energy - //! equation. This method specifies this profile. - void setFixedTempProfile(vector& zfixed, vector& tfixed) { - m_zfix = zfixed; - m_tfix = tfixed; - } - - /** - * Set the temperature fixed point at grid point j, and disable the energy - * equation so that the solution will be held to this value. - */ - void setTemperature(size_t j, double t) { - m_fixedtemp[j] = t; - m_do_energy[j] = false; - } - - //! The fixed temperature value at point j. - double T_fixed(size_t j) const { - return m_fixedtemp[j]; - } - - /// Returns the mixture fraction at point j - /// Added by P. Wolf - March 2010 - /// Thanks to Alireza Najafiyazdi - double getMixFrac(size_t j) { - return m_zmixfrac[j]; - } - - /// Updates the mixture fraction at point j - /// Added by P. Wolf - March 2010 - /// Thanks to Alireza Najafiyazdi - void calcMixFrac(const double* x,size_t j); - - //! @} - - string componentName(size_t n) const override; - - size_t componentIndex(const string& name) const override; - - //! Returns true if the specified component is an active part of the solver state - virtual bool componentActive(size_t n) const; - - //! Print the solution. - void show(const double* x) override; - - shared_ptr asArray(const double* soln) const override; - void fromArray(SolutionArray& arr, double* soln) override; - - //! Set flow configuration for freely-propagating flames, using an internal point - //! with a fixed temperature as the condition to determine the inlet mass flux. - void setFreeFlow() { - // m_type = cFreeFlow; // AP : test to remove the domain type (not used in Flow1D.h) - m_dovisc = false; - m_isFree = true; - m_usesLambda = false; - } - - //! Set flow configuration for axisymmetric counterflow flames, using specified - //! inlet mass fluxes. - void setAxisymmetricFlow() { - // m_type = cAxisymmetricStagnationFlow; // AP : test to remove the domain type (not used in Flow1D.h) - m_dovisc = true; - m_isFree = false; - m_usesLambda = true; - } - - //! Set flow configuration for burner-stabilized flames, using specified inlet mass - //! fluxes. - void setUnstrainedFlow() { - // m_type = cAxisymmetricStagnationFlow; // AP : test to remove the domain type (not used in Flow1D.h) - m_dovisc = false; - m_isFree = false; - m_usesLambda = false; - } - - void setFlameletFlow() { - // m_type = cFlameletFlow; // AP : test to remove the domain type (not used in Flow1D.h) - m_dovisc = true; - m_isFree = false; - m_usesLambda = true; - } - - //! Return the type of flow domain being represented, either "Free Flame" or - //! "Axisymmetric Stagnation". - //! @see setFreeFlow setAxisymmetricFlow - //! @deprecated To be removed after %Cantera 3.0; replaced by type(). - virtual string flowType() const; - - virtual void setFuelSpecies(const std::string fuel) { - m_fuel = fuel; - } - - void solveEnergyEqn(size_t j=npos); - - //! Get the solving stage (used by IonFlow specialization) - //! @since New in %Cantera 3.0 - virtual size_t getSolvingStage() const; - - //! Solving stage mode for handling ionized species (used by IonFlow specialization) - //! - @c stage=1: the fluxes of charged species are set to zero - //! - @c stage=2: the electric field equation is solved, and the drift flux for - //! ionized species is evaluated - virtual void setSolvingStage(const size_t stage); - - //! Set to solve electric field in a point (used by IonFlow specialization) - virtual void solveElectricField(size_t j=npos); - - //! Set to fix voltage in a point (used by IonFlow specialization) - virtual void fixElectricField(size_t j=npos); - - //! Retrieve flag indicating whether electric field is solved or not (used by - //! IonFlow specialization) - virtual bool doElectricField(size_t j) const; - - //! Turn radiation on / off. - /*! - * The simple radiation model used was established by Liu and Rogg - * @cite liu1991. This model considers the radiation of CO2 and H2O. - * - * This model uses the optically thin limit and the gray-gas approximation to - * simply calculate a volume specified heat flux out of the Planck absorption - * coefficients, the boundary emissivities and the temperature. Polynomial lines - * calculate the species Planck coefficients for H2O and CO2. The data for the - * lines are taken from the RADCAL program @cite RADCAL. - * The coefficients for the polynomials are taken from - * [TNF Workshop](https://tnfworkshop.org/radiation/) material. - */ - void enableRadiation(bool doRadiation) { - m_do_radiation = doRadiation; - } - - //! Returns `true` if the radiation term in the energy equation is enabled - bool radiationEnabled() const { - return m_do_radiation; - } - - //! Return radiative heat loss at grid point j - double radiativeHeatLoss(size_t j) const { - return m_qdotRadiation[j]; - } - - //! Set the emissivities for the boundary values - /*! - * Reads the emissivities for the left and right boundary values in the - * radiative term and writes them into the variables, which are used for the - * calculation. - */ - void setBoundaryEmissivities(double e_left, double e_right); - - // Turn soot formation on / off. - // setSections - const size_t getSections() const{ - return m_nsoot; - } - - void setSections(size_t nSec) { - m_nsoot = nSec; - } - - void setPrecursors(std::vector id_precursors); - - void setSootLoglevel(size_t loglevel){ - soot_loglevel = loglevel; - } - - size_t getSootLoglevel(){ - return soot_loglevel; - } - - void enableCondensation(bool doCondensation) { - m_do_condensation = doCondensation; - } - bool condensationEnabled(){ - return m_do_condensation; - } - - void enableCoagulation(bool doCoagulation) { - m_do_coagulation = doCoagulation; - } - bool coagulationEnabled(){ - return m_do_coagulation; - } - - void setCollisionModel(std::string collisionModel){ - m_collision_model = collisionModel; - } - - std::string getCollisionModel(){ - return m_collision_model; - } - - void setSootMorphology(std::string morphologyModel){ - m_soot_morphology = morphologyModel; - } - - std::string getSootMorphology(){ - return m_soot_morphology; - } - - void enableRetroaction(bool doRetroaction){ - m_do_retroaction = doRetroaction; - } - bool retroactionEnabled(){ - return m_do_retroaction; - } - - void enableSootRadiation(bool do_soot_radiation){ - m_do_soot_radiation = do_soot_radiation; - } - - bool sootRadiationEnabled(){ - return m_do_soot_radiation; - } - - void enableSootSoret(bool do_soot_soret){ - m_do_soot_soret = do_soot_soret; - } - - bool sootSoretEnabled(){ - return m_do_soot_soret; - } - - void enableSurfaceGrowth(bool do_sg){ - m_do_sg = do_sg; - } - bool surfaceGrowthEnabled(){ - return m_do_sg; - } - - void enableOxidation(bool do_oxidation){ - m_do_oxidation = do_oxidation; - } - bool oxidationEnabled(){ - return m_do_oxidation; - } - - void enableTrashSection(double trash_section){ - if (trash_section > 0){ - m_trash_section = true; - dTrashLowLim = trash_section; - }else{ - m_trash_section = false; - dTrashLowLim = 0.0; - } - } - - bool trashSectionEnabled(){ - return m_trash_section; - } - - void setHaca(size_t haca_model){ - m_haca_model = haca_model; - } - - size_t getHaca(){ - return m_haca_model; - } - - double getKazakovTad(){ - return kazakovTad; - } - void setKazakovTad(double kazakov_tad){ - kazakovTad = kazakov_tad; - } - - void loadHaca(size_t m_haca_model){ - if (m_haca_model == 1){ //Mauss - // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] - double lambda = 1.0 / S_C2; - // Number of sites [-] - // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) - n_sites = lambda * S_C2; - // Mauss HACA-RC model - //1st order : [1/s] , [-], [J/mol] - //2nd order : [m3/kmol/s], [-], [J/mol] - // S-H + H <-> S* + H2 - ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; - ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; - // S-H + OH <-> S* + H2O - ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; - ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; - // S* + H <-> S-H - ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; - ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; - // S* + C2H2 <-> S-H - ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; - ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; - // S* <-> S-H + H - ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; - ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; - // S* + O2 -> S-H + 2CO - ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 8.4000e03; - // S* + O2 -> S-H + 2HCO - // S-H + OH -> S-H + CO - gamma_oh = 0.13; - }else if (m_haca_model == 11){ //Mauss tuned (Guo 2016) - // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] - double lambda = 1.0 / S_C2; - // Number of sites [-] - // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) - n_sites = lambda * S_C2; - // Mauss HACA-RC model - //1st order : [1/s] , [-], [J/mol] - //2nd order : [m3/kmol/s], [-], [J/mol] - // S-H + H <-> S* + H2 - ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; - ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; - // S-H + OH <-> S* + H2O - ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; - ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; - // S* + H <-> S-H - ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; - ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; - // S* + C2H2 <-> S-H - ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; - ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; - // S* <-> S-H + H - ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; - ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; - // S* + O2 -> S-H + 2CO - ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 190.000e03; - // S* + O2 -> S-H + 2HCO - // S-H + OH -> S-H + CO - gamma_oh = 0.10; - }else if (m_haca_model == 2){ //Blanquart - // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] - double lambda = 1.7e19; - // Number of sites [-] - // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) - n_sites = lambda * S_C2; - // Blanquart HACA model - //1st order : [1/s] , [-], [J/mol] - //2nd order : [m3/kmol/s], [-], [J/mol] - // S-H + H <-> S* + H2 - ak01f = 1.0e8 * 1e-3; nk01f = 1.8; ek01f = 68420.0; - ak01b = 8.68e4 * 1e-3; nk01b = 2.36; ek01b = 25460.0; - // S-H + OH <-> S* + H2O - ak02f = 6.72e1 * 1e-3; nk02f = 3.33; ek02f = 6090.0; - ak02b = 6.44e-1 * 1e-3; nk02b = 3.79; ek02b = 27960.0; - // S-H <-> S* + H - ak03f = 1.13e16; nk03f = -0.06; ek03f = 476050.0; - ak03b = 4.17e13 * 1e-3; nk03b = 0.15; ek03b = 0.0; - // S* + C2H2 -> S-H - ak04f = 2.52e9 * 1e-3; nk04f = 1.77; ek04f = 13540.0; - // S* + O2 -> S + 2CO - ak05f = 2.2e12 * 1e-3; nk05f = 0.0; ek05f = 31380.0; - // S-H + OH -> S-H + CO - gamma_oh = 0.13; - }else if (m_haca_model == 3){ - // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [m-2] - double lambda = 2.3e19; - // Number of sites [-] - // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) - n_sites = lambda * S_C2; - // Kazakov HACA model - //1st order : [1/s] , [-], [J/mol] - //2nd order : [m3/mol/s], [-], [J/mol] - // S-H + H <-> S* + H2 - ak01f = 2.5e14 * 1e-3; nk01f = 0.0; ek01f = 66900.0; - ak01b = 3.9e12 * 1e-3; nk01b = 0.0; ek01b = 39000.0; - // S* + H -> S-H - ak02f = 1.0e14 * 1e-3; nk02f = 0.0; ek02f = 0.0; - // S* + C2H2 -> S-H + H - ak03f = 8.4e11 * 1e-3; nk03f = 0.4; ek03f = 35100.0; - // S* + O2 -> S + 2CO - ak04f = 2.2e12 * 1e-3; nk04f = 0.0; ek04f = 31300.0; - // S-H + OH -> S-H + CO - gamma_oh = 0.13; - } - } - - void finalizeSoot(); - void loadSurface(); - //Initialize soot - void initSoot(); - void showSootInfo(); - // Sections generation and display - void sootCreationVol(); - void showSootSections(); - void sootCollisionModel(); - void getDistributionOrdre0(const double* x, size_t j); - // Soot source terms - void sootSource(const double* x, size_t j); - void sootDimerization(const double* x, size_t j); - void sootNucleation(const double* x, size_t j); - void sootCondensation(const double* x, size_t j); - void sootCoagulation(const double* x, size_t j); - void sootSurface(const double* x, size_t j); - void sootSurfaceInitialization(const double* x, size_t j); - void sootCollisionInverse(); - // Returns section name - std::string sectionName(size_t n) const { - return m_section_name[n]; - } - - const vector& vMin() const { - return vSectMin; - } - - const vector& vMax() const { - return vSectMax; - } - - const vector& vMean() const { - return vSectMean; - } - - const vector& dMean() const { - return dSectMean; - } - - const vector& dCol() const { - return dSectCol; - } - - const vector& aCol() const { - return aSectCol; - } - - const vector& sMean() const { - return sSectMean; - } - - const vector& thetaSoot() const { - return theta_surf; - } - - const vector& fractalPrefactor() const { - return kfractal; - } - - const vector& fractalDimension() const { - return Dfractal; - } - - const double rhoSoot() const { - return rho_soot; - } - - const double getSootInception(size_t j) const { - return m_qdotNucleation[j] * m_rho[j]; - } - - const double getSootCondensation(size_t k, size_t j) const { - return m_qdotCondensation(k,j) * m_rho[j]; - } - - const double getSootCoagulation(size_t k, size_t j) const { - return m_qdotCoagulation(k,j) * m_rho[j]; - } - - const double getSootSg(size_t k, size_t j) const { - return m_qdotSg(k,j) * m_rho[j]; - } - - const double getSootOxidation(size_t k, size_t j) const { - return m_qdotOxidation(k,j) * m_rho[j]; - } - - const double fv(const double* x, size_t j){ - double val = 0.0; - for (size_t k=0; k < m_nsoot; k++){ - val += Ys(x,k,j); - } - val *= m_rho[j] / rho_soot; - return val; - } - - const double sootPrimaryDiam(size_t k) const { - return 2.0 * rNucMean[k]; - } - - const double sootPrimaryPart(size_t k) const { - return nNucMean[k]; - } - - void setThick(double thickness){ - m_thick = thickness; - AVBPReadInputChem(); - } - - double getThick() const { - return m_thick; - } - - //! Return emissivity at left boundary - double leftEmissivity() const { return m_epsilon_left; } - - //! Return emissivity at right boundary - double rightEmissivity() const { return m_epsilon_right; } - - void fixTemperature(size_t j=npos); - - bool doEnergy(size_t j) { - return m_do_energy[j]; - } - - //! Change the grid size. Called after grid refinement. - void resize(size_t components, size_t points) override; - - //! Set the gas object state to be consistent with the solution at point j. - virtual void setGas(const double* x, size_t j); - - //! Set the gas state to be consistent with the solution at the midpoint - //! between j and j + 1. - virtual void setGasAtMidpoint(const double* x, size_t j); - - double density(size_t j) const { - return m_rho[j]; - } - - //! seems unused - double cpBar(size_t j) const { - return m_cpm[j]; - } - - double enthalpy(size_t j) const { - return m_h[j]; - } - - double thCond(size_t j) const { - return m_tcon[j]; - } - - double HR(size_t j) const { - return m_hr[j]; - } - - //! @deprecated To be removed after %Cantera 3.0. Superseded by isFree() - virtual bool fixed_mdot(); - - /** - * Retrieve flag indicating whether flow is freely propagating. - * The flow is unstrained and the axial mass flow rate is not specified. - * For free flame propagation, the axial velocity is determined by the solver. - * @since New in %Cantera 3.0 - */ - bool isFree() const { - return m_isFree; - } - - /** - * Retrieve flag indicating whether flow uses radial momentum. - * If `true`, radial momentum equation for @f$ V @f$ as well as - * @f$ d\Lambda/dz = 0 @f$ are solved; if `false`, @f$ \Lambda(z) = 0 @f$ and - * @f$ V(z) = 0 @f$ by definition. - * @since New in %Cantera 3.0 - */ - bool isStrained() const { - return m_usesLambda; - } - - void setViscosityFlag(bool dovisc) { - m_dovisc = dovisc; - } - - - // P. Wolf - void AVBPReadInputPea(); - - //+++++++++++++++++++++++++++++++++++++++++++++++++++ - // B. Franzelli modifications to perform thickening - //+++++++++++++++++++++++++++++++++++++++++++++++++++ - void AVBPReadInputChem(); - void AVBPcompute_local_thick(double* x,size_t j); - - double AVBPthick(size_t j) const { - return avbp_thick[j]; - } - - /** - * Evaluate the residual function for axisymmetric stagnation flow. If - * j == npos, the residual function is evaluated at all grid points. - * Otherwise, the residual function is only evaluated at grid points - * j-1, j, and j+1. This option is used to efficiently evaluate the - * Jacobian numerically. - */ - void eval(size_t j, double* x, double* r, integer* mask, double rdt) override; - - //! Evaluate all residual components at the right boundary. - virtual void evalRightBoundary(double* x, double* res, int* diag, double rdt); - - void evalContinuity(size_t j, double* x, double* r, int* diag, double rdt) override; - -protected: - double wdot(size_t k, size_t j) const { - return m_wdot(k,j); - } - - //! Write the net production rates at point `j` into array `m_wdot` - // void getWdot(double* x, size_t j) { - // setGas(x,j); - // m_kin->getNetProductionRates(&m_wdot(0,j)); - // } -/// write the net production rates at point j into array m_wdot -/// Modified by P. Wolf March 2010 - Thanks to Alireza N. -/// when PEA activated: production rates depends on mixture fraction at point j -/// WARNING: the following is valid only for fuel/AIR right now - void getWdot(double *x, size_t j) - { - double zloc; - double phi; - setGas(x, j); // We'll need to set the gas before retrieving - // std::cout << "after setGas" << std::endl; - zloc = getMixFrac(j); // the Mixture Fraction and calculating wdot - phi = zloc / (1. - zloc) * phi_cst; - - switch (avbp_ipea) - { - case 0: - m_kin->getNetProductionRates(&m_wdot(0, j)); - break; - // ipea = 1, apply the PEA on fuel oxydation reaction only - case 1: - double pea_f; // pea correction function - // Now set the PEA correction function - pea_f = 0.5 * (1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) - + avbp_pea_coeffs[2] / 4. * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) - * (1. + tanh((avbp_pea_coeffs[5] - phi) / avbp_pea_coeffs[6])); - - // Multiply reaction rate of reaction 1 by the pea coeff - m_kin->setMultiplier(1, pea_f); - // Get the net production rates for all species - m_kin->getNetProductionRates(&m_wdot(0, j)); - // Restore the original reaction rates (not necessary) - m_kin->setMultiplier(1, 1.0 / pea_f); - break; - // ipea = 2, apply PEA on both reactions - case 2: - // TEST 081014: differencie bien les cas - double pea2_f[2]; // pea correction function - // Now set the PEA correction function - pea2_f[0] = 2. / ((1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) - + avbp_pea_coeffs[2] * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) - + avbp_pea_coeffs[5] * (1. + tanh((phi - avbp_pea_coeffs[6]) / avbp_pea_coeffs[7]))); - - pea2_f[1] = 0.5 * ((1. + tanh((avbp_pea_coeffs[8] - phi) / avbp_pea_coeffs[9])) - + avbp_pea_coeffs[10] * (1. + tanh((phi - avbp_pea_coeffs[11]) / avbp_pea_coeffs[12])) - + avbp_pea_coeffs[13] * (1. + tanh((phi - avbp_pea_coeffs[14]) / avbp_pea_coeffs[15])) - * (1. + tanh((avbp_pea_coeffs[16] - phi) / avbp_pea_coeffs[17]))); - // Multiply reaction rates by the pea coeff - if (m_kin->nReactions() == 2) - { - for (size_t n = 0; n < m_kin->nReactions(); n++) - { - m_kin->setMultiplier(n, pea2_f[n]); - } - // Get the net production rates for all species - m_kin->getNetProductionRates(&m_wdot(0, j)); - // Restore the original reaction rates (not necessary) - for (size_t n = 0; n < m_kin->nReactions(); n++) - { - m_kin->setMultiplier(n, 1.0 / pea2_f[n]); - } - } - else - { - throw CanteraError("getWdot", "ipea = 2 but there ain't 2 reactions"); - } - break; - // ipea = 3, apply PEA on both reactions (for CM2 only) - case 3: - double pea3_f[2]; // pea correction function - - // Now set the PEA correction function - if (phi > 1.0) - { - // pea3_f[0] = max(avbp_pea_coeffs[0]*phi*phi + avbp_pea_coeffs[1]*phi + avbp_pea_coeffs[2],0.0); - pea3_f[0] = avbp_pea_coeffs[0] * phi * phi + avbp_pea_coeffs[1] * phi + avbp_pea_coeffs[2]; - } - else - { - pea3_f[0] = 1; - } - pea3_f[1] = pea3_f[0]; - - // Multiply reaction rates by the pea coeff - if (m_kin->nReactions() == 2) - { - for (size_t n = 0; n < m_kin->nReactions(); n++) - { - m_kin->setMultiplier(n, pea2_f[n]); - } - - // Get the net production rates for all species - m_kin->getNetProductionRates(&m_wdot(0, j)); - - // Restore the original reaction rates (not necessary) - for (size_t n = 0; n < m_kin->nReactions(); n++) - { - m_kin->setMultiplier(n, 1.0 / pea2_f[n]); - } - } - else - { - throw CanteraError("getWdot", "ipea = 3 but there ain't 2 reactions"); - } - - break; - - default: - throw CanteraError("getWdot", "ipea is set to a weird value"); - break; - } - } - - //! Evaluate the residual function. This function is called in eval - //! after updateProperties is called. - virtual void evalResidual(double* x, double* rsd, int* diag, - double rdt, size_t jmin, size_t jmax); - - /** - * Update the thermodynamic properties from point j0 to point j1 - * (inclusive), based on solution x. - */ - virtual void updateThermo(const double* x, size_t j0, size_t j1) { - for (size_t j = j0; j <= j1; j++) { - setGas(x,j); - m_rho[j] = m_thermo->density(); - m_wtm[j] = m_thermo->meanMolecularWeight(); - m_cp[j] = m_thermo->cp_mass(); - m_thermo->getPartialMolarEnthalpies(&m_hk(0, j)); - } - } - - //-------------------------------- - // central-differenced derivatives - //-------------------------------- - double cdif1(const double*x, size_t n, size_t j) const { - double c1 = (x[index(n,j+1)] - x[index(n,j-1)]); - return c1/(z(j+1) - z(j-1)); - } - - //! seems unused - double cdif2(const double* x, size_t n, size_t j, - const double* f) const { - double c1 = (f[j] + f[j-1])*(x[index(n,j)] - x[index(n,j-1)]); - double c2 = (f[j+1] + f[j])*(x[index(n,j+1)] - x[index(n,j)]); - return (c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); - } - - //! @name Solution components - //! @{ - - virtual double T(const double* x, size_t j) const { - return x[index(c_offset_T, j)]; - } - virtual double& T(double* x, size_t j) { - return x[index(c_offset_T, j)]; - } - virtual double T_prev(size_t j) const { - return prevSoln(c_offset_T, j); - } - - double rho_u(const double* x, size_t j) const { - return m_rho[j]*x[index(c_offset_U, j)]; - } - - double u(const double* x, size_t j) const { - return x[index(c_offset_U, j)]; - } - - double V(const double* x, size_t j) const { - return x[index(c_offset_V, j)]; - } - double V_prev(size_t j) const { - return prevSoln(c_offset_V, j); - } - - double lambda(const double* x, size_t j) const { - return x[index(c_offset_L, j)]; - } - - virtual double Y(const double* x, size_t k, size_t j) const { - return x[index(c_offset_Y + k, j)]; - } - - virtual double& Y(double* x, size_t k, size_t j) { - return x[index(c_offset_Y + k, j)]; - } - - virtual double Y_prev(size_t k, size_t j) const { - return prevSoln(c_offset_Y + k, j); - } - - //Soot - double Ys(const double* x, size_t k, size_t j) const { - return x[index(c_offset_S+k, j)]; - } - - double& Ys(double* x, size_t k, size_t j) { - return x[index(c_offset_S+k, j)]; - } - - double Ys_prev(size_t k, size_t j) const { - return prevSoln(c_offset_S + k, j); - } - //---- - - double X(const double* x, size_t k, size_t j) const { - return m_wtm[j]*Y(x,k,j)/m_wt[k]; - } - - double flux(size_t k, size_t j) const { - return m_flux(k, j); - } - //! @} - - //! @name convective spatial derivatives. - //! - //! These use upwind differencing, assuming u(z) is negative - //! @{ - double dVdz(const double* x, size_t j) const { - size_t jloc = (u(x,j) > 0.0 ? j : j + 1); - return (V(x,jloc) - V(x,jloc-1))/m_dz[jloc-1]; - } - - double dYdz(const double* x, size_t k, size_t j) const { - size_t jloc = (u(x,j) > 0.0 ? j : j + 1); - return (Y(x,k,jloc) - Y(x,k,jloc-1))/m_dz[jloc-1]; - } - - // Soot - double dYsdz(const double* x, size_t k, size_t j) const { - size_t jloc = (u(x,j) > 0.0 ? j : j + 1); - return (Ys(x,k,jloc) - Ys(x,k,jloc-1))/m_dz[jloc-1]; - } - - double dTdz(const double* x, size_t j) const { - size_t jloc = (u(x,j) > 0.0 ? j : j + 1); - return (T(x,jloc) - T(x,jloc-1))/m_dz[jloc-1]; - } - //! @} - - double shear(const double* x, size_t j) const { - double c1 = m_visc[j-1]*(V(x,j) - V(x,j-1)); - double c2 = m_visc[j]*(V(x,j+1) - V(x,j)); - return 2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); - } - - double divHeatFlux(const double* x, size_t j) const { - double c1 = m_tcon[j-1]*(T(x,j) - T(x,j-1)); - double c2 = m_tcon[j]*(T(x,j+1) - T(x,j)); - return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); - } - - double AVBPdivHeatFlux(const double* x, size_t j) const { - double c1 = avbp_thick[j-1]*m_tcon[j-1]*(T(x,j) - T(x,j-1)); - double c2 = avbp_thick[j]*m_tcon[j]*(T(x,j+1) - T(x,j)); - return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); - } - - size_t mindex(size_t k, size_t j, size_t m) { - return m*m_nsp*m_nsp + m_nsp*j + k; - } - - //! Update the diffusive mass fluxes. - virtual void updateDiffFluxes(const double* x, size_t j0, size_t j1); - virtual void updateSootDiffFluxes(const double* x, size_t j0, size_t j1); - - //! Get the gradient of species specific molar enthalpies - virtual void grad_hk(const double* x, size_t j); - - //--------------------------------------------------------- - // member data - //--------------------------------------------------------- - - double m_press = -1.0; // pressure - - // grid parameters - vector m_dz; - - // mixture thermo properties - vector m_rho; - vector m_wtm; - - // P. Wolf - vector m_zmixfrac; - - vector m_cpm; - vector m_h; - - // species thermo properties - vector m_wt; - vector m_cp; - - // transport properties - vector m_ybar; - vector m_visc; - vector m_tcon; - vector m_diff; - vector m_multidiff; - Array2D m_dthermal; - Array2D m_flux; - - //! Array of size #m_nsp by #m_points for saving molar enthalpies - Array2D m_hk; - - //! Array of size #m_nsp by #m_points-1 for saving enthalpy fluxes - Array2D m_dhk_dz; - - // production rates - vector m_hr; - Array2D m_wdot; - - size_t m_nsp; //!< Number of species in the mechanism - size_t m_neq; //!< Number of non-species equations - size_t m_nsoot; - std::string m_fuel; - - ThermoPhase* m_thermo = nullptr; - Kinetics* m_kin = nullptr; - Transport* m_trans = nullptr; - - MultiJac* m_jac = nullptr; - - // boundary emissivities for the radiation calculations - double m_epsilon_left = 0.0; - double m_epsilon_right = 0.0; - - //! Indices within the ThermoPhase of the radiating species. First index is - //! for CO2, second is for H2O. - vector m_kRadiating; - - // Pierre WOLF: added parameters for input_pea.dat - size_t avbp_ipea = 0; - std::string avbp_fuel; - vector avbp_pea_coeffs; - double phi_cst; - - //+++++++++++++++++++++++++++++++++++++++++++++++++++ - // B. Franzelli modifications to perform thickening - // input_chem parameters - //+++++++++++++++++++++++++++++++++++++++++++++++++++ - double avbp_fthick; - vector avbp_thick; - double m_thick = 1.0; - - // flags - vector m_do_energy; - bool m_do_soret = false; - vector m_do_species; - bool m_do_multicomponent = false; - - //! flag for the radiative heat loss - bool m_do_radiation = false; - - //! radiative heat loss vector - vector m_qdotRadiation; - - // ---------------------- - // SOOT RELATED VARIABLES - // ---------------------- - bool m_do_soot_soret = true; - bool m_do_condensation = false; - bool m_do_soot_radiation = false; - bool m_do_coagulation = false; - std::string m_soot_morphology; - bool m_do_retroaction = false; - bool m_do_sg = false; - bool m_do_oxidation = false; - bool m_trash_section = false; - std::string m_collision_model = "rodrigues"; - size_t soot_loglevel=1; - size_t c_offset_S = 6; - size_t n_PAH = 0; - size_t m_haca_model; - double Y_PAH; - double C_PAH; - double dTrashLowLim; - vector W_PAH; - double W_C; - vector n_C; - double N_dimer; - double beta_dimer; - double r_dimer; - double V_dimer; - double beta_fm; - double n_sites; - double kazakovTad; - double ksg; - double kox; - vector sootConsumption; - vector vSectMin; - vector vSectMax; - vector dSectMean; - vector dSectCol; - vector rSectCol; - vector aSectCol; - vector vSectMean; - vector sSectMean; - vector Dfractal; - vector kfractal; - vector nNucMean; - vector rNucMean; - vector rSmolMean; - vector PAMean; - vector m_qdotNucleation; - Array2D m_qdotCondensation; - Array2D m_qdotCoagulation; - Array2D m_qdotSg; - Array2D m_qdotOxidation; - vector q; - vector theta_surf; - vector jpower; - vector kpower; - vector mpower; - vector vc2power; - vector vc2powerm; - vector vmax_kpower; - vector vmin_kpower; - vector vmax_jpower; - vector vmin_jpower; - vector vmax_mpower; - vector vmin_mpower; - vector vmaxmc2_kpower; - vector vminpc2_kpower; - vector vmaxmc2_jpower; - vector vminpc2_jpower; - vector vmaxmc2_mpower; - vector vminpc2_mpower; - vector vc2powervect; - vector vc2powermvect; - vector m_section_name; - vector m_precursors; - Array2D m_soot_diff ; - Array2D m_soot_soret ; - Array2D collision_mat; - //Surface reactions - double ak00f, nk00f, ek00f, ak01f, nk01f, ek01f, ak02f, nk02f, ek02f, - ak03f, nk03f, ek03f, ak04f, nk04f, ek04f, ak05f, nk05f, ek05f, - ak06f, nk06f, ek06f, ak07f, nk07f, ek07f; - double ak00b, nk00b, ek00b, ak01b, nk01b, ek01b, ak02b, nk02b, ek02b, - ak03b, nk03b, ek03b, ak04b, nk04b, ek04b, ak05b, nk05b, ek05b, - ak06b, nk06b, ek06b, ak07b, nk07b, ek07b; - double gamma_oh; - // ----------------------------- - // END OF SOOT RELATED VARIABLES - // ----------------------------- - - // fixed T and Y values - vector m_fixedtemp; - vector m_zfix; - vector m_tfix; - - //! Index of species with a large mass fraction at each boundary, for which - //! the mass fraction may be calculated as 1 minus the sum of the other mass - //! fractions - size_t m_kExcessLeft = 0; - size_t m_kExcessRight = 0; - - bool m_dovisc; - bool m_isFree; - bool m_usesLambda; - - //! Update the transport properties at grid points in the range from `j0` - //! to `j1`, based on solution `x`. - virtual void updateTransport(double* x, size_t j0, size_t j1); - -public: - //! Location of the point where temperature is fixed - double m_zfixed = Undef; - - //! Temperature at the point used to fix the flame location - double m_tfixed = -1.0; - -// private: -// vector m_ybar; -}; - -} - -#endif diff --git a/interfaces/cython/cantera/_onedim.pxd b/interfaces/cython/cantera/_onedim.pxd index 8e77fe12f20..b3ec4179ef8 100644 --- a/interfaces/cython/cantera/_onedim.pxd +++ b/interfaces/cython/cantera/_onedim.pxd @@ -106,7 +106,6 @@ cdef extern from "cantera/oneD/Flow1D.h": void setSections(size_t) size_t getSections() void setFlameletFlow() - string flowType() void setPrecursors(vector[size_t]&) @@ -216,8 +215,8 @@ cdef extern from "cantera/thermo/IdealGasPhase.h": cdef cppclass CxxIdealGasPhase "Cantera::IdealGasPhase" cdef extern from "cantera/oneD/Flamelet.h": - cdef cppclass CxxFlamelet "Cantera::Flamelet" (CxxStFlow): - CxxFlamelet(CxxStFlow*) + cdef cppclass CxxFlamelet "Cantera::Flamelet" (CxxFlow1D): + CxxFlamelet(CxxFlow1D*) double chiSt() #except +translate_exception double zSt() #except +translate_exception void setChiSt(double) #except +translate_exception @@ -239,7 +238,7 @@ cdef class ReactingSurface1D(Boundary1D): cdef class FlowBase(Domain1D): cdef CxxFlow1D* flow -cdef class FlameletFlow(_FlowBase): +cdef class FlameletFlow(FlowBase): cdef CxxFlamelet* flamelet cdef class Sim1D: diff --git a/interfaces/cython/cantera/_onedim.pyx b/interfaces/cython/cantera/_onedim.pyx index 4cc2ecdc033..d3f45f8425a 100644 --- a/interfaces/cython/cantera/_onedim.pyx +++ b/interfaces/cython/cantera/_onedim.pyx @@ -418,21 +418,6 @@ cdef class ReactingSurface1D(Boundary1D): gas phase. """ _domain_type = "reacting-surface" - def __cinit__(self, _SolutionBase phase, *args, name="", **kwargs): - # once legacy path is removed, the parent __cinit__ is sufficient - self.legacy = phase.phase_of_matter == "gas" - if self.legacy: - # legacy pathway - deprecation is handled in __init__ - self.surf = new CxxReactingSurf1D() - self.domain = (self.surf) - else: - self._domain = CxxNewDomain1D(stringify(self._domain_type), phase._base, stringify(name), - #add kwargs if kwargs provided - kwargs['sections'] if 'sections' in kwargs else 0, - ) - self.domain = self._domain.get() - self.surf = self.domain - self.boundary = (self.surf) def __init__(self, _SolutionBase phase, name=None): gas = None @@ -1171,18 +1156,6 @@ cdef class FlowBase(Domain1D): """ self.flow.setFlameletFlow() - property flow_type: - """ - Return the type of flow domain being represented, either "Free Flame" or - "Axisymmetric Stagnation". - - .. deprecated:: 3.0 - - Method to be removed after Cantera 3.0; superseded by `domain_type`. - """ - def __get__(self): - return pystr(self.flow.flowType()) - @property def type(self): """ diff --git a/samples/python/AVBP/1-runBurner.py b/samples/python/AVBP/1-runBurner.py index 25902d7b859..879f0688c3b 100644 --- a/samples/python/AVBP/1-runBurner.py +++ b/samples/python/AVBP/1-runBurner.py @@ -44,7 +44,7 @@ f.flame.set_fixed_temp_profile(z/max(z), T) # Setting the transport model to mixture-averaged -f.transport_model = 'Mix' +f.transport_model = 'mixture-averaged' # Setting mesh refinement criteria f.set_refine_criteria(ratio=2.0, slope=0.1, curve=0.1) @@ -53,7 +53,7 @@ f.solve(1, 'refine') # Showing the result -f.show_solution() +f.show() # Saving the result if ct.__version__ >= '2.5.0': diff --git a/samples/python/AVBP/2-restoreBurner.py b/samples/python/AVBP/2-restoreBurner.py index 3dd46de3365..606ff010df4 100644 --- a/samples/python/AVBP/2-restoreBurner.py +++ b/samples/python/AVBP/2-restoreBurner.py @@ -19,10 +19,10 @@ z, T = np.genfromtxt('./inputs/T_vs_x.dat').T # Creating flame object of the same size as the experimental flame with 25 soot sections -f = ct.BurnerFlame(gas=gas, width=z[-1], sections = 25) +f = ct.BurnerFlame(gas=gas, width=z[-1], sections = 2) # Setting transport model -f.transport_model = 'Mix' +f.transport_model = 'mixture-averaged' # Setting up soot calculation f.soot_setup(precursors =['A2'], @@ -51,4 +51,4 @@ if ct.__version__ >= '2.5.0': f.save('./RESULTS/%s.yaml' % mech,'sooting',overwrite=True) else: - f.save('./RESULTS/%s.xml' % mech,'sooting') \ No newline at end of file + f.save('./RESULTS/%s.xml' % mech,'sooting') diff --git a/samples/python/AVBP/RESULTS/BISETTI.xml b/samples/python/AVBP/RESULTS/BISETTI.xml deleted file mode 100644 index 239852c413e..00000000000 --- a/samples/python/AVBP/RESULTS/BISETTI.xml +++ /dev/null @@ -1,7624 +0,0 @@ - - - Thu Dec 28 11:45:10 2023 - none - - - - - - 2.980000000000000E+02 - 7.909433454451480E-02 - 0.000000000000000E+00 - 6.615775966700881E-01 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 2.009771930182301E-01 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 1.374452103116817E-01 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 0.000000000000000E+00 - 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temperature: 298.0 - pressure: 1.01325e+05 - mass-fractions: - N2: 0.6615842988823729 - O2: 0.2009704738662205 - C2H4: 0.1374452272514067 - flame: - Ys12: [-2.936810996752164e-22, -2.901974044126986e-22, -2.861412055025573e-22, - -2.845760420388120e-22, -2.791878899208235e-22, -2.753557512952252e-22, - -2.726182799211595e-22, -2.660333112178819e-22, -2.600526248356532e-22, - -2.539612806708918e-22, -2.476933850668903e-22, -2.389798597917e-22, - -2.346173730584655e-22, -2.318296553765535e-22, -2.274017101007241e-22, - -2.269700222665681e-22, -2.206624434491741e-22, -2.155700264763560e-22, - -2.111842260634649e-22, -2.080331121932468e-22, -2.033968591060562e-22, - -1.989903672008091e-22, -1.963815114933063e-22, -1.934461254633198e-22, - -1.891526970489431e-22, -1.863373490307378e-22, -1.864158323004905e-22, - -1.853630450219231e-22, -1.835246565635225e-22, -1.848100761964268e-22, - -1.884128463388945e-22, -1.938761260795531e-22, -2.105839198735709e-22, - -2.363993524560882e-22, -2.551403476237335e-22, -2.780167146750925e-22, - 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size: 154 - type: unstrained-flow - points: 154 - tolerances: - transient-abstol: 1.0e-11 - steady-reltol: 1.0e-04 - steady-abstol: 1.0e-09 - transient-reltol: 1.0e-04 - transport-model: mixture-averaged - phase: - name: gas - source: ./BISETTI.yaml - radiation-enabled: false - energy-enabled: false - Soret-enabled: false - species-enabled: true - refine-criteria: - ratio: 2.0 - slope: 0.1 - curve: 0.1 - prune: 0.0 - grid-min: 1.0e-10 - max-points: 1000 - basis: mass - components: [grid, velocity, T, D, AR, N2, S-CH2, T-CH2, O, H2, H, OH, H2O, O2, HO2, - CH, CO, HCO, CH2O, CH3, CO2, CH4, C2H3, C2H4, C2H5, C2H, HCCO, C2H2, - C3H3, A-C3H5, N-C3H7, C2H6, P-C3H4, A-C3H4, A1, A1-, C5H5, C3H6, C4H8, - C5H6, A2, C5H10, C5H11, A1C2H2, A1CH2, A1CHO, A1CH3, C7H15, N-C7H16, - A1C2H*, A2-, A1C2H] - outlet: - size: 0 - type: outlet - points: 1 diff --git a/samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml b/samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml deleted file mode 100644 index 65b36ca51cd..00000000000 --- a/samples/python/AVBP/RESULTS/CH4-O2-converged-flamelet-Lu.xml +++ /dev/null @@ -1,1844 +0,0 @@ - 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1.834531444376107e-14, 8.337372154444206e-15, 3.782440555268464e-15, - 1.712179079056678e-15, 7.733458046375476e-16, 3.486864330420177e-16, - 1.570538030743587e-16, 7.072998636725401e-17, 3.187935806731292e-17, - 1.439210423784746e-17, 6.511063151224956e-18, 2.945867167310686e-18, - 6.201938504786157e-19, 1.306772531749248e-19, 6.847637315797411e-21, - 3.970099950544625e-22, -1.716948145959151e-23, 2.097239934018185e-23, - 2.029223671651144e-23, 1.039150043002606e-22, 8.572315829734414e-25, - 9.969350204483684e-26, 2.206213741426378e-26, 8.491437863994048e-27, - 4.716602785763271e-27, 3.074147504932471e-27, 2.066824137239012e-27, - 1.340188612079251e-27, 7.845386992529860e-28, 3.490018573822431e-28, 0.0] - type: flamelet-flow - size: 144 - points: 145 - tolerances: - steady-reltol: 1.0e-04 - steady-abstol: 1.0e-09 - transient-reltol: 1.0e-04 - transient-abstol: 1.0e-11 - transport-model: mixture-averaged - phase: - name: gas - source: ././inputs/Lu.yaml - radiation-enabled: false - energy-enabled: true - Soret-enabled: false - species-enabled: true - refine-criteria: - ratio: 4.0 - slope: 0.1 - curve: 0.1 - prune: 0.0 - grid-min: 1.0e-10 - max-points: 1000 - basis: mass - components: [grid, T, D, H2, H, O, O2, OH, H2O, HO2, H2O2, CH3, CH4, CO, CO2, CH2O, - CH3OH, C2H2, C2H4, C2H6, CH2CO, N2] - fuel_inlet: - size: 1 - type: inlet - points: 1 - mass-flux: 0.2 - temperature: 300.0 - pressure: 1.01325e+05 - mass-fractions: - CH4: 1.0 diff --git a/src/kinetics/CustomKinetics.cpp b/src/kinetics/CustomKinetics.cpp index cc4b08c6449..bd03c243077 100644 --- a/src/kinetics/CustomKinetics.cpp +++ b/src/kinetics/CustomKinetics.cpp @@ -19,7 +19,7 @@ using namespace std; namespace Cantera { - CustomKinetics::CustomKinetics() : GasKinetics() + CustomKinetics::CustomKinetics() : BulkKinetics() { printf("WARNING: Using customized kinetics from f90 file.\n"); handle = dlopen("customkinetics.so", RTLD_LAZY); diff --git a/src/oneD/Boundary1D.cpp b/src/oneD/Boundary1D.cpp index bf70d14737d..b07d6f7dc89 100644 --- a/src/oneD/Boundary1D.cpp +++ b/src/oneD/Boundary1D.cpp @@ -36,7 +36,7 @@ void Boundary1D::_init(size_t n) if (!r.isConnector()) { // multi-point domain m_left_nv = r.nComponents(); - if (m_type == cFlameletFlow) { + if (domainType() == "flamelet-flow") { if (m_left_nv > c_offset_Yflamelet) { m_left_nsp = m_left_nv - c_offset_Yflamelet; } else { @@ -69,7 +69,7 @@ void Boundary1D::_init(size_t n) if (!r.isConnector()) { // multi-point domain m_right_nv = r.nComponents(); - if (m_type == cFlameletFlow) { + if (domainType() == "flamelet-flow") { if (m_right_nv > c_offset_Yflamelet) { m_right_nsp = m_right_nv - c_offset_Yflamelet; } else { diff --git a/src/oneD/DomainFactory.cpp b/src/oneD/DomainFactory.cpp index 4760701df96..6ed0e7519f0 100644 --- a/src/oneD/DomainFactory.cpp +++ b/src/oneD/DomainFactory.cpp @@ -8,7 +8,6 @@ #include "cantera/oneD/Flow1D.h" #include "cantera/oneD/Flamelet.h" #include "cantera/oneD/IonFlow.h" -#include "cantera/oneD/StFlow.h" #include "cantera/transport/Transport.h" namespace Cantera @@ -40,11 +39,11 @@ DomainFactory::DomainFactory() reg("reacting-surface", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new ReactingSurf1D(solution, id); }); - reg("gas-flow", [](shared_ptr solution, const string& id) { - return new Flow1D(solution, id); + reg("gas-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + return new Flow1D(solution, id, sections); }); reg("legacy-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { - return new StFlow(solution, id, sections); + return new Flow1D(solution, id, sections); }); reg("ion-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { return new IonFlow(solution, id); @@ -54,7 +53,7 @@ DomainFactory::DomainFactory() if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new StFlow(solution, id, sections); + ret = new Flow1D(solution, id, sections); } ret->setFreeFlow(); return ret; @@ -74,13 +73,13 @@ DomainFactory::DomainFactory() if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new StFlow(solution, id, sections); + ret = new Flow1D(solution, id, sections); } ret->setUnstrainedFlow(); return ret; }); reg("flamelet-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { - StFlow* ret; + Flow1D* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { diff --git a/src/oneD/Flamelet.cpp b/src/oneD/Flamelet.cpp index 96efc38633d..abe1a311b8d 100644 --- a/src/oneD/Flamelet.cpp +++ b/src/oneD/Flamelet.cpp @@ -1,12 +1,8 @@ // ! Flamelet definitions // - -#include "cantera/transport/TransportBase.h" #include "cantera/numerics/funcs.h" - - #include "cantera/base/SolutionArray.h" -#include "cantera/oneD/StFlow.h" +#include "cantera/oneD/Flow1D.h" #include "cantera/oneD/refine.h" #include "cantera/transport/Transport.h" #include "cantera/transport/TransportFactory.h" @@ -24,20 +20,20 @@ namespace Cantera { Flamelet::Flamelet(IdealGasPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : - StFlow(ph, nsp, nsoot, neq, points) { + Flow1D(ph, nsp, nsoot, neq, points) { m_dovisc = true; m_updateChi = true; m_do_unityLewisNumber = true; } Flamelet::Flamelet(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) - : StFlow(th.get(), nsp, nsoot, neq, points) { + : Flow1D(th.get(), nsp, nsoot, neq, points) { m_solution = Solution::create(); m_solution->setThermo(th); } Flamelet::Flamelet(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) - : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) { + : Flow1D(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) { m_solution = sol; m_id = id; m_kin = m_solution->kinetics().get(); @@ -50,7 +46,7 @@ Flamelet::Flamelet(shared_ptr sol, const string& id, size_t nsoot, siz if (m_trans->transportModel() == "none") { // @deprecated - warn_deprecated("StFlow", + warn_deprecated("Flow1D", "An appropriate transport model\nshould be set when instantiating the " "Solution ('gas') object.\nImplicit setting of the transport model " "is deprecated and\nwill be removed after Cantera 3.0."); diff --git a/src/oneD/Flow1D.cpp b/src/oneD/Flow1D.cpp index e677bcba609..a95392a976a 100644 --- a/src/oneD/Flow1D.cpp +++ b/src/oneD/Flow1D.cpp @@ -10,15 +10,19 @@ #include "cantera/transport/TransportFactory.h" #include "cantera/numerics/funcs.h" #include "cantera/base/global.h" +#include "cantera/base/Parser.h" +#include using namespace std; namespace Cantera { -Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t points) : - Domain1D(nsp+c_offset_Y, points), - m_nsp(nsp) +Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : + Domain1D(nsp, points, 0.0, nsoot, neq), // CERFACS : c_offset_Y is not added like in the official cantera release because in Domain1D.cpp we resize with nsoot and neq. + m_nsp(nsp), + m_neq(neq), + m_nsoot(nsoot) { m_points = points; @@ -28,9 +32,12 @@ Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t points) : m_thermo = ph; size_t nsp2 = m_thermo->nSpecies(); - if (nsp2 != m_nsp) { + m_nv = m_neq + m_nsp + m_nsoot; + + // CERFACS : I don't understand why do we do that ? nsp2 will always be different than nsp if we have soots. And even if we have soots, the domain size should already have the correct size. + if (nsp2 + m_nsoot != m_nsp) { m_nsp = nsp2; - Domain1D::resize(m_nsp+c_offset_Y, points); + Domain1D::resize(m_nv, points); } // make a local copy of the species molecular weight vector @@ -39,11 +46,6 @@ Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t points) : // set pressure based on associated thermo object setPressure(m_thermo->pressure()); - // the species mass fractions are the last components in the solution - // vector, so the total number of components is the number of species - // plus the offset of the first mass fraction. - m_nv = c_offset_Y + m_nsp; - // enable all species equations by default m_do_species.resize(m_nsp, true); @@ -60,23 +62,31 @@ Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t points) : m_qdotRadiation.resize(m_points, 0.0); //-------------- default solution bounds -------------------- - setBounds(c_offset_U, -1e20, 1e20); // no bounds on u - setBounds(c_offset_V, -1e20, 1e20); // no bounds on V - setBounds(c_offset_T, 200.0, 2*m_thermo->maxTemp()); // temperature bounds - setBounds(c_offset_L, -1e20, 1e20); // lambda should be negative - setBounds(c_offset_E, -1e20, 1e20); // no bounds on electric field - setBounds(c_offset_Uo, -1e20, 1e20); // no bounds on Uo + if (m_neq == 1) { + setBounds(c_offset_Tflamelet, 200.0, 2*m_thermo->maxTemp()); // temperature bounds + } else { + setBounds(c_offset_U, -1e20, 1e20); // no bounds on u + setBounds(c_offset_V, -1e20, 1e20); // no bounds on V + setBounds(c_offset_T, 200.0, 2*m_thermo->maxTemp()); // temperature bounds + setBounds(c_offset_L, -1e20, 1e20); // lambda should be negative + setBounds(c_offset_E, -1e20, 1e20); // no bounds on electric field + setBounds(c_offset_Uo, -1e20, 1e20); // no bounds on Uo + } // mass fraction bounds for (size_t k = 0; k < m_nsp; k++) { - setBounds(c_offset_Y+k, -1.0e-7, 1.0e5); + setBounds(m_neq+k, -1.0e-7, 1.0e5); } //-------------------- grid refinement ------------------------- - m_refiner->setActive(c_offset_U, false); - m_refiner->setActive(c_offset_V, false); - m_refiner->setActive(c_offset_T, false); - m_refiner->setActive(c_offset_L, false); - m_refiner->setActive(c_offset_Uo, false); + if (m_neq == 1) { + m_refiner->setActive(c_offset_Tflamelet, false); + } else { + m_refiner->setActive(c_offset_U, false); + m_refiner->setActive(c_offset_V, false); + m_refiner->setActive(c_offset_T, false); + m_refiner->setActive(c_offset_L, false); + m_refiner->setActive(c_offset_Uo, false); + } vector gr; for (size_t ng = 0; ng < m_points; ng++) { @@ -88,18 +98,32 @@ Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t points) : m_kRadiating.resize(2, npos); m_kRadiating[0] = m_thermo->speciesIndex("CO2"); m_kRadiating[1] = m_thermo->speciesIndex("H2O"); + + // P. Wolf + //---------------------AVBP PEA initialization------------------- + AVBPReadInputPea(); + + // B. Franzelli + //---------------------AVBP thickening initialisation------------ + AVBPReadInputChem(); + + // E. Lameloise + //---------------------Soot computation initialisation----------- + if (m_nsoot > 0){ + initSoot(); + } } -Flow1D::Flow1D(shared_ptr th, size_t nsp, size_t points) - : Flow1D(th.get(), nsp, points) +Flow1D::Flow1D(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) + : Flow1D(th.get(), nsp, nsoot, neq, points) { auto sol = Solution::create(); sol->setThermo(th); setSolution(sol); } -Flow1D::Flow1D(shared_ptr sol, const string& id, size_t points) - : Flow1D(sol->thermo().get(), sol->thermo()->nSpecies(), points) +Flow1D::Flow1D(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) + : Flow1D(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) { setSolution(sol); m_id = id; @@ -165,8 +189,11 @@ void Flow1D::resize(size_t ncomponents, size_t points) m_rho.resize(m_points, 0.0); m_wtm.resize(m_points, 0.0); m_cp.resize(m_points, 0.0); + m_h.resize(m_points, 0.0); + m_hr.resize(m_points, 0.0); m_visc.resize(m_points, 0.0); m_tcon.resize(m_points, 0.0); + avbp_thick.resize(m_points,0.0); m_diff.resize(m_nsp*m_points); if (m_do_multicomponent) { @@ -183,6 +210,21 @@ void Flow1D::resize(size_t ncomponents, size_t points) m_dz.resize(m_points-1); m_z.resize(m_points); + + // P. Wolf + m_zmixfrac.resize(m_points); + + // Soot + if (m_nsoot > 0){ + sootConsumption.resize(m_nsp, m_points, 0.0); + m_soot_diff.resize(m_nsoot, m_points, 0.0); + m_soot_soret.resize(m_nsoot, m_points, 0.0); + m_qdotNucleation.resize(m_points, 0.0); + m_qdotCondensation.resize(m_nsoot, m_points, 0.0); + m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); + m_qdotSg.resize(m_nsoot, m_points, 0.0); + m_qdotOxidation.resize(m_nsoot, m_points, 0.0); + } } void Flow1D::setupGrid(size_t n, const double* z) @@ -200,6 +242,17 @@ void Flow1D::setupGrid(size_t n, const double* z) } } +void Flow1D::setupGrid(size_t n) +{ + resize(m_nv, n); + + m_z[0] = 0.0; + for (size_t j = 1; j < m_points; j++) { + m_z[j] = (double) j / ( (double) (n-1) ); + m_dz[j-1] = m_z[j] - m_z[j-1]; + } +} + void Flow1D::resetBadValues(double* xg) { double* x = xg + loc(); @@ -244,6 +297,10 @@ void Flow1D::setGas(const double* x, size_t j) const double* yy = x + m_nv*j + c_offset_Y; m_thermo->setMassFractions_NoNorm(yy); m_thermo->setPressure(m_press); + // P. Wolf + if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ + calcMixFrac(x,j); + } } void Flow1D::setGasAtMidpoint(const double* x, size_t j) @@ -256,6 +313,34 @@ void Flow1D::setGasAtMidpoint(const double* x, size_t j) } m_thermo->setMassFractions_NoNorm(m_ybar.data()); m_thermo->setPressure(m_press); + // P. Wolf + if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ + calcMixFrac(x,j); + } +} + + /// Calculates and updates the mixture fraction at point j + /// WARNING: Only correct if no Carbon atoms in the oxidizer line + /// and pure fuel in the fuel line + /// Added by P. Wolf - March 2010 + /// Thanks to Alireza Najafiyazdi + +void Flow1D::calcMixFrac(const double* x, size_t j) { + size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom + size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel + double Z_C = 0.0; // passive scalar for C atom + double Z_C_F; // value of the passive scalar in fuel line + double W_C = this->m_thermo->atomicWeight(id_C); // Molecular weight of C atom + double W_fuel = this->m_thermo->molecularWeight(id_fuel); + double n_C; // Number of C atoms in each species + + for (size_t k=0; km_nsp; k++) { + n_C = this->m_thermo->nAtoms(k,id_C); + Z_C += n_C*x[index(c_offset_Y + k, j)]/this->m_thermo->molecularWeight(k); + } + Z_C = Z_C*W_C; + Z_C_F = W_C*this->m_thermo->nAtoms(id_fuel,id_C)/W_fuel; + m_zmixfrac[j] = Z_C/Z_C_F; // ie Z_C=0 in oxidizer line } void Flow1D::_finalize(const double* x) @@ -334,16 +419,26 @@ void Flow1D::eval(size_t jGlobal, double* xGlobal, double* rsdGlobal, if (m_do_radiation) { // Calculation of qdotRadiation computeRadiation(x, jmin, jmax); } + for (size_t j = jmin; j <= jmax; j++) { + if (m_nsoot > 0){ + getDistributionOrdre0(x,j); + } + AVBPcompute_local_thick(x,j); + } + // CERFACS : Do not change the eval order : Soot -> Species -> Energy evalContinuity(x, rsd, diag, rdt, jmin, jmax); evalMomentum(x, rsd, diag, rdt, jmin, jmax); + evalSoot(x, rsd, diag, rdt, jmin, jmax); + evalSpecies(x, rsd, diag, rdt, jmin, jmax); evalEnergy(x, rsd, diag, rdt, jmin, jmax); evalLambda(x, rsd, diag, rdt, jmin, jmax); evalElectricField(x, rsd, diag, rdt, jmin, jmax); evalUo(x, rsd, diag, rdt, jmin, jmax); - evalSpecies(x, rsd, diag, rdt, jmin, jmax); + } + void Flow1D::updateProperties(size_t jg, double* x, size_t jmin, size_t jmax) { // properties are computed for grid points from j0 to j1 @@ -366,6 +461,9 @@ void Flow1D::updateProperties(size_t jg, double* x, size_t jmin, size_t jmax) // update the species diffusive mass fluxes whether or not a // Jacobian is being evaluated updateDiffFluxes(x, j0, j1); + if (m_nsoot > 0){ + updateSootDiffFluxes(x, j0, j1); + } } void Flow1D::updateTransport(double* x, size_t j0, size_t j1) @@ -478,6 +576,7 @@ void Flow1D::computeRadiation(double* x, size_t jmin, size_t jmax) double boundary_Rad_left = m_epsilon_left * StefanBoltz * pow(T(x, 0), 4); double boundary_Rad_right = m_epsilon_right * StefanBoltz * pow(T(x, m_points - 1), 4); + // loop over all grid points for (size_t j = jmin; j < jmax; j++) { // calculation of the mean Planck absorption coefficient double k_P = 0; @@ -499,6 +598,12 @@ void Flow1D::computeRadiation(double* x, size_t jmin, size_t jmax) k_P_CO2 /= k_P_ref; k_P += m_press * X(x, m_kRadiating[0], j) * k_P_CO2; } + // absorption coefficient for soot + if (m_nsoot != 0 && m_do_soot_radiation) { + double k_P_soot = 0.0; + k_P_soot = 3.83 * CRad0 * fv(x,j) * T(x,j) / CRad2; + k_P += k_P_soot; + } // Calculation of the radiative heat loss term double radiative_heat_loss = 2 * k_P *(2 * StefanBoltz * pow(T(x, j), 4) @@ -657,16 +762,18 @@ void Flow1D::evalEnergy(double* x, double* rsd, int* diag, size_t j1 = std::min(jmax, m_points-2); for (size_t j = j0; j <= j1; j++) { if (m_do_energy[j]) { + setGas(x,j); grad_hk(x, j); double sum = 0.0; + double sum2 = 0.0; for (size_t k = 0; k < m_nsp; k++) { - double flxk = 0.5*(m_flux(k, j-1) + m_flux(k, j)); + double flxk = 0.5*(m_flux(k, j-1)*avbp_thick[j-1] + m_flux(k, j)*avbp_thick[j]); sum += m_wdot(k, j)*m_hk(k, j); - sum += flxk * m_dhk_dz(k, j) / m_wt[k]; + sum2 += flxk * m_dhk_dz(k, j) / m_wt[k]; } rsd[index(c_offset_T, j)] = - m_cp[j]*rho_u(x, j)*dTdz(x, j) - - conduction(x, j) - sum; + - AVBPdivHeatFlux(x, j) - sum/avbp_thick[j] - sum2; rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); rsd[index(c_offset_T, j)] -= rdt*(T(x, j) - T_prev(j)); rsd[index(c_offset_T, j)] -= (m_qdotRadiation[j] / (m_rho[j] * m_cp[j])); @@ -726,7 +833,7 @@ void Flow1D::evalSpecies(double* x, double* rsd, int* diag, double sum = 0.0; for (size_t k = 0; k < m_nsp; k++) { sum += Y(x,k,jmin); - rsd[index(c_offset_Y+k, jmin)] = -(m_flux(k, jmin) + + rsd[index(c_offset_Y+k, jmin)] = -(m_flux(k, jmin) * avbp_thick[jmin] + rho_u(x, jmin) * Y(x, k, jmin)); } rsd[index(c_offset_Y + leftExcessSpecies(), jmin)] = 1.0 - sum; @@ -735,9 +842,14 @@ void Flow1D::evalSpecies(double* x, double* rsd, int* diag, if (jmax == m_points - 1) { // right boundary double sum = 0.0; + if (m_nsoot > 0){ + for (size_t k = 0; k < m_nsoot; k++){ + if (m_do_retroaction){sum += Ys(x,k,jmax);} // CERFACS : Done for right Bnd but not for left ?? Maybe not needed because there are no soot at the inlet ? + } + } for (size_t k = 0; k < m_nsp; k++) { sum += Y(x,k,jmax); - rsd[index(k+c_offset_Y, jmax)] = m_flux(k, jmax-1) + + rsd[index(k+c_offset_Y, jmax)] = m_flux(k, jmax-1) * avbp_thick[jmax-1] + rho_u(x, jmax)*Y(x, k, jmax); } rsd[index(c_offset_Y + rightExcessSpecies(), jmax)] = 1.0 - sum; @@ -748,10 +860,18 @@ void Flow1D::evalSpecies(double* x, double* rsd, int* diag, size_t j0 = std::max(jmin, 1); size_t j1 = std::min(jmax, m_points-2); for (size_t j = j0; j <= j1; j++) { + getWdot(x,j); + + for (size_t k = 0; k < m_nsp; k++) { + + if (m_nsoot > 0 && m_do_retroaction){ + m_wdot(k,j) -= sootConsumption(k,j); + } + } for (size_t k = 0; k < m_nsp; k++) { double convec = rho_u(x, j)*dYdz(x, k, j); - double diffus = 2*(m_flux(k, j) - m_flux(k, j-1)) / (z(j+1) - z(j-1)); - rsd[index(c_offset_Y + k, j)] = (m_wt[k]*m_wdot(k, j) + double diffus = 2*(m_flux(k, j)*avbp_thick[j] - m_flux(k, j-1)*avbp_thick[j-1]) / (z(j+1) - z(j-1)); + rsd[index(c_offset_Y + k, j)] = (m_wt[k]*m_wdot(k, j)/avbp_thick[j] - convec - diffus) / m_rho[j] - rdt*(Y(x, k, j) - Y_prev(k, j)); diag[index(c_offset_Y + k, j)] = 1; @@ -768,10 +888,57 @@ void Flow1D::evalElectricField(double* x, double* rsd, int* diag, } } -void Flow1D::evalContinuity(size_t j, double* x, double* rsd, int* diag, double rdt) +void Flow1D::evalSoot(double* x, double* rsd, int* diag, + double rdt, size_t jmin, size_t jmax) { - throw CanteraError("Flow1D::evalContinuity", - "Overloaded by StFlow; to be removed after Cantera 3.1"); + if (m_nsoot > 0){ + if (jmin == 0) { // left boundary + for (size_t k = 0; k < m_nsoot; k++){ + rsd[index(c_offset_S + k, jmin)] = - (m_soot_diff(k,jmin) + + rho_u(x,jmin)* Ys(x,k,jmin)); + diag[index(c_offset_S + k, jmin)] = 0; + } + } + if (jmax == m_points - 1) { // right boundary + for (size_t k = 0; k < m_nsoot; k++){ //right boundary + rsd[index(c_offset_S + k, jmax)] = + m_soot_diff(k,jmax-1) + rho_u(x,jmax)*Ys(x,k,jmax); + diag[index(c_offset_S + k, jmax)] = 0; + } + } + // j0 and j1 are constrained to only interior points + size_t j0 = std::max(jmin, 1); + size_t j1 = std::min(jmax, m_points-2); + for (size_t j = j0; j <= j1; j++) { // interior points + sootSource(x,j); + for (size_t k = 0; k < m_nsoot; k++){ + // Convection + double soot_convec = rho_u(x,j)*dYsdz(x,k,j); + // Diffusion + double soot_diffus = 2.0 * (m_soot_diff(k,j) - m_soot_diff(k,j-1)) + / (z(j+1) - z(j-1)); + // Thermophoresis + double soot_soret = 2.0 * (m_soot_soret(k,j) - m_soot_soret(k,j-1)) + / (z(j+1) - z(j-1)); + // Source terms [m3/kg/s] + double soot_source = 0; + soot_source += (k == 0 ? m_qdotNucleation[j] : 0.0); + soot_source += (m_do_condensation ? m_qdotCondensation(k,j) : 0.0); + + soot_source += (m_do_coagulation ? m_qdotCoagulation(k,j) : 0.0); + soot_source += (m_do_sg ? m_qdotSg(k,j) : 0.0); + soot_source += (m_do_oxidation ? m_qdotOxidation(k,j) : 0.0); + // kg/s/m^3 + soot_source *= (rho_soot * m_rho[j]); + if(k == m_nsoot - 1 && m_trash_section){soot_source = 0.0;} + // Residual + rsd[index(c_offset_S + k, j)] = + (soot_source - soot_convec + soot_diffus + soot_soret) / m_rho[j] + - rdt * (Ys(x,k,j) - Ys_prev(k,j)); + diag[index(c_offset_S + k, j)] = 1; + } + } + } } void Flow1D::show(const double* x) @@ -809,6 +976,8 @@ string Flow1D::componentName(size_t n) const default: if (n >= c_offset_Y && n < (c_offset_Y + m_nsp)) { return m_thermo->speciesName(n - c_offset_Y); + } else if (n >= c_offset_S && n < (c_offset_S + m_nsoot)) { + return sectionName(n-c_offset_S); } else { return ""; } @@ -829,13 +998,15 @@ size_t Flow1D::componentIndex(const string& name) const return c_offset_E; } else if (name == "Uo") { return c_offset_Uo; + } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()) { + return stoi(name.substr(2))+c_offset_S; // offset not required in previous version, why? } else { for (size_t n=c_offset_Y; npressure(); + vector did_section(m_nsoot,false); + bool wrote_header = false; const auto grid = arr.getComponent("grid").as>(); setupGrid(nPoints(), &grid[0]); @@ -967,15 +1140,41 @@ void Flow1D::fromArray(SolutionArray& arr, double* soln) string name = componentName(i); if (arr.hasComponent(name)) { const vector data = arr.getComponent(name).as>(); + if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ + size_t n = stoi(name.substr(2)); + did_section[n]=true; + writelog("Adding soot section to soln "+name+"\n"); + } for (size_t j = 0; j < nPoints(); j++) { soln[index(i,j)] = data[j]; } + } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ + size_t n = stoi(name.substr(2)); + did_section[n]=true; + writelog("Creating soot section in soln "+name+"\n"); + for (size_t j = 0; j < nPoints(); j++) { + soln[index(n+c_offset_S,j)] = 0.0; + } } else { warn_user("Flow1D::fromArray", "Saved state does not contain values for " "component '{}' in domain '{}'.", name, id()); } } + if (soot_loglevel >= 1 && m_nsoot != 0) { + wrote_header = false; + for (size_t ks = 0; ks < m_nsoot; ks++) { + if (did_section[ks] == false) { + if (!wrote_header) { + writelog("\n\n"); + writelog("Missing data for soot sections:\n"); + wrote_header = true; + } + writelog(m_section_name[ks]+" "); + } + } + } + updateProperties(npos, soln + loc(), 0, m_points - 1); setMeta(arr.meta()); } @@ -1148,6 +1347,1014 @@ void Flow1D::fixTemperature(size_t j) } } +/* ------------------------------------------------------------------------ + Reads the mixture_database.dat file and sets accordingly the PEA function(s) + P. Wolf modif by J. Wirtz +--------------------------------------------------------------------------*/ +void Flow1D::AVBPReadInputPea() { + Parser parser; + Param* param; + + ifstream avbp_mixturedb("mixture_database.dat"); + if (avbp_mixturedb.good()){ + parser.parseFile("mixture_database.dat"); + // In case of pea, the name of the gas should be the same than the one in the mixture_database. + // Get number of mixtures in database + size_t n_mixtures = parser.nbParamOccurence("mixture_name"); + size_t idx_beg = std::string::npos; + size_t idx_end = std::string::npos; + // Loop through all occurences of keyword "mixture name" + for (size_t i=0; i< n_mixtures; ++i) { + param = parser.getParam("mixture_name",i); + std::string current_str = param->readString(0); + // Check if mixture_name is the one requested in the cti file + if ( current_str == m_thermo->name() ) { + // Store bounding idx to get important info + idx_beg = parser.getParamNumber("mixture_name",i); + idx_end = parser.getParamNumber("mixture_name",i+1); + + // Get the fuel of the 2-step chemistry + param = parser.getParam("species_name", idx_beg, idx_end); + for (size_t i=0; ireadString(i); + if (avbp_species.find('C')!=string::npos && avbp_species.find('H')!=string::npos){ + avbp_fuel = avbp_species; + } + if (avbp_species == "H2"){ + avbp_fuel = avbp_species; + } + + } + + // Check if PEA method and search for the coefficient + if (parser.checkParam("pea_method", idx_beg, idx_end) == true){ + param = parser.getParam("pea_method", idx_beg, idx_end); + std::string avbp_pea = param->readString(0); + if (avbp_pea == "pea1"){ + avbp_ipea = 1; + cout<<"ipea set to 1, PEA_1 will be applied"<readDouble(i); + } + } + else if (avbp_pea == "pea2") { + avbp_ipea = 2; + cout<<"ipea set to 2, PEA_2 will be applied"<readDouble(i); + } + param = parser.getParam("pea_coeff", idx_beg, idx_end, 1); + for (size_t i=0; i<10; i++) { + avbp_pea_coeffs[i+8] = param->readDouble(i); + } + + } + else{ + throw CanteraError("readAvbpInputPEA","ipea is set to a weird value"); + } + } + else { + avbp_ipea = 0; + } + } + else { + // pea not considered as mixture_name (mixture_database.dat) does not correspond to gas name (cti) + avbp_ipea = 0; + } + + // calculate the global equivalence ratio phi_cst + if ((avbp_ipea==1)||(avbp_ipea==2)){ + size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom + size_t id_H = this->m_thermo->elementIndex("H"); // Index of H atom + size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel + size_t id_ox = this->m_thermo->speciesIndex("O2"); // Index of O2 + size_t n_C = this->m_thermo->nAtoms(id_fuel,id_C); + size_t n_H = this->m_thermo->nAtoms(id_fuel,id_H); + //Calculate in mass units phi = s_m*Yf/Yo + phi_cst = (n_C + n_H/4)*this->m_thermo->molecularWeight(id_ox)/this->m_thermo->molecularWeight(id_fuel); + phi_cst = phi_cst*1./0.2333; // WARNING: valid only for Fuel/AIR mixture + } + + if (avbp_ipea!=0){ + break; + } + + } + } + else { + avbp_ipea = 0; + } +} +/********** + Reading the AVBP input_chem.dat + B. Franzelli +*************/ +void Flow1D::AVBPReadInputChem() { + avbp_fthick = m_thick; + if (avbp_fthick > 1.0) { + cout << "INFO: Thickening applied with constant value." << endl; + } + else { + avbp_fthick = 1.0; + } +} +void Flow1D::AVBPcompute_local_thick(double* x,size_t j){ + avbp_thick[j] = avbp_fthick; +} + +//----------------------// +// SOOT RELATED MTEHODS // +//----------------------// +void Flow1D::initSoot(){ + //---------------------------------------------------- + // Initializes soot computation + //---------------------------------------------------- + + // Sets offset of soot sections in solution array + // Resizes necessay arrays + // Sets sections names "YsXX", disables refinement on soot and sets clipping + + // Offset definition + c_offset_S = c_offset_Y + m_nsp; + // Array allocation + m_section_name.resize(m_nsoot); + sootConsumption.resize(m_nsp, m_points, 0.0); + q.resize(m_nsoot,0.0); + vSectMin.resize(m_nsoot, 0.0); + vSectMax.resize(m_nsoot, 0.0); + vSectMean.resize(m_nsoot, 0.0); + sSectMean.resize(m_nsoot, 0.0); + dSectMean.resize(m_nsoot, 0.0); + dSectCol.resize(m_nsoot, 0.0); + kfractal.resize(m_nsoot, 1.0); + Dfractal.resize(m_nsoot, 3); + nNucMean.resize(m_nsoot, 0.0); + rNucMean.resize(m_nsoot, 0.0); + rSectCol.resize(m_nsoot, 0.0); + aSectCol.resize(m_nsoot, 0.0); + theta_surf.resize(m_nsoot,2.0); + m_soot_diff.resize(m_nsoot, m_points, 0.0); + m_soot_soret.resize(m_nsoot, m_points, 0.0); + m_qdotNucleation.resize(m_points, 0.0); + m_qdotCondensation.resize(m_nsoot, m_points, 0.0); + m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); + collision_mat.resize(m_nsoot, m_nsoot, 0.0); + m_qdotSg.resize(m_nsoot, m_points, 0.0); + m_qdotOxidation.resize(m_nsoot, m_points, 0.0); + // Sections setup + for (size_t k = 0; k < m_nsoot; k++) { + std::string string_k = std::to_string(k); + m_section_name[k] = "Ys" + string_k; + m_refiner->setActive(c_offset_S+k, false); + setBounds(c_offset_S + k, -1.0e-5, 1e5); + } + +} + +void Flow1D::setPrecursors(vector id_precursors){ + //---------------------------------------------------- + // Recovers precursor data for further computation + //---------------------------------------------------- + + if (m_nsoot <= 0){ + writelog("\n--> CANTERA SOOT : no sections :(\n"); + return; + } + size_t id_C = m_thermo->elementIndex("C"); + W_C = m_thermo->atomicWeight(id_C); + n_PAH = id_precursors.size(); + m_precursors.resize(n_PAH); + W_PAH.resize(n_PAH,0.0); + n_C.resize(n_PAH,0.0); + for (size_t k = 0; k != n_PAH; k++){ + m_precursors[k] = id_precursors[k] - c_offset_Y; + W_PAH[k] = m_thermo->molecularWeight(m_precursors[k]); + n_C[k] = m_thermo->nAtoms(m_precursors[k],id_C); + } +} + +void Flow1D::finalizeSoot(){ + //---------------------------------------------------- + // Soot setup finalization + //---------------------------------------------------- + // Creates soot volumes + sootCreationVol(); + // Computes collision matrix + sootCollisionInverse(); + // Load surface reactions + if (m_do_sg || m_do_oxidation){ + loadHaca(m_haca_model); + loadSurface();} + + if (soot_loglevel >= 1){showSootInfo();} + if (soot_loglevel >= 2){showSootSections();} +} + +void Flow1D::sootCreationVol(){ + // Sections creations + // PAH list boundaries + size_t n_C_min = *min_element(n_C.begin(),n_C.end()); + size_t n_C_max = *max_element(n_C.begin(),n_C.end()); + // First section lower boundary : smallest possible dimer + vSectMin[0] = 2.0 * (double)n_C_min * V_C2; + // First section upper boundary : biggest possible dimer + vSectMax[0] = V_C2 * max(2.0 * n_C_min + n_C_max, 2.0 * n_C_max); + // Following sections : geometrical progression + vSectMin[1] = vSectMax[0]; + if (m_trash_section){ + double vTrashLowLim = Pi * pow(dTrashLowLim,3.0) / 6; + for (size_t k = 1; k < m_nsoot - 2; k++){ + double exponent = double(k) / double(m_nsoot-2); + vSectMax[k] = vSectMin[1] * pow(vTrashLowLim / vSectMin[1],exponent); + vSectMin[k+1] = vSectMax[k]; + } + vSectMax[m_nsoot - 2] = vTrashLowLim; + vSectMin[m_nsoot - 1] = vTrashLowLim; + }else{ + for (size_t k = 1; k < m_nsoot - 1; k++){ + double exponent = double(k) / double(m_nsoot-1); + vSectMax[k] = vSectMin[1] * pow(bigSoot / vSectMin[1],exponent); + vSectMin[k+1] = vSectMax[k]; + } + } + + vSectMax[m_nsoot-1] = bigSoot; + // Building mean values + for (size_t k = 0; k < m_nsoot; k++){ + vSectMean[k] = (vSectMax[k] + vSectMin[k]) / 2.0 ; //(vSectMax[k] - vSectMin[k]) / log (vSectMax[k] / vSectMin[k]); + dSectMean[k] = pow(6 / Pi * vSectMean[k], 1.0 / 3.0); + } + + // Sections morphology + for (size_t k = 0; k < m_nsoot; k++){ + if (vSectMean[k] >= vlim1){ + // Fractal dimension + Dfractal[k] = Df; + // Fractal prefactor + kfractal[k] = 4.46 * pow(Dfractal[k], -2.08); + } + } + + if (m_soot_morphology == "sphere" || m_soot_morphology == "rodrigues"){ + // Soot morphological properties as defined by P. Rodrigues (PhD Thesis, 2018) + // For spheres, theta = 2.0 + for (size_t k = 0; k < m_nsoot; k++){ + if (m_soot_morphology == "rodrigues" && vSectMin[k] >= vlim1){ + theta_surf[k] = (3.0 * (log(vSectMean[k] / vlim1)) + + 2.0 * (log(vlim1 / V_C2))) + / (log(vSectMean[k] / V_C2)); + if (k == m_nsoot-1 && m_trash_section){theta_surf[k] = theta_surf[k-1];} + } + // Collision diameter + dSectCol[k] = 6 / pow(36 * Pi, 1.0 /Dfractal[k]) + * pow(vSectMean[k], (Dfractal[k]-2.0) / Dfractal[k]) + * pow(S_C2 * + pow(vSectMean[k]/V_C2,theta_surf[k] / 3.0),(3.0-Dfractal[k]) / Dfractal[k]); + // Collision radius + rSectCol[k] = dSectCol[k] / 2.0; + // Collision cross-section + aSectCol[k] = Pi * pow(rSectCol[k], 2.0); + // Surface area + sSectMean[k] = S_C2 * pow(vSectMean[k] / V_C2, theta_surf[k] / 3.0); + // Nuclei number + nNucMean[k] = pow(sSectMean[k], 2) / (36. * Pi * pow(vSectMean[k], 2.)); + // Nuclei radius[m] + rNucMean[k] = 3. * vSectMean[k] / sSectMean[k]; + } + // // From P. Rodrigues, trick to help numerical stability (not tested its impact) + // dSectCol[m_nsoot-1] = dSectMean[m_nsoot-1]; + // rSectCol[m_nsoot-1] = dSectCol[m_nsoot-1] / 2.0; + // aSectCol[m_nsoot-1] = Pi * pow(rSectCol[m_nsoot-1], 2.0); + }else if (m_soot_morphology == "thajudeen"){ + // Soot morphological properties as defined by Thajudeen (2012) + for (size_t k = 0; k < m_nsoot; k++){ + // Nuclei number + nNucMean[k] = max(1., vSectMean[k] / vlim1); + // Nuclei radius + rNucMean[k] = min(pow(3.0 * vSectMean[k] / (4.0 * Pi), 1./3.), pow(3.0 * vlim1 / (4.0 * Pi), 1.0/3.0)); + if (vSectMean[k] >= vlim1){ + // Collision radius (Smoluchowski radius) + double alpha1 = 0.253 * pow(Dfractal[k], 2.0) - 1.209 * Dfractal[k] + 1.433; + double alpha2 = -0.218 * pow(Dfractal[k], 2.0) + 0.964 * Dfractal[k] - 0.180; + double phi_r = 1 / (alpha1 * log(nNucMean[k]) + alpha2); + rSectCol[k] = rNucMean[k] * phi_r * pow(nNucMean[k] / kfractal[k], 1/Dfractal[k]); + // Collision cross-section (Projected Area) + double alpha3 = 0.439 * pow(Dfractal[k], 2.0) - 2.221 * Dfractal[k] + 2.787; + double alpha4 = -0.232 * pow(Dfractal[k], 3.0) + 1.273 * pow(Dfractal[k], 2.0) - 2.183 * Dfractal[k] + 1.906; + double phi_p = pow(nNucMean[k], -alpha3) / alpha4; + aSectCol[k] = Pi * pow(rNucMean[k], 2.) * phi_p * pow(nNucMean[k] / kfractal[k], 2.0/Dfractal[k]); + }else{ + rSectCol[k] = dSectMean[k] / 2.; + aSectCol[k] = Pi * pow(rSectCol[k], 2.); + } + //Collision diameter ("Smoluchowski diameter") + dSectCol[k] = 2. * rSectCol[k]; + // Surface area (computed from smoluchowski radius, close to Rodrigues definition) + sSectMean[k] = Pi * pow(dSectCol[k], 2.); + // theta parameter (needed for surface reactions) + theta_surf[k] = 3. * log(sSectMean[k]/S_C2) / log(vSectMean[k]/V_C2); + } + } +} + +void Flow1D::sootCollisionInverse(){ + //---------------------------------------------------- + // Computes colision matrix (coagulation) + //---------------------------------------------------- + + for (size_t k = 0; k < m_nsoot; k++){ + for (size_t l = k; l < m_nsoot; l++){ + for (size_t m = l; m < m_nsoot; m++){ + double vol_min = vSectMin[l] + vSectMin[k]; + if(vol_min <= vSectMax[m] && vol_min >= vSectMin[m]){ + collision_mat(k,l) = m; + } + } + } + } +} + +void Flow1D::loadSurface(){ + //---------------------------------------------------- + // Resizes and compute surface reactions arrays + //---------------------------------------------------- + + kpower.resize(m_nsoot,0.0); + mpower.resize(m_nsoot,0.0); + vc2power.resize(m_nsoot,0.0); + vc2powerm.resize(m_nsoot,0.0); + vmax_kpower.resize(m_nsoot,0.0); + vmin_kpower.resize(m_nsoot,0.0); + vmax_mpower.resize(m_nsoot,0.0); + vmin_mpower.resize(m_nsoot,0.0); + vmaxmc2_kpower.resize(m_nsoot,0.0); + vminpc2_kpower.resize(m_nsoot,0.0); + vmaxmc2_mpower.resize(m_nsoot,0.0); + vminpc2_mpower.resize(m_nsoot,0.0); + vc2powervect.resize(m_nsoot,0.0); + vc2powermvect.resize(m_nsoot,0.0); + for (size_t k = 0; k < m_nsoot; k++){ + kpower[k] = (theta_surf[k] + 3.0)/3.0; + mpower[k] = theta_surf[k]/3.0; + vc2power[k] = (3.0 - theta_surf[k] )/3.0; + vc2powerm[k] = - mpower[k]; + vmax_kpower[k] = pow(vSectMax[k],kpower[k]); + vmin_kpower[k] = pow(vSectMin[k],kpower[k]); + vmax_mpower[k] = pow(vSectMax[k],mpower[k]); + vmin_mpower[k] = pow(vSectMin[k],mpower[k]); + vmaxmc2_kpower[k] = pow(vSectMax[k] - V_C2,kpower[k]); + vminpc2_kpower[k] = pow(vSectMin[k] + V_C2,kpower[k]); + vmaxmc2_mpower[k] = pow(vSectMax[k] - V_C2,mpower[k]); + vminpc2_mpower[k] = pow(vSectMin[k] + V_C2,mpower[k]); + vc2powervect[k] = pow(V_C2,vc2power[k]); + vc2powermvect[k] = pow(V_C2,vc2powerm[k]); + } +} + +void Flow1D::showSootInfo(){ + writelog("\n{:=^47}{:9}{:=^47}", "", "SOOT INFO", ""); + writelog("\n{:21}{:2}{}", "NUMBER OF SECTIONS", ":", m_nsoot); + writelog("\n{:21}{:1}","PRECURSORS", ":"); + for (size_t k = 0; k != n_PAH; k++){ + writelog(" {}", m_thermo->speciesName(m_precursors[k])); + } + if (dTrashLowLim > 0){writelog("\n{:21}{:2}{} m", "MAX DIAMETER", ":", dTrashLowLim);} + writelog("\n{:21}{:2}{}", "AGGREGATES MORPHOLOGY", ":", m_soot_morphology); + writelog("\n{:21}{:2}{}", "RETROACTION", ":", m_do_retroaction); + writelog("\n{:21}{:2}{}", "CONDENSATION", ":", m_do_condensation); + writelog("\n{:21}{:2}{}", "COAGULATION", ":", m_do_coagulation); + writelog("\n{:21}{:2}{}", "SURFACE GROWTH", ":", m_do_sg); + writelog("\n{:21}{:2}{}", "OXIDATION", ":", m_do_oxidation); + if (m_do_sg || m_do_oxidation){ + writelog("\n{:21}{:2}", "HACA MODEL", ":"); + if (m_haca_model == 1){ + writelog("Mauss"); + }else if (m_haca_model == 2){ + writelog("Blanquart"); + }else if (m_haca_model == 3){ + writelog("Kazakov"); + writelog("\n{:21}{:2}{}{:2}", "-> Flame temperature", ":", kazakovTad, " K"); + } + } + writelog("\n{:21}{:2}{}", "RADIATIVE HEAT LOSSES", ":", m_do_soot_radiation); + writelog("\n{:21}{:2}{}", "SORET EFFECT", ":", m_do_soot_soret); + writeline('=', 103, false, true); + writelog("\n"); +} +void Flow1D::showSootSections(){ + //---------------------------------------------------- + // Displays section informations + //---------------------------------------------------- + + if (m_nsoot <= 0){ + writelog ("\nSOOT INFO : no sections to show :("); + return; + } + writelog("\n{:=^36}{:30}{:=^37}", "", "SOOT SECTIONS INFO (SI UNITS)", ""); + writelog("\n Section Vol. min. Vol. mean Vol. max. Diam. mean Diam. coll"); + writeline('-', 103, false, true); + for (size_t k = 0; k < m_nsoot; k++) { + writelog("\n {:10d} {:10.4g} {:10.4g} {:10.4g} {:10.4g} {:10.4g}", + k,vSectMin[k],vSectMean[k],vSectMax[k],dSectMean[k],dSectCol[k]); + } + writeline('=', 103, false, true); + writelog("\n"); +} + +void Flow1D::sootSource(const double* x, size_t j) { + //---------------------------------------------------- + // Computes soot source terms + //---------------------------------------------------- + // Dimerization + sootDimerization(x,j); + // Nucleation + sootNucleation(x,j); + // Condensation + if (m_do_condensation){sootCondensation(x,j);} + // Coagulation + if (m_do_coagulation){sootCoagulation(x,j);} + // Surface chemistry + if (m_do_sg || m_do_oxidation){sootSurface(x,j);} +} + +void Flow1D::sootDimerization(const double* x, size_t j){ + //---------------------------------------------------- + // Computes dimerization source term + //---------------------------------------------------- + double omega = 0, c_dimer = 0; + double V_k, d2_k, omega_k, C_k, gamma_k, k_k; + for (size_t k = 0; k < n_PAH; k++){ + // PAH volume [m3] + V_k = n_C[k] * V_C2 / 2.0; + // Squared PAH diameter [m2] + d2_k = pow(6.0 * V_k / Pi, 2.0/3.0); + // PAH concentraiton [kmol/m3] + C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; + // PAH sticking coefficient [-] + gamma_k = Cn_cst * pow(W_PAH[k], 4.0); + // Reaction rate constant [m3/kmol/s] + k_k = sqrt(4.0 * Pi * Boltzmann * T(x,j) / (W_C * n_C[k] / Avogadro)) * d2_k * Avogadro; + // PAH dimerization reaction rate [kmol/m3/s] + omega_k = gamma_k * k_k * pow(C_k, 2.0); + // PAH consumption [kmol/m3/s] (x2 because 2 mol PAH -> 1 mol dimer) + sootConsumption(m_precursors[k],j) = 2 * omega_k; + // Adds PAH contribution to overall local dimerization rate sootConsumption[index(k,j)] + omega += omega_k; + // Adds PAH contribution to overall dimer carbon atoms + c_dimer += omega_k * n_C[k]; + } + // Overall dimerization rate [1/kg/s] + r_dimer = omega * Avogadro / m_rho[j]; + // Overall dimer volume [m3] + V_dimer = c_dimer * V_C2 / omega; + + // double K00 = 0, cdimer = 0; + // double V_k, d_k, kdimfwd_k, K00_k, C_k; + // for (size_t k = 0; k < n_PAH; k++){ + // // PAH volume [m3] + // V_k = n_C[k] * V_C2 / 2.0; + // // PAH diameter [m] + // d_k = pow(6.0 * V_k / Pi, 1.0/3.0); + // // PAH concentraiton [mol/m3] + // C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; + // // m6/s/kg/mol2 + // kdimfwd_k = Cn_cst * pow(W_PAH[k], 4.0) / m_rho[j] + // * sqrt((4.0 * Pi * Boltzmann * T(x,j)) / ((W_C / Avogadro) * n_C[k])) + // * pow(d_k, 2.0) * pow(Avogadro, 2.0) ; + // // (mol.g^(-1).s^(-1)) + // K00_k = pow(C_k, 2.0) * kdimfwd_k / Avogadro; + // // (mol.g^(-1).s^(-1)) + // K00 += K00_k; + // cdimer += K00_k * n_C[k]; + // // Precursor consumption (mol/m3/s) + // // (x2 because 2 mol PAH -> 1 mol dimer) + // sootConsumption[m_precursors[k]] = 2 * K00_k * m_rho[j]; + // } + // // Dimerization rate [1/kg/s] + // r_dimer = K00 * Avogadro; + // // Equivalent dimer volume [m3] + // V_dimer = cdimer * V_C2 / K00; +} + +void Flow1D::sootNucleation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute nucleation source terms + //---------------------------------------------------- + // [m(11/2)/s/kg] + beta_fm = sqrt(Pi * Boltzmann * T(x,j) + / (rho_soot * 2.0)) / m_rho[j]; + // Dimer collision frequency [m6/s/kg] + beta_dimer = eps_nucl * beta_fm * sqrt(2.0 / V_dimer) + * pow (2.0 * pow(6.0 * V_dimer / Pi, 1.0 / 3.0), 2.0); + // // Dimer particle density [1/m3] + // N_dimer = sqrt((r_dimer / beta_dimer)); + // // Source term for nucleation [m3/kg/s] + // m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer, 2.0); + + // Dimer diameter [m] + double d_dimer = 2.0 * pow(3.0 * V_dimer / (4.0 * Pi), 1.0/3.0); + // Dimer mass [kg] + double m_dimer = V_dimer * rho_soot; + // Reaction rate constant [m3/kmol/s] + // k_nuc = beta_dimer * m_rho[j] * Avogadro / 2 + double k_nuc = eps_nucl * Avogadro * pow(d_dimer, 2.0) + * sqrt(4.0 * Pi * Boltzmann * T(x, j) / m_dimer); + // Dimer concentration (QSS Assumption) [kmol/m3] + double C_dimer = sqrt((r_dimer / Avogadro * m_rho[j]) / (2.0 * k_nuc)); + // Dimer number concentration [1/m3] + N_dimer = C_dimer * Avogadro; + // Nucleation reaction rate [kmol/m3/s] + double omega_nuc = k_nuc * pow(C_dimer, 2.0); + // Nucleation rate [m3/kg/s] + m_qdotNucleation[j] = omega_nuc * Avogadro * V_dimer / m_rho[j] * 2.0; + +} + +void Flow1D::sootCondensation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute condensation source term and corrects + // nucleation source term + //---------------------------------------------------- + + double kCond = 0; + double interval, vmoy, term1, term2, term3; + vector beta_cond(m_nsoot,0.0); + for (size_t k = 0; k < m_nsoot; k++){ + // Condensation collision kernel[m6/s/kg] + beta_cond[k] = eps_cond * beta_fm * sqrt(1.0/vSectMean[k]+1.0/V_dimer) + * pow(dSectCol[k] + pow(6.0 / Pi * V_dimer, 1.0/3.0), 2.0); + // Collisional frequency between a dimer and any soot particle [m3/s/kg] + kCond += beta_cond[k] * (q[k] * (vSectMax[k] - vSectMin[k]) / (vSectMean[k])); + } + // Correction of dimer density and nucleation source term + N_dimer = - (kCond / (2.0 * beta_dimer)) + + sqrt((r_dimer / beta_dimer) + + pow(kCond / (2.0 * beta_dimer),2.0)); + // Nucleation source term [m3/kg/1] + m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer,2.0); + + // Condensation source terms + for (size_t k = 0; k < m_nsoot; k++){ + interval = (vSectMax[k] - V_dimer) - vSectMin[k]; + vmoy = ((vSectMax[k] - V_dimer) + vSectMin[k]) / 2; + term1 = N_dimer * beta_cond[k] * q[k] / vmoy * V_dimer * interval; + if ( k==0 ){ + term2 = 0.0; + term3 = 0.0; + }else{ + interval = vSectMax[k-1] - (vSectMax[k-1] - V_dimer); + vmoy = (vSectMax[k-1] + (vSectMax[k-1] - V_dimer)) / 2; + term2 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * V_dimer * interval; + term3 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * vmoy * interval; + } + m_qdotCondensation(k,j) = term1 + term2 + term3; + if ( k>0 ){ + m_qdotCondensation(k-1,j) -= term3; + } + } +} + + +void Flow1D::sootCoagulation(const double* x, size_t j){ + //---------------------------------------------------- + // Compute coagulation source terms + //---------------------------------------------------- + + for (size_t k = 0; k < m_nsoot; k++){ + m_qdotCoagulation(k,j) = 0.0; + } + // Viscosity (Cantera) [Pa.s-1] [CLEAN BUT SLOW] + // setGas(x,j); + // double visc = m_trans->viscosity(); + // Viscosity (Sutherland, air) [Pa.s-1] [TRASH BUT QUICK] + double visc = Csut1 * pow(T(x,j),1.5) / (T(x,j) + Csut2); + // Mean free path [m] + double mfp_rod = Boltzmann * T(x,j) / (sqrt(2.0) * Pi * pow(d_gaz,2.0) * m_press); + double mfp_tha = 66.4e-7 * (101325. / m_press) * (T(x,j) / 293.) * (1. + 110./293.) / (1 + 110. / T(x,j)); + double beta_coag_lk = 0.0; + for (size_t k = 0; k < m_nsoot; k++){ + for (size_t l = k; l < m_nsoot; l++){ + if (m_collision_model == "rodrigues" || m_collision_model == "sphere"){ + //Cunnningham numbers [-] + double Cu_k = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[k]; + double Cu_l = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[l]; + // Coagulation rate in continuous regime [m^6.kg^(-1).s-(-1)] + double beta_cont_lk = (2.0 * Boltzmann * T(x,j)) / (3.0 * visc) + * (dSectCol[l] + dSectCol[k]) + * (Cu_l / dSectCol[l] + Cu_k / dSectCol[k]) + / m_rho[j]; + // Coagulation rate in free molecular regime [m^6.kg^(-1).s-(-1)] + double beta_fm_lk = eps_coag * beta_fm + * sqrt(1 / vSectMean[k] + 1 / vSectMean[l]) + * pow(dSectCol[k] + dSectCol[l], 2.0); + // Overall coagulation rate [m^6.kg^(-1).s-(-1)] + beta_coag_lk = (beta_fm_lk * beta_cont_lk) + / (beta_fm_lk + beta_cont_lk); + }else if (m_collision_model == "thajudeen"){ + double reduced_mass = rho_soot * vSectMean[k] * vSectMean[l] / (vSectMean[k] + vSectMean[l]); + double smoluchowski_radius = rNucMean[k] * (1.203 - (0.4315*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])) * pow(rSectCol[k]/rNucMean[k] + rSectCol[l]/rNucMean[k], 0.8806 + (0.3497*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])); + double kn_diff_k = mfp_tha * Pi * rSectCol[k] / aSectCol[k]; + double kn_diff_l = mfp_tha * Pi * rSectCol[l] / aSectCol[l]; + double f_k = (6.0 * Pi * rSectCol[k] * visc) / (1 + kn_diff_k * (1.257 + 0.4 * exp(-1.1/kn_diff_k))); + double f_l = (6.0 * Pi * rSectCol[l] * visc) / (1 + kn_diff_l * (1.257 + 0.4 * exp(-1.1/kn_diff_l))); + double friction_coefficient = f_k * f_l / (f_k + f_l); + double projected_area = pow(smoluchowski_radius, 2.0) * Pi; + double kn_diff = (sqrt(Boltzmann * T(x,j) * reduced_mass) * Pi * smoluchowski_radius) / (friction_coefficient * projected_area); + double H = (4.0 * Pi * pow(kn_diff, 2.0) + 25.836 * pow(kn_diff, 3.0) + eps_coag * sqrt(8.0 * Pi) * 11.211 * pow(kn_diff, 4.0)) / (1 + 3.502 * kn_diff + 7.211 * pow(kn_diff, 2.0) + 11.211 * pow(kn_diff, 3.0)); + beta_coag_lk = (H * friction_coefficient * pow(projected_area, 2.0)) / (reduced_mass * pow(Pi, 2.0) * smoluchowski_radius) / m_rho[j]; + } + // Section of the particle corresponding to the coagulation of (l,k)y + size_t m = collision_mat(k,l); + // Loss of mass in section l due to coagulation with k + double terml = beta_coag_lk * q[l] * q[k] / vSectMean[k] + * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); + // Loss of mass in section k due to coagulation with l + double termk = beta_coag_lk * q[l] * q[k] / vSectMean[l] + * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); + double termm, termmplus; + // Gain in mass in m and m+1 thanks to coagulation of (l,k) + if (vSectMax[l] + vSectMax[k] <= vSectMax[m]){ + termm = terml + termk; + termmplus = 0.0; + }else{ + termm = (terml + termk) + * (vSectMax[m] - (vSectMin[k] + vSectMin[l])) + / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); + termmplus = (terml + termk) + * (vSectMax[k]+vSectMax[l]-vSectMax[m]) + / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); + } + if (m < m_nsoot-1){ + m_qdotCoagulation(m+1,j) += termmplus; + }else{ + termm = terml + termk; + } + m_qdotCoagulation(m,j) += termm; + m_qdotCoagulation(l,j) -= terml; + m_qdotCoagulation(k,j) -= termk; + } + } +} + +void Flow1D::updateSootDiffFluxes(const double* x, size_t j0, size_t j1) +{ + //---------------------------------------------------- + // Computes soot molecular and thermal diffusion fluxes + //---------------------------------------------------- + for (size_t j = j0; j < j1; j++) { + // Evaluate gas at midpoints : j->j+1/2 + double Tmid = 0.5 * (T(x,j)+T(x,j+1)); + // [CLEAN BUT SLOW] + // setGasAtMidpoint(x,j); + // double wtm = m_thermo->meanMolecularWeight(); + // double rho = m_thermo->density(); + // double visco = m_trans->viscosity(); + // [TRASH BUT QUICK] + double wtm = 0.5*(m_wtm[j]+m_wtm[j+1]); + double rho = 0.5*(m_rho[j]+m_rho[j+1]); + double visco = Csut1 * pow(Tmid,1.5) / (Tmid + Csut2); + // Evaluate centered differencies at j+1/2 + double dT = T(x,j+1)-T(x,j); + double dz = z(j+1) - z(j); + // Evaluate viscosity + for (size_t k = 0; k < m_nsoot; k++){ + // Evaluate soot mass fraction at j+1/2 + + double Ysmid = 0.5 * (Ys(x,k,j)+Ys(x,k,j+1)); + // Evaluate centered differencies at j+1/2 + double dYs = Ys(x,k,j+1) - Ys(x,k,j); + //Evaluate diffusion coefficient at j+1/2 + double Ds = 3 / (2 * rho_soot * pow(dSectMean[k], 2.0) + * (1 + alphaT * Pi / 8)) + * sqrt ((wtm*Boltzmann*Tmid)/(2*Pi*Avogadro)); + // Evaluate soot mass diffusion flux at j+1/2 + m_soot_diff(k,j) = rho * Ds * dYs/dz; + // Evaluate soot mass soret flux at j+1/2 + if (m_do_soot_soret){ + m_soot_soret(k,j) = C_soot_soret * visco * Ysmid * dT/dz / Tmid; + } + } + } +} + +void Flow1D::sootSurface(const double* x, size_t j){ + //---------------------------------------------------- + // Compute surface chemistry source terms + //---------------------------------------------------- + + // Computes reaction rates + sootSurfaceInitialization(x,j); + double term1, term2, term3; + //--------------- + // SURFACE GROWTH + //--------------- + if (m_do_sg){ + for (size_t k = 0; k < m_nsoot; k++){ + term1 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] + * (vmaxmc2_mpower[k] - vmin_mpower[k]); + if (k==0){ + term2 = 0.0; + term3 = 0.0; + }else{ + term2 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k-1] / mpower[k-1] * q[k-1] + * (vmax_mpower[k-1] - vmaxmc2_mpower[k-1]); + term3 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powermvect[k-1] / kpower[k-1] * q[k-1] + * (vmax_kpower[k-1] - vmaxmc2_kpower[k-1]); + } + // Surface growth source term [m3/kg/s] + m_qdotSg(k,j) = term1 + term2 + term3; + if (k > 0){m_qdotSg(k-1,j) -= term3;} + } + } + //---------- + // OXYDATION + //---------- + if (m_do_oxidation){ + for (size_t k=m_nsoot; k --> 0;){ + term1 = alpha_surf * kox / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] + * (vmax_mpower[k] - vminpc2_mpower[k]); + if (k==m_nsoot-1){ + term2 = 0.0; + term3 = 0.0; + }else if (k==m_nsoot-2 && m_trash_section) { + term2 = 0.0; + term3 = 0.0; + }else{ + term2 = alpha_surf * kox / m_rho[j] * vc2powervect[k+1] / mpower[k+1] * q[k+1] + * (vminpc2_mpower[k+1] - vmin_mpower[k+1]); + term3 = alpha_surf * kox / m_rho[j] * vc2powermvect[k+1] / kpower[k+1] * q[k+1] + * (vminpc2_kpower[k+1] - vmin_kpower[k+1]); + } + // Oxidation source term [m3/kg/s] + m_qdotOxidation(k,j) = - (term1 + term2 - term3); + if (k < m_nsoot - 1){ + m_qdotOxidation(k+1,j) -= term3; + } + } + } +} + +void Flow1D::sootSurfaceInitialization(const double* x, size_t j){ + // Recover species concentrations [kmol/m3] + double conc_H = 0, conc_H2 = 0, conc_OH = 0, conc_H2O = 0, conc_C2H2 = 0, conc_O2 = 0; + double k01f = 0, k01b = 0, k02f = 0, k02b = 0, k03f = 0, k03b = 0, k04f = 0, k04b = 0; + double k05f = 0, k05b = 0, k06f = 0, k06bisf = 0; + double r01f = 0, r01b = 0, r02f = 0, r02b = 0, r03f = 0, r03b = 0, r04f = 0, r04b = 0; + double r05f = 0, r05b = 0, r06f = 0, r06bisf = 0, r07f = 0; + double ko2, koh, kd, krev, chi, chip, chic, alpha_kazakov; + size_t k; + // Recover molar concentrations + k = m_thermo->speciesIndex("H"); + if (k != npos){conc_H = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("H2"); + if (k != npos){conc_H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){conc_H2O = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){conc_C2H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("O2"); + if (k != npos){conc_O2 = Y(x,k,j) * m_rho[j] / m_wt[k];} + k = m_thermo->speciesIndex("OH"); + if (k != npos){conc_OH = Y(x,k,j) * m_rho[j] / m_wt[k];} + // SI units + double slt = 1.0e3 / GasConstant / T(x,j); // 1e3 because GasConstant in J/kmol/K + double T_log=log(T(x,j)); + if (m_haca_model == 1 || m_haca_model == 11){ //Mauss + // Arrhenius constants + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); // [m3/kmol/s] + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); // [m3/kmol/s] + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); // [m3/kmol/s] + k02b = ak02b * exp(nk02b*T_log - ek02b*slt); // [m3/kmol/s] + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [m3/kmol/s] + k03b = ak03b * exp(nk03b*T_log - ek03b*slt); // [1/s] + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); // [m3/kmol/s] + k04b = ak04b * exp(nk04b*T_log - ek04b*slt); // [1/s] + k05f = ak05f * exp(nk05f*T_log - ek05f*slt); // [1/s] + k05b = ak05b * exp(nk05b*T_log - ek05b*slt); // [m3/kmol/s] + k06f = ak06f * exp(nk06f*T_log - ek06f*slt); // [m3/kmol/s] + k06bisf = k06f; + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_OH; + r02b = k02b * conc_H2O; + r03f = k03f * conc_H; + r03b = k03b; + r04f = k04f * conc_C2H2; + r04b = k04b; + r05f = k05f; + r05b = k05b * conc_H; + r06f = k06f * conc_O2; + r06bisf = k06bisf * conc_O2; + r07f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + double fk10 = r05f / (r04b+r06bisf+r05f); + double A_QSS = (r01f + r02f + r03b + r07f + r05b * (1.0 - fk10)) / (r01b + r02b + r03f + r04f * fk10); + double B_QSS = r04f / ( r04b + r06bisf + r05f); + double D_QSS = r05b / (r04b + r06f + r05f); + + chi = 1.0; + chip = chi * A_QSS; + chic = chi * (A_QSS*B_QSS + D_QSS); + // Partial reaction rates[1/s] + koh = r07f * chi; + kd = r04f * chip; + ko2 = r06f * (chip + chic); + krev = r04b * chic; + // Partial surface growth and oxidation rates [1/s] + ksg = kd - krev; + kox = ko2 + koh; + } else if (m_haca_model == 2){ //Blanquart + // Arrhenius constants [m3/kmol/s] + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); + k02b = ak02b * exp(nk02b*T_log - ek02b*slt); + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [1/s] + k03b = ak03b * exp(nk03b*T_log - ek03b*slt); + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); + k05f = ak05f * exp(nk05f*T_log - ek05f*slt); + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_OH; + r02b = k02b * conc_H2O; + r03f = k03f; + r03b = k03b * conc_H; + r04f = k04f * conc_C2H2; + r05f = k05f * conc_O2; + r06f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + chi = (r01f + r02f + r03f) / (r01b + r02b + r03b + r04f + r05f); // * 1.7e15; + // Oxidation O2 [must be 1/s] + ko2 = chi * r05f; + // Oxidation OH [1/s] + koh = r06f * chi; + // Oxidation + kox = ko2 + koh; + // Surface growth [1/s] + ksg = chi * r04f; + } else if (m_haca_model == 3){ //Kazakov + // Fraction of sites available at the surface of the particle for reaction [-] + alpha_kazakov = (1.0 + tanh(8.168e3/kazakovTad - 4.57)) / 2.0; + // Arrhenius constants [m3/kmol/s] + k01f = ak01f * exp(nk01f*T_log - ek01f*slt); + k01b = ak01b * exp(nk01b*T_log - ek01b*slt); + k02f = ak02f * exp(nk02f*T_log - ek02f*slt); + k03f = ak03f * exp(nk03f*T_log - ek03f*slt); + k04f = ak04f * exp(nk04f*T_log - ek04f*slt); + // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] + r01f = k01f * conc_H; + r01b = k01b * conc_H2; + r02f = k02f * conc_H; + r03f = k03f * conc_C2H2; + r04f = k04f * conc_O2; + r05f = Avogadro * S_C2 * gamma_oh * conc_OH * + pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); + // From QSS [-] + chi = r01f / (r01b + r02f + r03f + r04f); // * 2.3e14 + // Oxidation O2 [1/s] + ko2 = alpha_kazakov * chi * r04f; + // Oxidation OH [1/s] + koh = r05f * chi; + //Oxidation [1/s] + kox = ko2 + koh; + // Surface growth [1/s] + ksg = alpha_kazakov * chi * r03f; + } + //------------------------- + // RETROACTION ON GAS PHASE + //------------------------- + if (m_do_retroaction){ + double deltaQ = 0.0, soot_surface = 0.0; + for (size_t k = 0; k < m_nsoot; k++){ + deltaQ += vc2powervect[k] / mpower[k] * q[k] * (vmax_mpower[k]-vmin_mpower[k]); + } + //Overall active sites concentration [kmol/m3] + soot_surface = alpha_surf * n_sites * deltaQ / (V_C2 * Avogadro); // n_sites added here + // Surface chemistry reaction rates [kmol/s/m3] + double w01f = 0, w01b = 0, w02f = 0, w02b = 0, w03f = 0, w03b = 0; + double w04f = 0, w04b = 0, w05f = 0, w05b = 0, w06f = 0, w06bisf = 0; + double w07f = 0; + if (m_do_sg || m_do_oxidation){ + // Reaction rates for reactions occuring on both oxidation & surface growth + if (m_haca_model == 1){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chip; + w02f = r02f * soot_surface * chi; + w02b = r02b * soot_surface * chip; + w03f = r03f * soot_surface * chip; + w03b = r03b * soot_surface * chi; + w05f = r05f * soot_surface * chic; + w05b = r05b * soot_surface * chi; + w06bisf = r06bisf * soot_surface * chic; + }else if (m_haca_model == 2){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chi; + w02f = r02f * soot_surface * chi; + w02b = r02b * soot_surface * chi; + w03f = r03f * soot_surface * chi; + w03b = r03b * soot_surface * chi; + }else if (m_haca_model == 3){ + w01f = r01f * soot_surface * chi; + w01b = r01b * soot_surface * chi; + w02f = r02f * soot_surface * chi; + } + } + // Reaction rates for reactions occuring on surfacce growth only + if (m_do_sg){ + if (m_haca_model == 1){ + w04f = r04f * soot_surface * chip; + w04b = r04b * soot_surface * chic; + }else if (m_haca_model == 2){ + w04f = r04f * soot_surface * chi; + }else if (m_haca_model == 3){ + w03f = r03f * soot_surface * chi; + } + } + // Reaction rates for reactions occuring on oxidation only + if (m_do_oxidation){ + if (m_haca_model == 1){ + // Reaction rates [kmol/m3/s] + w06f = r06f * soot_surface * chip; + w07f = r07f * soot_surface * chi; + }else if (m_haca_model == 2){ + w05f = r05f * soot_surface * chi; + w06f = r06f * soot_surface * chi; + }else if (m_haca_model == 3){ + w04f = r04f * soot_surface * chi; + w05f = r05f * soot_surface * chi; + } + } + + // Gaseous species consumption [kmol/s/m3] + if (m_haca_model == 1){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption(k,j) = - (w01f - w01b) - (w03f - w03b) + (w05f - w05b);} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption(k,j) = (w04f - w04b);} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption(k,j) = (w01f - w01b);} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption(k,j) = - w06f - w06bisf;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption(k,j) = 2.0 * w06f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption(k,j) = - (w02f - w02b) - w07f;} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){sootConsumption(k,j) = + (w02f - w02b);} + k = m_thermo->speciesIndex("HCO"); + if (k != npos){sootConsumption(k,j) = 2.0 * w06bisf + w07f;} + k = m_thermo->speciesIndex("CH"); + if (k != npos){sootConsumption(k,j) = w07f;} + }else if (m_haca_model == 2){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption(k,j) = -(w01f-w01b) + (w03f-w03b) + w04f;} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption(k,j) = -w04f;} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption(k,j) = (w01f-w01b) + w05f + w06f;} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption(k,j) = -w05f;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption(k,j) = 2.0 * w05f + w06f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption(k,j) = -(w02f-w02b) - w06f;} + k = m_thermo->speciesIndex("H2O"); + if (k != npos){sootConsumption(k,j) = (w02f-w02b);} + }else if (m_haca_model == 3){ + k = m_thermo->speciesIndex("H"); + if (k != npos){sootConsumption(k,j) = -(w01f-w01b) - w02f + w03f;} + k = m_thermo->speciesIndex("C2H2"); + if (k != npos){sootConsumption(k,j) = -w03f;} + k = m_thermo->speciesIndex("H2"); + if (k != npos){sootConsumption(k,j) = (w01f-w01b) + w05f;} + k = m_thermo->speciesIndex("O2"); + if (k != npos){sootConsumption(k,j) = -w04f;} + k = m_thermo->speciesIndex("CO"); + if (k != npos){sootConsumption(k,j) = 2.0 * w04f + w05f;} + k = m_thermo->speciesIndex("OH"); + if (k != npos){sootConsumption(k,j) = - w05f;} + } + } +} + +void Flow1D::getDistributionOrdre0(const double* x, size_t j){ + for (size_t k = 0; k < m_nsoot; k++){ + // Soot volume fraction density [1/m3] + q[k] = m_rho[j] * Ys(x,k,j) / (rho_soot * (vSectMax[k] - vSectMin[k])); + } +} +//-----------------------------// +// END OF SOOT RELATED METHODS // +//-----------------------------// + void Flow1D::grad_hk(const double* x, size_t j) { size_t jloc = (u(x, j) > 0.0 ? j : j + 1); diff --git a/src/oneD/IonFlow.cpp b/src/oneD/IonFlow.cpp index 2c13c406b55..58e5cba7c4c 100644 --- a/src/oneD/IonFlow.cpp +++ b/src/oneD/IonFlow.cpp @@ -16,7 +16,7 @@ namespace Cantera { IonFlow::IonFlow(ThermoPhase* ph, size_t nsp, size_t points) : - StFlow(ph, nsp, 0, c_offset_Y, points) + Flow1D(ph, nsp, 0, c_offset_Y, points) { // make a local copy of species charge for (size_t k = 0; k < m_nsp; k++) { diff --git a/src/oneD/StFlow.cpp b/src/oneD/StFlow.cpp deleted file mode 100644 index 10e8259bd1e..00000000000 --- a/src/oneD/StFlow.cpp +++ /dev/null @@ -1,2293 +0,0 @@ -//! @file StFlow.cpp - -// This file is part of Cantera. See License.txt in the top-level directory or -// at https://cantera.org/license.txt for license and copyright information. - -#include "cantera/oneD/StFlow.h" -#include "cantera/base/global.h" -#include "cantera/base/Parser.h" -#include - -using namespace std; - -namespace Cantera -{ - -StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : - Domain1D(nsp, points, 0.0, nsoot, neq), - m_nsp(nsp), - m_neq(neq), - m_nsoot(nsoot) -{ - m_type = cFlowType; - m_points = points; - - if (ph == 0) { - return; // used to create a dummy object - } - m_thermo = ph; - - size_t nsp2 = m_thermo->nSpecies(); - // the species mass fractions are the last components in the solution - // vector, so the total number of components is the number of species - // plus the offset of the first mass fraction. - - - m_nv = m_neq + m_nsp + m_nsoot; - if (nsp2 + m_nsoot != m_nsp) { - m_nsp = nsp2; - Domain1D::resize(m_nv, points); - } - - // make a local copy of the species molecular weight vector - m_wt = m_thermo->molecularWeights(); - - // set pressure based on associated thermo object - setPressure(m_thermo->pressure()); - - // the species mass fractions are the last components in the solution - // vector, so the total number of components is the number of species - // plus the offset of the first mass fraction. - // m_nv = c_offset_Y + m_nsp; - - // enable all species equations by default - m_do_species.resize(m_nsp, true); - - // but turn off the energy equation at all points - m_do_energy.resize(m_points,false); - - m_diff.resize(m_nsp*m_points); - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_flux.resize(m_nsp,m_points); - m_wdot.resize(m_nsp,m_points, 0.0); - m_hk.resize(m_nsp, m_points, 0.0); - m_dhk_dz.resize(m_nsp, m_points - 1, 0.0); - m_ybar.resize(m_nsp); - m_qdotRadiation.resize(m_points, 0.0); - - //-------------- default solution bounds -------------------- - if (m_neq == 1) { - setBounds(c_offset_Tflamelet, 200.0, 2*m_thermo->maxTemp()); // temperature bounds - } else { - setBounds(c_offset_U, -1e20, 1e20); // no bounds on u - setBounds(c_offset_V, -1e20, 1e20); // V - setBounds(c_offset_T, 200.0, 2*m_thermo->maxTemp()); // temperature bounds - setBounds(c_offset_L, -1e20, 1e20); // lambda should be negative - setBounds(c_offset_E, -1e20, 1e20); // no bounds for inactive component - } - // mass fraction bounds - for (size_t k = 0; k < m_nsp; k++) { - setBounds(m_neq+k, -1.0e-7, 1.0e5); - } - - //-------------------- grid refinement ------------------------- - if (m_neq == 1) { - m_refiner->setActive(c_offset_Tflamelet, false); - } else { - m_refiner->setActive(c_offset_U, false); - m_refiner->setActive(c_offset_V, false); - m_refiner->setActive(c_offset_T, false); - m_refiner->setActive(c_offset_L, false); - } - - vector gr; - for (size_t ng = 0; ng < m_points; ng++) { - gr.push_back(1.0*ng/m_points); - } - setupGrid(m_points, gr.data()); - - // Find indices for radiating species - m_kRadiating.resize(2, npos); - m_kRadiating[0] = m_thermo->speciesIndex("CO2"); - m_kRadiating[1] = m_thermo->speciesIndex("H2O"); - - // P. Wolf - //---------------------AVBP PEA initialization------------------- - AVBPReadInputPea(); - - // B. Franzelli - //---------------------AVBP thickening initialisation------------ - AVBPReadInputChem(); - - // E. Lameloise - //---------------------Soot computation initialisation----------- - if (m_nsoot > 0){ - initSoot(); - } -} - -StFlow::StFlow(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) - : StFlow(th.get(), nsp, nsoot, neq, points) -{ - warn_deprecated("StFlow::StFlow", - "To be removed after Cantera 3.1. Class replaced by Flow1D."); -} - -StFlow::StFlow(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) - : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) -{ - m_solution = sol; - m_id = id; - m_kin = m_solution->kinetics().get(); - m_trans = m_solution->transport().get(); - - m_solution->registerChangedCallback(this, [this]() { - setKinetics(m_solution->kinetics()); - setTransport(m_solution->transport()); - }); - - if (m_trans->transportModel() == "none") { - // @deprecated - warn_deprecated("StFlow", - "An appropriate transport model\nshould be set when instantiating the " - "Solution ('gas') object.\nImplicit setting of the transport model " - "is deprecated and\nwill be removed after Cantera 3.0."); - setTransportModel("mixture-averaged"); - } - -} - -StFlow::~StFlow() -{ - if (m_solution) { - m_solution->removeChangedCallback(this); - } -} - -string StFlow::type() const { - if (m_isFree) { - return "free-flow"; - } - if (m_usesLambda) { - return "axisymmetric-flow"; - } - return "unstrained-flow"; -} - -void StFlow::setThermo(ThermoPhase& th) { - warn_deprecated("StFlow::setThermo", "To be removed after Cantera 3.0."); - m_thermo = &th; -} - -void StFlow::setKinetics(shared_ptr kin) -{ - if (!m_solution) { - // @todo remove after Cantera 3.0 - throw CanteraError("StFlow::setKinetics", - "Unable to update object that was not constructed from smart pointers."); - } - m_kin = kin.get(); - m_solution->setKinetics(kin); -} - -void StFlow::setKinetics(Kinetics& kin) -{ - warn_deprecated("StFlow::setKinetics(Kinetics&)", "To be removed after Cantera 3.0." - " Replaced by setKinetics(shared_ptr)."); - m_kin = &kin; -} - -void StFlow::setTransport(shared_ptr trans) -{ - if (!m_solution) { - // @todo remove after Cantera 3.0 - throw CanteraError("StFlow::setTransport", - "Unable to update object that was not constructed from smart pointers."); - } - if (!trans) { - throw CanteraError("StFlow::setTransport", "Unable to set empty transport."); - } - m_trans = trans.get(); - if (m_trans->transportModel() == "none") { - throw CanteraError("StFlow::setTransport", "Invalid Transport model 'none'."); - } - m_do_multicomponent = (m_trans->transportModel() == "multicomponent" || - m_trans->transportModel() == "multicomponent-CK"); - - m_diff.resize(m_nsp * m_points); - if (m_do_multicomponent) { - m_multidiff.resize(m_nsp * m_nsp*m_points); - m_dthermal.resize(m_nsp, m_points, 0.0); - } - m_solution->setTransport(trans); -} - -void StFlow::resize(size_t ncomponents, size_t points) -{ - Domain1D::resize(ncomponents, points); - m_rho.resize(m_points, 0.0); - m_wtm.resize(m_points, 0.0); - m_cp.resize(m_points, 0.0); - m_h.resize(m_points, 0.0); - m_hr.resize(m_points, 0.0); - m_visc.resize(m_points, 0.0); - m_tcon.resize(m_points, 0.0); - avbp_thick.resize(m_points,0.0); - - m_diff.resize(m_nsp*m_points); - if (m_do_multicomponent) { - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_dthermal.resize(m_nsp, m_points, 0.0); - } - m_flux.resize(m_nsp,m_points); - m_wdot.resize(m_nsp,m_points, 0.0); - m_hk.resize(m_nsp, m_points, 0.0); - m_dhk_dz.resize(m_nsp, m_points - 1, 0.0); - m_do_energy.resize(m_points,false); - m_qdotRadiation.resize(m_points, 0.0); - m_fixedtemp.resize(m_points); - - m_dz.resize(m_points-1); - m_z.resize(m_points); - - // P. Wolf - m_zmixfrac.resize(m_points); - // Soot - if (m_nsoot > 0){ - sootConsumption.resize(m_nsp, 0.0); - m_soot_diff.resize(m_nsoot, m_points, 0.0); - m_soot_soret.resize(m_nsoot, m_points, 0.0); - m_qdotNucleation.resize(m_points, 0.0); - m_qdotCondensation.resize(m_nsoot, m_points, 0.0); - m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); - m_qdotSg.resize(m_nsoot, m_points, 0.0); - m_qdotOxidation.resize(m_nsoot, m_points, 0.0); - } -} - -void StFlow::setupGrid(size_t n, const double* z) -{ - resize(m_nv, n); - - m_z[0] = z[0]; - for (size_t j = 1; j < m_points; j++) { - if (z[j] <= z[j-1]) { - throw CanteraError("StFlow::setupGrid", - "grid points must be monotonically increasing"); - } - m_z[j] = z[j]; - m_dz[j-1] = m_z[j] - m_z[j-1]; - } -} - -void StFlow::setupGrid(size_t n) -{ - resize(m_nv, n); - - m_z[0] = 0.0; - for (size_t j = 1; j < m_points; j++) { - m_z[j] = (double) j / ( (double) (n-1) ); - m_dz[j-1] = m_z[j] - m_z[j-1]; - } -} - -void StFlow::resetBadValues(double* xg) -{ - double* x = xg + loc(); - for (size_t j = 0; j < m_points; j++) { - double* Y = x + m_nv*j + c_offset_Y; - m_thermo->setMassFractions(Y); - m_thermo->getMassFractions(Y); - } -} - -void StFlow::setTransportModel(const string& trans) -{ - if (!m_solution) { - // @todo remove after Cantera 3.0 - throw CanteraError("StFlow::setTransportModel", - "Unable to set Transport manager by name as object was not initialized\n" - "from a Solution manager: set Transport object directly instead."); - } - m_solution->setTransportModel(trans); -} - -string StFlow::transportModel() const { - return m_trans->transportModel(); -} - -void StFlow::setTransport(Transport& trans) -{ - warn_deprecated("StFlow::setTransport(Transport&)", "To be removed after" - " Cantera 3.0. Replaced by setTransport(shared_ptr)."); - m_trans = &trans; - if (m_trans->transportModel() == "none") { - throw CanteraError("StFlow::setTransport", - "Invalid Transport model 'none'."); - } - m_do_multicomponent = (m_trans->transportModel() == "multicomponent" || - m_trans->transportModel() == "multicomponent-CK"); - - m_diff.resize(m_nsp*m_points); - if (m_do_multicomponent) { - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_dthermal.resize(m_nsp, m_points, 0.0); - } -} - -void StFlow::_getInitialSoln(double* x) -{ - for (size_t j = 0; j < m_points; j++) { - T(x,j) = m_thermo->temperature(); - m_thermo->getMassFractions(&Y(x, 0, j)); - m_rho[j] = m_thermo->density(); - } -} - -void StFlow::setGas(const double* x, size_t j) -{ - m_thermo->setTemperature(T(x,j)); - const double* yy = x + m_nv*j + c_offset_Y; - m_thermo->setMassFractions_NoNorm(yy); - m_thermo->setPressure(m_press); - // P. Wolf - if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ - calcMixFrac(x,j); - } -} - -void StFlow::setGasAtMidpoint(const double* x, size_t j) -{ - m_thermo->setTemperature(0.5*(T(x,j)+T(x,j+1))); - const double* yyj = x + m_nv*j + c_offset_Y; - const double* yyjp = x + m_nv*(j+1) + c_offset_Y; - for (size_t k = 0; k < m_nsp; k++) { - m_ybar[k] = 0.5*(yyj[k] + yyjp[k]); - } - m_thermo->setMassFractions_NoNorm(m_ybar.data()); - m_thermo->setPressure(m_press); - // P. Wolf - if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ - calcMixFrac(x,j); - } -} - - /// Calculates and updates the mixture fraction at point j - /// WARNING: Only correct if no Carbon atoms in the oxidizer line - /// and pure fuel in the fuel line - /// Added by P. Wolf - March 2010 - /// Thanks to Alireza Najafiyazdi - -void StFlow::calcMixFrac(const double* x, size_t j) { - size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom - size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel - double Z_C = 0.0; // passive scalar for C atom - double Z_C_F; // value of the passive scalar in fuel line - double W_C = this->m_thermo->atomicWeight(id_C); // Molecular weight of C atom - double W_fuel = this->m_thermo->molecularWeight(id_fuel); - double n_C; // Number of C atoms in each species - - for (size_t k=0; km_nsp; k++) { - n_C = this->m_thermo->nAtoms(k,id_C); - Z_C += n_C*x[index(c_offset_Y + k, j)]/this->m_thermo->molecularWeight(k); - } - Z_C = Z_C*W_C; - Z_C_F = W_C*this->m_thermo->nAtoms(id_fuel,id_C)/W_fuel; - m_zmixfrac[j] = Z_C/Z_C_F; // ie Z_C=0 in oxidizer line -} - -bool StFlow::fixed_mdot() { - warn_deprecated("StFlow::fixed_mdot", "To be removed after" - " Cantera 3.0. Replaced by isFree()."); - return !m_isFree; -} - -void StFlow::_finalize(const double* x) -{ - if (!m_do_multicomponent && m_do_soret) { - throw CanteraError("StFlow::_finalize", - "Thermal diffusion (the Soret effect) is enabled, and requires " - "using a multicomponent transport model."); - } - - size_t nz = m_zfix.size(); - bool e = m_do_energy[0]; - for (size_t j = 0; j < m_points; j++) { - if (e || nz == 0) { - m_fixedtemp[j] = T(x, j); - } else { - double zz = (z(j) - z(0))/(z(m_points - 1) - z(0)); - double tt = linearInterp(zz, m_zfix, m_tfix); - m_fixedtemp[j] = tt; - } - } - if (e) { - solveEnergyEqn(); - } - - if (m_isFree) { - // If the domain contains the temperature fixed point, make sure that it - // is correctly set. This may be necessary when the grid has been modified - // externally. - if (m_tfixed != Undef) { - for (size_t j = 0; j < m_points; j++) { - if (z(j) == m_zfixed) { - return; // fixed point is already set correctly - } - } - - for (size_t j = 0; j < m_points - 1; j++) { - // Find where the temperature profile crosses the current - // fixed temperature. - if ((T(x, j) - m_tfixed) * (T(x, j+1) - m_tfixed) <= 0.0) { - m_tfixed = T(x, j+1); - m_zfixed = z(j+1); - return; - } - } - } - } -} - -void StFlow::eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) -{ - // if evaluating a Jacobian, and the global point is outside the domain of - // influence for this domain, then skip evaluating the residual - if (jg != npos && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) { - return; - } - - // start of local part of global arrays - double* x = xg + loc(); - double* rsd = rg + loc(); - integer* diag = diagg + loc(); - - size_t jmin, jmax; - if (jg == npos) { // evaluate all points - jmin = 0; - jmax = m_points - 1; - } else { // evaluate points for Jacobian - size_t jpt = (jg == 0) ? 0 : jg - firstPoint(); - jmin = std::max(jpt, 1) - 1; - jmax = std::min(jpt+1,m_points-1); - } - - updateProperties(jg, x, jmin, jmax); - evalResidual(x, rsd, diag, rdt, jmin, jmax); -} - -void StFlow::updateProperties(size_t jg, double* x, size_t jmin, size_t jmax) -{ - // properties are computed for grid points from j0 to j1 - size_t j0 = std::max(jmin, 1) - 1; - size_t j1 = std::min(jmax+1,m_points-1); - - updateThermo(x, j0, j1); - if (jg == npos || m_force_full_update) { - // update transport properties only if a Jacobian is not being - // evaluated, or if specifically requested - updateTransport(x, j0, j1); - } - if (jg == npos) { - double* Yleft = x + index(c_offset_Y, jmin); - m_kExcessLeft = distance(Yleft, max_element(Yleft, Yleft + m_nsp)); - double* Yright = x + index(c_offset_Y, jmax); - m_kExcessRight = distance(Yright, max_element(Yright, Yright + m_nsp)); - } - - // update the species diffusive mass fluxes whether or not a - // Jacobian is being evaluated - updateDiffFluxes(x, j0, j1); - if (m_nsoot > 0){ - updateSootDiffFluxes(x, j0, j1); - } -} - -void StFlow::evalResidual(double* x, double* rsd, int* diag, - double rdt, size_t jmin, size_t jmax) -{ - //---------------------------------------------------- - // evaluate the residual equations at all required - // grid points - //---------------------------------------------------- - - // calculation of qdotRadiation (see docstring of enableRadiation) - if (m_do_radiation) { - // variable definitions for the Planck absorption coefficient and the - // radiation calculation: - double k_P_ref = 1.0*OneAtm; - - // polynomial coefficients: - const double c_H2O[6] = {-0.23093, -1.12390, 9.41530, -2.99880, - 0.51382, -1.86840e-5}; - const double c_CO2[6] = {18.741, -121.310, 273.500, -194.050, - 56.310, -5.8169}; - - // calculation of the two boundary values - double boundary_Rad_left = m_epsilon_left * StefanBoltz * pow(T(x, 0), 4); - double boundary_Rad_right = m_epsilon_right * StefanBoltz * pow(T(x, m_points - 1), 4); - - // loop over all grid points - for (size_t j = jmin; j < jmax; j++) { - // helping variable for the calculation - double radiative_heat_loss = 0; - - // calculation of the mean Planck absorption coefficient - double k_P = 0; - // absorption coefficient for H2O - if (m_kRadiating[1] != npos) { - double k_P_H2O = 0; - for (size_t n = 0; n <= 5; n++) { - k_P_H2O += c_H2O[n] * pow(1000 / T(x, j), (double) n); - } - k_P_H2O /= k_P_ref; - k_P += m_press * X(x, m_kRadiating[1], j) * k_P_H2O; - } - // absorption coefficient for CO2 - if (m_kRadiating[0] != npos) { - double k_P_CO2 = 0; - for (size_t n = 0; n <= 5; n++) { - k_P_CO2 += c_CO2[n] * pow(1000 / T(x, j), (double) n); - } - k_P_CO2 /= k_P_ref; - k_P += m_press * X(x, m_kRadiating[0], j) * k_P_CO2; - } - // absorption coefficient for soot - if (m_nsoot != 0 && m_do_soot_radiation) { - double k_P_soot = 0.0; - k_P_soot = 3.83 * CRad0 * fv(x,j) * T(x,j) / CRad2; - k_P += k_P_soot; - } - - // calculation of the radiative heat loss term - radiative_heat_loss = 2 * k_P *(2 * StefanBoltz * pow(T(x, j), 4) - - boundary_Rad_left - boundary_Rad_right); - - // set the radiative heat loss vector - m_qdotRadiation[j] = radiative_heat_loss; - } - } - - for (size_t j = jmin; j <= jmax; j++) { - //---------------------------------------------- - // left boundary - //---------------------------------------------- - if (m_nsoot > 0){ - getDistributionOrdre0(x,j); - } - //avbp_thick.resize(m_points,avbp_fthick); ///////////////////////////// NEW to handle pytest - AVBPcompute_local_thick(x,j); - double thick_j = avbp_thick[j]; - - if (j == 0) { - // these may be modified by a boundary object - - // Continuity. This propagates information right-to-left, since - // rho_u at point 0 is dependent on rho_u at point 1, but not on - // mdot from the inlet. - rsd[index(c_offset_U,0)] = - -(rho_u(x,1) - rho_u(x,0))/m_dz[0] - -(density(1)*V(x,1) + density(0)*V(x,0)); - - // the inlet (or other) object connected to this one will modify - // these equations by subtracting its values for V, T, and mdot. As - // a result, these residual equations will force the solution - // variables to the values for the boundary object - rsd[index(c_offset_V,0)] = V(x,0); - rsd[index(c_offset_T,0)] = T(x,0); - if (m_usesLambda) { - rsd[index(c_offset_L, 0)] = -rho_u(x, 0); - } else { - rsd[index(c_offset_L, 0)] = lambda(x, 0); - diag[index(c_offset_L, 0)] = 0; - } - - // The default boundary condition for species is zero flux. However, - // the boundary object may modify this. - double sum = 0.0; - for (size_t k = 0; k < m_nsp; k++) { - sum += Y(x,k,0); - rsd[index(c_offset_Y + k, 0)] = -// no thick -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); - -(m_flux(k,0) * thick_j + rho_u(x,0)* Y(x,k,0)); - } - rsd[index(c_offset_Y + leftExcessSpecies(), 0)] = 1.0 - sum; - if (m_nsoot > 0){ - for (size_t k = 0; k < m_nsoot; k++){ - rsd[index(c_offset_S + k, 0)] = - (m_soot_diff(k,0) - + rho_u(x,0)* Ys(x,k,0)); - } - } - - // set residual of poisson's equ to zero - rsd[index(c_offset_E, 0)] = x[index(c_offset_E, j)]; - } else if (j == m_points - 1) { - evalRightBoundary(x, rsd, diag, rdt); - } else { // interior points - evalContinuity(j, x, rsd, diag, rdt); - // set residual of poisson's equ to zero - rsd[index(c_offset_E, j)] = x[index(c_offset_E, j)]; - - //------------------------------------------------ - // Radial momentum equation - // - // \rho dV/dt + \rho u dV/dz + \rho V^2 - // = d(\mu dV/dz)/dz - lambda - //------------------------------------------------- - AVBPcompute_local_thick(x,j); - double thick_j = avbp_thick[j]; - double inv_thick = 1.0 / thick_j; - double thick_prev = avbp_thick[j-1]; - - if (m_usesLambda) { - rsd[index(c_offset_V,j)] = - (shear(x, j) - lambda(x, j) - rho_u(x, j) * dVdz(x, j) - - m_rho[j] * V(x, j) * V(x, j)) / m_rho[j] - - rdt * (V(x, j) - V_prev(j)); - diag[index(c_offset_V, j)] = 1; - } else { - rsd[index(c_offset_V, j)] = V(x, j); - diag[index(c_offset_V, j)] = 0; - } - - //------------------------------------------------- - // Soot equation - // - // \rho u dYs/dz + d(-0.554 \mu 1/T dT/dx Ys)/dz - // = d(\rho Ds dYs/dz)/dz + \rhos \rho qdots - // - // convection - Thermophoresis = Diffusion + Source - //------------------------------------------------- - if (m_nsoot > 0) { - sootSource(x,j); - for (size_t k = 0; k < m_nsoot; k++){ - // Convection - double soot_convec = rho_u(x,j)*dYsdz(x,k,j); - // Diffusion - double soot_diffus = 2.0 * (m_soot_diff(k,j) - m_soot_diff(k,j-1)) - / (z(j+1) - z(j-1)); - // Thermophoresis - double soot_soret = 2.0 * (m_soot_soret(k,j) - m_soot_soret(k,j-1)) - / (z(j+1) - z(j-1)); - // Source terms [m3/kg/s] - double soot_source = 0; - soot_source += (k == 0 ? m_qdotNucleation[j] : 0.0); - soot_source += (m_do_condensation ? m_qdotCondensation(k,j) : 0.0); - soot_source += (m_do_coagulation ? m_qdotCoagulation(k,j) : 0.0); - soot_source += (m_do_sg ? m_qdotSg(k,j) : 0.0); - soot_source += (m_do_oxidation ? m_qdotOxidation(k,j) : 0.0); - // kg/s/m^3 - soot_source *= (rho_soot * m_rho[j]); - if(k == m_nsoot - 1 && m_trash_section){soot_source = 0.0;} - // Residual - rsd[index(c_offset_S + k, j)] = - (soot_source - soot_convec + soot_diffus + soot_soret) / m_rho[j] - - rdt * (Ys(x,k,j) - Ys_prev(k,j)); - diag[index(c_offset_S + k, j)] = 1; - } - } - //------------------------------------------------- - // Species equations - // - // \rho dY_k/dt + \rho u dY_k/dz + dJ_k/dz - // = M_k\omega_k - //------------------------------------------------- - getWdot(x,j); - if (m_nsoot > 0 && m_do_retroaction){ - for (size_t k=0; k < m_nsp; k++){ - // (kmol.m^(-3).s^(-1)) - m_wdot(k,j) -= sootConsumption[k]; - } - } - for (size_t k = 0; k < m_nsp; k++) { - double convec = rho_u(x,j)*dYdz(x,k,j); -// no thick double diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) - double diffus = 2.0*(m_flux(k,j)*thick_j - m_flux(k,j-1)*thick_prev) - / (z(j+1) - z(j-1)); - rsd[index(c_offset_Y + k, j)] - = (m_wt[k]*(wdot(k,j)*inv_thick) -// no thick = (m_wt[k]*(wdot(k,j)) - - convec - diffus)/m_rho[j] - - rdt*(Y(x,k,j) - Y_prev(k,j)); - diag[index(c_offset_Y + k, j)] = 1; - } - - //----------------------------------------------- - // energy equation - // - // \rho c_p dT/dt + \rho c_p u dT/dz - // = d(k dT/dz)/dz - // - sum_k(\omega_k h_k_ref) - // - sum_k(J_k c_p_k / M_k) dT/dz - //----------------------------------------------- - if (m_do_energy[j]) { - - setGas(x,j); - double dtdzj = dTdz(x,j); - double sum = 0.0; - double sum2 = 0.0; - - grad_hk(x, j); - for (size_t k = 0; k < m_nsp; k++) { -// no thick double flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); - double flxk = 0.5*(m_flux(k,j-1)*thick_prev + m_flux(k,j)*thick_j); - sum += wdot(k,j)*m_hk(k,j); - sum2 += flxk * m_dhk_dz(k,j) / m_wt[k]; - } - - rsd[index(c_offset_T, j)] = - m_cp[j]*rho_u(x,j)*dtdzj -// no thick //- divHeatFlux(x,j) - sum; - - AVBPdivHeatFlux(x,j) - sum*inv_thick - sum2; - - rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); - rsd[index(c_offset_T, j)] -= rdt*(T(x,j) - T_prev(j)); - rsd[index(c_offset_T, j)] -= (m_qdotRadiation[j] / (m_rho[j] * m_cp[j])); - diag[index(c_offset_T, j)] = 1; - } else { - // residual equations if the energy equation is disabled - rsd[index(c_offset_T, j)] = T(x,j) - T_fixed(j); - diag[index(c_offset_T, j)] = 0; - } - - if (m_usesLambda) { - rsd[index(c_offset_L, j)] = lambda(x, j) - lambda(x, j - 1); - } else { - rsd[index(c_offset_L, j)] = lambda(x, j); - } - diag[index(c_offset_L, j)] = 0; - } - } -} - -void StFlow::updateTransport(double* x, size_t j0, size_t j1) -{ - if (m_do_multicomponent) { - for (size_t j = j0; j < j1; j++) { - setGasAtMidpoint(x,j); - double wtm = m_thermo->meanMolecularWeight(); - double rho = m_thermo->density(); - m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0); - m_trans->getMultiDiffCoeffs(m_nsp, &m_multidiff[mindex(0,0,j)]); - - // Use m_diff as storage for the factor outside the summation - for (size_t k = 0; k < m_nsp; k++) { - m_diff[k+j*m_nsp] = m_wt[k] * rho / (wtm*wtm); - } - - m_tcon[j] = m_trans->thermalConductivity(); - if (m_do_soret) { - m_trans->getThermalDiffCoeffs(m_dthermal.ptrColumn(0) + j*m_nsp); - } - } - } else { // mixture averaged transport - for (size_t j = j0; j < j1; j++) { - setGasAtMidpoint(x,j); - m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0); - m_trans->getMixDiffCoeffs(&m_diff[j*m_nsp]); - m_tcon[j] = m_trans->thermalConductivity(); - } - } -} - -void StFlow::show(const double* x) -{ - writelog(" Pressure: {:10.4g} Pa\n", m_press); - - Domain1D::show(x); - - if (m_do_radiation) { - writeline('-', 79, false, true); - writelog("\n z radiative heat loss"); - writeline('-', 79, false, true); - for (size_t j = 0; j < m_points; j++) { - writelog("\n {:10.4g} {:10.4g}", m_z[j], m_qdotRadiation[j]); - } - writelog("\n"); - } -} - -void StFlow::updateDiffFluxes(const double* x, size_t j0, size_t j1) -{ - if (m_do_multicomponent) { - for (size_t j = j0; j < j1; j++) { - double dz = z(j+1) - z(j); - for (size_t k = 0; k < m_nsp; k++) { - double sum = 0.0; - for (size_t m = 0; m < m_nsp; m++) { - sum += m_wt[m] * m_multidiff[mindex(k,m,j)] * (X(x,m,j+1)-X(x,m,j)); - } - m_flux(k,j) = sum * m_diff[k+j*m_nsp] / dz; - } - } - } else { - for (size_t j = j0; j < j1; j++) { - double sum = 0.0; - double wtm = m_wtm[j]; - double rho = density(j); - double dz = z(j+1) - z(j); - for (size_t k = 0; k < m_nsp; k++) { - m_flux(k,j) = m_wt[k]*(rho*m_diff[k+m_nsp*j]/wtm); - m_flux(k,j) *= (X(x,k,j) - X(x,k,j+1))/dz; - sum -= m_flux(k,j); - } - // correction flux to insure that \sum_k Y_k V_k = 0. - for (size_t k = 0; k < m_nsp; k++) { - m_flux(k,j) += sum*Y(x,k,j); - } - } - } - - if (m_do_soret) { - for (size_t m = j0; m < j1; m++) { - double gradlogT = 2.0 * (T(x,m+1) - T(x,m)) / - ((T(x,m+1) + T(x,m)) * (z(m+1) - z(m))); - for (size_t k = 0; k < m_nsp; k++) { - m_flux(k,m) -= m_dthermal(k,m)*gradlogT; - } - } - } -} - -string StFlow::componentName(size_t n) const -{ - switch (n) { - case c_offset_U: - return "velocity"; - case c_offset_V: - return "spread_rate"; - case c_offset_T: - return "T"; - case c_offset_L: - return "lambda"; - case c_offset_E: - return "eField"; - default: - if (n >= c_offset_Y && n < (c_offset_Y + m_nsp)) { - return m_thermo->speciesName(n - c_offset_Y); - } else if (n >= c_offset_S && n < (c_offset_S + m_nsoot)) { - return sectionName(n-c_offset_S); - } else { - return ""; - } - } -} - -size_t StFlow::componentIndex(const string& name) const -{ - if (name=="velocity") { - return c_offset_U; - } else if (name=="spread_rate") { - return c_offset_V; - } else if (name=="T") { - return c_offset_T; - } else if (name=="lambda") { - return c_offset_L; - } else if (name == "eField") { - return c_offset_E; - } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()) { - return stoi(name.substr(2))+c_offset_S; // offset not required in previous version, why? - } else { - for (size_t n=c_offset_Y; ntransportModel(); - - state["phase"]["name"] = m_thermo->name(); - AnyValue source = m_thermo->input().getMetadata("filename"); - state["phase"]["source"] = source.empty() ? "" : source.asString(); - - state["radiation-enabled"] = m_do_radiation; - if (m_do_radiation) { - state["emissivity-left"] = m_epsilon_left; - state["emissivity-right"] = m_epsilon_right; - } - - set energy_flags(m_do_energy.begin(), m_do_energy.end()); - if (energy_flags.size() == 1) { - state["energy-enabled"] = m_do_energy[0]; - } else { - state["energy-enabled"] = m_do_energy; - } - - state["Soret-enabled"] = m_do_soret; - - set species_flags(m_do_species.begin(), m_do_species.end()); - if (species_flags.size() == 1) { - state["species-enabled"] = m_do_species[0]; - } else { - for (size_t k = 0; k < m_nsp; k++) { - state["species-enabled"][m_thermo->speciesName(k)] = m_do_species[k]; - } - } - - state["refine-criteria"]["ratio"] = m_refiner->maxRatio(); - state["refine-criteria"]["slope"] = m_refiner->maxDelta(); - state["refine-criteria"]["curve"] = m_refiner->maxSlope(); - state["refine-criteria"]["prune"] = m_refiner->prune(); - state["refine-criteria"]["grid-min"] = m_refiner->gridMin(); - state["refine-criteria"]["max-points"] = - static_cast(m_refiner->maxPoints()); - - if (m_zfixed != Undef) { - state["fixed-point"]["location"] = m_zfixed; - state["fixed-point"]["temperature"] = m_tfixed; - } - - return state; -} - -shared_ptr StFlow::asArray(const double* soln) const -{ - auto arr = SolutionArray::create( - m_solution, static_cast(nPoints()), getMeta()); - arr->addExtra("grid", false); // leading entry - AnyValue value; - value = m_z; - arr->setComponent("grid", value); - vector data(nPoints()); - for (size_t i = 0; i < nComponents(); i++) { - if (componentActive(i)) { - auto name = componentName(i); - for (size_t j = 0; j < nPoints(); j++) { - data[j] = soln[index(i, j)]; - } - if (!arr->hasComponent(name)) { - arr->addExtra(name, componentIndex(name) > c_offset_Y); - } - value = data; - arr->setComponent(name, value); - } - } - value = m_rho; - arr->setComponent("D", value); // use density rather than pressure - - if (m_do_radiation) { - arr->addExtra("radiative-heat-loss", true); // add at end - value = m_qdotRadiation; - arr->setComponent("radiative-heat-loss", value); - } - - return arr; -} - -void StFlow::fromArray(SolutionArray& arr, double* soln) -{ - Domain1D::setMeta(arr.meta()); - arr.setLoc(0); - auto phase = arr.thermo(); - m_press = phase->pressure(); - vector did_section(m_nsoot,false); - bool wrote_header = false; - - const auto grid = arr.getComponent("grid").as>(); - setupGrid(nPoints(), &grid[0]); - - for (size_t i = 0; i < nComponents(); i++) { - if (!componentActive(i)) { - continue; - } - string name = componentName(i); - if (arr.hasComponent(name)) { - const vector data = arr.getComponent(name).as>(); - if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ - size_t n = stoi(name.substr(2)); - did_section[n]=true; - writelog("Adding soot section to soln "+name+"\n"); - } - for (size_t j = 0; j < nPoints(); j++) { - soln[index(i,j)] = data[j]; - } - } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ - size_t n = stoi(name.substr(2)); - did_section[n]=true; - writelog("Creating soot section in soln "+name+"\n"); - for (size_t j = 0; j < nPoints(); j++) { - soln[index(n+c_offset_S,j)] = 0.0; - } - } else { - warn_user("StFlow::fromArray", "Saved state does not contain values for " - "component '{}' in domain '{}'.", name, id()); - } - } - - if (soot_loglevel >= 1 && m_nsoot != 0) { - wrote_header = false; - for (size_t ks = 0; ks < m_nsoot; ks++) { - if (did_section[ks] == false) { - if (!wrote_header) { - writelog("\n\n"); - writelog("Missing data for soot sections:\n"); - wrote_header = true; - } - writelog(m_section_name[ks]+" "); - } - } - } - - updateProperties(npos, soln + loc(), 0, m_points - 1); - setMeta(arr.meta()); -} - -string StFlow::flowType() const { - warn_deprecated("StFlow::flowType", - "To be removed after Cantera 3.0; superseded by 'type'."); - if (m_type == cFreeFlow) { - return "Free Flame"; - } else if (m_type == cAxisymmetricStagnationFlow) { - return "Axisymmetric Stagnation"; - } else if (m_type == cFlameletFlow){ - return "Flamelet"; - } else { - throw CanteraError("StFlow::flowType", "Unknown value for 'm_type'"); - } -} - -void StFlow::setMeta(const AnyMap& state) -{ - if (state.hasKey("energy-enabled")) { - const AnyValue& ee = state["energy-enabled"]; - if (ee.isScalar()) { - m_do_energy.assign(nPoints(), ee.asBool()); - } else { - m_do_energy = ee.asVector(nPoints()); - } - } - - setTransportModel(state.getString("transport-model", "mixture-averaged")); - - if (state.hasKey("Soret-enabled")) { - m_do_soret = state["Soret-enabled"].asBool(); - } - - if (state.hasKey("species-enabled")) { - const AnyValue& se = state["species-enabled"]; - if (se.isScalar()) { - m_do_species.assign(m_thermo->nSpecies(), se.asBool()); - } else { - m_do_species = se.asVector(m_thermo->nSpecies()); - } - } - - if (state.hasKey("radiation-enabled")) { - m_do_radiation = state["radiation-enabled"].asBool(); - if (m_do_radiation) { - m_epsilon_left = state["emissivity-left"].asDouble(); - m_epsilon_right = state["emissivity-right"].asDouble(); - } - } - - if (state.hasKey("refine-criteria")) { - const AnyMap& criteria = state["refine-criteria"].as(); - double ratio = criteria.getDouble("ratio", m_refiner->maxRatio()); - double slope = criteria.getDouble("slope", m_refiner->maxDelta()); - double curve = criteria.getDouble("curve", m_refiner->maxSlope()); - double prune = criteria.getDouble("prune", m_refiner->prune()); - m_refiner->setCriteria(ratio, slope, curve, prune); - - if (criteria.hasKey("grid-min")) { - m_refiner->setGridMin(criteria["grid-min"].asDouble()); - } - if (criteria.hasKey("max-points")) { - m_refiner->setMaxPoints(criteria["max-points"].asInt()); - } - } - - if (state.hasKey("fixed-point")) { - m_zfixed = state["fixed-point"]["location"].asDouble(); - m_tfixed = state["fixed-point"]["temperature"].asDouble(); - } -} - -void StFlow::solveEnergyEqn(size_t j) -{ - bool changed = false; - if (j == npos) { - for (size_t i = 0; i < m_points; i++) { - if (!m_do_energy[i]) { - changed = true; - } - m_do_energy[i] = true; - } - } else { - if (!m_do_energy[j]) { - changed = true; - } - m_do_energy[j] = true; - } - m_refiner->setActive(c_offset_U, true); - m_refiner->setActive(c_offset_V, true); - m_refiner->setActive(c_offset_T, true); - if (changed) { - needJacUpdate(); - } -} - -size_t StFlow::getSolvingStage() const -{ - throw NotImplementedError("StFlow::getSolvingStage", - "Not used by '{}' objects.", type()); -} - -void StFlow::setSolvingStage(const size_t stage) -{ - throw NotImplementedError("StFlow::setSolvingStage", - "Not used by '{}' objects.", type()); -} - -void StFlow::solveElectricField(size_t j) -{ - throw NotImplementedError("StFlow::solveElectricField", - "Not used by '{}' objects.", type()); -} - -void StFlow::fixElectricField(size_t j) -{ - throw NotImplementedError("StFlow::fixElectricField", - "Not used by '{}' objects.", type()); -} - -bool StFlow::doElectricField(size_t j) const -{ - throw NotImplementedError("StFlow::doElectricField", - "Not used by '{}' objects.", type()); -} - -void StFlow::setBoundaryEmissivities(double e_left, double e_right) -{ - if (e_left < 0 || e_left > 1) { - throw CanteraError("StFlow::setBoundaryEmissivities", - "The left boundary emissivity must be between 0.0 and 1.0!"); - } else if (e_right < 0 || e_right > 1) { - throw CanteraError("StFlow::setBoundaryEmissivities", - "The right boundary emissivity must be between 0.0 and 1.0!"); - } else { - m_epsilon_left = e_left; - m_epsilon_right = e_right; - } -} - -void StFlow::fixTemperature(size_t j) -{ - bool changed = false; - if (j == npos) { - for (size_t i = 0; i < m_points; i++) { - if (m_do_energy[i]) { - changed = true; - } - m_do_energy[i] = false; - } - } else { - if (m_do_energy[j]) { - changed = true; - } - m_do_energy[j] = false; - } - m_refiner->setActive(c_offset_U, false); - m_refiner->setActive(c_offset_V, false); - m_refiner->setActive(c_offset_T, false); - if (changed) { - needJacUpdate(); - } -} -/* ------------------------------------------------------------------------ - Reads the mixture_database.dat file and sets accordingly the PEA function(s) - P. Wolf modif by J. Wirtz ---------------------------------------------------------------------------*/ -void StFlow::AVBPReadInputPea() { - Parser parser; - Param* param; - - ifstream avbp_mixturedb("mixture_database.dat"); - if (avbp_mixturedb.good()){ - parser.parseFile("mixture_database.dat"); - // In case of pea, the name of the gas should be the same than the one in the mixture_database. - // Get number of mixtures in database - size_t n_mixtures = parser.nbParamOccurence("mixture_name"); - size_t idx_beg = std::string::npos; - size_t idx_end = std::string::npos; - // Loop through all occurences of keyword "mixture name" - for (size_t i=0; i< n_mixtures; ++i) { - param = parser.getParam("mixture_name",i); - std::string current_str = param->readString(0); - // Check if mixture_name is the one requested in the cti file - if ( current_str == m_thermo->name() ) { - // Store bounding idx to get important info - idx_beg = parser.getParamNumber("mixture_name",i); - idx_end = parser.getParamNumber("mixture_name",i+1); - - // Get the fuel of the 2-step chemistry - param = parser.getParam("species_name", idx_beg, idx_end); - for (size_t i=0; ireadString(i); - if (avbp_species.find('C')!=string::npos && avbp_species.find('H')!=string::npos){ - avbp_fuel = avbp_species; - } - if (avbp_species == "H2"){ - avbp_fuel = avbp_species; - } - - } - - // Check if PEA method and search for the coefficient - if (parser.checkParam("pea_method", idx_beg, idx_end) == true){ - param = parser.getParam("pea_method", idx_beg, idx_end); - std::string avbp_pea = param->readString(0); - if (avbp_pea == "pea1"){ - avbp_ipea = 1; - cout<<"ipea set to 1, PEA_1 will be applied"<readDouble(i); - } - } - else if (avbp_pea == "pea2") { - avbp_ipea = 2; - cout<<"ipea set to 2, PEA_2 will be applied"<readDouble(i); - } - param = parser.getParam("pea_coeff", idx_beg, idx_end, 1); - for (size_t i=0; i<10; i++) { - avbp_pea_coeffs[i+8] = param->readDouble(i); - } - - } - else{ - throw CanteraError("readAvbpInputPEA","ipea is set to a weird value"); - } - } - else { - avbp_ipea = 0; - } - } - else { - // pea not considered as mixture_name (mixture_database.dat) does not correspond to gas name (cti) - avbp_ipea = 0; - } - - // calculate the global equivalence ratio phi_cst - if ((avbp_ipea==1)||(avbp_ipea==2)){ - size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom - size_t id_H = this->m_thermo->elementIndex("H"); // Index of H atom - size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel - size_t id_ox = this->m_thermo->speciesIndex("O2"); // Index of O2 - size_t n_C = this->m_thermo->nAtoms(id_fuel,id_C); - size_t n_H = this->m_thermo->nAtoms(id_fuel,id_H); - //Calculate in mass units phi = s_m*Yf/Yo - phi_cst = (n_C + n_H/4)*this->m_thermo->molecularWeight(id_ox)/this->m_thermo->molecularWeight(id_fuel); - phi_cst = phi_cst*1./0.2333; // WARNING: valid only for Fuel/AIR mixture - } - - if (avbp_ipea!=0){ - break; - } - - } - } - else { - avbp_ipea = 0; - } -} -/********** - Reading the AVBP input_chem.dat - B. Franzelli -*************/ -void StFlow::AVBPReadInputChem() { - avbp_fthick = m_thick; - if (avbp_fthick > 1.0) { - cout << "INFO: Thickening applied with constant value." << endl; - } - else { - avbp_fthick = 1.0; - } -} -void StFlow::AVBPcompute_local_thick(double* x,size_t j){ - avbp_thick[j] = avbp_fthick; -} - -//----------------------// -// SOOT RELATED MTEHODS // -//----------------------// -void StFlow::initSoot(){ - //---------------------------------------------------- - // Initializes soot computation - //---------------------------------------------------- - - // Sets offset of soot sections in solution array - // Resizes necessay arrays - // Sets sections names "YsXX", disables refinement on soot and sets clipping - - // Offset definition - c_offset_S = c_offset_Y + m_nsp; - // Array allocation - m_section_name.resize(m_nsoot); - sootConsumption.resize(m_nsp, 0.0); - q.resize(m_nsoot,0.0); - vSectMin.resize(m_nsoot, 0.0); - vSectMax.resize(m_nsoot, 0.0); - vSectMean.resize(m_nsoot, 0.0); - sSectMean.resize(m_nsoot, 0.0); - dSectMean.resize(m_nsoot, 0.0); - dSectCol.resize(m_nsoot, 0.0); - kfractal.resize(m_nsoot, 1.0); - Dfractal.resize(m_nsoot, 3); - nNucMean.resize(m_nsoot, 0.0); - rNucMean.resize(m_nsoot, 0.0); - rSectCol.resize(m_nsoot, 0.0); - aSectCol.resize(m_nsoot, 0.0); - theta_surf.resize(m_nsoot,2.0); - m_soot_diff.resize(m_nsoot, m_points, 0.0); - m_soot_soret.resize(m_nsoot, m_points, 0.0); - m_qdotNucleation.resize(m_points, 0.0); - m_qdotCondensation.resize(m_nsoot, m_points, 0.0); - m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); - collision_mat.resize(m_nsoot, m_nsoot, 0.0); - m_qdotSg.resize(m_nsoot, m_points, 0.0); - m_qdotOxidation.resize(m_nsoot, m_points, 0.0); - // Sections setup - for (size_t k = 0; k < m_nsoot; k++) { - std::string string_k = std::to_string(k); - m_section_name[k] = "Ys" + string_k; - m_refiner->setActive(c_offset_S+k, false); - setBounds(c_offset_S + k, -1.0e-5, 1e5); - } - -} - -void StFlow::setPrecursors(vector id_precursors){ - //---------------------------------------------------- - // Recovers precursor data for further computation - //---------------------------------------------------- - - if (m_nsoot <= 0){ - writelog("\n--> CANTERA SOOT : no sections :(\n"); - return; - } - size_t id_C = m_thermo->elementIndex("C"); - W_C = m_thermo->atomicWeight(id_C); - n_PAH = id_precursors.size(); - m_precursors.resize(n_PAH); - W_PAH.resize(n_PAH,0.0); - n_C.resize(n_PAH,0.0); - for (size_t k = 0; k != n_PAH; k++){ - m_precursors[k] = id_precursors[k] - c_offset_Y; - W_PAH[k] = m_thermo->molecularWeight(m_precursors[k]); - n_C[k] = m_thermo->nAtoms(m_precursors[k],id_C); - } -} - -void StFlow::finalizeSoot(){ - //---------------------------------------------------- - // Soot setup finalization - //---------------------------------------------------- - // Creates soot volumes - sootCreationVol(); - // Computes collision matrix - sootCollisionInverse(); - // Load surface reactions - if (m_do_sg || m_do_oxidation){ - loadHaca(m_haca_model); - loadSurface();} - - if (soot_loglevel >= 1){showSootInfo();} - if (soot_loglevel >= 2){showSootSections();} -} - -void StFlow::sootCreationVol(){ - // Sections creations - // PAH list boundaries - size_t n_C_min = *min_element(n_C.begin(),n_C.end()); - size_t n_C_max = *max_element(n_C.begin(),n_C.end()); - // First section lower boundary : smallest possible dimer - vSectMin[0] = 2.0 * (double)n_C_min * V_C2; - // First section upper boundary : biggest possible dimer - vSectMax[0] = V_C2 * max(2.0 * n_C_min + n_C_max, 2.0 * n_C_max); - // Following sections : geometrical progression - vSectMin[1] = vSectMax[0]; - if (m_trash_section){ - double vTrashLowLim = Pi * pow(dTrashLowLim,3.0) / 6; - for (size_t k = 1; k < m_nsoot - 2; k++){ - double exponent = double(k) / double(m_nsoot-2); - vSectMax[k] = vSectMin[1] * pow(vTrashLowLim / vSectMin[1],exponent); - vSectMin[k+1] = vSectMax[k]; - } - vSectMax[m_nsoot - 2] = vTrashLowLim; - vSectMin[m_nsoot - 1] = vTrashLowLim; - }else{ - for (size_t k = 1; k < m_nsoot - 1; k++){ - double exponent = double(k) / double(m_nsoot-1); - vSectMax[k] = vSectMin[1] * pow(bigSoot / vSectMin[1],exponent); - vSectMin[k+1] = vSectMax[k]; - } - } - - vSectMax[m_nsoot-1] = bigSoot; - // Building mean values - for (size_t k = 0; k < m_nsoot; k++){ - vSectMean[k] = (vSectMax[k] + vSectMin[k]) / 2.0 ; //(vSectMax[k] - vSectMin[k]) / log (vSectMax[k] / vSectMin[k]); - dSectMean[k] = pow(6 / Pi * vSectMean[k], 1.0 / 3.0); - } - - // Sections morphology - for (size_t k = 0; k < m_nsoot; k++){ - if (vSectMean[k] >= vlim1){ - // Fractal dimension - Dfractal[k] = Df; - // Fractal prefactor - kfractal[k] = 4.46 * pow(Dfractal[k], -2.08); - } - } - - if (m_soot_morphology == "sphere" || m_soot_morphology == "rodrigues"){ - // Soot morphological properties as defined by P. Rodrigues (PhD Thesis, 2018) - // For spheres, theta = 2.0 - for (size_t k = 0; k < m_nsoot; k++){ - if (m_soot_morphology == "rodrigues" && vSectMin[k] >= vlim1){ - theta_surf[k] = (3.0 * (log(vSectMean[k] / vlim1)) - + 2.0 * (log(vlim1 / V_C2))) - / (log(vSectMean[k] / V_C2)); - if (k == m_nsoot-1 && m_trash_section){theta_surf[k] = theta_surf[k-1];} - } - // Collision diameter - dSectCol[k] = 6 / pow(36 * Pi, 1.0 /Dfractal[k]) - * pow(vSectMean[k], (Dfractal[k]-2.0) / Dfractal[k]) - * pow(S_C2 * - pow(vSectMean[k]/V_C2,theta_surf[k] / 3.0),(3.0-Dfractal[k]) / Dfractal[k]); - // Collision radius - rSectCol[k] = dSectCol[k] / 2.0; - // Collision cross-section - aSectCol[k] = Pi * pow(rSectCol[k], 2.0); - // Surface area - sSectMean[k] = S_C2 * pow(vSectMean[k] / V_C2, theta_surf[k] / 3.0); - // Nuclei number - nNucMean[k] = pow(sSectMean[k], 2) / (36. * Pi * pow(vSectMean[k], 2.)); - // Nuclei radius[m] - rNucMean[k] = 3. * vSectMean[k] / sSectMean[k]; - } - // // From P. Rodrigues, trick to help numerical stability (not tested its impact) - // dSectCol[m_nsoot-1] = dSectMean[m_nsoot-1]; - // rSectCol[m_nsoot-1] = dSectCol[m_nsoot-1] / 2.0; - // aSectCol[m_nsoot-1] = Pi * pow(rSectCol[m_nsoot-1], 2.0); - }else if (m_soot_morphology == "thajudeen"){ - // Soot morphological properties as defined by Thajudeen (2012) - for (size_t k = 0; k < m_nsoot; k++){ - // Nuclei number - nNucMean[k] = max(1., vSectMean[k] / vlim1); - // Nuclei radius - rNucMean[k] = min(pow(3.0 * vSectMean[k] / (4.0 * Pi), 1./3.), pow(3.0 * vlim1 / (4.0 * Pi), 1.0/3.0)); - if (vSectMean[k] >= vlim1){ - // Collision radius (Smoluchowski radius) - double alpha1 = 0.253 * pow(Dfractal[k], 2.0) - 1.209 * Dfractal[k] + 1.433; - double alpha2 = -0.218 * pow(Dfractal[k], 2.0) + 0.964 * Dfractal[k] - 0.180; - double phi_r = 1 / (alpha1 * log(nNucMean[k]) + alpha2); - rSectCol[k] = rNucMean[k] * phi_r * pow(nNucMean[k] / kfractal[k], 1/Dfractal[k]); - // Collision cross-section (Projected Area) - double alpha3 = 0.439 * pow(Dfractal[k], 2.0) - 2.221 * Dfractal[k] + 2.787; - double alpha4 = -0.232 * pow(Dfractal[k], 3.0) + 1.273 * pow(Dfractal[k], 2.0) - 2.183 * Dfractal[k] + 1.906; - double phi_p = pow(nNucMean[k], -alpha3) / alpha4; - aSectCol[k] = Pi * pow(rNucMean[k], 2.) * phi_p * pow(nNucMean[k] / kfractal[k], 2.0/Dfractal[k]); - }else{ - rSectCol[k] = dSectMean[k] / 2.; - aSectCol[k] = Pi * pow(rSectCol[k], 2.); - } - //Collision diameter ("Smoluchowski diameter") - dSectCol[k] = 2. * rSectCol[k]; - // Surface area (computed from smoluchowski radius, close to Rodrigues definition) - sSectMean[k] = Pi * pow(dSectCol[k], 2.); - // theta parameter (needed for surface reactions) - theta_surf[k] = 3. * log(sSectMean[k]/S_C2) / log(vSectMean[k]/V_C2); - } - } -} - -void StFlow::sootCollisionInverse(){ - //---------------------------------------------------- - // Computes colision matrix (coagulation) - //---------------------------------------------------- - - for (size_t k = 0; k < m_nsoot; k++){ - for (size_t l = k; l < m_nsoot; l++){ - for (size_t m = l; m < m_nsoot; m++){ - double vol_min = vSectMin[l] + vSectMin[k]; - if(vol_min <= vSectMax[m] && vol_min >= vSectMin[m]){ - collision_mat(k,l) = m; - } - } - } - } -} - -void StFlow::loadSurface(){ - //---------------------------------------------------- - // Resizes and compute surface reactions arrays - //---------------------------------------------------- - - kpower.resize(m_nsoot,0.0); - mpower.resize(m_nsoot,0.0); - vc2power.resize(m_nsoot,0.0); - vc2powerm.resize(m_nsoot,0.0); - vmax_kpower.resize(m_nsoot,0.0); - vmin_kpower.resize(m_nsoot,0.0); - vmax_mpower.resize(m_nsoot,0.0); - vmin_mpower.resize(m_nsoot,0.0); - vmaxmc2_kpower.resize(m_nsoot,0.0); - vminpc2_kpower.resize(m_nsoot,0.0); - vmaxmc2_mpower.resize(m_nsoot,0.0); - vminpc2_mpower.resize(m_nsoot,0.0); - vc2powervect.resize(m_nsoot,0.0); - vc2powermvect.resize(m_nsoot,0.0); - for (size_t k = 0; k < m_nsoot; k++){ - kpower[k] = (theta_surf[k] + 3.0)/3.0; - mpower[k] = theta_surf[k]/3.0; - vc2power[k] = (3.0 - theta_surf[k] )/3.0; - vc2powerm[k] = - mpower[k]; - vmax_kpower[k] = pow(vSectMax[k],kpower[k]); - vmin_kpower[k] = pow(vSectMin[k],kpower[k]); - vmax_mpower[k] = pow(vSectMax[k],mpower[k]); - vmin_mpower[k] = pow(vSectMin[k],mpower[k]); - vmaxmc2_kpower[k] = pow(vSectMax[k] - V_C2,kpower[k]); - vminpc2_kpower[k] = pow(vSectMin[k] + V_C2,kpower[k]); - vmaxmc2_mpower[k] = pow(vSectMax[k] - V_C2,mpower[k]); - vminpc2_mpower[k] = pow(vSectMin[k] + V_C2,mpower[k]); - vc2powervect[k] = pow(V_C2,vc2power[k]); - vc2powermvect[k] = pow(V_C2,vc2powerm[k]); - } -} - -void StFlow::showSootInfo(){ - writelog("\n{:=^47}{:9}{:=^47}", "", "SOOT INFO", ""); - writelog("\n{:21}{:2}{}", "NUMBER OF SECTIONS", ":", m_nsoot); - writelog("\n{:21}{:1}","PRECURSORS", ":"); - for (size_t k = 0; k != n_PAH; k++){ - writelog(" {}", m_thermo->speciesName(m_precursors[k])); - } - if (dTrashLowLim > 0){writelog("\n{:21}{:2}{} m", "MAX DIAMETER", ":", dTrashLowLim);} - writelog("\n{:21}{:2}{}", "AGGREGATES MORPHOLOGY", ":", m_soot_morphology); - writelog("\n{:21}{:2}{}", "RETROACTION", ":", m_do_retroaction); - writelog("\n{:21}{:2}{}", "CONDENSATION", ":", m_do_condensation); - writelog("\n{:21}{:2}{}", "COAGULATION", ":", m_do_coagulation); - writelog("\n{:21}{:2}{}", "SURFACE GROWTH", ":", m_do_sg); - writelog("\n{:21}{:2}{}", "OXIDATION", ":", m_do_oxidation); - if (m_do_sg || m_do_oxidation){ - writelog("\n{:21}{:2}", "HACA MODEL", ":"); - if (m_haca_model == 1){ - writelog("Mauss"); - }else if (m_haca_model == 2){ - writelog("Blanquart"); - }else if (m_haca_model == 3){ - writelog("Kazakov"); - writelog("\n{:21}{:2}{}{:2}", "-> Flame temperature", ":", kazakovTad, " K"); - } - } - writelog("\n{:21}{:2}{}", "RADIATIVE HEAT LOSSES", ":", m_do_soot_radiation); - writelog("\n{:21}{:2}{}", "SORET EFFECT", ":", m_do_soot_soret); - writeline('=', 103, false, true); - writelog("\n"); -} -void StFlow::showSootSections(){ - //---------------------------------------------------- - // Displays section informations - //---------------------------------------------------- - - if (m_nsoot <= 0){ - writelog ("\nSOOT INFO : no sections to show :("); - return; - } - writelog("\n{:=^36}{:30}{:=^37}", "", "SOOT SECTIONS INFO (SI UNITS)", ""); - writelog("\n Section Vol. min. Vol. mean Vol. max. Diam. mean Diam. coll"); - writeline('-', 103, false, true); - for (size_t k = 0; k < m_nsoot; k++) { - writelog("\n {:10d} {:10.4g} {:10.4g} {:10.4g} {:10.4g} {:10.4g}", - k,vSectMin[k],vSectMean[k],vSectMax[k],dSectMean[k],dSectCol[k]); - } - writeline('=', 103, false, true); - writelog("\n"); -} - -void StFlow::sootSource(const double* x, size_t j) { - //---------------------------------------------------- - // Computes soot source terms - //---------------------------------------------------- - // Dimerization - sootDimerization(x,j); - // Nucleation - sootNucleation(x,j); - // Condensation - if (m_do_condensation){sootCondensation(x,j);} - // Coagulation - if (m_do_coagulation){sootCoagulation(x,j);} - // Surface chemistry - if (m_do_sg || m_do_oxidation){sootSurface(x,j);} -} - -void StFlow::sootDimerization(const double* x, size_t j){ - //---------------------------------------------------- - // Computes dimerization source term - //---------------------------------------------------- - double omega = 0, c_dimer = 0; - double V_k, d2_k, omega_k, C_k, gamma_k, k_k; - for (size_t k = 0; k < n_PAH; k++){ - // PAH volume [m3] - V_k = n_C[k] * V_C2 / 2.0; - // Squared PAH diameter [m2] - d2_k = pow(6.0 * V_k / Pi, 2.0/3.0); - // PAH concentraiton [kmol/m3] - C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; - // PAH sticking coefficient [-] - gamma_k = Cn_cst * pow(W_PAH[k], 4.0); - // Reaction rate constant [m3/kmol/s] - k_k = sqrt(4.0 * Pi * Boltzmann * T(x,j) / (W_C * n_C[k] / Avogadro)) * d2_k * Avogadro; - // PAH dimerization reaction rate [kmol/m3/s] - omega_k = gamma_k * k_k * pow(C_k, 2.0); - // PAH consumption [kmol/m3/s] (x2 because 2 mol PAH -> 1 mol dimer) - sootConsumption[m_precursors[k]] = 2 * omega_k; - // Adds PAH contribution to overall local dimerization rate - omega += omega_k; - // Adds PAH contribution to overall dimer carbon atoms - c_dimer += omega_k * n_C[k]; - - } - // Overall dimerization rate [1/kg/s] - r_dimer = omega * Avogadro / m_rho[j]; - // Overall dimer volume [m3] - V_dimer = c_dimer * V_C2 / omega; - - // double K00 = 0, cdimer = 0; - // double V_k, d_k, kdimfwd_k, K00_k, C_k; - // for (size_t k = 0; k < n_PAH; k++){ - // // PAH volume [m3] - // V_k = n_C[k] * V_C2 / 2.0; - // // PAH diameter [m] - // d_k = pow(6.0 * V_k / Pi, 1.0/3.0); - // // PAH concentraiton [mol/m3] - // C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; - // // m6/s/kg/mol2 - // kdimfwd_k = Cn_cst * pow(W_PAH[k], 4.0) / m_rho[j] - // * sqrt((4.0 * Pi * Boltzmann * T(x,j)) / ((W_C / Avogadro) * n_C[k])) - // * pow(d_k, 2.0) * pow(Avogadro, 2.0) ; - // // (mol.g^(-1).s^(-1)) - // K00_k = pow(C_k, 2.0) * kdimfwd_k / Avogadro; - // // (mol.g^(-1).s^(-1)) - // K00 += K00_k; - // cdimer += K00_k * n_C[k]; - // // Precursor consumption (mol/m3/s) - // // (x2 because 2 mol PAH -> 1 mol dimer) - // sootConsumption[m_precursors[k]] = 2 * K00_k * m_rho[j]; - // } - // // Dimerization rate [1/kg/s] - // r_dimer = K00 * Avogadro; - // // Equivalent dimer volume [m3] - // V_dimer = cdimer * V_C2 / K00; -} - -void StFlow::sootNucleation(const double* x, size_t j){ - //---------------------------------------------------- - // Compute nucleation source terms - //---------------------------------------------------- - // [m(11/2)/s/kg] - beta_fm = sqrt(Pi * Boltzmann * T(x,j) - / (rho_soot * 2.0)) / m_rho[j]; - // Dimer collision frequency [m6/s/kg] - beta_dimer = eps_nucl * beta_fm * sqrt(2.0 / V_dimer) - * pow (2.0 * pow(6.0 * V_dimer / Pi, 1.0 / 3.0), 2.0); - // // Dimer particle density [1/m3] - // N_dimer = sqrt((r_dimer / beta_dimer)); - // // Source term for nucleation [m3/kg/s] - // m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer, 2.0); - - // Dimer diameter [m] - double d_dimer = 2.0 * pow(3.0 * V_dimer / (4.0 * Pi), 1.0/3.0); - // Dimer mass [kg] - double m_dimer = V_dimer * rho_soot; - // Reaction rate constant [m3/kmol/s] - // k_nuc = beta_dimer * m_rho[j] * Avogadro / 2 - double k_nuc = eps_nucl * Avogadro * pow(d_dimer, 2.0) - * sqrt(4.0 * Pi * Boltzmann * T(x, j) / m_dimer); - // Dimer concentration (QSS Assumption) [kmol/m3] - double C_dimer = sqrt((r_dimer / Avogadro * m_rho[j]) / (2.0 * k_nuc)); - // Dimer number concentration [1/m3] - N_dimer = C_dimer * Avogadro; - // Nucleation reaction rate [kmol/m3/s] - double omega_nuc = k_nuc * pow(C_dimer, 2.0); - // Nucleation rate [m3/kg/s] - m_qdotNucleation[j] = omega_nuc * Avogadro * V_dimer / m_rho[j] * 2.0; - -} - -void StFlow::sootCondensation(const double* x, size_t j){ - //---------------------------------------------------- - // Compute condensation source term and corrects - // nucleation source term - //---------------------------------------------------- - - double kCond = 0; - double interval, vmoy, term1, term2, term3; - vector beta_cond(m_nsoot,0.0); - for (size_t k = 0; k < m_nsoot; k++){ - // Condensation collision kernel[m6/s/kg] - beta_cond[k] = eps_cond * beta_fm * sqrt(1.0/vSectMean[k]+1.0/V_dimer) - * pow(dSectCol[k] + pow(6.0 / Pi * V_dimer, 1.0/3.0), 2.0); - // Collisional frequency between a dimer and any soot particle [m3/s/kg] - kCond += beta_cond[k] * (q[k] * (vSectMax[k] - vSectMin[k]) / (vSectMean[k])); - } - // Correction of dimer density and nucleation source term - N_dimer = - (kCond / (2.0 * beta_dimer)) - + sqrt((r_dimer / beta_dimer) - + pow(kCond / (2.0 * beta_dimer),2.0)); - // Nucleation source term [m3/kg/1] - m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer,2.0); - - // Condensation source terms - for (size_t k = 0; k < m_nsoot; k++){ - interval = (vSectMax[k] - V_dimer) - vSectMin[k]; - vmoy = ((vSectMax[k] - V_dimer) + vSectMin[k]) / 2; - term1 = N_dimer * beta_cond[k] * q[k] / vmoy * V_dimer * interval; - if ( k==0 ){ - term2 = 0.0; - term3 = 0.0; - }else{ - interval = vSectMax[k-1] - (vSectMax[k-1] - V_dimer); - vmoy = (vSectMax[k-1] + (vSectMax[k-1] - V_dimer)) / 2; - term2 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * V_dimer * interval; - term3 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * vmoy * interval; - } - m_qdotCondensation(k,j) = term1 + term2 + term3; - if ( k>0 ){ - m_qdotCondensation(k-1,j) -= term3; - } - } -} - - -void StFlow::sootCoagulation(const double* x, size_t j){ - //---------------------------------------------------- - // Compute coagulation source terms - //---------------------------------------------------- - - for (size_t k = 0; k < m_nsoot; k++){ - m_qdotCoagulation(k,j) = 0.0; - } - // Viscosity (Cantera) [Pa.s-1] [CLEAN BUT SLOW] - // setGas(x,j); - // double visc = m_trans->viscosity(); - // Viscosity (Sutherland, air) [Pa.s-1] [TRASH BUT QUICK] - double visc = Csut1 * pow(T(x,j),1.5) / (T(x,j) + Csut2); - // Mean free path [m] - double mfp_rod = Boltzmann * T(x,j) / (sqrt(2.0) * Pi * pow(d_gaz,2.0) * m_press); - double mfp_tha = 66.4e-7 * (101325. / m_press) * (T(x,j) / 293.) * (1. + 110./293.) / (1 + 110. / T(x,j)); - double beta_coag_lk = 0.0; - for (size_t k = 0; k < m_nsoot; k++){ - for (size_t l = k; l < m_nsoot; l++){ - if (m_collision_model == "rodrigues" || m_collision_model == "sphere"){ - //Cunnningham numbers [-] - double Cu_k = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[k]; - double Cu_l = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[l]; - // Coagulation rate in continuous regime [m^6.kg^(-1).s-(-1)] - double beta_cont_lk = (2.0 * Boltzmann * T(x,j)) / (3.0 * visc) - * (dSectCol[l] + dSectCol[k]) - * (Cu_l / dSectCol[l] + Cu_k / dSectCol[k]) - / m_rho[j]; - // Coagulation rate in free molecular regime [m^6.kg^(-1).s-(-1)] - double beta_fm_lk = eps_coag * beta_fm - * sqrt(1 / vSectMean[k] + 1 / vSectMean[l]) - * pow(dSectCol[k] + dSectCol[l], 2.0); - // Overall coagulation rate [m^6.kg^(-1).s-(-1)] - beta_coag_lk = (beta_fm_lk * beta_cont_lk) - / (beta_fm_lk + beta_cont_lk); - }else if (m_collision_model == "thajudeen"){ - double reduced_mass = rho_soot * vSectMean[k] * vSectMean[l] / (vSectMean[k] + vSectMean[l]); - double smoluchowski_radius = rNucMean[k] * (1.203 - (0.4315*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])) * pow(rSectCol[k]/rNucMean[k] + rSectCol[l]/rNucMean[k], 0.8806 + (0.3497*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])); - double kn_diff_k = mfp_tha * Pi * rSectCol[k] / aSectCol[k]; - double kn_diff_l = mfp_tha * Pi * rSectCol[l] / aSectCol[l]; - double f_k = (6.0 * Pi * rSectCol[k] * visc) / (1 + kn_diff_k * (1.257 + 0.4 * exp(-1.1/kn_diff_k))); - double f_l = (6.0 * Pi * rSectCol[l] * visc) / (1 + kn_diff_l * (1.257 + 0.4 * exp(-1.1/kn_diff_l))); - double friction_coefficient = f_k * f_l / (f_k + f_l); - double projected_area = pow(smoluchowski_radius, 2.0) * Pi; - double kn_diff = (sqrt(Boltzmann * T(x,j) * reduced_mass) * Pi * smoluchowski_radius) / (friction_coefficient * projected_area); - double H = (4.0 * Pi * pow(kn_diff, 2.0) + 25.836 * pow(kn_diff, 3.0) + eps_coag * sqrt(8.0 * Pi) * 11.211 * pow(kn_diff, 4.0)) / (1 + 3.502 * kn_diff + 7.211 * pow(kn_diff, 2.0) + 11.211 * pow(kn_diff, 3.0)); - beta_coag_lk = (H * friction_coefficient * pow(projected_area, 2.0)) / (reduced_mass * pow(Pi, 2.0) * smoluchowski_radius) / m_rho[j]; - } - // Section of the particle corresponding to the coagulation of (l,k)y - size_t m = collision_mat(k,l); - // Loss of mass in section l due to coagulation with k - double terml = beta_coag_lk * q[l] * q[k] / vSectMean[k] - * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); - // Loss of mass in section k due to coagulation with l - double termk = beta_coag_lk * q[l] * q[k] / vSectMean[l] - * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); - double termm, termmplus; - // Gain in mass in m and m+1 thanks to coagulation of (l,k) - if (vSectMax[l] + vSectMax[k] <= vSectMax[m]){ - termm = terml + termk; - termmplus = 0.0; - }else{ - termm = (terml + termk) - * (vSectMax[m] - (vSectMin[k] + vSectMin[l])) - / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); - termmplus = (terml + termk) - * (vSectMax[k]+vSectMax[l]-vSectMax[m]) - / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); - } - if (m < m_nsoot-1){ - m_qdotCoagulation(m+1,j) += termmplus; - }else{ - termm = terml + termk; - } - m_qdotCoagulation(m,j) += termm; - m_qdotCoagulation(l,j) -= terml; - m_qdotCoagulation(k,j) -= termk; - } - } -} - -void StFlow::updateSootDiffFluxes(const double* x, size_t j0, size_t j1) -{ - //---------------------------------------------------- - // Computes soot molecular and thermal diffusion fluxes - //---------------------------------------------------- - for (size_t j = j0; j < j1; j++) { - // Evaluate gas at midpoints : j->j+1/2 - double Tmid = 0.5 * (T(x,j)+T(x,j+1)); - // [CLEAN BUT SLOW] - // setGasAtMidpoint(x,j); - // double wtm = m_thermo->meanMolecularWeight(); - // double rho = m_thermo->density(); - // double visco = m_trans->viscosity(); - // [TRASH BUT QUICK] - double wtm = 0.5*(m_wtm[j]+m_wtm[j+1]); - double rho = 0.5*(m_rho[j]+m_rho[j+1]); - double visco = Csut1 * pow(Tmid,1.5) / (Tmid + Csut2); - // Evaluate centered differencies at j+1/2 - double dT = T(x,j+1)-T(x,j); - double dz = z(j+1) - z(j); - // Evaluate viscosity - for (size_t k = 0; k < m_nsoot; k++){ - // Evaluate soot mass fraction at j+1/2 - - double Ysmid = 0.5 * (Ys(x,k,j)+Ys(x,k,j+1)); - // Evaluate centered differencies at j+1/2 - double dYs = Ys(x,k,j+1) - Ys(x,k,j); - //Evaluate diffusion coefficient at j+1/2 - double Ds = 3 / (2 * rho_soot * pow(dSectMean[k], 2.0) - * (1 + alphaT * Pi / 8)) - * sqrt ((wtm*Boltzmann*Tmid)/(2*Pi*Avogadro)); - // Evaluate soot mass diffusion flux at j+1/2 - m_soot_diff(k,j) = rho * Ds * dYs/dz; - // Evaluate soot mass soret flux at j+1/2 - if (m_do_soot_soret){ - m_soot_soret(k,j) = C_soot_soret * visco * Ysmid * dT/dz / Tmid; - } - } - } -} - -void StFlow::sootSurface(const double* x, size_t j){ - //---------------------------------------------------- - // Compute surface chemistry source terms - //---------------------------------------------------- - - // Computes reaction rates - sootSurfaceInitialization(x,j); - double term1, term2, term3; - //--------------- - // SURFACE GROWTH - //--------------- - if (m_do_sg){ - for (size_t k = 0; k < m_nsoot; k++){ - term1 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] - * (vmaxmc2_mpower[k] - vmin_mpower[k]); - if (k==0){ - term2 = 0.0; - term3 = 0.0; - }else{ - term2 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k-1] / mpower[k-1] * q[k-1] - * (vmax_mpower[k-1] - vmaxmc2_mpower[k-1]); - term3 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powermvect[k-1] / kpower[k-1] * q[k-1] - * (vmax_kpower[k-1] - vmaxmc2_kpower[k-1]); - } - // Surface growth source term [m3/kg/s] - m_qdotSg(k,j) = term1 + term2 + term3; - if (k > 0){m_qdotSg(k-1,j) -= term3;} - } - } - //---------- - // OXYDATION - //---------- - if (m_do_oxidation){ - for (size_t k=m_nsoot; k --> 0;){ - term1 = alpha_surf * kox / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] - * (vmax_mpower[k] - vminpc2_mpower[k]); - if (k==m_nsoot-1){ - term2 = 0.0; - term3 = 0.0; - }else if (k==m_nsoot-2 && m_trash_section) { - term2 = 0.0; - term3 = 0.0; - }else{ - term2 = alpha_surf * kox / m_rho[j] * vc2powervect[k+1] / mpower[k+1] * q[k+1] - * (vminpc2_mpower[k+1] - vmin_mpower[k+1]); - term3 = alpha_surf * kox / m_rho[j] * vc2powermvect[k+1] / kpower[k+1] * q[k+1] - * (vminpc2_kpower[k+1] - vmin_kpower[k+1]); - } - // Oxidation source term [m3/kg/s] - m_qdotOxidation(k,j) = - (term1 + term2 - term3); - if (k < m_nsoot - 1){ - m_qdotOxidation(k+1,j) -= term3; - } - } - } -} - -void StFlow::sootSurfaceInitialization(const double* x, size_t j){ - // Recover species concentrations [kmol/m3] - double conc_H = 0, conc_H2 = 0, conc_OH = 0, conc_H2O = 0, conc_C2H2 = 0, conc_O2 = 0; - double k01f = 0, k01b = 0, k02f = 0, k02b = 0, k03f = 0, k03b = 0, k04f = 0, k04b = 0; - double k05f = 0, k05b = 0, k06f = 0, k06bisf = 0; - double r01f = 0, r01b = 0, r02f = 0, r02b = 0, r03f = 0, r03b = 0, r04f = 0, r04b = 0; - double r05f = 0, r05b = 0, r06f = 0, r06bisf = 0, r07f = 0; - double ko2, koh, kd, krev, chi, chip, chic, alpha_kazakov; - size_t k; - // Recover molar concentrations - k = m_thermo->speciesIndex("H"); - if (k != npos){conc_H = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("H2"); - if (k != npos){conc_H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("H2O"); - if (k != npos){conc_H2O = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("C2H2"); - if (k != npos){conc_C2H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("O2"); - if (k != npos){conc_O2 = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("OH"); - if (k != npos){conc_OH = Y(x,k,j) * m_rho[j] / m_wt[k];} - // SI units - double slt = 1.0e3 / GasConstant / T(x,j); // 1e3 because GasConstant in J/kmol/K - double T_log=log(T(x,j)); - if (m_haca_model == 1 || m_haca_model == 11){ //Mauss - // Arrhenius constants - k01f = ak01f * exp(nk01f*T_log - ek01f*slt); // [m3/kmol/s] - k01b = ak01b * exp(nk01b*T_log - ek01b*slt); // [m3/kmol/s] - k02f = ak02f * exp(nk02f*T_log - ek02f*slt); // [m3/kmol/s] - k02b = ak02b * exp(nk02b*T_log - ek02b*slt); // [m3/kmol/s] - k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [m3/kmol/s] - k03b = ak03b * exp(nk03b*T_log - ek03b*slt); // [1/s] - k04f = ak04f * exp(nk04f*T_log - ek04f*slt); // [m3/kmol/s] - k04b = ak04b * exp(nk04b*T_log - ek04b*slt); // [1/s] - k05f = ak05f * exp(nk05f*T_log - ek05f*slt); // [1/s] - k05b = ak05b * exp(nk05b*T_log - ek05b*slt); // [m3/kmol/s] - k06f = ak06f * exp(nk06f*T_log - ek06f*slt); // [m3/kmol/s] - k06bisf = k06f; - // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] - r01f = k01f * conc_H; - r01b = k01b * conc_H2; - r02f = k02f * conc_OH; - r02b = k02b * conc_H2O; - r03f = k03f * conc_H; - r03b = k03b; - r04f = k04f * conc_C2H2; - r04b = k04b; - r05f = k05f; - r05b = k05b * conc_H; - r06f = k06f * conc_O2; - r06bisf = k06bisf * conc_O2; - r07f = Avogadro * S_C2 * gamma_oh * conc_OH * - pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); - // From QSS [-] - double fk10 = r05f / (r04b+r06bisf+r05f); - double A_QSS = (r01f + r02f + r03b + r07f + r05b * (1.0 - fk10)) / (r01b + r02b + r03f + r04f * fk10); - double B_QSS = r04f / ( r04b + r06bisf + r05f); - double D_QSS = r05b / (r04b + r06f + r05f); - - chi = 1.0; - chip = chi * A_QSS; - chic = chi * (A_QSS*B_QSS + D_QSS); - // Partial reaction rates[1/s] - koh = r07f * chi; - kd = r04f * chip; - ko2 = r06f * (chip + chic); - krev = r04b * chic; - // Partial surface growth and oxidation rates [1/s] - ksg = kd - krev; - kox = ko2 + koh; - } else if (m_haca_model == 2){ //Blanquart - // Arrhenius constants [m3/kmol/s] - k01f = ak01f * exp(nk01f*T_log - ek01f*slt); - k01b = ak01b * exp(nk01b*T_log - ek01b*slt); - k02f = ak02f * exp(nk02f*T_log - ek02f*slt); - k02b = ak02b * exp(nk02b*T_log - ek02b*slt); - k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [1/s] - k03b = ak03b * exp(nk03b*T_log - ek03b*slt); - k04f = ak04f * exp(nk04f*T_log - ek04f*slt); - k05f = ak05f * exp(nk05f*T_log - ek05f*slt); - // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] - r01f = k01f * conc_H; - r01b = k01b * conc_H2; - r02f = k02f * conc_OH; - r02b = k02b * conc_H2O; - r03f = k03f; - r03b = k03b * conc_H; - r04f = k04f * conc_C2H2; - r05f = k05f * conc_O2; - r06f = Avogadro * S_C2 * gamma_oh * conc_OH * - pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); - // From QSS [-] - chi = (r01f + r02f + r03f) / (r01b + r02b + r03b + r04f + r05f); // * 1.7e15; - // Oxidation O2 [must be 1/s] - ko2 = chi * r05f; - // Oxidation OH [1/s] - koh = r06f * chi; - // Oxidation - kox = ko2 + koh; - // Surface growth [1/s] - ksg = chi * r04f; - } else if (m_haca_model == 3){ //Kazakov - // Fraction of sites available at the surface of the particle for reaction [-] - alpha_kazakov = (1.0 + tanh(8.168e3/kazakovTad - 4.57)) / 2.0; - // Arrhenius constants [m3/kmol/s] - k01f = ak01f * exp(nk01f*T_log - ek01f*slt); - k01b = ak01b * exp(nk01b*T_log - ek01b*slt); - k02f = ak02f * exp(nk02f*T_log - ek02f*slt); - k03f = ak03f * exp(nk03f*T_log - ek03f*slt); - k04f = ak04f * exp(nk04f*T_log - ek04f*slt); - // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] - r01f = k01f * conc_H; - r01b = k01b * conc_H2; - r02f = k02f * conc_H; - r03f = k03f * conc_C2H2; - r04f = k04f * conc_O2; - r05f = Avogadro * S_C2 * gamma_oh * conc_OH * - pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); - // From QSS [-] - chi = r01f / (r01b + r02f + r03f + r04f); // * 2.3e14 - // Oxidation O2 [1/s] - ko2 = alpha_kazakov * chi * r04f; - // Oxidation OH [1/s] - koh = r05f * chi; - //Oxidation [1/s] - kox = ko2 + koh; - // Surface growth [1/s] - ksg = alpha_kazakov * chi * r03f; - } - //------------------------- - // RETROACTION ON GAS PHASE - //------------------------- - if (m_do_retroaction){ - double deltaQ = 0.0, soot_surface = 0.0; - for (size_t k = 0; k < m_nsoot; k++){ - deltaQ += vc2powervect[k] / mpower[k] * q[k] * (vmax_mpower[k]-vmin_mpower[k]); - } - //Overall active sites concentration [kmol/m3] - soot_surface = alpha_surf * n_sites * deltaQ / (V_C2 * Avogadro); // n_sites added here - // Surface chemistry reaction rates [kmol/s/m3] - double w01f = 0, w01b = 0, w02f = 0, w02b = 0, w03f = 0, w03b = 0; - double w04f = 0, w04b = 0, w05f = 0, w05b = 0, w06f = 0, w06bisf = 0; - double w07f = 0; - if (m_do_sg || m_do_oxidation){ - // Reaction rates for reactions occuring on both oxidation & surface growth - if (m_haca_model == 1){ - w01f = r01f * soot_surface * chi; - w01b = r01b * soot_surface * chip; - w02f = r02f * soot_surface * chi; - w02b = r02b * soot_surface * chip; - w03f = r03f * soot_surface * chip; - w03b = r03b * soot_surface * chi; - w05f = r05f * soot_surface * chic; - w05b = r05b * soot_surface * chi; - w06bisf = r06bisf * soot_surface * chic; - }else if (m_haca_model == 2){ - w01f = r01f * soot_surface * chi; - w01b = r01b * soot_surface * chi; - w02f = r02f * soot_surface * chi; - w02b = r02b * soot_surface * chi; - w03f = r03f * soot_surface * chi; - w03b = r03b * soot_surface * chi; - }else if (m_haca_model == 3){ - w01f = r01f * soot_surface * chi; - w01b = r01b * soot_surface * chi; - w02f = r02f * soot_surface * chi; - } - } - // Reaction rates for reactions occuring on surfacce growth only - if (m_do_sg){ - if (m_haca_model == 1){ - w04f = r04f * soot_surface * chip; - w04b = r04b * soot_surface * chic; - }else if (m_haca_model == 2){ - w04f = r04f * soot_surface * chi; - }else if (m_haca_model == 3){ - w03f = r03f * soot_surface * chi; - } - } - // Reaction rates for reactions occuring on oxidation only - if (m_do_oxidation){ - if (m_haca_model == 1){ - // Reaction rates [kmol/m3/s] - w06f = r06f * soot_surface * chip; - w07f = r07f * soot_surface * chi; - }else if (m_haca_model == 2){ - w05f = r05f * soot_surface * chi; - w06f = r06f * soot_surface * chi; - }else if (m_haca_model == 3){ - w04f = r04f * soot_surface * chi; - w05f = r05f * soot_surface * chi; - } - } - - // Gaseous species consumption [kmol/s/m3] - if (m_haca_model == 1){ - k = m_thermo->speciesIndex("H"); - if (k != npos){sootConsumption[k] = - (w01f - w01b) - (w03f - w03b) + (w05f - w05b);} - k = m_thermo->speciesIndex("C2H2"); - if (k != npos){sootConsumption[k] = (w04f - w04b);} - k = m_thermo->speciesIndex("H2"); - if (k != npos){sootConsumption[k] = (w01f - w01b);} - k = m_thermo->speciesIndex("O2"); - if (k != npos){sootConsumption[k] = - w06f - w06bisf;} - k = m_thermo->speciesIndex("CO"); - if (k != npos){sootConsumption[k] = 2.0 * w06f;} - k = m_thermo->speciesIndex("OH"); - if (k != npos){sootConsumption[k] = - (w02f - w02b) - w07f;} - k = m_thermo->speciesIndex("H2O"); - if (k != npos){sootConsumption[k] = + (w02f - w02b);} - k = m_thermo->speciesIndex("HCO"); - if (k != npos){sootConsumption[k] = 2.0 * w06bisf + w07f;} - k = m_thermo->speciesIndex("CH"); - if (k != npos){sootConsumption[k] = w07f;} - }else if (m_haca_model == 2){ - k = m_thermo->speciesIndex("H"); - if (k != npos){sootConsumption[k] = -(w01f-w01b) + (w03f-w03b) + w04f;} - k = m_thermo->speciesIndex("C2H2"); - if (k != npos){sootConsumption[k] = -w04f;} - k = m_thermo->speciesIndex("H2"); - if (k != npos){sootConsumption[k] = (w01f-w01b) + w05f + w06f;} - k = m_thermo->speciesIndex("O2"); - if (k != npos){sootConsumption[k] = -w05f;} - k = m_thermo->speciesIndex("CO"); - if (k != npos){sootConsumption[k] = 2.0 * w05f + w06f;} - k = m_thermo->speciesIndex("OH"); - if (k != npos){sootConsumption[k] = -(w02f-w02b) - w06f;} - k = m_thermo->speciesIndex("H2O"); - if (k != npos){sootConsumption[k] = (w02f-w02b);} - }else if (m_haca_model == 3){ - k = m_thermo->speciesIndex("H"); - if (k != npos){sootConsumption[k] = -(w01f-w01b) - w02f + w03f;} - k = m_thermo->speciesIndex("C2H2"); - if (k != npos){sootConsumption[k] = -w03f;} - k = m_thermo->speciesIndex("H2"); - if (k != npos){sootConsumption[k] = (w01f-w01b) + w05f;} - k = m_thermo->speciesIndex("O2"); - if (k != npos){sootConsumption[k] = -w04f;} - k = m_thermo->speciesIndex("CO"); - if (k != npos){sootConsumption[k] = 2.0 * w04f + w05f;} - k = m_thermo->speciesIndex("OH"); - if (k != npos){sootConsumption[k] = - w05f;} - } - } -} - -void StFlow::getDistributionOrdre0(const double* x, size_t j){ - for (size_t k = 0; k < m_nsoot; k++){ - // Soot volume fraction density [1/m3] - q[k] = m_rho[j] * Ys(x,k,j) / (rho_soot * (vSectMax[k] - vSectMin[k])); - } -} -//-----------------------------// -// END OF SOOT RELATED METHODS // -//-----------------------------// - -void StFlow::evalRightBoundary(double* x, double* rsd, int* diag, double rdt) -{ - size_t j = m_points - 1; - AVBPcompute_local_thick(x,j); - double thick_prev = avbp_thick[j-1]; - - // the boundary object connected to the right of this one may modify or - // replace these equations. The default boundary conditions are zero u, V, - // and T, and zero diffusive flux for all species. - - rsd[index(c_offset_V,j)] = V(x,j); - diag[index(c_offset_V,j)] = 0; - double sum = 0.0; - // set residual of poisson's equ to zero - rsd[index(c_offset_E, j)] = x[index(c_offset_E, j)]; - if (m_nsoot > 0){ - for (size_t k = 0; k < m_nsoot; k++){ - if (m_do_retroaction){sum += Ys(x,k,j);} - rsd[index(c_offset_S + k, j)] = - m_soot_diff(k,j-1) + rho_u(x,j)*Ys(x,k,j); - } - } - for (size_t k = 0; k < m_nsp; k++) { - sum += Y(x,k,j); - rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1)*thick_prev + rho_u(x,j)*Y(x,k,j); -// no thick rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); - } - rsd[index(c_offset_Y + rightExcessSpecies(), j)] = 1.0 - sum; - diag[index(c_offset_Y + rightExcessSpecies(), j)] = 0; - if (m_usesLambda) { - rsd[index(c_offset_U, j)] = rho_u(x, j); - } else { - rsd[index(c_offset_U, j)] = rho_u(x, j) - rho_u(x, j-1); - } - - rsd[index(c_offset_L, j)] = lambda(x, j) - lambda(x, j-1); - diag[index(c_offset_L, j)] = 0; - rsd[index(c_offset_T, j)] = T(x, j); -} - -void StFlow::evalContinuity(size_t j, double* x, double* rsd, int* diag, double rdt) -{ - //algebraic constraint - diag[index(c_offset_U, j)] = 0; - //---------------------------------------------- - // Continuity equation - // - // d(\rho u)/dz + 2\rho V = 0 - //---------------------------------------------- - if (m_usesLambda) { - // Note that this propagates the mass flow rate information to the left - // (j+1 -> j) from the value specified at the right boundary. The - // lambda information propagates in the opposite direction. - rsd[index(c_offset_U,j)] = - -(rho_u(x,j+1) - rho_u(x,j))/m_dz[j] - -(density(j+1)*V(x,j+1) + density(j)*V(x,j)); - } else if (m_isFree) { - // terms involving V are zero as V=0 by definition - if (grid(j) > m_zfixed) { - rsd[index(c_offset_U,j)] = - - (rho_u(x,j) - rho_u(x,j-1))/m_dz[j-1]; - } else if (grid(j) == m_zfixed) { - if (m_do_energy[j]) { - rsd[index(c_offset_U,j)] = (T(x,j) - m_tfixed); - } else { - rsd[index(c_offset_U,j)] = (rho_u(x,j) - - m_rho[0]*0.3); // why 0.3? - } - } else if (grid(j) < m_zfixed) { - rsd[index(c_offset_U,j)] = - - (rho_u(x,j+1) - rho_u(x,j))/m_dz[j]; - } - } else { - // unstrained with fixed mass flow rate - rsd[index(c_offset_U, j)] = rho_u(x, j) - rho_u(x, j - 1); - } -} - -} // namespace diff --git a/test/oneD/test_oneD.cpp b/test/oneD/test_oneD.cpp index df838747e70..9ad78963460 100644 --- a/test/oneD/test_oneD.cpp +++ b/test/oneD/test_oneD.cpp @@ -5,7 +5,7 @@ #include "cantera/core.h" #include "cantera/onedim.h" #include "cantera/oneD/DomainFactory.h" -#include "cantera/oneD/StFlow.h" +#include "cantera/oneD/Flow1D.h" #include "cantera/oneD/IonFlow.h" using namespace Cantera; @@ -103,97 +103,6 @@ TEST(onedim, freeflame) } } -TEST(onedim, legacy) -{ - //! @todo: Remove after Cantera 3.1 - auto sol = newSolution("h2o2.yaml", "ohmech", "mixture-averaged"); - auto gas = sol->thermo(); - size_t nsp = gas->nSpecies(); - - // reactants - double uin = .3; - double T = 300; - double P = 101325; - string X = "H2:0.65, O2:0.5, AR:2"; - gas->setState_TPX(T, P, X); - double rho_in = gas->density(); - vector yin(nsp); - gas->getMassFractions(&yin[0]); - - // product estimate - gas->equilibrate("HP"); - vector yout(nsp); - gas->getMassFractions(&yout[0]); - double rho_out = gas->density(); - double Tad = gas->temperature(); - - // flow - suppress_deprecation_warnings(); - auto flow = newDomain("legacy-flow", sol); - make_deprecation_warnings_fatal(); - flow->setID("flow"); - flow->setFreeFlow(); - - // grid - int nz = 21; - double lz = 0.02; - vector z(nz); - double dz = lz; - dz /= (double)(nz - 1); - for (int iz = 0; iz < nz; iz++) { - z[iz] = iz * dz; - } - flow->setupGrid(nz, &z[0]); - - // inlet - auto inlet = newDomain("inlet", sol); - inlet->setMoleFractions(X); - inlet->setMdot(uin * rho_in); - inlet->setTemperature(T); - - // outlet - auto outlet = newDomain("outlet", sol); - double uout = inlet->mdot() / rho_out; - - // set up simulation - vector> domains { inlet, flow, outlet }; - Sim1D flame(domains); - int dom = static_cast(flame.domainIndex("flow")); - ASSERT_EQ(dom, 1); - - // set up initial guess - vector locs{0.0, 0.3, 0.7, 1.0}; - vector value{uin, uin, uout, uout}; - flame.setInitialGuess("velocity", locs, value); - value = {T, T, Tad, Tad}; - flame.setInitialGuess("T", locs, value); - for (size_t i = 0; i < nsp; i++) { - value = {yin[i], yin[i], yout[i], yout[i]}; - flame.setInitialGuess(gas->speciesName(i), locs, value); - } - - // simulation settings - double ratio = 15.0; - double slope = 0.3; - double curve = 0.5; - flame.setRefineCriteria(dom, ratio, slope, curve); - flame.setFixedTemperature(0.85 * T + .15 * Tad); - - // solve - flow->solveEnergyEqn(); - bool refine_grid = false; - int loglevel = 0; - flame.solve(loglevel, refine_grid); - - ASSERT_EQ(flow->nPoints(), static_cast(nz + 1)); - size_t comp = flow->componentIndex("T"); - double Tprev = flame.value(dom, comp, 0); - for (size_t n = 0; n < flow->nPoints(); n++) { - T = flame.value(dom, comp, n); - ASSERT_GE(T, Tprev); - Tprev = T; - } -} TEST(onedim, flame_types) { From 46d63f39673bc7e2fb71113e6743c814ec1f89bd Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 8 Jul 2025 16:39:56 +0200 Subject: [PATCH 31/98] Small bugfixes following merge Changes to be committed: deleted: ../../../include/cantera/oneD/StFlow.h modified: ../../../interfaces/cython/cantera/_onedim.pxd deleted: ../../../src/oneD/StFlow.cpp --- include/cantera/oneD/StFlow.h | 1257 -------------- interfaces/cython/cantera/_onedim.pxd | 3 - src/oneD/StFlow.cpp | 2310 ------------------------- 3 files changed, 3570 deletions(-) delete mode 100644 include/cantera/oneD/StFlow.h delete mode 100644 src/oneD/StFlow.cpp diff --git a/include/cantera/oneD/StFlow.h b/include/cantera/oneD/StFlow.h deleted file mode 100644 index dc4b3b36fd6..00000000000 --- a/include/cantera/oneD/StFlow.h +++ /dev/null @@ -1,1257 +0,0 @@ -//! @file StFlow.h - -// This file is part of Cantera. See License.txt in the top-level directory or -// at https://cantera.org/license.txt for license and copyright information. - -#ifndef CT_STFLOW_H -#define CT_STFLOW_H - -#include "Domain1D.h" -#include "cantera/base/Array.h" -#include "cantera/base/Solution.h" -#include "cantera/thermo/ThermoPhase.h" -#include "cantera/kinetics/Kinetics.h" - -namespace Cantera -{ - -//------------------------------------------ -// constants -//------------------------------------------ - -//! Offsets of solution components in the 1D solution array. -enum offset -{ - c_offset_U //! axial velocity - , c_offset_V //! strain rate - , c_offset_T //! temperature - , c_offset_L //! (1/r)dP/dr - , c_offset_E //! electric poisson's equation - , c_offset_Y //! mass fractions -}; - -//! Offsets of solution components in the 1D solution array for mixture fraction space -enum offset_z -{ - c_offset_Tflamelet, //! Temperature - c_offset_Yflamelet, //! Species mass fractions - // c_offset_Chi not used -}; - -class Transport; - -//! @defgroup flowGroup Flow Domains -//! One-dimensional flow domains. -//! @ingroup onedGroup - -/** - * This class represents 1D flow domains that satisfy the one-dimensional - * similarity solution for chemically-reacting, axisymmetric flows. - * @ingroup flowGroup - */ -class StFlow : public Domain1D -{ -public: - //-------------------------------- - // construction and destruction - //-------------------------------- - - //! Create a new flow domain. - //! @param ph Object representing the gas phase. This object will be used - //! to evaluate all thermodynamic, kinetic, and transport properties. - //! @param nsp Number of species. - //! @param points Initial number of grid points - //! @param n_eq Number of non-species equations (default = 4 for spatial resolution) - - //StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t points = 1); - StFlow(ThermoPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); - - //! Delegating constructor - StFlow(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); - - //! Create a new flow domain. - //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and - //! transport properties - //! @param id name of flow domain - //! @param points initial number of grid points - StFlow(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Y, size_t points=1); - - virtual ~StFlow(); // virtual kw required for derived class destructors (flamelet) - - virtual string type() const override; - - //! @name Problem Specification - //! @{ - - void setupGrid(size_t n, const double* z) override; - void setupGrid(size_t n); - - virtual void resetBadValues(double* xg) override; - - ThermoPhase& phase() { - return *m_thermo; - } - - Kinetics& kinetics() { - return *m_kin; - } - - /** - * Set the thermo manager. - * - * @deprecated To be removed after %Cantera 3.0 (unused) - */ - void setThermo(ThermoPhase& th); - - void setKinetics(shared_ptr kin) override; - - //! Set the kinetics manager. - //! @deprecated To be removed after %Cantera 3.0; - //! replaced by Domain1D::setKinetics() - void setKinetics(Kinetics& kin); - - void setTransport(shared_ptr trans) override; - - //! Set transport model to existing instance - //! @deprecated To be removed after %Cantera 3.0; - //! replaced by Domain1D::setKinetics() - void setTransport(Transport& trans); - - //! Set the transport model - //! @since New in %Cantera 3.0. - void setTransportModel(const string& trans); - - //! Retrieve transport model - //! @since New in %Cantera 3.0. - string transportModel() const; - - //! Enable thermal diffusion, also known as Soret diffusion. - //! Requires that multicomponent transport properties be - //! enabled to carry out calculations. - void enableSoret(bool withSoret) { - m_do_soret = withSoret; - } - bool withSoret() const { - return m_do_soret; - } - - //! Set the pressure. Since the flow equations are for the limit of small - //! Mach number, the pressure is very nearly constant throughout the flow. - void setPressure(double p) { - m_press = p; - } - - //! The current pressure [Pa]. - double pressure() const { - return m_press; - } - - //! Set the number of non-species equations - void setNequation(size_t neq){ - m_neq = neq; - } - - //! The current number of non-species equations - size_t nEq(){ - return m_neq; - } - - //! Write the initial solution estimate into array x. - void _getInitialSoln(double* x) override; - - void _finalize(const double* x) override; - - //! Sometimes it is desired to carry out the simulation using a specified - //! temperature profile, rather than computing it by solving the energy - //! equation. This method specifies this profile. - void setFixedTempProfile(vector& zfixed, vector& tfixed) { - m_zfix = zfixed; - m_tfix = tfixed; - } - - /** - * Set the temperature fixed point at grid point j, and disable the energy - * equation so that the solution will be held to this value. - */ - void setTemperature(size_t j, double t) { - m_fixedtemp[j] = t; - m_do_energy[j] = false; - } - - //! The fixed temperature value at point j. - double T_fixed(size_t j) const { - return m_fixedtemp[j]; - } - - /// Returns the mixture fraction at point j - /// Added by P. Wolf - March 2010 - /// Thanks to Alireza Najafiyazdi - double getMixFrac(size_t j) { - return m_zmixfrac[j]; - } - - /// Updates the mixture fraction at point j - /// Added by P. Wolf - March 2010 - /// Thanks to Alireza Najafiyazdi - void calcMixFrac(const double* x,size_t j); - - //! @} - - string componentName(size_t n) const override; - - size_t componentIndex(const string& name) const override; - - //! Returns true if the specified component is an active part of the solver state - virtual bool componentActive(size_t n) const; - - //! Print the solution. - void show(const double* x) override; - - shared_ptr asArray(const double* soln) const override; - void fromArray(SolutionArray& arr, double* soln) override; - - //! Set flow configuration for freely-propagating flames, using an internal point - //! with a fixed temperature as the condition to determine the inlet mass flux. - void setFreeFlow() { - m_type = cFreeFlow; - m_dovisc = false; - m_isFree = true; - m_usesLambda = false; - } - - //! Set flow configuration for axisymmetric counterflow flames, using specified - //! inlet mass fluxes. - void setAxisymmetricFlow() { - m_type = cAxisymmetricStagnationFlow; - m_dovisc = true; - m_isFree = false; - m_usesLambda = true; - } - - //! Set flow configuration for burner-stabilized flames, using specified inlet mass - //! fluxes. - void setUnstrainedFlow() { - m_type = cAxisymmetricStagnationFlow; - m_dovisc = false; - m_isFree = false; - m_usesLambda = false; - } - - void setFlameletFlow() { - m_type = cFlameletFlow; - m_dovisc = true; - m_isFree = false; - m_usesLambda = true; - } - - //! Return the type of flow domain being represented, either "Free Flame" or - //! "Axisymmetric Stagnation". - //! @see setFreeFlow setAxisymmetricFlow - //! @deprecated To be removed after %Cantera 3.0; replaced by type(). - virtual string flowType() const; - - virtual void setFuelSpecies(const std::string fuel) { - m_fuel = fuel; - } - - void solveEnergyEqn(size_t j=npos); - - //! Get the solving stage (used by IonFlow specialization) - //! @since New in %Cantera 3.0 - virtual size_t getSolvingStage() const; - - //! Solving stage mode for handling ionized species (used by IonFlow specialization) - //! - @c stage=1: the fluxes of charged species are set to zero - //! - @c stage=2: the electric field equation is solved, and the drift flux for - //! ionized species is evaluated - virtual void setSolvingStage(const size_t stage); - - //! Set to solve electric field in a point (used by IonFlow specialization) - virtual void solveElectricField(size_t j=npos); - - //! Set to fix voltage in a point (used by IonFlow specialization) - virtual void fixElectricField(size_t j=npos); - - //! Retrieve flag indicating whether electric field is solved or not (used by - //! IonFlow specialization) - virtual bool doElectricField(size_t j) const; - - //! Turn radiation on / off. - /*! - * The simple radiation model used was established by Liu and Rogg - * @cite liu1991. This model considers the radiation of CO2 and H2O. - * - * This model uses the optically thin limit and the gray-gas approximation to - * simply calculate a volume specified heat flux out of the Planck absorption - * coefficients, the boundary emissivities and the temperature. Polynomial lines - * calculate the species Planck coefficients for H2O and CO2. The data for the - * lines are taken from the RADCAL program @cite RADCAL. - * The coefficients for the polynomials are taken from - * [TNF Workshop](https://tnfworkshop.org/radiation/) material. - */ - void enableRadiation(bool doRadiation) { - m_do_radiation = doRadiation; - } - - //! Returns `true` if the radiation term in the energy equation is enabled - bool radiationEnabled() const { - return m_do_radiation; - } - - //! Return radiative heat loss at grid point j - double radiativeHeatLoss(size_t j) const { - return m_qdotRadiation[j]; - } - - //! Set the emissivities for the boundary values - /*! - * Reads the emissivities for the left and right boundary values in the - * radiative term and writes them into the variables, which are used for the - * calculation. - */ - void setBoundaryEmissivities(double e_left, double e_right); - - // Turn soot formation on / off. - // setSections - const size_t getSections() const{ - return m_nsoot; - } - - void setSections(size_t nSec) { - m_nsoot = nSec; - } - - void setPrecursors(std::vector id_precursors); - - void setSootLoglevel(size_t loglevel){ - soot_loglevel = loglevel; - } - - size_t getSootLoglevel(){ - return soot_loglevel; - } - - void enableCondensation(bool doCondensation) { - m_do_condensation = doCondensation; - } - bool condensationEnabled(){ - return m_do_condensation; - } - - void enableCoagulation(bool doCoagulation) { - m_do_coagulation = doCoagulation; - } - bool coagulationEnabled(){ - return m_do_coagulation; - } - - void setCollisionModel(std::string collisionModel){ - m_collision_model = collisionModel; - } - - std::string getCollisionModel(){ - return m_collision_model; - } - - void setSootMorphology(std::string morphologyModel){ - m_soot_morphology = morphologyModel; - } - - std::string getSootMorphology(){ - return m_soot_morphology; - } - - void enableRetroaction(bool doRetroaction){ - m_do_retroaction = doRetroaction; - } - bool retroactionEnabled(){ - return m_do_retroaction; - } - - void enableSootRadiation(bool do_soot_radiation){ - m_do_soot_radiation = do_soot_radiation; - } - - bool sootRadiationEnabled(){ - return m_do_soot_radiation; - } - - void enableSootSoret(bool do_soot_soret){ - m_do_soot_soret = do_soot_soret; - } - - bool sootSoretEnabled(){ - return m_do_soot_soret; - } - - void enableSurfaceGrowth(bool do_sg){ - m_do_sg = do_sg; - } - bool surfaceGrowthEnabled(){ - return m_do_sg; - } - - void enableOxidation(bool do_oxidation){ - m_do_oxidation = do_oxidation; - } - bool oxidationEnabled(){ - return m_do_oxidation; - } - - void enableTrashSection(double trash_section){ - if (trash_section > 0){ - m_trash_section = true; - dTrashLowLim = trash_section; - }else{ - m_trash_section = false; - dTrashLowLim = 0.0; - } - } - - bool trashSectionEnabled(){ - return m_trash_section; - } - - void setHaca(size_t haca_model){ - m_haca_model = haca_model; - } - - size_t getHaca(){ - return m_haca_model; - } - - double getKazakovTad(){ - return kazakovTad; - } - void setKazakovTad(double kazakov_tad){ - kazakovTad = kazakov_tad; - } - - void loadHaca(size_t m_haca_model){ - if (m_haca_model == 1){ //Mauss - // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] - double lambda = 1.0 / S_C2; - // Number of sites [-] - // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) - n_sites = lambda * S_C2; - // Mauss HACA-RC model - //1st order : [1/s] , [-], [J/mol] - //2nd order : [m3/kmol/s], [-], [J/mol] - // S-H + H <-> S* + H2 - ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; - ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; - // S-H + OH <-> S* + H2O - ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; - ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; - // S* + H <-> S-H - ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; - ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; - // S* + C2H2 <-> S-H - ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; - ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; - // S* <-> S-H + H - ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; - ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; - // S* + O2 -> S-H + 2CO - ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 8.4000e03; - // S* + O2 -> S-H + 2HCO - // S-H + OH -> S-H + CO - gamma_oh = 0.13; - }else if (m_haca_model == 11){ //Mauss tuned (Guo 2016) - // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] - double lambda = 1.0 / S_C2; - // Number of sites [-] - // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) - n_sites = lambda * S_C2; - // Mauss HACA-RC model - //1st order : [1/s] , [-], [J/mol] - //2nd order : [m3/kmol/s], [-], [J/mol] - // S-H + H <-> S* + H2 - ak01f = 1.000e14 * 1e-3, nk01f = 0.000e00, ek01f = 0.0000e00; - ak01b = 1.439e13 * 1e-3, nk01b = 0.000e00, ek01b = -37.63e03; - // S-H + OH <-> S* + H2O - ak02f = 1.630e08 * 1e-3, nk02f = 1.400e00, ek02f = 6.1000e03; - ak02b = 1.101e08 * 1e-3, nk02b = 1.400e00, ek02b = 31.140e03; - // S* + H <-> S-H - ak03f = 1.000e13 * 1e-3, nk03f = 0.000e00, ek03f = 0.00000e0; - ak03b = 0.000e00, nk03b = 0.000e00, ek03b = 0.00000e0; - // S* + C2H2 <-> S-H - ak04f = 3.500e13 * 1e-3, nk04f = 0.000e00, ek04f = 0.00000e0; - ak04b = 3.225e14, nk04b = 0.000e00, ek04b = 181.69e03; - // S* <-> S-H + H - ak05f = 1.000e10, nk05f = 0.000e00, ek05f = 20.000e03; - ak05b = 8.770e11 * 1e-3, nk05b = 0.000e00, ek05b = 74.440e03; - // S* + O2 -> S-H + 2CO - ak06f = 1.000e12 * 1e-3, nk06f = 0.000e00, ek06f = 190.000e03; - // S* + O2 -> S-H + 2HCO - // S-H + OH -> S-H + CO - gamma_oh = 0.10; - }else if (m_haca_model == 2){ //Blanquart - // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [1/m2] - double lambda = 1.7e19; - // Number of sites [-] - // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) - n_sites = lambda * S_C2; - // Blanquart HACA model - //1st order : [1/s] , [-], [J/mol] - //2nd order : [m3/kmol/s], [-], [J/mol] - // S-H + H <-> S* + H2 - ak01f = 1.0e8 * 1e-3; nk01f = 1.8; ek01f = 68420.0; - ak01b = 8.68e4 * 1e-3; nk01b = 2.36; ek01b = 25460.0; - // S-H + OH <-> S* + H2O - ak02f = 6.72e1 * 1e-3; nk02f = 3.33; ek02f = 6090.0; - ak02b = 6.44e-1 * 1e-3; nk02b = 3.79; ek02b = 27960.0; - // S-H <-> S* + H - ak03f = 1.13e16; nk03f = -0.06; ek03f = 476050.0; - ak03b = 4.17e13 * 1e-3; nk03b = 0.15; ek03b = 0.0; - // S* + C2H2 -> S-H - ak04f = 2.52e9 * 1e-3; nk04f = 1.77; ek04f = 13540.0; - // S* + O2 -> S + 2CO - ak05f = 2.2e12 * 1e-3; nk05f = 0.0; ek05f = 31380.0; - // S-H + OH -> S-H + CO - gamma_oh = 0.13; - }else if (m_haca_model == 3){ - // Number of sites at the particle's surface per unit surface (each site occupies S_C2) [m-2] - double lambda = 2.3e19; - // Number of sites [-] - // Used in sootSurface to compute lambda * s = lambda * s_c2 * (v/v_c2)^(theta/3) - n_sites = lambda * S_C2; - // Kazakov HACA model - //1st order : [1/s] , [-], [J/mol] - //2nd order : [m3/mol/s], [-], [J/mol] - // S-H + H <-> S* + H2 - ak01f = 2.5e14 * 1e-3; nk01f = 0.0; ek01f = 66900.0; - ak01b = 3.9e12 * 1e-3; nk01b = 0.0; ek01b = 39000.0; - // S* + H -> S-H - ak02f = 1.0e14 * 1e-3; nk02f = 0.0; ek02f = 0.0; - // S* + C2H2 -> S-H + H - ak03f = 8.4e11 * 1e-3; nk03f = 0.4; ek03f = 35100.0; - // S* + O2 -> S + 2CO - ak04f = 2.2e12 * 1e-3; nk04f = 0.0; ek04f = 31300.0; - // S-H + OH -> S-H + CO - gamma_oh = 0.13; - } - } - - void finalizeSoot(); - void loadSurface(); - //Initialize soot - void initSoot(); - void showSootInfo(); - // Sections generation and display - void sootCreationVol(); - void showSootSections(); - void sootCollisionModel(); - void getDistributionOrdre0(const double* x, size_t j); - // Soot source terms - void sootSource(const double* x, size_t j); - void sootDimerization(const double* x, size_t j); - void sootNucleation(const double* x, size_t j); - void sootCondensation(const double* x, size_t j); - void sootCoagulation(const double* x, size_t j); - void sootSurface(const double* x, size_t j); - void sootSurfaceInitialization(const double* x, size_t j); - void sootCollisionInverse(); - // Returns section name - std::string sectionName(size_t n) const { - return m_section_name[n]; - } - - const vector& vMin() const { - return vSectMin; - } - - const vector& vMax() const { - return vSectMax; - } - - const vector& vMean() const { - return vSectMean; - } - - const vector& dMean() const { - return dSectMean; - } - - const vector& dCol() const { - return dSectCol; - } - - const vector& aCol() const { - return aSectCol; - } - - const vector& sMean() const { - return sSectMean; - } - - const vector& thetaSoot() const { - return theta_surf; - } - - const vector& fractalPrefactor() const { - return kfractal; - } - - const vector& fractalDimension() const { - return Dfractal; - } - - const double rhoSoot() const { - return rho_soot; - } - - const double getSootInception(size_t j) const { - return m_qdotNucleation[j] * m_rho[j]; - } - - const double getSootCondensation(size_t k, size_t j) const { - return m_qdotCondensation(k,j) * m_rho[j]; - } - - const double getSootCoagulation(size_t k, size_t j) const { - return m_qdotCoagulation(k,j) * m_rho[j]; - } - - const double getSootSg(size_t k, size_t j) const { - return m_qdotSg(k,j) * m_rho[j]; - } - - const double getSootOxidation(size_t k, size_t j) const { - return m_qdotOxidation(k,j) * m_rho[j]; - } - - const double fv(const double* x, size_t j){ - double val = 0.0; - for (size_t k=0; k < m_nsoot; k++){ - val += Ys(x,k,j); - } - val *= m_rho[j] / rho_soot; - return val; - } - - const double sootPrimaryDiam(size_t k) const { - return 2.0 * rNucMean[k]; - } - - const double sootPrimaryPart(size_t k) const { - return nNucMean[k]; - } - - void setThick(double thickness){ - m_thick = thickness; - AVBPReadInputChem(); - } - - double getThick() const { - return m_thick; - } - - //! Return emissivity at left boundary - double leftEmissivity() const { return m_epsilon_left; } - - //! Return emissivity at right boundary - double rightEmissivity() const { return m_epsilon_right; } - - void fixTemperature(size_t j=npos); - - bool doEnergy(size_t j) { - return m_do_energy[j]; - } - - //! Change the grid size. Called after grid refinement. - void resize(size_t components, size_t points) override; - - //! Set the gas object state to be consistent with the solution at point j. - virtual void setGas(const double* x, size_t j); - - //! Set the gas state to be consistent with the solution at the midpoint - //! between j and j + 1. - virtual void setGasAtMidpoint(const double* x, size_t j); - - double density(size_t j) const { - return m_rho[j]; - } - - //! seems unused - double cpBar(size_t j) const { - return m_cpm[j]; - } - - double enthalpy(size_t j) const { - return m_h[j]; - } - - double thCond(size_t j) const { - return m_tcon[j]; - } - - double HR(size_t j) const { - return m_hr[j]; - } - - //! @deprecated To be removed after %Cantera 3.0. Superseded by isFree() - virtual bool fixed_mdot(); - - /** - * Retrieve flag indicating whether flow is freely propagating. - * The flow is unstrained and the axial mass flow rate is not specified. - * For free flame propagation, the axial velocity is determined by the solver. - * @since New in %Cantera 3.0 - */ - bool isFree() const { - return m_isFree; - } - - /** - * Retrieve flag indicating whether flow uses radial momentum. - * If `true`, radial momentum equation for @f$ V @f$ as well as - * @f$ d\Lambda/dz = 0 @f$ are solved; if `false`, @f$ \Lambda(z) = 0 @f$ and - * @f$ V(z) = 0 @f$ by definition. - * @since New in %Cantera 3.0 - */ - bool isStrained() const { - return m_usesLambda; - } - - void setViscosityFlag(bool dovisc) { - m_dovisc = dovisc; - } - - - // P. Wolf - void AVBPReadInputPea(); - - //+++++++++++++++++++++++++++++++++++++++++++++++++++ - // B. Franzelli modifications to perform thickening - //+++++++++++++++++++++++++++++++++++++++++++++++++++ - void AVBPReadInputChem(); - void AVBPcompute_local_thick(double* x,size_t j); - - double AVBPthick(size_t j) const { - return avbp_thick[j]; - } - - /** - * Evaluate the residual function for axisymmetric stagnation flow. If - * j == npos, the residual function is evaluated at all grid points. - * Otherwise, the residual function is only evaluated at grid points - * j-1, j, and j+1. This option is used to efficiently evaluate the - * Jacobian numerically. - */ - void eval(size_t j, double* x, double* r, integer* mask, double rdt) override; - - //! Evaluate all residual components at the right boundary. - virtual void evalRightBoundary(double* x, double* res, int* diag, double rdt); - - //! Evaluate the residual corresponding to the continuity equation at all - //! interior grid points. - virtual void evalContinuity(size_t j, double* x, double* r, int* diag, double rdt); - - //! Index of the species on the left boundary with the largest mass fraction - size_t leftExcessSpecies() const { - return m_kExcessLeft; - } - - //! Index of the species on the right boundary with the largest mass fraction - size_t rightExcessSpecies() const { - return m_kExcessRight; - } - -protected: - AnyMap getMeta() const override; - void setMeta(const AnyMap& state) override; - - double wdot(size_t k, size_t j) const { - return m_wdot(k,j); - } - - //! Write the net production rates at point `j` into array `m_wdot` - // void getWdot(double* x, size_t j) { - // setGas(x,j); - // m_kin->getNetProductionRates(&m_wdot(0,j)); - // } -/// write the net production rates at point j into array m_wdot -/// Modified by P. Wolf March 2010 - Thanks to Alireza N. -/// when PEA activated: production rates depends on mixture fraction at point j -/// WARNING: the following is valid only for fuel/AIR right now - void getWdot(double *x, size_t j) - { - double zloc; - double phi; - setGas(x, j); // We'll need to set the gas before retrieving - // std::cout << "after setGas" << std::endl; - zloc = getMixFrac(j); // the Mixture Fraction and calculating wdot - phi = zloc / (1. - zloc) * phi_cst; - - switch (avbp_ipea) - { - case 0: - m_kin->getNetProductionRates(&m_wdot(0, j)); - break; - // ipea = 1, apply the PEA on fuel oxydation reaction only - case 1: - double pea_f; // pea correction function - // Now set the PEA correction function - pea_f = 0.5 * (1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) - + avbp_pea_coeffs[2] / 4. * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) - * (1. + tanh((avbp_pea_coeffs[5] - phi) / avbp_pea_coeffs[6])); - - // Multiply reaction rate of reaction 1 by the pea coeff - m_kin->setMultiplier(1, pea_f); - // Get the net production rates for all species - m_kin->getNetProductionRates(&m_wdot(0, j)); - // Restore the original reaction rates (not necessary) - m_kin->setMultiplier(1, 1.0 / pea_f); - break; - // ipea = 2, apply PEA on both reactions - case 2: - // TEST 081014: differencie bien les cas - double pea2_f[2]; // pea correction function - // Now set the PEA correction function - pea2_f[0] = 2. / ((1. + tanh((avbp_pea_coeffs[0] - phi) / avbp_pea_coeffs[1])) - + avbp_pea_coeffs[2] * (1. + tanh((phi - avbp_pea_coeffs[3]) / avbp_pea_coeffs[4])) - + avbp_pea_coeffs[5] * (1. + tanh((phi - avbp_pea_coeffs[6]) / avbp_pea_coeffs[7]))); - - pea2_f[1] = 0.5 * ((1. + tanh((avbp_pea_coeffs[8] - phi) / avbp_pea_coeffs[9])) - + avbp_pea_coeffs[10] * (1. + tanh((phi - avbp_pea_coeffs[11]) / avbp_pea_coeffs[12])) - + avbp_pea_coeffs[13] * (1. + tanh((phi - avbp_pea_coeffs[14]) / avbp_pea_coeffs[15])) - * (1. + tanh((avbp_pea_coeffs[16] - phi) / avbp_pea_coeffs[17]))); - // Multiply reaction rates by the pea coeff - if (m_kin->nReactions() == 2) - { - for (size_t n = 0; n < m_kin->nReactions(); n++) - { - m_kin->setMultiplier(n, pea2_f[n]); - } - // Get the net production rates for all species - m_kin->getNetProductionRates(&m_wdot(0, j)); - // Restore the original reaction rates (not necessary) - for (size_t n = 0; n < m_kin->nReactions(); n++) - { - m_kin->setMultiplier(n, 1.0 / pea2_f[n]); - } - } - else - { - throw CanteraError("getWdot", "ipea = 2 but there ain't 2 reactions"); - } - break; - // ipea = 3, apply PEA on both reactions (for CM2 only) - case 3: - double pea3_f[2]; // pea correction function - - // Now set the PEA correction function - if (phi > 1.0) - { - // pea3_f[0] = max(avbp_pea_coeffs[0]*phi*phi + avbp_pea_coeffs[1]*phi + avbp_pea_coeffs[2],0.0); - pea3_f[0] = avbp_pea_coeffs[0] * phi * phi + avbp_pea_coeffs[1] * phi + avbp_pea_coeffs[2]; - } - else - { - pea3_f[0] = 1; - } - pea3_f[1] = pea3_f[0]; - - // Multiply reaction rates by the pea coeff - if (m_kin->nReactions() == 2) - { - for (size_t n = 0; n < m_kin->nReactions(); n++) - { - m_kin->setMultiplier(n, pea2_f[n]); - } - - // Get the net production rates for all species - m_kin->getNetProductionRates(&m_wdot(0, j)); - - // Restore the original reaction rates (not necessary) - for (size_t n = 0; n < m_kin->nReactions(); n++) - { - m_kin->setMultiplier(n, 1.0 / pea2_f[n]); - } - } - else - { - throw CanteraError("getWdot", "ipea = 3 but there ain't 2 reactions"); - } - - break; - - default: - throw CanteraError("getWdot", "ipea is set to a weird value"); - break; - } - } - - //! Update the properties (thermo, transport, and diffusion flux). - //! This function is called in eval after the points which need - //! to be updated are defined. - virtual void updateProperties(size_t jg, double* x, size_t jmin, size_t jmax); - - //! Evaluate the residual function. This function is called in eval - //! after updateProperties is called. - virtual void evalResidual(double* x, double* rsd, int* diag, - double rdt, size_t jmin, size_t jmax); - - /** - * Update the thermodynamic properties from point j0 to point j1 - * (inclusive), based on solution x. - */ - virtual void updateThermo(const double* x, size_t j0, size_t j1) { - for (size_t j = j0; j <= j1; j++) { - setGas(x,j); - m_rho[j] = m_thermo->density(); - m_wtm[j] = m_thermo->meanMolecularWeight(); - m_cp[j] = m_thermo->cp_mass(); - m_thermo->getPartialMolarEnthalpies(&m_hk(0, j)); - } - } - - //-------------------------------- - // central-differenced derivatives - //-------------------------------- - double cdif1(const double*x, size_t n, size_t j) const { - double c1 = (x[index(n,j+1)] - x[index(n,j-1)]); - return c1/(z(j+1) - z(j-1)); - } - - //! seems unused - double cdif2(const double* x, size_t n, size_t j, - const double* f) const { - double c1 = (f[j] + f[j-1])*(x[index(n,j)] - x[index(n,j-1)]); - double c2 = (f[j+1] + f[j])*(x[index(n,j+1)] - x[index(n,j)]); - return (c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); - } - - //! @name Solution components - //! @{ - - virtual double T(const double* x, size_t j) const { - return x[index(c_offset_T, j)]; - } - virtual double& T(double* x, size_t j) { - return x[index(c_offset_T, j)]; - } - virtual double T_prev(size_t j) const { - return prevSoln(c_offset_T, j); - } - - double rho_u(const double* x, size_t j) const { - return m_rho[j]*x[index(c_offset_U, j)]; - } - - double u(const double* x, size_t j) const { - return x[index(c_offset_U, j)]; - } - - double V(const double* x, size_t j) const { - return x[index(c_offset_V, j)]; - } - double V_prev(size_t j) const { - return prevSoln(c_offset_V, j); - } - - double lambda(const double* x, size_t j) const { - return x[index(c_offset_L, j)]; - } - - virtual double Y(const double* x, size_t k, size_t j) const { - return x[index(c_offset_Y + k, j)]; - } - - virtual double& Y(double* x, size_t k, size_t j) { - return x[index(c_offset_Y + k, j)]; - } - - virtual double Y_prev(size_t k, size_t j) const { - return prevSoln(c_offset_Y + k, j); - } - - //Soot - double Ys(const double* x, size_t k, size_t j) const { - return x[index(c_offset_S+k, j)]; - } - - double& Ys(double* x, size_t k, size_t j) { - return x[index(c_offset_S+k, j)]; - } - - double Ys_prev(size_t k, size_t j) const { - return prevSoln(c_offset_S + k, j); - } - //---- - - double X(const double* x, size_t k, size_t j) const { - return m_wtm[j]*Y(x,k,j)/m_wt[k]; - } - - double flux(size_t k, size_t j) const { - return m_flux(k, j); - } - //! @} - - //! @name convective spatial derivatives. - //! - //! These use upwind differencing, assuming u(z) is negative - //! @{ - double dVdz(const double* x, size_t j) const { - size_t jloc = (u(x,j) > 0.0 ? j : j + 1); - return (V(x,jloc) - V(x,jloc-1))/m_dz[jloc-1]; - } - - double dYdz(const double* x, size_t k, size_t j) const { - size_t jloc = (u(x,j) > 0.0 ? j : j + 1); - return (Y(x,k,jloc) - Y(x,k,jloc-1))/m_dz[jloc-1]; - } - - // Soot - double dYsdz(const double* x, size_t k, size_t j) const { - size_t jloc = (u(x,j) > 0.0 ? j : j + 1); - return (Ys(x,k,jloc) - Ys(x,k,jloc-1))/m_dz[jloc-1]; - } - - double dTdz(const double* x, size_t j) const { - size_t jloc = (u(x,j) > 0.0 ? j : j + 1); - return (T(x,jloc) - T(x,jloc-1))/m_dz[jloc-1]; - } - //! @} - - double shear(const double* x, size_t j) const { - double c1 = m_visc[j-1]*(V(x,j) - V(x,j-1)); - double c2 = m_visc[j]*(V(x,j+1) - V(x,j)); - return 2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); - } - - double divHeatFlux(const double* x, size_t j) const { - double c1 = m_tcon[j-1]*(T(x,j) - T(x,j-1)); - double c2 = m_tcon[j]*(T(x,j+1) - T(x,j)); - return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); - } - - double AVBPdivHeatFlux(const double* x, size_t j) const { - double c1 = avbp_thick[j-1]*m_tcon[j-1]*(T(x,j) - T(x,j-1)); - double c2 = avbp_thick[j]*m_tcon[j]*(T(x,j+1) - T(x,j)); - return -2.0*(c2/(z(j+1) - z(j)) - c1/(z(j) - z(j-1)))/(z(j+1) - z(j-1)); - } - - size_t mindex(size_t k, size_t j, size_t m) { - return m*m_nsp*m_nsp + m_nsp*j + k; - } - - //! Update the diffusive mass fluxes. - virtual void updateDiffFluxes(const double* x, size_t j0, size_t j1); - virtual void updateSootDiffFluxes(const double* x, size_t j0, size_t j1); - - //! Get the gradient of species specific molar enthalpies - virtual void grad_hk(const double* x, size_t j); - - //--------------------------------------------------------- - // member data - //--------------------------------------------------------- - - double m_press = -1.0; // pressure - - // grid parameters - vector m_dz; - - // mixture thermo properties - vector m_rho; - vector m_wtm; - - // P. Wolf - vector m_zmixfrac; - - vector m_cpm; - vector m_h; - - // species thermo properties - vector m_wt; - vector m_cp; - - // transport properties - vector m_ybar; - vector m_visc; - vector m_tcon; - vector m_diff; - vector m_multidiff; - Array2D m_dthermal; - Array2D m_flux; - - //! Array of size #m_nsp by #m_points for saving molar enthalpies - Array2D m_hk; - - //! Array of size #m_nsp by #m_points-1 for saving enthalpy fluxes - Array2D m_dhk_dz; - - // production rates - vector m_hr; - Array2D m_wdot; - - size_t m_nsp; //!< Number of species in the mechanism - size_t m_neq; //!< Number of non-species equations - size_t m_nsoot; - std::string m_fuel; - - ThermoPhase* m_thermo = nullptr; - Kinetics* m_kin = nullptr; - Transport* m_trans = nullptr; - - MultiJac* m_jac = nullptr; - - // boundary emissivities for the radiation calculations - double m_epsilon_left = 0.0; - double m_epsilon_right = 0.0; - - //! Indices within the ThermoPhase of the radiating species. First index is - //! for CO2, second is for H2O. - vector m_kRadiating; - - // Pierre WOLF: added parameters for input_pea.dat - size_t avbp_ipea = 0; - std::string avbp_fuel; - vector avbp_pea_coeffs; - double phi_cst; - - //+++++++++++++++++++++++++++++++++++++++++++++++++++ - // B. Franzelli modifications to perform thickening - // input_chem parameters - //+++++++++++++++++++++++++++++++++++++++++++++++++++ - double avbp_fthick; - vector avbp_thick; - double m_thick = 1.0; - - // flags - vector m_do_energy; - bool m_do_soret = false; - vector m_do_species; - bool m_do_multicomponent = false; - - //! flag for the radiative heat loss - bool m_do_radiation = false; - - //! radiative heat loss vector - vector m_qdotRadiation; - - // ---------------------- - // SOOT RELATED VARIABLES - // ---------------------- - bool m_do_soot_soret = true; - bool m_do_condensation = false; - bool m_do_soot_radiation = false; - bool m_do_coagulation = false; - std::string m_soot_morphology; - bool m_do_retroaction = false; - bool m_do_sg = false; - bool m_do_oxidation = false; - bool m_trash_section = false; - std::string m_collision_model = "rodrigues"; - size_t soot_loglevel=1; - size_t c_offset_S = 6; - size_t n_PAH = 0; - size_t m_haca_model; - double Y_PAH; - double C_PAH; - double dTrashLowLim; - vector W_PAH; - double W_C; - vector n_C; - double N_dimer; - double beta_dimer; - double r_dimer; - double V_dimer; - double beta_fm; - double n_sites; - double kazakovTad; - double ksg; - double kox; - vector sootConsumption; - vector vSectMin; - vector vSectMax; - vector dSectMean; - vector dSectCol; - vector rSectCol; - vector aSectCol; - vector vSectMean; - vector sSectMean; - vector Dfractal; - vector kfractal; - vector nNucMean; - vector rNucMean; - vector rSmolMean; - vector PAMean; - vector m_qdotNucleation; - Array2D m_qdotCondensation; - Array2D m_qdotCoagulation; - Array2D m_qdotSg; - Array2D m_qdotOxidation; - vector q; - vector theta_surf; - vector jpower; - vector kpower; - vector mpower; - vector vc2power; - vector vc2powerm; - vector vmax_kpower; - vector vmin_kpower; - vector vmax_jpower; - vector vmin_jpower; - vector vmax_mpower; - vector vmin_mpower; - vector vmaxmc2_kpower; - vector vminpc2_kpower; - vector vmaxmc2_jpower; - vector vminpc2_jpower; - vector vmaxmc2_mpower; - vector vminpc2_mpower; - vector vc2powervect; - vector vc2powermvect; - vector m_section_name; - vector m_precursors; - Array2D m_soot_diff ; - Array2D m_soot_soret ; - Array2D collision_mat; - //Surface reactions - double ak00f, nk00f, ek00f, ak01f, nk01f, ek01f, ak02f, nk02f, ek02f, - ak03f, nk03f, ek03f, ak04f, nk04f, ek04f, ak05f, nk05f, ek05f, - ak06f, nk06f, ek06f, ak07f, nk07f, ek07f; - double ak00b, nk00b, ek00b, ak01b, nk01b, ek01b, ak02b, nk02b, ek02b, - ak03b, nk03b, ek03b, ak04b, nk04b, ek04b, ak05b, nk05b, ek05b, - ak06b, nk06b, ek06b, ak07b, nk07b, ek07b; - double gamma_oh; - // ----------------------------- - // END OF SOOT RELATED VARIABLES - // ----------------------------- - - // fixed T and Y values - vector m_fixedtemp; - vector m_zfix; - vector m_tfix; - - //! Index of species with a large mass fraction at each boundary, for which - //! the mass fraction may be calculated as 1 minus the sum of the other mass - //! fractions - size_t m_kExcessLeft = 0; - size_t m_kExcessRight = 0; - - bool m_dovisc; - bool m_isFree; - bool m_usesLambda; - - //! Update the transport properties at grid points in the range from `j0` - //! to `j1`, based on solution `x`. - virtual void updateTransport(double* x, size_t j0, size_t j1); - -public: - //! Location of the point where temperature is fixed - double m_zfixed = Undef; - - //! Temperature at the point used to fix the flame location - double m_tfixed = -1.0; - -// private: -// vector m_ybar; -}; - -} - -#endif diff --git a/interfaces/cython/cantera/_onedim.pxd b/interfaces/cython/cantera/_onedim.pxd index d22bc13b0dc..b3ec4179ef8 100644 --- a/interfaces/cython/cantera/_onedim.pxd +++ b/interfaces/cython/cantera/_onedim.pxd @@ -241,9 +241,6 @@ cdef class FlowBase(Domain1D): cdef class FlameletFlow(FlowBase): cdef CxxFlamelet* flamelet -cdef class FlameletFlow(_FlowBase): - cdef CxxFlamelet* flamelet - cdef class Sim1D: cdef CxxSim1D* sim cdef readonly object domains diff --git a/src/oneD/StFlow.cpp b/src/oneD/StFlow.cpp deleted file mode 100644 index e71b0f8244d..00000000000 --- a/src/oneD/StFlow.cpp +++ /dev/null @@ -1,2310 +0,0 @@ -//! @file StFlow.cpp - -// This file is part of Cantera. See License.txt in the top-level directory or -// at https://cantera.org/license.txt for license and copyright information. - -#include "cantera/base/SolutionArray.h" -#include "cantera/oneD/StFlow.h" -#include "cantera/oneD/refine.h" -#include "cantera/transport/Transport.h" -#include "cantera/transport/TransportFactory.h" -#include "cantera/numerics/funcs.h" -#include "cantera/base/global.h" -#include "cantera/base/Parser.h" -#include - -using namespace std; - -namespace Cantera -{ - -StFlow::StFlow(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : - Domain1D(nsp, points, 0.0, nsoot, neq), - m_nsp(nsp), - m_neq(neq), - m_nsoot(nsoot) -{ - m_type = cFlowType; - m_points = points; - - if (ph == 0) { - return; // used to create a dummy object - } - m_thermo = ph; - - size_t nsp2 = m_thermo->nSpecies(); - // the species mass fractions are the last components in the solution - // vector, so the total number of components is the number of species - // plus the offset of the first mass fraction. - - - m_nv = m_neq + m_nsp + m_nsoot; - if (nsp2 + m_nsoot != m_nsp) { - m_nsp = nsp2; - Domain1D::resize(m_nv, points); - } - - // make a local copy of the species molecular weight vector - m_wt = m_thermo->molecularWeights(); - - // set pressure based on associated thermo object - setPressure(m_thermo->pressure()); - - // the species mass fractions are the last components in the solution - // vector, so the total number of components is the number of species - // plus the offset of the first mass fraction. - // m_nv = c_offset_Y + m_nsp; - - // enable all species equations by default - m_do_species.resize(m_nsp, true); - - // but turn off the energy equation at all points - m_do_energy.resize(m_points,false); - - m_diff.resize(m_nsp*m_points); - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_flux.resize(m_nsp,m_points); - m_wdot.resize(m_nsp,m_points, 0.0); - m_hk.resize(m_nsp, m_points, 0.0); - m_dhk_dz.resize(m_nsp, m_points - 1, 0.0); - m_ybar.resize(m_nsp); - m_qdotRadiation.resize(m_points, 0.0); - - //-------------- default solution bounds -------------------- - if (m_neq == 1) { - setBounds(c_offset_Tflamelet, 200.0, 2*m_thermo->maxTemp()); // temperature bounds - } else { - setBounds(c_offset_U, -1e20, 1e20); // no bounds on u - setBounds(c_offset_V, -1e20, 1e20); // V - setBounds(c_offset_T, 200.0, 2*m_thermo->maxTemp()); // temperature bounds - setBounds(c_offset_L, -1e20, 1e20); // lambda should be negative - setBounds(c_offset_E, -1e20, 1e20); // no bounds for inactive component - } - // mass fraction bounds - for (size_t k = 0; k < m_nsp; k++) { - setBounds(m_neq+k, -1.0e-7, 1.0e5); - } - - //-------------------- grid refinement ------------------------- - if (m_neq == 1) { - m_refiner->setActive(c_offset_Tflamelet, false); - } else { - m_refiner->setActive(c_offset_U, false); - m_refiner->setActive(c_offset_V, false); - m_refiner->setActive(c_offset_T, false); - m_refiner->setActive(c_offset_L, false); - } - - vector gr; - for (size_t ng = 0; ng < m_points; ng++) { - gr.push_back(1.0*ng/m_points); - } - setupGrid(m_points, gr.data()); - - // Find indices for radiating species - m_kRadiating.resize(2, npos); - m_kRadiating[0] = m_thermo->speciesIndex("CO2"); - m_kRadiating[1] = m_thermo->speciesIndex("H2O"); - - // P. Wolf - //---------------------AVBP PEA initialization------------------- - AVBPReadInputPea(); - - // B. Franzelli - //---------------------AVBP thickening initialisation------------ - AVBPReadInputChem(); - - // E. Lameloise - //---------------------Soot computation initialisation----------- - if (m_nsoot > 0){ - initSoot(); - } -} - -StFlow::StFlow(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) - : StFlow(th.get(), nsp, nsoot, neq, points) -{ - m_solution = Solution::create(); - m_solution->setThermo(th); -} - -StFlow::StFlow(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) - : StFlow(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) -{ - m_solution = sol; - m_id = id; - m_kin = m_solution->kinetics().get(); - m_trans = m_solution->transport().get(); - - m_solution->registerChangedCallback(this, [this]() { - setKinetics(m_solution->kinetics()); - setTransport(m_solution->transport()); - }); - - if (m_trans->transportModel() == "none") { - // @deprecated - warn_deprecated("StFlow", - "An appropriate transport model\nshould be set when instantiating the " - "Solution ('gas') object.\nImplicit setting of the transport model " - "is deprecated and\nwill be removed after Cantera 3.0."); - setTransportModel("mixture-averaged"); - } - -} - -StFlow::~StFlow() -{ - if (m_solution) { - m_solution->removeChangedCallback(this); - } -} - -string StFlow::type() const { - if (m_isFree) { - return "free-flow"; - } - if (m_usesLambda) { - return "axisymmetric-flow"; - } - return "unstrained-flow"; -} - -void StFlow::setThermo(ThermoPhase& th) { - warn_deprecated("StFlow::setThermo", "To be removed after Cantera 3.0."); - m_thermo = &th; -} - -void StFlow::setKinetics(shared_ptr kin) -{ - if (!m_solution) { - // @todo remove after Cantera 3.0 - throw CanteraError("StFlow::setKinetics", - "Unable to update object that was not constructed from smart pointers."); - } - m_kin = kin.get(); - m_solution->setKinetics(kin); -} - -void StFlow::setKinetics(Kinetics& kin) -{ - warn_deprecated("StFlow::setKinetics(Kinetics&)", "To be removed after Cantera 3.0." - " Replaced by setKinetics(shared_ptr)."); - m_kin = &kin; -} - -void StFlow::setTransport(shared_ptr trans) -{ - if (!m_solution) { - // @todo remove after Cantera 3.0 - throw CanteraError("StFlow::setTransport", - "Unable to update object that was not constructed from smart pointers."); - } - if (!trans) { - throw CanteraError("StFlow::setTransport", "Unable to set empty transport."); - } - m_trans = trans.get(); - if (m_trans->transportModel() == "none") { - throw CanteraError("StFlow::setTransport", "Invalid Transport model 'none'."); - } - m_do_multicomponent = (m_trans->transportModel() == "multicomponent" || - m_trans->transportModel() == "multicomponent-CK"); - - m_diff.resize(m_nsp * m_points); - if (m_do_multicomponent) { - m_multidiff.resize(m_nsp * m_nsp*m_points); - m_dthermal.resize(m_nsp, m_points, 0.0); - } - m_solution->setTransport(trans); -} - -void StFlow::resize(size_t ncomponents, size_t points) -{ - Domain1D::resize(ncomponents, points); - m_rho.resize(m_points, 0.0); - m_wtm.resize(m_points, 0.0); - m_cp.resize(m_points, 0.0); - m_h.resize(m_points, 0.0); - m_hr.resize(m_points, 0.0); - m_visc.resize(m_points, 0.0); - m_tcon.resize(m_points, 0.0); - avbp_thick.resize(m_points,0.0); - - m_diff.resize(m_nsp*m_points); - if (m_do_multicomponent) { - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_dthermal.resize(m_nsp, m_points, 0.0); - } - m_flux.resize(m_nsp,m_points); - m_wdot.resize(m_nsp,m_points, 0.0); - m_hk.resize(m_nsp, m_points, 0.0); - m_dhk_dz.resize(m_nsp, m_points - 1, 0.0); - m_do_energy.resize(m_points,false); - m_qdotRadiation.resize(m_points, 0.0); - m_fixedtemp.resize(m_points); - - m_dz.resize(m_points-1); - m_z.resize(m_points); - - // P. Wolf - m_zmixfrac.resize(m_points); - // Soot - if (m_nsoot > 0){ - sootConsumption.resize(m_nsp, 0.0); - m_soot_diff.resize(m_nsoot, m_points, 0.0); - m_soot_soret.resize(m_nsoot, m_points, 0.0); - m_qdotNucleation.resize(m_points, 0.0); - m_qdotCondensation.resize(m_nsoot, m_points, 0.0); - m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); - m_qdotSg.resize(m_nsoot, m_points, 0.0); - m_qdotOxidation.resize(m_nsoot, m_points, 0.0); - } -} - -void StFlow::setupGrid(size_t n, const double* z) -{ - resize(m_nv, n); - - m_z[0] = z[0]; - for (size_t j = 1; j < m_points; j++) { - if (z[j] <= z[j-1]) { - throw CanteraError("StFlow::setupGrid", - "grid points must be monotonically increasing"); - } - m_z[j] = z[j]; - m_dz[j-1] = m_z[j] - m_z[j-1]; - } -} - -void StFlow::setupGrid(size_t n) -{ - resize(m_nv, n); - - m_z[0] = 0.0; - for (size_t j = 1; j < m_points; j++) { - m_z[j] = (double) j / ( (double) (n-1) ); - m_dz[j-1] = m_z[j] - m_z[j-1]; - } -} - -void StFlow::resetBadValues(double* xg) -{ - double* x = xg + loc(); - for (size_t j = 0; j < m_points; j++) { - double* Y = x + m_nv*j + c_offset_Y; - m_thermo->setMassFractions(Y); - m_thermo->getMassFractions(Y); - } -} - -void StFlow::setTransportModel(const string& trans) -{ - if (!m_solution) { - // @todo remove after Cantera 3.0 - throw CanteraError("StFlow::setTransportModel", - "Unable to set Transport manager by name as object was not initialized\n" - "from a Solution manager: set Transport object directly instead."); - } - m_solution->setTransportModel(trans); -} - -string StFlow::transportModel() const { - return m_trans->transportModel(); -} - -void StFlow::setTransport(Transport& trans) -{ - warn_deprecated("StFlow::setTransport(Transport&)", "To be removed after" - " Cantera 3.0. Replaced by setTransport(shared_ptr)."); - m_trans = &trans; - if (m_trans->transportModel() == "none") { - throw CanteraError("StFlow::setTransport", - "Invalid Transport model 'none'."); - } - m_do_multicomponent = (m_trans->transportModel() == "multicomponent" || - m_trans->transportModel() == "multicomponent-CK"); - - m_diff.resize(m_nsp*m_points); - if (m_do_multicomponent) { - m_multidiff.resize(m_nsp*m_nsp*m_points); - m_dthermal.resize(m_nsp, m_points, 0.0); - } -} - -void StFlow::_getInitialSoln(double* x) -{ - for (size_t j = 0; j < m_points; j++) { - T(x,j) = m_thermo->temperature(); - m_thermo->getMassFractions(&Y(x, 0, j)); - m_rho[j] = m_thermo->density(); - } -} - -void StFlow::setGas(const double* x, size_t j) -{ - m_thermo->setTemperature(T(x,j)); - const double* yy = x + m_nv*j + c_offset_Y; - m_thermo->setMassFractions_NoNorm(yy); - m_thermo->setPressure(m_press); - // P. Wolf - if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ - calcMixFrac(x,j); - } -} - -void StFlow::setGasAtMidpoint(const double* x, size_t j) -{ - m_thermo->setTemperature(0.5*(T(x,j)+T(x,j+1))); - const double* yyj = x + m_nv*j + c_offset_Y; - const double* yyjp = x + m_nv*(j+1) + c_offset_Y; - for (size_t k = 0; k < m_nsp; k++) { - m_ybar[k] = 0.5*(yyj[k] + yyjp[k]); - } - m_thermo->setMassFractions_NoNorm(m_ybar.data()); - m_thermo->setPressure(m_press); - // P. Wolf - if ((avbp_ipea==1)||(avbp_ipea==2)||(avbp_ipea==3)){ - calcMixFrac(x,j); - } -} - - /// Calculates and updates the mixture fraction at point j - /// WARNING: Only correct if no Carbon atoms in the oxidizer line - /// and pure fuel in the fuel line - /// Added by P. Wolf - March 2010 - /// Thanks to Alireza Najafiyazdi - -void StFlow::calcMixFrac(const double* x, size_t j) { - size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom - size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel - double Z_C = 0.0; // passive scalar for C atom - double Z_C_F; // value of the passive scalar in fuel line - double W_C = this->m_thermo->atomicWeight(id_C); // Molecular weight of C atom - double W_fuel = this->m_thermo->molecularWeight(id_fuel); - double n_C; // Number of C atoms in each species - - for (size_t k=0; km_nsp; k++) { - n_C = this->m_thermo->nAtoms(k,id_C); - Z_C += n_C*x[index(c_offset_Y + k, j)]/this->m_thermo->molecularWeight(k); - } - Z_C = Z_C*W_C; - Z_C_F = W_C*this->m_thermo->nAtoms(id_fuel,id_C)/W_fuel; - m_zmixfrac[j] = Z_C/Z_C_F; // ie Z_C=0 in oxidizer line -} - -bool StFlow::fixed_mdot() { - warn_deprecated("StFlow::fixed_mdot", "To be removed after" - " Cantera 3.0. Replaced by isFree()."); - return !m_isFree; -} - -void StFlow::_finalize(const double* x) -{ - if (!m_do_multicomponent && m_do_soret) { - throw CanteraError("StFlow::_finalize", - "Thermal diffusion (the Soret effect) is enabled, and requires " - "using a multicomponent transport model."); - } - - size_t nz = m_zfix.size(); - bool e = m_do_energy[0]; - for (size_t j = 0; j < m_points; j++) { - if (e || nz == 0) { - m_fixedtemp[j] = T(x, j); - } else { - double zz = (z(j) - z(0))/(z(m_points - 1) - z(0)); - double tt = linearInterp(zz, m_zfix, m_tfix); - m_fixedtemp[j] = tt; - } - } - if (e) { - solveEnergyEqn(); - } - - if (m_isFree) { - // If the domain contains the temperature fixed point, make sure that it - // is correctly set. This may be necessary when the grid has been modified - // externally. - if (m_tfixed != Undef) { - for (size_t j = 0; j < m_points; j++) { - if (z(j) == m_zfixed) { - return; // fixed point is already set correctly - } - } - - for (size_t j = 0; j < m_points - 1; j++) { - // Find where the temperature profile crosses the current - // fixed temperature. - if ((T(x, j) - m_tfixed) * (T(x, j+1) - m_tfixed) <= 0.0) { - m_tfixed = T(x, j+1); - m_zfixed = z(j+1); - return; - } - } - } - } -} - -void StFlow::eval(size_t jg, double* xg, double* rg, integer* diagg, double rdt) -{ - // if evaluating a Jacobian, and the global point is outside the domain of - // influence for this domain, then skip evaluating the residual - if (jg != npos && (jg + 1 < firstPoint() || jg > lastPoint() + 1)) { - return; - } - - // start of local part of global arrays - double* x = xg + loc(); - double* rsd = rg + loc(); - integer* diag = diagg + loc(); - - size_t jmin, jmax; - if (jg == npos) { // evaluate all points - jmin = 0; - jmax = m_points - 1; - } else { // evaluate points for Jacobian - size_t jpt = (jg == 0) ? 0 : jg - firstPoint(); - jmin = std::max(jpt, 1) - 1; - jmax = std::min(jpt+1,m_points-1); - } - - updateProperties(jg, x, jmin, jmax); - evalResidual(x, rsd, diag, rdt, jmin, jmax); -} - -void StFlow::updateProperties(size_t jg, double* x, size_t jmin, size_t jmax) -{ - // properties are computed for grid points from j0 to j1 - size_t j0 = std::max(jmin, 1) - 1; - size_t j1 = std::min(jmax+1,m_points-1); - - updateThermo(x, j0, j1); - if (jg == npos || m_force_full_update) { - // update transport properties only if a Jacobian is not being - // evaluated, or if specifically requested - updateTransport(x, j0, j1); - } - if (jg == npos) { - double* Yleft = x + index(c_offset_Y, jmin); - m_kExcessLeft = distance(Yleft, max_element(Yleft, Yleft + m_nsp)); - double* Yright = x + index(c_offset_Y, jmax); - m_kExcessRight = distance(Yright, max_element(Yright, Yright + m_nsp)); - } - - // update the species diffusive mass fluxes whether or not a - // Jacobian is being evaluated - updateDiffFluxes(x, j0, j1); - if (m_nsoot > 0){ - updateSootDiffFluxes(x, j0, j1); - } -} - -void StFlow::evalResidual(double* x, double* rsd, int* diag, - double rdt, size_t jmin, size_t jmax) -{ - //---------------------------------------------------- - // evaluate the residual equations at all required - // grid points - //---------------------------------------------------- - - // calculation of qdotRadiation (see docstring of enableRadiation) - if (m_do_radiation) { - // variable definitions for the Planck absorption coefficient and the - // radiation calculation: - double k_P_ref = 1.0*OneAtm; - - // polynomial coefficients: - const double c_H2O[6] = {-0.23093, -1.12390, 9.41530, -2.99880, - 0.51382, -1.86840e-5}; - const double c_CO2[6] = {18.741, -121.310, 273.500, -194.050, - 56.310, -5.8169}; - - // calculation of the two boundary values - double boundary_Rad_left = m_epsilon_left * StefanBoltz * pow(T(x, 0), 4); - double boundary_Rad_right = m_epsilon_right * StefanBoltz * pow(T(x, m_points - 1), 4); - - // loop over all grid points - for (size_t j = jmin; j < jmax; j++) { - // helping variable for the calculation - double radiative_heat_loss = 0; - - // calculation of the mean Planck absorption coefficient - double k_P = 0; - // absorption coefficient for H2O - if (m_kRadiating[1] != npos) { - double k_P_H2O = 0; - for (size_t n = 0; n <= 5; n++) { - k_P_H2O += c_H2O[n] * pow(1000 / T(x, j), (double) n); - } - k_P_H2O /= k_P_ref; - k_P += m_press * X(x, m_kRadiating[1], j) * k_P_H2O; - } - // absorption coefficient for CO2 - if (m_kRadiating[0] != npos) { - double k_P_CO2 = 0; - for (size_t n = 0; n <= 5; n++) { - k_P_CO2 += c_CO2[n] * pow(1000 / T(x, j), (double) n); - } - k_P_CO2 /= k_P_ref; - k_P += m_press * X(x, m_kRadiating[0], j) * k_P_CO2; - } - // absorption coefficient for soot - if (m_nsoot != 0 && m_do_soot_radiation) { - double k_P_soot = 0.0; - k_P_soot = 3.83 * CRad0 * fv(x,j) * T(x,j) / CRad2; - k_P += k_P_soot; - } - - // calculation of the radiative heat loss term - radiative_heat_loss = 2 * k_P *(2 * StefanBoltz * pow(T(x, j), 4) - - boundary_Rad_left - boundary_Rad_right); - - // set the radiative heat loss vector - m_qdotRadiation[j] = radiative_heat_loss; - } - } - - for (size_t j = jmin; j <= jmax; j++) { - //---------------------------------------------- - // left boundary - //---------------------------------------------- - if (m_nsoot > 0){ - getDistributionOrdre0(x,j); - } - //avbp_thick.resize(m_points,avbp_fthick); ///////////////////////////// NEW to handle pytest - AVBPcompute_local_thick(x,j); - double thick_j = avbp_thick[j]; - - if (j == 0) { - // these may be modified by a boundary object - - // Continuity. This propagates information right-to-left, since - // rho_u at point 0 is dependent on rho_u at point 1, but not on - // mdot from the inlet. - rsd[index(c_offset_U,0)] = - -(rho_u(x,1) - rho_u(x,0))/m_dz[0] - -(density(1)*V(x,1) + density(0)*V(x,0)); - - // the inlet (or other) object connected to this one will modify - // these equations by subtracting its values for V, T, and mdot. As - // a result, these residual equations will force the solution - // variables to the values for the boundary object - rsd[index(c_offset_V,0)] = V(x,0); - rsd[index(c_offset_T,0)] = T(x,0); - if (m_usesLambda) { - rsd[index(c_offset_L, 0)] = -rho_u(x, 0); - } else { - rsd[index(c_offset_L, 0)] = lambda(x, 0); - diag[index(c_offset_L, 0)] = 0; - } - - // The default boundary condition for species is zero flux. However, - // the boundary object may modify this. - double sum = 0.0; - for (size_t k = 0; k < m_nsp; k++) { - sum += Y(x,k,0); - rsd[index(c_offset_Y + k, 0)] = -// no thick -(m_flux(k,0) + rho_u(x,0)* Y(x,k,0)); - -(m_flux(k,0) * thick_j + rho_u(x,0)* Y(x,k,0)); - } - rsd[index(c_offset_Y + leftExcessSpecies(), 0)] = 1.0 - sum; - if (m_nsoot > 0){ - for (size_t k = 0; k < m_nsoot; k++){ - rsd[index(c_offset_S + k, 0)] = - (m_soot_diff(k,0) - + rho_u(x,0)* Ys(x,k,0)); - } - } - - // set residual of poisson's equ to zero - rsd[index(c_offset_E, 0)] = x[index(c_offset_E, j)]; - } else if (j == m_points - 1) { - evalRightBoundary(x, rsd, diag, rdt); - } else { // interior points - evalContinuity(j, x, rsd, diag, rdt); - // set residual of poisson's equ to zero - rsd[index(c_offset_E, j)] = x[index(c_offset_E, j)]; - - //------------------------------------------------ - // Radial momentum equation - // - // \rho dV/dt + \rho u dV/dz + \rho V^2 - // = d(\mu dV/dz)/dz - lambda - //------------------------------------------------- - AVBPcompute_local_thick(x,j); - double thick_j = avbp_thick[j]; - double inv_thick = 1.0 / thick_j; - double thick_prev = avbp_thick[j-1]; - - if (m_usesLambda) { - rsd[index(c_offset_V,j)] = - (shear(x, j) - lambda(x, j) - rho_u(x, j) * dVdz(x, j) - - m_rho[j] * V(x, j) * V(x, j)) / m_rho[j] - - rdt * (V(x, j) - V_prev(j)); - diag[index(c_offset_V, j)] = 1; - } else { - rsd[index(c_offset_V, j)] = V(x, j); - diag[index(c_offset_V, j)] = 0; - } - - //------------------------------------------------- - // Soot equation - // - // \rho u dYs/dz + d(-0.554 \mu 1/T dT/dx Ys)/dz - // = d(\rho Ds dYs/dz)/dz + \rhos \rho qdots - // - // convection - Thermophoresis = Diffusion + Source - //------------------------------------------------- - if (m_nsoot > 0) { - sootSource(x,j); - for (size_t k = 0; k < m_nsoot; k++){ - // Convection - double soot_convec = rho_u(x,j)*dYsdz(x,k,j); - // Diffusion - double soot_diffus = 2.0 * (m_soot_diff(k,j) - m_soot_diff(k,j-1)) - / (z(j+1) - z(j-1)); - // Thermophoresis - double soot_soret = 2.0 * (m_soot_soret(k,j) - m_soot_soret(k,j-1)) - / (z(j+1) - z(j-1)); - // Source terms [m3/kg/s] - double soot_source = 0; - soot_source += (k == 0 ? m_qdotNucleation[j] : 0.0); - soot_source += (m_do_condensation ? m_qdotCondensation(k,j) : 0.0); - soot_source += (m_do_coagulation ? m_qdotCoagulation(k,j) : 0.0); - soot_source += (m_do_sg ? m_qdotSg(k,j) : 0.0); - soot_source += (m_do_oxidation ? m_qdotOxidation(k,j) : 0.0); - // kg/s/m^3 - soot_source *= (rho_soot * m_rho[j]); - if(k == m_nsoot - 1 && m_trash_section){soot_source = 0.0;} - // Residual - rsd[index(c_offset_S + k, j)] = - (soot_source - soot_convec + soot_diffus + soot_soret) / m_rho[j] - - rdt * (Ys(x,k,j) - Ys_prev(k,j)); - diag[index(c_offset_S + k, j)] = 1; - } - } - //------------------------------------------------- - // Species equations - // - // \rho dY_k/dt + \rho u dY_k/dz + dJ_k/dz - // = M_k\omega_k - //------------------------------------------------- - getWdot(x,j); - if (m_nsoot > 0 && m_do_retroaction){ - for (size_t k=0; k < m_nsp; k++){ - // (kmol.m^(-3).s^(-1)) - m_wdot(k,j) -= sootConsumption[k]; - } - } - for (size_t k = 0; k < m_nsp; k++) { - double convec = rho_u(x,j)*dYdz(x,k,j); -// no thick double diffus = 2.0*(m_flux(k,j) - m_flux(k,j-1)) - double diffus = 2.0*(m_flux(k,j)*thick_j - m_flux(k,j-1)*thick_prev) - / (z(j+1) - z(j-1)); - rsd[index(c_offset_Y + k, j)] - = (m_wt[k]*(wdot(k,j)*inv_thick) -// no thick = (m_wt[k]*(wdot(k,j)) - - convec - diffus)/m_rho[j] - - rdt*(Y(x,k,j) - Y_prev(k,j)); - diag[index(c_offset_Y + k, j)] = 1; - } - - //----------------------------------------------- - // energy equation - // - // \rho c_p dT/dt + \rho c_p u dT/dz - // = d(k dT/dz)/dz - // - sum_k(\omega_k h_k_ref) - // - sum_k(J_k c_p_k / M_k) dT/dz - //----------------------------------------------- - if (m_do_energy[j]) { - - setGas(x,j); - double dtdzj = dTdz(x,j); - double sum = 0.0; - double sum2 = 0.0; - - grad_hk(x, j); - for (size_t k = 0; k < m_nsp; k++) { -// no thick double flxk = 0.5*(m_flux(k,j-1) + m_flux(k,j)); - double flxk = 0.5*(m_flux(k,j-1)*thick_prev + m_flux(k,j)*thick_j); - sum += wdot(k,j)*m_hk(k,j); - sum2 += flxk * m_dhk_dz(k,j) / m_wt[k]; - } - - rsd[index(c_offset_T, j)] = - m_cp[j]*rho_u(x,j)*dtdzj -// no thick //- divHeatFlux(x,j) - sum; - - AVBPdivHeatFlux(x,j) - sum*inv_thick - sum2; - - rsd[index(c_offset_T, j)] /= (m_rho[j]*m_cp[j]); - rsd[index(c_offset_T, j)] -= rdt*(T(x,j) - T_prev(j)); - rsd[index(c_offset_T, j)] -= (m_qdotRadiation[j] / (m_rho[j] * m_cp[j])); - diag[index(c_offset_T, j)] = 1; - } else { - // residual equations if the energy equation is disabled - rsd[index(c_offset_T, j)] = T(x,j) - T_fixed(j); - diag[index(c_offset_T, j)] = 0; - } - - if (m_usesLambda) { - rsd[index(c_offset_L, j)] = lambda(x, j) - lambda(x, j - 1); - } else { - rsd[index(c_offset_L, j)] = lambda(x, j); - } - diag[index(c_offset_L, j)] = 0; - } - } -} - -void StFlow::updateTransport(double* x, size_t j0, size_t j1) -{ - if (m_do_multicomponent) { - for (size_t j = j0; j < j1; j++) { - setGasAtMidpoint(x,j); - double wtm = m_thermo->meanMolecularWeight(); - double rho = m_thermo->density(); - m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0); - m_trans->getMultiDiffCoeffs(m_nsp, &m_multidiff[mindex(0,0,j)]); - - // Use m_diff as storage for the factor outside the summation - for (size_t k = 0; k < m_nsp; k++) { - m_diff[k+j*m_nsp] = m_wt[k] * rho / (wtm*wtm); - } - - m_tcon[j] = m_trans->thermalConductivity(); - if (m_do_soret) { - m_trans->getThermalDiffCoeffs(m_dthermal.ptrColumn(0) + j*m_nsp); - } - } - } else { // mixture averaged transport - for (size_t j = j0; j < j1; j++) { - setGasAtMidpoint(x,j); - m_visc[j] = (m_dovisc ? m_trans->viscosity() : 0.0); - m_trans->getMixDiffCoeffs(&m_diff[j*m_nsp]); - m_tcon[j] = m_trans->thermalConductivity(); - } - } -} - -void StFlow::show(const double* x) -{ - writelog(" Pressure: {:10.4g} Pa\n", m_press); - - Domain1D::show(x); - - if (m_do_radiation) { - writeline('-', 79, false, true); - writelog("\n z radiative heat loss"); - writeline('-', 79, false, true); - for (size_t j = 0; j < m_points; j++) { - writelog("\n {:10.4g} {:10.4g}", m_z[j], m_qdotRadiation[j]); - } - writelog("\n"); - } -} - -void StFlow::updateDiffFluxes(const double* x, size_t j0, size_t j1) -{ - if (m_do_multicomponent) { - for (size_t j = j0; j < j1; j++) { - double dz = z(j+1) - z(j); - for (size_t k = 0; k < m_nsp; k++) { - double sum = 0.0; - for (size_t m = 0; m < m_nsp; m++) { - sum += m_wt[m] * m_multidiff[mindex(k,m,j)] * (X(x,m,j+1)-X(x,m,j)); - } - m_flux(k,j) = sum * m_diff[k+j*m_nsp] / dz; - } - } - } else { - for (size_t j = j0; j < j1; j++) { - double sum = 0.0; - double wtm = m_wtm[j]; - double rho = density(j); - double dz = z(j+1) - z(j); - for (size_t k = 0; k < m_nsp; k++) { - m_flux(k,j) = m_wt[k]*(rho*m_diff[k+m_nsp*j]/wtm); - m_flux(k,j) *= (X(x,k,j) - X(x,k,j+1))/dz; - sum -= m_flux(k,j); - } - // correction flux to insure that \sum_k Y_k V_k = 0. - for (size_t k = 0; k < m_nsp; k++) { - m_flux(k,j) += sum*Y(x,k,j); - } - } - } - - if (m_do_soret) { - for (size_t m = j0; m < j1; m++) { - double gradlogT = 2.0 * (T(x,m+1) - T(x,m)) / - ((T(x,m+1) + T(x,m)) * (z(m+1) - z(m))); - for (size_t k = 0; k < m_nsp; k++) { - m_flux(k,m) -= m_dthermal(k,m)*gradlogT; - } - } - } -} - -string StFlow::componentName(size_t n) const -{ - switch (n) { - case c_offset_U: - return "velocity"; - case c_offset_V: - return "spread_rate"; - case c_offset_T: - return "T"; - case c_offset_L: - return "lambda"; - case c_offset_E: - return "eField"; - default: - if (n >= c_offset_Y && n < (c_offset_Y + m_nsp)) { - return m_thermo->speciesName(n - c_offset_Y); - } else if (n >= c_offset_S && n < (c_offset_S + m_nsoot)) { - return sectionName(n-c_offset_S); - } else { - return ""; - } - } -} - -size_t StFlow::componentIndex(const string& name) const -{ - if (name=="velocity") { - return c_offset_U; - } else if (name=="spread_rate") { - return c_offset_V; - } else if (name=="T") { - return c_offset_T; - } else if (name=="lambda") { - return c_offset_L; - } else if (name == "eField") { - return c_offset_E; - } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()) { - return stoi(name.substr(2))+c_offset_S; // offset not required in previous version, why? - } else { - for (size_t n=c_offset_Y; ntransportModel(); - - state["phase"]["name"] = m_thermo->name(); - AnyValue source = m_thermo->input().getMetadata("filename"); - state["phase"]["source"] = source.empty() ? "" : source.asString(); - - state["radiation-enabled"] = m_do_radiation; - if (m_do_radiation) { - state["emissivity-left"] = m_epsilon_left; - state["emissivity-right"] = m_epsilon_right; - } - - set energy_flags(m_do_energy.begin(), m_do_energy.end()); - if (energy_flags.size() == 1) { - state["energy-enabled"] = m_do_energy[0]; - } else { - state["energy-enabled"] = m_do_energy; - } - - state["Soret-enabled"] = m_do_soret; - - set species_flags(m_do_species.begin(), m_do_species.end()); - if (species_flags.size() == 1) { - state["species-enabled"] = m_do_species[0]; - } else { - for (size_t k = 0; k < m_nsp; k++) { - state["species-enabled"][m_thermo->speciesName(k)] = m_do_species[k]; - } - } - - state["refine-criteria"]["ratio"] = m_refiner->maxRatio(); - state["refine-criteria"]["slope"] = m_refiner->maxDelta(); - state["refine-criteria"]["curve"] = m_refiner->maxSlope(); - state["refine-criteria"]["prune"] = m_refiner->prune(); - state["refine-criteria"]["grid-min"] = m_refiner->gridMin(); - state["refine-criteria"]["max-points"] = - static_cast(m_refiner->maxPoints()); - - if (m_zfixed != Undef) { - state["fixed-point"]["location"] = m_zfixed; - state["fixed-point"]["temperature"] = m_tfixed; - } - - return state; -} - -shared_ptr StFlow::asArray(const double* soln) const -{ - auto arr = SolutionArray::create( - m_solution, static_cast(nPoints()), getMeta()); - arr->addExtra("grid", false); // leading entry - AnyValue value; - value = m_z; - arr->setComponent("grid", value); - vector data(nPoints()); - for (size_t i = 0; i < nComponents(); i++) { - if (componentActive(i)) { - auto name = componentName(i); - for (size_t j = 0; j < nPoints(); j++) { - data[j] = soln[index(i, j)]; - } - if (!arr->hasComponent(name)) { - arr->addExtra(name, componentIndex(name) > c_offset_Y); - } - value = data; - arr->setComponent(name, value); - } - } - value = m_rho; - arr->setComponent("D", value); // use density rather than pressure - - if (m_do_radiation) { - arr->addExtra("radiative-heat-loss", true); // add at end - value = m_qdotRadiation; - arr->setComponent("radiative-heat-loss", value); - } - - return arr; -} - -void StFlow::fromArray(SolutionArray& arr, double* soln) -{ - Domain1D::setMeta(arr.meta()); - arr.setLoc(0); - auto phase = arr.thermo(); - m_press = phase->pressure(); - vector did_section(m_nsoot,false); - bool wrote_header = false; - - const auto grid = arr.getComponent("grid").as>(); - setupGrid(nPoints(), &grid[0]); - - for (size_t i = 0; i < nComponents(); i++) { - if (!componentActive(i)) { - continue; - } - string name = componentName(i); - if (arr.hasComponent(name)) { - const vector data = arr.getComponent(name).as>(); - if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ - size_t n = stoi(name.substr(2)); - did_section[n]=true; - writelog("Adding soot section to soln "+name+"\n"); - } - for (size_t j = 0; j < nPoints(); j++) { - soln[index(i,j)] = data[j]; - } - } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ - size_t n = stoi(name.substr(2)); - did_section[n]=true; - writelog("Creating soot section in soln "+name+"\n"); - for (size_t j = 0; j < nPoints(); j++) { - soln[index(n+c_offset_S,j)] = 0.0; - } - } else { - warn_user("StFlow::fromArray", "Saved state does not contain values for " - "component '{}' in domain '{}'.", name, id()); - } - } - - if (soot_loglevel >= 1 && m_nsoot != 0) { - wrote_header = false; - for (size_t ks = 0; ks < m_nsoot; ks++) { - if (did_section[ks] == false) { - if (!wrote_header) { - writelog("\n\n"); - writelog("Missing data for soot sections:\n"); - wrote_header = true; - } - writelog(m_section_name[ks]+" "); - } - } - } - - updateProperties(npos, soln + loc(), 0, m_points - 1); - setMeta(arr.meta()); -} - -string StFlow::flowType() const { - warn_deprecated("StFlow::flowType", - "To be removed after Cantera 3.0; superseded by 'type'."); - if (m_type == cFreeFlow) { - return "Free Flame"; - } else if (m_type == cAxisymmetricStagnationFlow) { - return "Axisymmetric Stagnation"; - } else if (m_type == cFlameletFlow){ - return "Flamelet"; - } else { - throw CanteraError("StFlow::flowType", "Unknown value for 'm_type'"); - } -} - -void StFlow::setMeta(const AnyMap& state) -{ - if (state.hasKey("energy-enabled")) { - const AnyValue& ee = state["energy-enabled"]; - if (ee.isScalar()) { - m_do_energy.assign(nPoints(), ee.asBool()); - } else { - m_do_energy = ee.asVector(nPoints()); - } - } - - setTransportModel(state.getString("transport-model", "mixture-averaged")); - - if (state.hasKey("Soret-enabled")) { - m_do_soret = state["Soret-enabled"].asBool(); - } - - if (state.hasKey("species-enabled")) { - const AnyValue& se = state["species-enabled"]; - if (se.isScalar()) { - m_do_species.assign(m_thermo->nSpecies(), se.asBool()); - } else { - m_do_species = se.asVector(m_thermo->nSpecies()); - } - } - - if (state.hasKey("radiation-enabled")) { - m_do_radiation = state["radiation-enabled"].asBool(); - if (m_do_radiation) { - m_epsilon_left = state["emissivity-left"].asDouble(); - m_epsilon_right = state["emissivity-right"].asDouble(); - } - } - - if (state.hasKey("refine-criteria")) { - const AnyMap& criteria = state["refine-criteria"].as(); - double ratio = criteria.getDouble("ratio", m_refiner->maxRatio()); - double slope = criteria.getDouble("slope", m_refiner->maxDelta()); - double curve = criteria.getDouble("curve", m_refiner->maxSlope()); - double prune = criteria.getDouble("prune", m_refiner->prune()); - m_refiner->setCriteria(ratio, slope, curve, prune); - - if (criteria.hasKey("grid-min")) { - m_refiner->setGridMin(criteria["grid-min"].asDouble()); - } - if (criteria.hasKey("max-points")) { - m_refiner->setMaxPoints(criteria["max-points"].asInt()); - } - } - - if (state.hasKey("fixed-point")) { - m_zfixed = state["fixed-point"]["location"].asDouble(); - m_tfixed = state["fixed-point"]["temperature"].asDouble(); - } -} - -void StFlow::solveEnergyEqn(size_t j) -{ - bool changed = false; - if (j == npos) { - for (size_t i = 0; i < m_points; i++) { - if (!m_do_energy[i]) { - changed = true; - } - m_do_energy[i] = true; - } - } else { - if (!m_do_energy[j]) { - changed = true; - } - m_do_energy[j] = true; - } - m_refiner->setActive(c_offset_U, true); - m_refiner->setActive(c_offset_V, true); - m_refiner->setActive(c_offset_T, true); - if (changed) { - needJacUpdate(); - } -} - -size_t StFlow::getSolvingStage() const -{ - throw NotImplementedError("StFlow::getSolvingStage", - "Not used by '{}' objects.", type()); -} - -void StFlow::setSolvingStage(const size_t stage) -{ - throw NotImplementedError("StFlow::setSolvingStage", - "Not used by '{}' objects.", type()); -} - -void StFlow::solveElectricField(size_t j) -{ - throw NotImplementedError("StFlow::solveElectricField", - "Not used by '{}' objects.", type()); -} - -void StFlow::fixElectricField(size_t j) -{ - throw NotImplementedError("StFlow::fixElectricField", - "Not used by '{}' objects.", type()); -} - -bool StFlow::doElectricField(size_t j) const -{ - throw NotImplementedError("StFlow::doElectricField", - "Not used by '{}' objects.", type()); -} - -void StFlow::setBoundaryEmissivities(double e_left, double e_right) -{ - if (e_left < 0 || e_left > 1) { - throw CanteraError("StFlow::setBoundaryEmissivities", - "The left boundary emissivity must be between 0.0 and 1.0!"); - } else if (e_right < 0 || e_right > 1) { - throw CanteraError("StFlow::setBoundaryEmissivities", - "The right boundary emissivity must be between 0.0 and 1.0!"); - } else { - m_epsilon_left = e_left; - m_epsilon_right = e_right; - } -} - -void StFlow::fixTemperature(size_t j) -{ - bool changed = false; - if (j == npos) { - for (size_t i = 0; i < m_points; i++) { - if (m_do_energy[i]) { - changed = true; - } - m_do_energy[i] = false; - } - } else { - if (m_do_energy[j]) { - changed = true; - } - m_do_energy[j] = false; - } - m_refiner->setActive(c_offset_U, false); - m_refiner->setActive(c_offset_V, false); - m_refiner->setActive(c_offset_T, false); - if (changed) { - needJacUpdate(); - } -} -/* ------------------------------------------------------------------------ - Reads the mixture_database.dat file and sets accordingly the PEA function(s) - P. Wolf modif by J. Wirtz ---------------------------------------------------------------------------*/ -void StFlow::AVBPReadInputPea() { - Parser parser; - Param* param; - - ifstream avbp_mixturedb("mixture_database.dat"); - if (avbp_mixturedb.good()){ - parser.parseFile("mixture_database.dat"); - // In case of pea, the name of the gas should be the same than the one in the mixture_database. - // Get number of mixtures in database - size_t n_mixtures = parser.nbParamOccurence("mixture_name"); - size_t idx_beg = std::string::npos; - size_t idx_end = std::string::npos; - // Loop through all occurences of keyword "mixture name" - for (size_t i=0; i< n_mixtures; ++i) { - param = parser.getParam("mixture_name",i); - std::string current_str = param->readString(0); - // Check if mixture_name is the one requested in the cti file - if ( current_str == m_thermo->name() ) { - // Store bounding idx to get important info - idx_beg = parser.getParamNumber("mixture_name",i); - idx_end = parser.getParamNumber("mixture_name",i+1); - - // Get the fuel of the 2-step chemistry - param = parser.getParam("species_name", idx_beg, idx_end); - for (size_t i=0; ireadString(i); - if (avbp_species.find('C')!=string::npos && avbp_species.find('H')!=string::npos){ - avbp_fuel = avbp_species; - } - if (avbp_species == "H2"){ - avbp_fuel = avbp_species; - } - - } - - // Check if PEA method and search for the coefficient - if (parser.checkParam("pea_method", idx_beg, idx_end) == true){ - param = parser.getParam("pea_method", idx_beg, idx_end); - std::string avbp_pea = param->readString(0); - if (avbp_pea == "pea1"){ - avbp_ipea = 1; - cout<<"ipea set to 1, PEA_1 will be applied"<readDouble(i); - } - } - else if (avbp_pea == "pea2") { - avbp_ipea = 2; - cout<<"ipea set to 2, PEA_2 will be applied"<readDouble(i); - } - param = parser.getParam("pea_coeff", idx_beg, idx_end, 1); - for (size_t i=0; i<10; i++) { - avbp_pea_coeffs[i+8] = param->readDouble(i); - } - - } - else{ - throw CanteraError("readAvbpInputPEA","ipea is set to a weird value"); - } - } - else { - avbp_ipea = 0; - } - } - else { - // pea not considered as mixture_name (mixture_database.dat) does not correspond to gas name (cti) - avbp_ipea = 0; - } - - // calculate the global equivalence ratio phi_cst - if ((avbp_ipea==1)||(avbp_ipea==2)){ - size_t id_C = this->m_thermo->elementIndex("C"); // Index of C atom - size_t id_H = this->m_thermo->elementIndex("H"); // Index of H atom - size_t id_fuel = this->m_thermo->speciesIndex(avbp_fuel); // Index of fuel - size_t id_ox = this->m_thermo->speciesIndex("O2"); // Index of O2 - size_t n_C = this->m_thermo->nAtoms(id_fuel,id_C); - size_t n_H = this->m_thermo->nAtoms(id_fuel,id_H); - //Calculate in mass units phi = s_m*Yf/Yo - phi_cst = (n_C + n_H/4)*this->m_thermo->molecularWeight(id_ox)/this->m_thermo->molecularWeight(id_fuel); - phi_cst = phi_cst*1./0.2333; // WARNING: valid only for Fuel/AIR mixture - } - - if (avbp_ipea!=0){ - break; - } - - } - } - else { - avbp_ipea = 0; - } -} -/********** - Reading the AVBP input_chem.dat - B. Franzelli -*************/ -void StFlow::AVBPReadInputChem() { - avbp_fthick = m_thick; - if (avbp_fthick > 1.0) { - cout << "INFO: Thickening applied with constant value." << endl; - } - else { - avbp_fthick = 1.0; - } -} -void StFlow::AVBPcompute_local_thick(double* x,size_t j){ - avbp_thick[j] = avbp_fthick; -} - -//----------------------// -// SOOT RELATED MTEHODS // -//----------------------// -void StFlow::initSoot(){ - //---------------------------------------------------- - // Initializes soot computation - //---------------------------------------------------- - - // Sets offset of soot sections in solution array - // Resizes necessay arrays - // Sets sections names "YsXX", disables refinement on soot and sets clipping - - // Offset definition - c_offset_S = c_offset_Y + m_nsp; - // Array allocation - m_section_name.resize(m_nsoot); - sootConsumption.resize(m_nsp, 0.0); - q.resize(m_nsoot,0.0); - vSectMin.resize(m_nsoot, 0.0); - vSectMax.resize(m_nsoot, 0.0); - vSectMean.resize(m_nsoot, 0.0); - sSectMean.resize(m_nsoot, 0.0); - dSectMean.resize(m_nsoot, 0.0); - dSectCol.resize(m_nsoot, 0.0); - kfractal.resize(m_nsoot, 1.0); - Dfractal.resize(m_nsoot, 3); - nNucMean.resize(m_nsoot, 0.0); - rNucMean.resize(m_nsoot, 0.0); - rSectCol.resize(m_nsoot, 0.0); - aSectCol.resize(m_nsoot, 0.0); - theta_surf.resize(m_nsoot,2.0); - m_soot_diff.resize(m_nsoot, m_points, 0.0); - m_soot_soret.resize(m_nsoot, m_points, 0.0); - m_qdotNucleation.resize(m_points, 0.0); - m_qdotCondensation.resize(m_nsoot, m_points, 0.0); - m_qdotCoagulation.resize(m_nsoot, m_points, 0.0); - collision_mat.resize(m_nsoot, m_nsoot, 0.0); - m_qdotSg.resize(m_nsoot, m_points, 0.0); - m_qdotOxidation.resize(m_nsoot, m_points, 0.0); - // Sections setup - for (size_t k = 0; k < m_nsoot; k++) { - std::string string_k = std::to_string(k); - m_section_name[k] = "Ys" + string_k; - m_refiner->setActive(c_offset_S+k, false); - setBounds(c_offset_S + k, -1.0e-5, 1e5); - } - -} - -void StFlow::setPrecursors(vector id_precursors){ - //---------------------------------------------------- - // Recovers precursor data for further computation - //---------------------------------------------------- - - if (m_nsoot <= 0){ - writelog("\n--> CANTERA SOOT : no sections :(\n"); - return; - } - size_t id_C = m_thermo->elementIndex("C"); - W_C = m_thermo->atomicWeight(id_C); - n_PAH = id_precursors.size(); - m_precursors.resize(n_PAH); - W_PAH.resize(n_PAH,0.0); - n_C.resize(n_PAH,0.0); - for (size_t k = 0; k != n_PAH; k++){ - m_precursors[k] = id_precursors[k] - c_offset_Y; - W_PAH[k] = m_thermo->molecularWeight(m_precursors[k]); - n_C[k] = m_thermo->nAtoms(m_precursors[k],id_C); - } -} - -void StFlow::finalizeSoot(){ - //---------------------------------------------------- - // Soot setup finalization - //---------------------------------------------------- - // Creates soot volumes - sootCreationVol(); - // Computes collision matrix - sootCollisionInverse(); - // Load surface reactions - if (m_do_sg || m_do_oxidation){ - loadHaca(m_haca_model); - loadSurface();} - - if (soot_loglevel >= 1){showSootInfo();} - if (soot_loglevel >= 2){showSootSections();} -} - -void StFlow::sootCreationVol(){ - // Sections creations - // PAH list boundaries - size_t n_C_min = *min_element(n_C.begin(),n_C.end()); - size_t n_C_max = *max_element(n_C.begin(),n_C.end()); - // First section lower boundary : smallest possible dimer - vSectMin[0] = 2.0 * (double)n_C_min * V_C2; - // First section upper boundary : biggest possible dimer - vSectMax[0] = V_C2 * max(2.0 * n_C_min + n_C_max, 2.0 * n_C_max); - // Following sections : geometrical progression - vSectMin[1] = vSectMax[0]; - if (m_trash_section){ - double vTrashLowLim = Pi * pow(dTrashLowLim,3.0) / 6; - for (size_t k = 1; k < m_nsoot - 2; k++){ - double exponent = double(k) / double(m_nsoot-2); - vSectMax[k] = vSectMin[1] * pow(vTrashLowLim / vSectMin[1],exponent); - vSectMin[k+1] = vSectMax[k]; - } - vSectMax[m_nsoot - 2] = vTrashLowLim; - vSectMin[m_nsoot - 1] = vTrashLowLim; - }else{ - for (size_t k = 1; k < m_nsoot - 1; k++){ - double exponent = double(k) / double(m_nsoot-1); - vSectMax[k] = vSectMin[1] * pow(bigSoot / vSectMin[1],exponent); - vSectMin[k+1] = vSectMax[k]; - } - } - - vSectMax[m_nsoot-1] = bigSoot; - // Building mean values - for (size_t k = 0; k < m_nsoot; k++){ - vSectMean[k] = (vSectMax[k] + vSectMin[k]) / 2.0 ; //(vSectMax[k] - vSectMin[k]) / log (vSectMax[k] / vSectMin[k]); - dSectMean[k] = pow(6 / Pi * vSectMean[k], 1.0 / 3.0); - } - - // Sections morphology - for (size_t k = 0; k < m_nsoot; k++){ - if (vSectMean[k] >= vlim1){ - // Fractal dimension - Dfractal[k] = Df; - // Fractal prefactor - kfractal[k] = 4.46 * pow(Dfractal[k], -2.08); - } - } - - if (m_soot_morphology == "sphere" || m_soot_morphology == "rodrigues"){ - // Soot morphological properties as defined by P. Rodrigues (PhD Thesis, 2018) - // For spheres, theta = 2.0 - for (size_t k = 0; k < m_nsoot; k++){ - if (m_soot_morphology == "rodrigues" && vSectMin[k] >= vlim1){ - theta_surf[k] = (3.0 * (log(vSectMean[k] / vlim1)) - + 2.0 * (log(vlim1 / V_C2))) - / (log(vSectMean[k] / V_C2)); - if (k == m_nsoot-1 && m_trash_section){theta_surf[k] = theta_surf[k-1];} - } - // Collision diameter - dSectCol[k] = 6 / pow(36 * Pi, 1.0 /Dfractal[k]) - * pow(vSectMean[k], (Dfractal[k]-2.0) / Dfractal[k]) - * pow(S_C2 * - pow(vSectMean[k]/V_C2,theta_surf[k] / 3.0),(3.0-Dfractal[k]) / Dfractal[k]); - // Collision radius - rSectCol[k] = dSectCol[k] / 2.0; - // Collision cross-section - aSectCol[k] = Pi * pow(rSectCol[k], 2.0); - // Surface area - sSectMean[k] = S_C2 * pow(vSectMean[k] / V_C2, theta_surf[k] / 3.0); - // Nuclei number - nNucMean[k] = pow(sSectMean[k], 2) / (36. * Pi * pow(vSectMean[k], 2.)); - // Nuclei radius[m] - rNucMean[k] = 3. * vSectMean[k] / sSectMean[k]; - } - // // From P. Rodrigues, trick to help numerical stability (not tested its impact) - // dSectCol[m_nsoot-1] = dSectMean[m_nsoot-1]; - // rSectCol[m_nsoot-1] = dSectCol[m_nsoot-1] / 2.0; - // aSectCol[m_nsoot-1] = Pi * pow(rSectCol[m_nsoot-1], 2.0); - }else if (m_soot_morphology == "thajudeen"){ - // Soot morphological properties as defined by Thajudeen (2012) - for (size_t k = 0; k < m_nsoot; k++){ - // Nuclei number - nNucMean[k] = max(1., vSectMean[k] / vlim1); - // Nuclei radius - rNucMean[k] = min(pow(3.0 * vSectMean[k] / (4.0 * Pi), 1./3.), pow(3.0 * vlim1 / (4.0 * Pi), 1.0/3.0)); - if (vSectMean[k] >= vlim1){ - // Collision radius (Smoluchowski radius) - double alpha1 = 0.253 * pow(Dfractal[k], 2.0) - 1.209 * Dfractal[k] + 1.433; - double alpha2 = -0.218 * pow(Dfractal[k], 2.0) + 0.964 * Dfractal[k] - 0.180; - double phi_r = 1 / (alpha1 * log(nNucMean[k]) + alpha2); - rSectCol[k] = rNucMean[k] * phi_r * pow(nNucMean[k] / kfractal[k], 1/Dfractal[k]); - // Collision cross-section (Projected Area) - double alpha3 = 0.439 * pow(Dfractal[k], 2.0) - 2.221 * Dfractal[k] + 2.787; - double alpha4 = -0.232 * pow(Dfractal[k], 3.0) + 1.273 * pow(Dfractal[k], 2.0) - 2.183 * Dfractal[k] + 1.906; - double phi_p = pow(nNucMean[k], -alpha3) / alpha4; - aSectCol[k] = Pi * pow(rNucMean[k], 2.) * phi_p * pow(nNucMean[k] / kfractal[k], 2.0/Dfractal[k]); - }else{ - rSectCol[k] = dSectMean[k] / 2.; - aSectCol[k] = Pi * pow(rSectCol[k], 2.); - } - //Collision diameter ("Smoluchowski diameter") - dSectCol[k] = 2. * rSectCol[k]; - // Surface area (computed from smoluchowski radius, close to Rodrigues definition) - sSectMean[k] = Pi * pow(dSectCol[k], 2.); - // theta parameter (needed for surface reactions) - theta_surf[k] = 3. * log(sSectMean[k]/S_C2) / log(vSectMean[k]/V_C2); - } - } -} - -void StFlow::sootCollisionInverse(){ - //---------------------------------------------------- - // Computes colision matrix (coagulation) - //---------------------------------------------------- - - for (size_t k = 0; k < m_nsoot; k++){ - for (size_t l = k; l < m_nsoot; l++){ - for (size_t m = l; m < m_nsoot; m++){ - double vol_min = vSectMin[l] + vSectMin[k]; - if(vol_min <= vSectMax[m] && vol_min >= vSectMin[m]){ - collision_mat(k,l) = m; - } - } - } - } -} - -void StFlow::loadSurface(){ - //---------------------------------------------------- - // Resizes and compute surface reactions arrays - //---------------------------------------------------- - - kpower.resize(m_nsoot,0.0); - mpower.resize(m_nsoot,0.0); - vc2power.resize(m_nsoot,0.0); - vc2powerm.resize(m_nsoot,0.0); - vmax_kpower.resize(m_nsoot,0.0); - vmin_kpower.resize(m_nsoot,0.0); - vmax_mpower.resize(m_nsoot,0.0); - vmin_mpower.resize(m_nsoot,0.0); - vmaxmc2_kpower.resize(m_nsoot,0.0); - vminpc2_kpower.resize(m_nsoot,0.0); - vmaxmc2_mpower.resize(m_nsoot,0.0); - vminpc2_mpower.resize(m_nsoot,0.0); - vc2powervect.resize(m_nsoot,0.0); - vc2powermvect.resize(m_nsoot,0.0); - for (size_t k = 0; k < m_nsoot; k++){ - kpower[k] = (theta_surf[k] + 3.0)/3.0; - mpower[k] = theta_surf[k]/3.0; - vc2power[k] = (3.0 - theta_surf[k] )/3.0; - vc2powerm[k] = - mpower[k]; - vmax_kpower[k] = pow(vSectMax[k],kpower[k]); - vmin_kpower[k] = pow(vSectMin[k],kpower[k]); - vmax_mpower[k] = pow(vSectMax[k],mpower[k]); - vmin_mpower[k] = pow(vSectMin[k],mpower[k]); - vmaxmc2_kpower[k] = pow(vSectMax[k] - V_C2,kpower[k]); - vminpc2_kpower[k] = pow(vSectMin[k] + V_C2,kpower[k]); - vmaxmc2_mpower[k] = pow(vSectMax[k] - V_C2,mpower[k]); - vminpc2_mpower[k] = pow(vSectMin[k] + V_C2,mpower[k]); - vc2powervect[k] = pow(V_C2,vc2power[k]); - vc2powermvect[k] = pow(V_C2,vc2powerm[k]); - } -} - -void StFlow::showSootInfo(){ - writelog("\n{:=^47}{:9}{:=^47}", "", "SOOT INFO", ""); - writelog("\n{:21}{:2}{}", "NUMBER OF SECTIONS", ":", m_nsoot); - writelog("\n{:21}{:1}","PRECURSORS", ":"); - for (size_t k = 0; k != n_PAH; k++){ - writelog(" {}", m_thermo->speciesName(m_precursors[k])); - } - if (dTrashLowLim > 0){writelog("\n{:21}{:2}{} m", "MAX DIAMETER", ":", dTrashLowLim);} - writelog("\n{:21}{:2}{}", "AGGREGATES MORPHOLOGY", ":", m_soot_morphology); - writelog("\n{:21}{:2}{}", "RETROACTION", ":", m_do_retroaction); - writelog("\n{:21}{:2}{}", "CONDENSATION", ":", m_do_condensation); - writelog("\n{:21}{:2}{}", "COAGULATION", ":", m_do_coagulation); - writelog("\n{:21}{:2}{}", "SURFACE GROWTH", ":", m_do_sg); - writelog("\n{:21}{:2}{}", "OXIDATION", ":", m_do_oxidation); - if (m_do_sg || m_do_oxidation){ - writelog("\n{:21}{:2}", "HACA MODEL", ":"); - if (m_haca_model == 1){ - writelog("Mauss"); - }else if (m_haca_model == 2){ - writelog("Blanquart"); - }else if (m_haca_model == 3){ - writelog("Kazakov"); - writelog("\n{:21}{:2}{}{:2}", "-> Flame temperature", ":", kazakovTad, " K"); - } - } - writelog("\n{:21}{:2}{}", "RADIATIVE HEAT LOSSES", ":", m_do_soot_radiation); - writelog("\n{:21}{:2}{}", "SORET EFFECT", ":", m_do_soot_soret); - writeline('=', 103, false, true); - writelog("\n"); -} -void StFlow::showSootSections(){ - //---------------------------------------------------- - // Displays section informations - //---------------------------------------------------- - - if (m_nsoot <= 0){ - writelog ("\nSOOT INFO : no sections to show :("); - return; - } - writelog("\n{:=^36}{:30}{:=^37}", "", "SOOT SECTIONS INFO (SI UNITS)", ""); - writelog("\n Section Vol. min. Vol. mean Vol. max. Diam. mean Diam. coll"); - writeline('-', 103, false, true); - for (size_t k = 0; k < m_nsoot; k++) { - writelog("\n {:10d} {:10.4g} {:10.4g} {:10.4g} {:10.4g} {:10.4g}", - k,vSectMin[k],vSectMean[k],vSectMax[k],dSectMean[k],dSectCol[k]); - } - writeline('=', 103, false, true); - writelog("\n"); -} - -void StFlow::sootSource(const double* x, size_t j) { - //---------------------------------------------------- - // Computes soot source terms - //---------------------------------------------------- - // Dimerization - sootDimerization(x,j); - // Nucleation - sootNucleation(x,j); - // Condensation - if (m_do_condensation){sootCondensation(x,j);} - // Coagulation - if (m_do_coagulation){sootCoagulation(x,j);} - // Surface chemistry - if (m_do_sg || m_do_oxidation){sootSurface(x,j);} -} - -void StFlow::sootDimerization(const double* x, size_t j){ - //---------------------------------------------------- - // Computes dimerization source term - //---------------------------------------------------- - double omega = 0, c_dimer = 0; - double V_k, d2_k, omega_k, C_k, gamma_k, k_k; - for (size_t k = 0; k < n_PAH; k++){ - // PAH volume [m3] - V_k = n_C[k] * V_C2 / 2.0; - // Squared PAH diameter [m2] - d2_k = pow(6.0 * V_k / Pi, 2.0/3.0); - // PAH concentraiton [kmol/m3] - C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; - // PAH sticking coefficient [-] - gamma_k = Cn_cst * pow(W_PAH[k], 4.0); - // Reaction rate constant [m3/kmol/s] - k_k = sqrt(4.0 * Pi * Boltzmann * T(x,j) / (W_C * n_C[k] / Avogadro)) * d2_k * Avogadro; - // PAH dimerization reaction rate [kmol/m3/s] - omega_k = gamma_k * k_k * pow(C_k, 2.0); - // PAH consumption [kmol/m3/s] (x2 because 2 mol PAH -> 1 mol dimer) - sootConsumption[m_precursors[k]] = 2 * omega_k; - // Adds PAH contribution to overall local dimerization rate - omega += omega_k; - // Adds PAH contribution to overall dimer carbon atoms - c_dimer += omega_k * n_C[k]; - - } - // Overall dimerization rate [1/kg/s] - r_dimer = omega * Avogadro / m_rho[j]; - // Overall dimer volume [m3] - V_dimer = c_dimer * V_C2 / omega; - - // double K00 = 0, cdimer = 0; - // double V_k, d_k, kdimfwd_k, K00_k, C_k; - // for (size_t k = 0; k < n_PAH; k++){ - // // PAH volume [m3] - // V_k = n_C[k] * V_C2 / 2.0; - // // PAH diameter [m] - // d_k = pow(6.0 * V_k / Pi, 1.0/3.0); - // // PAH concentraiton [mol/m3] - // C_k = m_rho[j] * Y(x,m_precursors[k],j) / W_PAH[k]; - // // m6/s/kg/mol2 - // kdimfwd_k = Cn_cst * pow(W_PAH[k], 4.0) / m_rho[j] - // * sqrt((4.0 * Pi * Boltzmann * T(x,j)) / ((W_C / Avogadro) * n_C[k])) - // * pow(d_k, 2.0) * pow(Avogadro, 2.0) ; - // // (mol.g^(-1).s^(-1)) - // K00_k = pow(C_k, 2.0) * kdimfwd_k / Avogadro; - // // (mol.g^(-1).s^(-1)) - // K00 += K00_k; - // cdimer += K00_k * n_C[k]; - // // Precursor consumption (mol/m3/s) - // // (x2 because 2 mol PAH -> 1 mol dimer) - // sootConsumption[m_precursors[k]] = 2 * K00_k * m_rho[j]; - // } - // // Dimerization rate [1/kg/s] - // r_dimer = K00 * Avogadro; - // // Equivalent dimer volume [m3] - // V_dimer = cdimer * V_C2 / K00; -} - -void StFlow::sootNucleation(const double* x, size_t j){ - //---------------------------------------------------- - // Compute nucleation source terms - //---------------------------------------------------- - // [m(11/2)/s/kg] - beta_fm = sqrt(Pi * Boltzmann * T(x,j) - / (rho_soot * 2.0)) / m_rho[j]; - // Dimer collision frequency [m6/s/kg] - beta_dimer = eps_nucl * beta_fm * sqrt(2.0 / V_dimer) - * pow (2.0 * pow(6.0 * V_dimer / Pi, 1.0 / 3.0), 2.0); - // // Dimer particle density [1/m3] - // N_dimer = sqrt((r_dimer / beta_dimer)); - // // Source term for nucleation [m3/kg/s] - // m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer, 2.0); - - // Dimer diameter [m] - double d_dimer = 2.0 * pow(3.0 * V_dimer / (4.0 * Pi), 1.0/3.0); - // Dimer mass [kg] - double m_dimer = V_dimer * rho_soot; - // Reaction rate constant [m3/kmol/s] - // k_nuc = beta_dimer * m_rho[j] * Avogadro / 2 - double k_nuc = eps_nucl * Avogadro * pow(d_dimer, 2.0) - * sqrt(4.0 * Pi * Boltzmann * T(x, j) / m_dimer); - // Dimer concentration (QSS Assumption) [kmol/m3] - double C_dimer = sqrt((r_dimer / Avogadro * m_rho[j]) / (2.0 * k_nuc)); - // Dimer number concentration [1/m3] - N_dimer = C_dimer * Avogadro; - // Nucleation reaction rate [kmol/m3/s] - double omega_nuc = k_nuc * pow(C_dimer, 2.0); - // Nucleation rate [m3/kg/s] - m_qdotNucleation[j] = omega_nuc * Avogadro * V_dimer / m_rho[j] * 2.0; - -} - -void StFlow::sootCondensation(const double* x, size_t j){ - //---------------------------------------------------- - // Compute condensation source term and corrects - // nucleation source term - //---------------------------------------------------- - - double kCond = 0; - double interval, vmoy, term1, term2, term3; - vector beta_cond(m_nsoot,0.0); - for (size_t k = 0; k < m_nsoot; k++){ - // Condensation collision kernel[m6/s/kg] - beta_cond[k] = eps_cond * beta_fm * sqrt(1.0/vSectMean[k]+1.0/V_dimer) - * pow(dSectCol[k] + pow(6.0 / Pi * V_dimer, 1.0/3.0), 2.0); - // Collisional frequency between a dimer and any soot particle [m3/s/kg] - kCond += beta_cond[k] * (q[k] * (vSectMax[k] - vSectMin[k]) / (vSectMean[k])); - } - // Correction of dimer density and nucleation source term - N_dimer = - (kCond / (2.0 * beta_dimer)) - + sqrt((r_dimer / beta_dimer) - + pow(kCond / (2.0 * beta_dimer),2.0)); - // Nucleation source term [m3/kg/1] - m_qdotNucleation[j] = V_dimer * beta_dimer * pow(N_dimer,2.0); - - // Condensation source terms - for (size_t k = 0; k < m_nsoot; k++){ - interval = (vSectMax[k] - V_dimer) - vSectMin[k]; - vmoy = ((vSectMax[k] - V_dimer) + vSectMin[k]) / 2; - term1 = N_dimer * beta_cond[k] * q[k] / vmoy * V_dimer * interval; - if ( k==0 ){ - term2 = 0.0; - term3 = 0.0; - }else{ - interval = vSectMax[k-1] - (vSectMax[k-1] - V_dimer); - vmoy = (vSectMax[k-1] + (vSectMax[k-1] - V_dimer)) / 2; - term2 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * V_dimer * interval; - term3 = N_dimer * beta_cond[k-1] * q[k-1] / vmoy * vmoy * interval; - } - m_qdotCondensation(k,j) = term1 + term2 + term3; - if ( k>0 ){ - m_qdotCondensation(k-1,j) -= term3; - } - } -} - - -void StFlow::sootCoagulation(const double* x, size_t j){ - //---------------------------------------------------- - // Compute coagulation source terms - //---------------------------------------------------- - - for (size_t k = 0; k < m_nsoot; k++){ - m_qdotCoagulation(k,j) = 0.0; - } - // Viscosity (Cantera) [Pa.s-1] [CLEAN BUT SLOW] - // setGas(x,j); - // double visc = m_trans->viscosity(); - // Viscosity (Sutherland, air) [Pa.s-1] [TRASH BUT QUICK] - double visc = Csut1 * pow(T(x,j),1.5) / (T(x,j) + Csut2); - // Mean free path [m] - double mfp_rod = Boltzmann * T(x,j) / (sqrt(2.0) * Pi * pow(d_gaz,2.0) * m_press); - double mfp_tha = 66.4e-7 * (101325. / m_press) * (T(x,j) / 293.) * (1. + 110./293.) / (1 + 110. / T(x,j)); - double beta_coag_lk = 0.0; - for (size_t k = 0; k < m_nsoot; k++){ - for (size_t l = k; l < m_nsoot; l++){ - if (m_collision_model == "rodrigues" || m_collision_model == "sphere"){ - //Cunnningham numbers [-] - double Cu_k = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[k]; - double Cu_l = 1 + 1.257 * 2.0 * mfp_rod / dSectCol[l]; - // Coagulation rate in continuous regime [m^6.kg^(-1).s-(-1)] - double beta_cont_lk = (2.0 * Boltzmann * T(x,j)) / (3.0 * visc) - * (dSectCol[l] + dSectCol[k]) - * (Cu_l / dSectCol[l] + Cu_k / dSectCol[k]) - / m_rho[j]; - // Coagulation rate in free molecular regime [m^6.kg^(-1).s-(-1)] - double beta_fm_lk = eps_coag * beta_fm - * sqrt(1 / vSectMean[k] + 1 / vSectMean[l]) - * pow(dSectCol[k] + dSectCol[l], 2.0); - // Overall coagulation rate [m^6.kg^(-1).s-(-1)] - beta_coag_lk = (beta_fm_lk * beta_cont_lk) - / (beta_fm_lk + beta_cont_lk); - }else if (m_collision_model == "thajudeen"){ - double reduced_mass = rho_soot * vSectMean[k] * vSectMean[l] / (vSectMean[k] + vSectMean[l]); - double smoluchowski_radius = rNucMean[k] * (1.203 - (0.4315*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])) * pow(rSectCol[k]/rNucMean[k] + rSectCol[l]/rNucMean[k], 0.8806 + (0.3497*(nNucMean[k] + nNucMean[l]))/(nNucMean[k]*Dfractal[k] + nNucMean[l]*Dfractal[l])); - double kn_diff_k = mfp_tha * Pi * rSectCol[k] / aSectCol[k]; - double kn_diff_l = mfp_tha * Pi * rSectCol[l] / aSectCol[l]; - double f_k = (6.0 * Pi * rSectCol[k] * visc) / (1 + kn_diff_k * (1.257 + 0.4 * exp(-1.1/kn_diff_k))); - double f_l = (6.0 * Pi * rSectCol[l] * visc) / (1 + kn_diff_l * (1.257 + 0.4 * exp(-1.1/kn_diff_l))); - double friction_coefficient = f_k * f_l / (f_k + f_l); - double projected_area = pow(smoluchowski_radius, 2.0) * Pi; - double kn_diff = (sqrt(Boltzmann * T(x,j) * reduced_mass) * Pi * smoluchowski_radius) / (friction_coefficient * projected_area); - double H = (4.0 * Pi * pow(kn_diff, 2.0) + 25.836 * pow(kn_diff, 3.0) + eps_coag * sqrt(8.0 * Pi) * 11.211 * pow(kn_diff, 4.0)) / (1 + 3.502 * kn_diff + 7.211 * pow(kn_diff, 2.0) + 11.211 * pow(kn_diff, 3.0)); - beta_coag_lk = (H * friction_coefficient * pow(projected_area, 2.0)) / (reduced_mass * pow(Pi, 2.0) * smoluchowski_radius) / m_rho[j]; - } - // Section of the particle corresponding to the coagulation of (l,k)y - size_t m = collision_mat(k,l); - // Loss of mass in section l due to coagulation with k - double terml = beta_coag_lk * q[l] * q[k] / vSectMean[k] - * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); - // Loss of mass in section k due to coagulation with l - double termk = beta_coag_lk * q[l] * q[k] / vSectMean[l] - * (vSectMax[l] - vSectMin[l]) * (vSectMax[k] - vSectMin[k]); - double termm, termmplus; - // Gain in mass in m and m+1 thanks to coagulation of (l,k) - if (vSectMax[l] + vSectMax[k] <= vSectMax[m]){ - termm = terml + termk; - termmplus = 0.0; - }else{ - termm = (terml + termk) - * (vSectMax[m] - (vSectMin[k] + vSectMin[l])) - / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); - termmplus = (terml + termk) - * (vSectMax[k]+vSectMax[l]-vSectMax[m]) - / (vSectMax[k]+vSectMax[l]-vSectMin[k]-vSectMin[l]); - } - if (m < m_nsoot-1){ - m_qdotCoagulation(m+1,j) += termmplus; - }else{ - termm = terml + termk; - } - m_qdotCoagulation(m,j) += termm; - m_qdotCoagulation(l,j) -= terml; - m_qdotCoagulation(k,j) -= termk; - } - } -} - -void StFlow::updateSootDiffFluxes(const double* x, size_t j0, size_t j1) -{ - //---------------------------------------------------- - // Computes soot molecular and thermal diffusion fluxes - //---------------------------------------------------- - for (size_t j = j0; j < j1; j++) { - // Evaluate gas at midpoints : j->j+1/2 - double Tmid = 0.5 * (T(x,j)+T(x,j+1)); - // [CLEAN BUT SLOW] - // setGasAtMidpoint(x,j); - // double wtm = m_thermo->meanMolecularWeight(); - // double rho = m_thermo->density(); - // double visco = m_trans->viscosity(); - // [TRASH BUT QUICK] - double wtm = 0.5*(m_wtm[j]+m_wtm[j+1]); - double rho = 0.5*(m_rho[j]+m_rho[j+1]); - double visco = Csut1 * pow(Tmid,1.5) / (Tmid + Csut2); - // Evaluate centered differencies at j+1/2 - double dT = T(x,j+1)-T(x,j); - double dz = z(j+1) - z(j); - // Evaluate viscosity - for (size_t k = 0; k < m_nsoot; k++){ - // Evaluate soot mass fraction at j+1/2 - - double Ysmid = 0.5 * (Ys(x,k,j)+Ys(x,k,j+1)); - // Evaluate centered differencies at j+1/2 - double dYs = Ys(x,k,j+1) - Ys(x,k,j); - //Evaluate diffusion coefficient at j+1/2 - double Ds = 3 / (2 * rho_soot * pow(dSectMean[k], 2.0) - * (1 + alphaT * Pi / 8)) - * sqrt ((wtm*Boltzmann*Tmid)/(2*Pi*Avogadro)); - // Evaluate soot mass diffusion flux at j+1/2 - m_soot_diff(k,j) = rho * Ds * dYs/dz; - // Evaluate soot mass soret flux at j+1/2 - if (m_do_soot_soret){ - m_soot_soret(k,j) = C_soot_soret * visco * Ysmid * dT/dz / Tmid; - } - } - } -} - -void StFlow::sootSurface(const double* x, size_t j){ - //---------------------------------------------------- - // Compute surface chemistry source terms - //---------------------------------------------------- - - // Computes reaction rates - sootSurfaceInitialization(x,j); - double term1, term2, term3; - //--------------- - // SURFACE GROWTH - //--------------- - if (m_do_sg){ - for (size_t k = 0; k < m_nsoot; k++){ - term1 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] - * (vmaxmc2_mpower[k] - vmin_mpower[k]); - if (k==0){ - term2 = 0.0; - term3 = 0.0; - }else{ - term2 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powervect[k-1] / mpower[k-1] * q[k-1] - * (vmax_mpower[k-1] - vmaxmc2_mpower[k-1]); - term3 = n_sites * alpha_surf * ksg / m_rho[j] * vc2powermvect[k-1] / kpower[k-1] * q[k-1] - * (vmax_kpower[k-1] - vmaxmc2_kpower[k-1]); - } - // Surface growth source term [m3/kg/s] - m_qdotSg(k,j) = term1 + term2 + term3; - if (k > 0){m_qdotSg(k-1,j) -= term3;} - } - } - //---------- - // OXYDATION - //---------- - if (m_do_oxidation){ - for (size_t k=m_nsoot; k --> 0;){ - term1 = alpha_surf * kox / m_rho[j] * vc2powervect[k] / mpower[k] * q[k] - * (vmax_mpower[k] - vminpc2_mpower[k]); - if (k==m_nsoot-1){ - term2 = 0.0; - term3 = 0.0; - }else if (k==m_nsoot-2 && m_trash_section) { - term2 = 0.0; - term3 = 0.0; - }else{ - term2 = alpha_surf * kox / m_rho[j] * vc2powervect[k+1] / mpower[k+1] * q[k+1] - * (vminpc2_mpower[k+1] - vmin_mpower[k+1]); - term3 = alpha_surf * kox / m_rho[j] * vc2powermvect[k+1] / kpower[k+1] * q[k+1] - * (vminpc2_kpower[k+1] - vmin_kpower[k+1]); - } - // Oxidation source term [m3/kg/s] - m_qdotOxidation(k,j) = - (term1 + term2 - term3); - if (k < m_nsoot - 1){ - m_qdotOxidation(k+1,j) -= term3; - } - } - } -} - -void StFlow::sootSurfaceInitialization(const double* x, size_t j){ - // Recover species concentrations [kmol/m3] - double conc_H = 0, conc_H2 = 0, conc_OH = 0, conc_H2O = 0, conc_C2H2 = 0, conc_O2 = 0; - double k01f = 0, k01b = 0, k02f = 0, k02b = 0, k03f = 0, k03b = 0, k04f = 0, k04b = 0; - double k05f = 0, k05b = 0, k06f = 0, k06bisf = 0; - double r01f = 0, r01b = 0, r02f = 0, r02b = 0, r03f = 0, r03b = 0, r04f = 0, r04b = 0; - double r05f = 0, r05b = 0, r06f = 0, r06bisf = 0, r07f = 0; - double ko2, koh, kd, krev, chi, chip, chic, alpha_kazakov; - size_t k; - // Recover molar concentrations - k = m_thermo->speciesIndex("H"); - if (k != npos){conc_H = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("H2"); - if (k != npos){conc_H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("H2O"); - if (k != npos){conc_H2O = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("C2H2"); - if (k != npos){conc_C2H2 = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("O2"); - if (k != npos){conc_O2 = Y(x,k,j) * m_rho[j] / m_wt[k];} - k = m_thermo->speciesIndex("OH"); - if (k != npos){conc_OH = Y(x,k,j) * m_rho[j] / m_wt[k];} - // SI units - double slt = 1.0e3 / GasConstant / T(x,j); // 1e3 because GasConstant in J/kmol/K - double T_log=log(T(x,j)); - if (m_haca_model == 1 || m_haca_model == 11){ //Mauss - // Arrhenius constants - k01f = ak01f * exp(nk01f*T_log - ek01f*slt); // [m3/kmol/s] - k01b = ak01b * exp(nk01b*T_log - ek01b*slt); // [m3/kmol/s] - k02f = ak02f * exp(nk02f*T_log - ek02f*slt); // [m3/kmol/s] - k02b = ak02b * exp(nk02b*T_log - ek02b*slt); // [m3/kmol/s] - k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [m3/kmol/s] - k03b = ak03b * exp(nk03b*T_log - ek03b*slt); // [1/s] - k04f = ak04f * exp(nk04f*T_log - ek04f*slt); // [m3/kmol/s] - k04b = ak04b * exp(nk04b*T_log - ek04b*slt); // [1/s] - k05f = ak05f * exp(nk05f*T_log - ek05f*slt); // [1/s] - k05b = ak05b * exp(nk05b*T_log - ek05b*slt); // [m3/kmol/s] - k06f = ak06f * exp(nk06f*T_log - ek06f*slt); // [m3/kmol/s] - k06bisf = k06f; - // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] - r01f = k01f * conc_H; - r01b = k01b * conc_H2; - r02f = k02f * conc_OH; - r02b = k02b * conc_H2O; - r03f = k03f * conc_H; - r03b = k03b; - r04f = k04f * conc_C2H2; - r04b = k04b; - r05f = k05f; - r05b = k05b * conc_H; - r06f = k06f * conc_O2; - r06bisf = k06bisf * conc_O2; - r07f = Avogadro * S_C2 * gamma_oh * conc_OH * - pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); - // From QSS [-] - double fk10 = r05f / (r04b+r06bisf+r05f); - double A_QSS = (r01f + r02f + r03b + r07f + r05b * (1.0 - fk10)) / (r01b + r02b + r03f + r04f * fk10); - double B_QSS = r04f / ( r04b + r06bisf + r05f); - double D_QSS = r05b / (r04b + r06f + r05f); - - chi = 1.0; - chip = chi * A_QSS; - chic = chi * (A_QSS*B_QSS + D_QSS); - // Partial reaction rates[1/s] - koh = r07f * chi; - kd = r04f * chip; - ko2 = r06f * (chip + chic); - krev = r04b * chic; - // Partial surface growth and oxidation rates [1/s] - ksg = kd - krev; - kox = ko2 + koh; - } else if (m_haca_model == 2){ //Blanquart - // Arrhenius constants [m3/kmol/s] - k01f = ak01f * exp(nk01f*T_log - ek01f*slt); - k01b = ak01b * exp(nk01b*T_log - ek01b*slt); - k02f = ak02f * exp(nk02f*T_log - ek02f*slt); - k02b = ak02b * exp(nk02b*T_log - ek02b*slt); - k03f = ak03f * exp(nk03f*T_log - ek03f*slt); // [1/s] - k03b = ak03b * exp(nk03b*T_log - ek03b*slt); - k04f = ak04f * exp(nk04f*T_log - ek04f*slt); - k05f = ak05f * exp(nk05f*T_log - ek05f*slt); - // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] - r01f = k01f * conc_H; - r01b = k01b * conc_H2; - r02f = k02f * conc_OH; - r02b = k02b * conc_H2O; - r03f = k03f; - r03b = k03b * conc_H; - r04f = k04f * conc_C2H2; - r05f = k05f * conc_O2; - r06f = Avogadro * S_C2 * gamma_oh * conc_OH * - pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); - // From QSS [-] - chi = (r01f + r02f + r03f) / (r01b + r02b + r03b + r04f + r05f); // * 1.7e15; - // Oxidation O2 [must be 1/s] - ko2 = chi * r05f; - // Oxidation OH [1/s] - koh = r06f * chi; - // Oxidation - kox = ko2 + koh; - // Surface growth [1/s] - ksg = chi * r04f; - } else if (m_haca_model == 3){ //Kazakov - // Fraction of sites available at the surface of the particle for reaction [-] - alpha_kazakov = (1.0 + tanh(8.168e3/kazakovTad - 4.57)) / 2.0; - // Arrhenius constants [m3/kmol/s] - k01f = ak01f * exp(nk01f*T_log - ek01f*slt); - k01b = ak01b * exp(nk01b*T_log - ek01b*slt); - k02f = ak02f * exp(nk02f*T_log - ek02f*slt); - k03f = ak03f * exp(nk03f*T_log - ek03f*slt); - k04f = ak04f * exp(nk04f*T_log - ek04f*slt); - // Partial (soot or soot radical concentration not accounted) surface chemistry reaction rates [1/s] - r01f = k01f * conc_H; - r01b = k01b * conc_H2; - r02f = k02f * conc_H; - r03f = k03f * conc_C2H2; - r04f = k04f * conc_O2; - r05f = Avogadro * S_C2 * gamma_oh * conc_OH * - pow(GasConstant * T(x,j)/(2* Pi * m_wt[k]), 0.5); - // From QSS [-] - chi = r01f / (r01b + r02f + r03f + r04f); // * 2.3e14 - // Oxidation O2 [1/s] - ko2 = alpha_kazakov * chi * r04f; - // Oxidation OH [1/s] - koh = r05f * chi; - //Oxidation [1/s] - kox = ko2 + koh; - // Surface growth [1/s] - ksg = alpha_kazakov * chi * r03f; - } - //------------------------- - // RETROACTION ON GAS PHASE - //------------------------- - if (m_do_retroaction){ - double deltaQ = 0.0, soot_surface = 0.0; - for (size_t k = 0; k < m_nsoot; k++){ - deltaQ += vc2powervect[k] / mpower[k] * q[k] * (vmax_mpower[k]-vmin_mpower[k]); - } - //Overall active sites concentration [kmol/m3] - soot_surface = alpha_surf * n_sites * deltaQ / (V_C2 * Avogadro); // n_sites added here - // Surface chemistry reaction rates [kmol/s/m3] - double w01f = 0, w01b = 0, w02f = 0, w02b = 0, w03f = 0, w03b = 0; - double w04f = 0, w04b = 0, w05f = 0, w05b = 0, w06f = 0, w06bisf = 0; - double w07f = 0; - if (m_do_sg || m_do_oxidation){ - // Reaction rates for reactions occuring on both oxidation & surface growth - if (m_haca_model == 1){ - w01f = r01f * soot_surface * chi; - w01b = r01b * soot_surface * chip; - w02f = r02f * soot_surface * chi; - w02b = r02b * soot_surface * chip; - w03f = r03f * soot_surface * chip; - w03b = r03b * soot_surface * chi; - w05f = r05f * soot_surface * chic; - w05b = r05b * soot_surface * chi; - w06bisf = r06bisf * soot_surface * chic; - }else if (m_haca_model == 2){ - w01f = r01f * soot_surface * chi; - w01b = r01b * soot_surface * chi; - w02f = r02f * soot_surface * chi; - w02b = r02b * soot_surface * chi; - w03f = r03f * soot_surface * chi; - w03b = r03b * soot_surface * chi; - }else if (m_haca_model == 3){ - w01f = r01f * soot_surface * chi; - w01b = r01b * soot_surface * chi; - w02f = r02f * soot_surface * chi; - } - } - // Reaction rates for reactions occuring on surfacce growth only - if (m_do_sg){ - if (m_haca_model == 1){ - w04f = r04f * soot_surface * chip; - w04b = r04b * soot_surface * chic; - }else if (m_haca_model == 2){ - w04f = r04f * soot_surface * chi; - }else if (m_haca_model == 3){ - w03f = r03f * soot_surface * chi; - } - } - // Reaction rates for reactions occuring on oxidation only - if (m_do_oxidation){ - if (m_haca_model == 1){ - // Reaction rates [kmol/m3/s] - w06f = r06f * soot_surface * chip; - w07f = r07f * soot_surface * chi; - }else if (m_haca_model == 2){ - w05f = r05f * soot_surface * chi; - w06f = r06f * soot_surface * chi; - }else if (m_haca_model == 3){ - w04f = r04f * soot_surface * chi; - w05f = r05f * soot_surface * chi; - } - } - - // Gaseous species consumption [kmol/s/m3] - if (m_haca_model == 1){ - k = m_thermo->speciesIndex("H"); - if (k != npos){sootConsumption[k] = - (w01f - w01b) - (w03f - w03b) + (w05f - w05b);} - k = m_thermo->speciesIndex("C2H2"); - if (k != npos){sootConsumption[k] = (w04f - w04b);} - k = m_thermo->speciesIndex("H2"); - if (k != npos){sootConsumption[k] = (w01f - w01b);} - k = m_thermo->speciesIndex("O2"); - if (k != npos){sootConsumption[k] = - w06f - w06bisf;} - k = m_thermo->speciesIndex("CO"); - if (k != npos){sootConsumption[k] = 2.0 * w06f;} - k = m_thermo->speciesIndex("OH"); - if (k != npos){sootConsumption[k] = - (w02f - w02b) - w07f;} - k = m_thermo->speciesIndex("H2O"); - if (k != npos){sootConsumption[k] = + (w02f - w02b);} - k = m_thermo->speciesIndex("HCO"); - if (k != npos){sootConsumption[k] = 2.0 * w06bisf + w07f;} - k = m_thermo->speciesIndex("CH"); - if (k != npos){sootConsumption[k] = w07f;} - }else if (m_haca_model == 2){ - k = m_thermo->speciesIndex("H"); - if (k != npos){sootConsumption[k] = -(w01f-w01b) + (w03f-w03b) + w04f;} - k = m_thermo->speciesIndex("C2H2"); - if (k != npos){sootConsumption[k] = -w04f;} - k = m_thermo->speciesIndex("H2"); - if (k != npos){sootConsumption[k] = (w01f-w01b) + w05f + w06f;} - k = m_thermo->speciesIndex("O2"); - if (k != npos){sootConsumption[k] = -w05f;} - k = m_thermo->speciesIndex("CO"); - if (k != npos){sootConsumption[k] = 2.0 * w05f + w06f;} - k = m_thermo->speciesIndex("OH"); - if (k != npos){sootConsumption[k] = -(w02f-w02b) - w06f;} - k = m_thermo->speciesIndex("H2O"); - if (k != npos){sootConsumption[k] = (w02f-w02b);} - }else if (m_haca_model == 3){ - k = m_thermo->speciesIndex("H"); - if (k != npos){sootConsumption[k] = -(w01f-w01b) - w02f + w03f;} - k = m_thermo->speciesIndex("C2H2"); - if (k != npos){sootConsumption[k] = -w03f;} - k = m_thermo->speciesIndex("H2"); - if (k != npos){sootConsumption[k] = (w01f-w01b) + w05f;} - k = m_thermo->speciesIndex("O2"); - if (k != npos){sootConsumption[k] = -w04f;} - k = m_thermo->speciesIndex("CO"); - if (k != npos){sootConsumption[k] = 2.0 * w04f + w05f;} - k = m_thermo->speciesIndex("OH"); - if (k != npos){sootConsumption[k] = - w05f;} - } - } -} - -void StFlow::getDistributionOrdre0(const double* x, size_t j){ - for (size_t k = 0; k < m_nsoot; k++){ - // Soot volume fraction density [1/m3] - q[k] = m_rho[j] * Ys(x,k,j) / (rho_soot * (vSectMax[k] - vSectMin[k])); - } -} -//-----------------------------// -// END OF SOOT RELATED METHODS // -//-----------------------------// - -void StFlow::evalRightBoundary(double* x, double* rsd, int* diag, double rdt) -{ - size_t j = m_points - 1; - AVBPcompute_local_thick(x,j); - double thick_prev = avbp_thick[j-1]; - - // the boundary object connected to the right of this one may modify or - // replace these equations. The default boundary conditions are zero u, V, - // and T, and zero diffusive flux for all species. - - rsd[index(c_offset_V,j)] = V(x,j); - diag[index(c_offset_V,j)] = 0; - double sum = 0.0; - // set residual of poisson's equ to zero - rsd[index(c_offset_E, j)] = x[index(c_offset_E, j)]; - if (m_nsoot > 0){ - for (size_t k = 0; k < m_nsoot; k++){ - if (m_do_retroaction){sum += Ys(x,k,j);} - rsd[index(c_offset_S + k, j)] = - m_soot_diff(k,j-1) + rho_u(x,j)*Ys(x,k,j); - } - } - for (size_t k = 0; k < m_nsp; k++) { - sum += Y(x,k,j); - rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1)*thick_prev + rho_u(x,j)*Y(x,k,j); -// no thick rsd[index(k+c_offset_Y,j)] = m_flux(k,j-1) + rho_u(x,j)*Y(x,k,j); - } - rsd[index(c_offset_Y + rightExcessSpecies(), j)] = 1.0 - sum; - diag[index(c_offset_Y + rightExcessSpecies(), j)] = 0; - if (m_usesLambda) { - rsd[index(c_offset_U, j)] = rho_u(x, j); - } else { - rsd[index(c_offset_U, j)] = rho_u(x, j) - rho_u(x, j-1); - } - - rsd[index(c_offset_L, j)] = lambda(x, j) - lambda(x, j-1); - diag[index(c_offset_L, j)] = 0; - rsd[index(c_offset_T, j)] = T(x, j); -} - -void StFlow::evalContinuity(size_t j, double* x, double* rsd, int* diag, double rdt) -{ - //algebraic constraint - diag[index(c_offset_U, j)] = 0; - //---------------------------------------------- - // Continuity equation - // - // d(\rho u)/dz + 2\rho V = 0 - //---------------------------------------------- - if (m_usesLambda) { - // Note that this propagates the mass flow rate information to the left - // (j+1 -> j) from the value specified at the right boundary. The - // lambda information propagates in the opposite direction. - rsd[index(c_offset_U,j)] = - -(rho_u(x,j+1) - rho_u(x,j))/m_dz[j] - -(density(j+1)*V(x,j+1) + density(j)*V(x,j)); - } else if (m_isFree) { - // terms involving V are zero as V=0 by definition - if (grid(j) > m_zfixed) { - rsd[index(c_offset_U,j)] = - - (rho_u(x,j) - rho_u(x,j-1))/m_dz[j-1]; - } else if (grid(j) == m_zfixed) { - if (m_do_energy[j]) { - rsd[index(c_offset_U,j)] = (T(x,j) - m_tfixed); - } else { - rsd[index(c_offset_U,j)] = (rho_u(x,j) - - m_rho[0]*0.3); // why 0.3? - } - } else if (grid(j) < m_zfixed) { - rsd[index(c_offset_U,j)] = - - (rho_u(x,j+1) - rho_u(x,j))/m_dz[j]; - } - } else { - // unstrained with fixed mass flow rate - rsd[index(c_offset_U, j)] = rho_u(x, j) - rho_u(x, j - 1); - } -} - -void StFlow::grad_hk(const double* x, size_t j) -{ - for(size_t k = 0; k < m_nsp; k++) { - if (u(x, j) > 0.0) { - m_dhk_dz(k,j) = (m_hk(k,j) - m_hk(k,j-1)) / m_dz[j - 1]; - } - else { - m_dhk_dz(k,j) = (m_hk(k,j+1) - m_hk(k,j)) / m_dz[j]; - } - } -} - -} // namespace From 64fd9a1b7ce9917aecd94a13a75711e0fa5f3530 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 9 Jul 2025 17:38:22 +0200 Subject: [PATCH 32/98] Change stflow_solveEnergyEqn to flow1D_solveEnergyEqn because stflow.* files has benn removed Changes to be committed: modified: ../../../test/clib/test_ctonedim.cpp --- test/clib/test_ctonedim.cpp | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/clib/test_ctonedim.cpp b/test/clib/test_ctonedim.cpp index 9462e4861b8..d416562c6c7 100644 --- a/test/clib/test_ctonedim.cpp +++ b/test/clib/test_ctonedim.cpp @@ -182,7 +182,7 @@ TEST(ctonedim, freeflame) sim1D_setFixedTemperature(flame, 0.85 * T + .15 * Tad); // solve and save - stflow_solveEnergyEqn(flow, 1); + flow1D_solveEnergyEqn(flow, 1); const char* refine_grid = "disabled"; int loglevel = 0; sim1D_solve(flame, loglevel, refine_grid); From 3d9059375c4c485ce258ecd59a3d2e9be504d8b9 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 9 Jul 2025 17:39:46 +0200 Subject: [PATCH 33/98] Remove grid variable that is deprecated (changed by z) + add missing declarations needed for remesh features Changes to be committed: modified: ../../../include/cantera/oneD/Domain1D.h modified: ../../../src/oneD/Sim1D.cpp --- include/cantera/oneD/Domain1D.h | 4 ++-- src/oneD/Sim1D.cpp | 34 ++++++++++++++++----------------- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/include/cantera/oneD/Domain1D.h b/include/cantera/oneD/Domain1D.h index ca4fe03a485..01d5aa8c30e 100644 --- a/include/cantera/oneD/Domain1D.h +++ b/include/cantera/oneD/Domain1D.h @@ -517,12 +517,12 @@ class Domain1D void setProfile(const string& name, double* values, double* soln); //! Access the array of grid coordinates [m] - vector& grid() { + vector& z() { return m_z; } //! Access the array of grid coordinates [m] - const vector& grid() const { + const vector& z() const { return m_z; } diff --git a/src/oneD/Sim1D.cpp b/src/oneD/Sim1D.cpp index 7e12d5000f6..335f9131970 100644 --- a/src/oneD/Sim1D.cpp +++ b/src/oneD/Sim1D.cpp @@ -425,9 +425,9 @@ void Sim1D::solve(int loglevel, const string& refine_grid) for (size_t n = 0; n < nDomains(); n++) { Domain1D& d = domain(n); - size_t length = d.grid().size(); + size_t length = d.z().size(); - domain_size += d.grid(length-1); + domain_size += d.z(length-1); } domain_size = domain_size/2.0; @@ -609,10 +609,10 @@ int Sim1D::refine(int loglevel) Refiner& r = d.refiner(); // Save the old grid corresponding to the converged solution - m_grid_last_ss.push_back(d.grid()); + m_grid_last_ss.push_back(d.z()); // determine where new points are needed - r.analyze(d.grid().size(), d.grid().data(), m_state->data() + start(n)); + r.analyze(d.z().size(), d.z().data(), m_state->data() + start(n)); if (loglevel > 0) { r.show(); @@ -698,8 +698,8 @@ double Sim1D::remesh(int loglevel, double dist_min, double domain_size) //from M // double this_distance = r.remeshFromSolution( d.grid().size(), // d.grid().data(), &m_state[start(n)], // dist_min, domain_size ); - double this_distance = r.remeshFromSolution( d.grid().size(), - d.grid().data(), m_state->data() + start(n), + double this_distance = r.remeshFromSolution( d.z().size(), + d.z().data(), m_state->data() + start(n), dist_min, domain_size ); distance += this_distance; @@ -716,9 +716,9 @@ double Sim1D::remesh(int loglevel, double dist_min, double domain_size) //from M // interpolation if (np_new>1) { - int m_old = r.indxtp(np_old,znew_curr,d.grid().data()); - double z0_old = d.grid(m_old ); - double z1_old = d.grid(m_old+1); + int m_old = r.indxtp(np_old,znew_curr,d.z().data()); + double z0_old = d.z(m_old ); + double z1_old = d.z(m_old+1); for (size_t i = 0; i < d.nComponents(); i++) { double x0_old = value(n,i,m_old ); @@ -767,7 +767,7 @@ void Sim1D::getRatio() //from MUTAGEN Domain1D& d = domain(n); Refiner& r = d.refiner(); // r.getRatio(d.grid().size(), d.grid().data(), &m_state[start(n)]); - r.getRatio(d.grid().size(), d.grid().data(), m_state->data() + start(n)); + r.getRatio(d.z().size(), d.z().data(), m_state->data() + start(n)); } } @@ -806,7 +806,7 @@ void Sim1D::addPoint(size_t ndomain, double zpoint, vector xpoint, int l if (np_old>0) { - if (zpoint xpoint, int l for (size_t m = 0; m < np_old; m++) { // check that zpoint is not in the current grid - if (zpoint==d.grid(m)) + if (zpoint==d.z(m)) { // add new position to the znew array znew.push_back(zpoint); @@ -835,7 +835,7 @@ void Sim1D::addPoint(size_t ndomain, double zpoint, vector xpoint, int l else { // add current position to the znew array - znew.push_back(d.grid(m)); + znew.push_back(d.z(m)); // add current data to the xnew array for (size_t i = 0; i < ncomp; i++) { @@ -845,8 +845,8 @@ void Sim1D::addPoint(size_t ndomain, double zpoint, vector xpoint, int l if (m!=np_old-1) { // current and next position - double z_curr = d.grid(m ); - double z_next = d.grid(m+1); + double z_curr = d.z(m ); + double z_next = d.z(m+1); // if the new point is in the current interval if ((z_curr xpoint, int l } } - if (d.grid(np_old-1) xpoint, int l for (size_t m = 0; m < np_old; m++) { // add current position to the znew array - znew.push_back(d.grid(m)); + znew.push_back(d.z(m)); // add current data to the xnew array for (size_t i = 0; i < ncomp; i++) { From b5500fe5cb2c878eeac1fe6312f90d72c13d0c3d Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 9 Jul 2025 19:52:00 +0200 Subject: [PATCH 34/98] Bugfixes for TestOnedim.test_width_grid + avoid crashed due to cantera error message avec flamelet computation Changes to be committed: modified: interfaces/cython/cantera/onedim.py modified: src/thermo/Phase.cpp --- interfaces/cython/cantera/onedim.py | 13 ++++++++++--- src/thermo/Phase.cpp | 6 ++++-- 2 files changed, 14 insertions(+), 5 deletions(-) diff --git a/interfaces/cython/cantera/onedim.py b/interfaces/cython/cantera/onedim.py index 4bdd5cda10b..0f181ed876c 100644 --- a/interfaces/cython/cantera/onedim.py +++ b/interfaces/cython/cantera/onedim.py @@ -2129,7 +2129,7 @@ class Flamelet(FlameBase): __slots__ = ('oxidizer_inlet', 'flame', 'fuel_inlet') _other = ('grid') - def __init__(self, gas, grid=None,): + def __init__(self, gas, grid=None, width=None): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -2144,6 +2144,9 @@ def __init__(self, gas, grid=None,): ``self.oxidizer_inlet``, ``self.flame``, and ``self.fuel_inlet``. """ + if width is not None: + warnings.warn("width parameter cannot be used with Flamelets, the width is fixed to 1. This parameter is available for consistency with other FlameBase subclasses and pytest",UserWarning) + #: `Inlet1D` at the left of the domain representing the fuel mixture self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas) self.fuel_inlet.T = gas.T @@ -2155,12 +2158,16 @@ def __init__(self, gas, grid=None,): #: `FlameletFlow` domain representing the flame self.flame = FlameletFlow(gas, name='flame') + # CERFACS : This part need to be added to comply with the pytest test_width_grid::test_width_grid + if width is not None: + if grid is not None: + raise ValueError("'grid' and 'width' arguments are mutually exclusive") + if grid is None: grid = np.array([0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0]) # Note: flamelet initialisation is very sensitive to the number of grid points. # Do not hesitate to try some: experience shows that between 10 and 20 is often a good guess - - grid = grid / max(grid) # Width of the grid must anyway be 1 because in Z-space + grid = np.asarray(grid) / max(grid) # Width of the grid must anyway be 1 because in Z-space super().__init__((self.oxidizer_inlet, self.flame, self.fuel_inlet), gas, grid) diff --git a/src/thermo/Phase.cpp b/src/thermo/Phase.cpp index dc0f6a4fd36..c0987d531cf 100644 --- a/src/thermo/Phase.cpp +++ b/src/thermo/Phase.cpp @@ -846,8 +846,10 @@ void Phase::addSpeciesAlias(const string& name, const string& alias) void Phase::removeSpeciesLock() { if (!m_nSpeciesLocks) { - throw CanteraError("Phase::removeSpeciesLock", - "ThermoPhase '{}' has no current species locks.", m_name); + // throw CanteraError("Phase::removeSpeciesLock", + // "ThermoPhase '{}' has no current species locks.", m_name); + // CERFACS : crash after computation of Flamelets because cantera wants to remove the species lock that doen't exist in this case, and send an error. Then, the error message has been convert into a user warning. + warn_user("Phase::removeSpeciesLock","ThermoPhase '{}' has no current species locks.", m_name); } m_nSpeciesLocks--; } From 6e19c61f60a6426029ec0eac53860170779ec286 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 22 Jul 2025 15:57:45 +0200 Subject: [PATCH 35/98] Remove samples/python/AVBP/RESULTS directory from .gitignore Changes to be committed: modified: ../../../.gitignore --- .gitignore | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 6b392c09aa9..6d111e3fb3e 100644 --- a/.gitignore +++ b/.gitignore @@ -55,5 +55,5 @@ doc/sphinx/matlab/*.rst reduced.yaml INSTALL_DIR/ *.code-workspace -samples/python/AVBP/RESULTS/ +samples/python/AVBP/RESULTS/* test_problems/cxx_samples/flamespeed.yaml From 1936cef27a415122199efcd38462105ba85cd666 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 22 Jul 2025 16:02:41 +0200 Subject: [PATCH 36/98] Create an additional .gitignore file in samples/python/AVBP/RESULTS/ to add an empty directory RESULT to the git repository Changes to be committed: modified: .gitignore new file: samples/python/AVBP/RESULTS/.gitignore --- .gitignore | 1 - samples/python/AVBP/RESULTS/.gitignore | 4 ++++ 2 files changed, 4 insertions(+), 1 deletion(-) create mode 100644 samples/python/AVBP/RESULTS/.gitignore diff --git a/.gitignore b/.gitignore index 6d111e3fb3e..23d55771f41 100644 --- a/.gitignore +++ b/.gitignore @@ -55,5 +55,4 @@ doc/sphinx/matlab/*.rst reduced.yaml INSTALL_DIR/ *.code-workspace -samples/python/AVBP/RESULTS/* test_problems/cxx_samples/flamespeed.yaml diff --git a/samples/python/AVBP/RESULTS/.gitignore b/samples/python/AVBP/RESULTS/.gitignore new file mode 100644 index 00000000000..5e7d2734cfc --- /dev/null +++ b/samples/python/AVBP/RESULTS/.gitignore @@ -0,0 +1,4 @@ +# Ignore everything in this directory +* +# Except this file +!.gitignore From 02f4896f86f27acd5fa9f7ddf4dcf1ac02eb6c35 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 22 Jul 2025 16:51:52 +0200 Subject: [PATCH 37/98] Update the pip install in install_cantera.py script Changes to be committed: modified: install_cantera.py --- install_cantera.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/install_cantera.py b/install_cantera.py index 4245b5d93a8..96d3891a4ff 100644 --- a/install_cantera.py +++ b/install_cantera.py @@ -90,8 +90,10 @@ def execute_with_live_display(command): subprocess.call('/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"', shell=True) subprocess.call('brew install boost', shell=True) subprocess.call('brew install gcc', shell=True) - subprocess.call('pip3 install numpy --no-use-pep517', shell=True) - subprocess.call('pip3 install cython', shell=True) + #subprocess.call('pip3 install numpy --no-use-pep517', shell=True) + subprocess.call('pip3 install numpy', shell=True) + subprocess.call('pip3 install cython==3.1.1', shell=True) + subprocess.call('pip3 install packaging', shell=True) subprocess.call('pip3 install scons==3.1.2', shell=True) subprocess.call('pip3 install wheel', shell=True) subprocess.call('pip3 install ruamel.yaml', shell=True) From 5ab8cb0a321aeb8e1ffb90280d5998fa56d3ea6c Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 22 Jul 2025 16:57:33 +0200 Subject: [PATCH 38/98] Update doc for install Changes to be committed: modified: README.rst modified: install_cantera.py --- README.rst | 17 ++++++----------- install_cantera.py | 2 +- 2 files changed, 7 insertions(+), 12 deletions(-) diff --git a/README.rst b/README.rst index 0e18a057356..d82930acf87 100644 --- a/README.rst +++ b/README.rst @@ -47,28 +47,23 @@ Follow the steps below for a **local** installation: python3 -m venv env_cantera source ~/env_cantera/bin/activate -2. Install specific python packages:: - - pip install numpy==1.26.4 - pip install scipy==1.13 - -3. (optional) Create an alias to load ``env_cantera``:: +2. (optional) Create an alias to load ``env_cantera``:: echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.zshrc source ~/.zshrc -4. Navigate to the Cantera directory:: +3. Navigate to the Cantera directory:: cd /Users/$USER/Documents/cantera-avbp -5. Switch to the right branch and run the installation script:: +4. Switch to the right branch and run the installation script:: git checkout dev_cantera-avbp python3 install_cantera.py -6. When prompted about NFS, answer ``no``. -7. Wait for the compilation and installation process to complete successfully. +5. When prompted about NFS, answer ``no``. +6. Wait for the compilation and installation process to complete successfully. If everything goes well, you should see the following message:: @@ -76,7 +71,7 @@ If everything goes well, you should see the following message:: To use this newly installed Cantera version, update your environment variables by adding the following lines to your.bashrc (or equivalent): - #cantera-avbp-3.0 + #cantera-avbp-3.1 export PYTHONPATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH export PKG_CONFIG_PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH export LD_LIBRARY_PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH diff --git a/install_cantera.py b/install_cantera.py index 96d3891a4ff..cac66d19d7a 100644 --- a/install_cantera.py +++ b/install_cantera.py @@ -131,7 +131,7 @@ def execute_with_live_display(command): print("To use this brandnew Cantera installation, you must update some of your environment variables.") print("To do so, you can add the following lines to your .bashrc (or equivalent):") text="""\ -#cantera-avbp-3.0 +#cantera-avbp-3.1 export PYTHONPATH={0}/lib/python{1}.{2}/site-packages:$PYTHONPATH export PKG_CONFIG_PATH={0}/lib/pkgconfig:$PKG_CONFIG_PATH export LD_LIBRARY_PATH={0}/lib:$LD_LIBRARY_PATH From 3f818a29340d47c4eb50b39a510d50b55af35250 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 29 Jul 2025 18:50:55 +0200 Subject: [PATCH 39/98] Add instal for CALYPSO MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Modifications qui seront validées : modifié : install_cantera.py supprimé : run_compil nouveau fichier : run_compil_CALYPSO --- install_cantera.py | 35 ++++++++++++++++++++++++++++++----- run_compil | 5 ----- run_compil_CALYPSO | 6 ++++++ 3 files changed, 36 insertions(+), 10 deletions(-) delete mode 100755 run_compil create mode 100755 run_compil_CALYPSO diff --git a/install_cantera.py b/install_cantera.py index cac66d19d7a..98b6868b6c5 100644 --- a/install_cantera.py +++ b/install_cantera.py @@ -15,6 +15,7 @@ if string_argument in ['yes', 'y']: argument = 'NFS' + cluster = input('On which cluster are you installing Cantera ? (KRAKEN/CALYPSO) ') elif string_argument in ['no', 'n']: argument = 'local' else: @@ -50,7 +51,12 @@ def fill_cantera_conf(file_path, install_dir_path): # use the output of ls /opt/homebrew/Cellar/boost/ to get the version number f.write(text.format(subprocess.check_output('ls /opt/homebrew/Cellar/boost/', shell=True).decode('utf-8').split('\n')[0])) else : - text = """\ + if cluster == 'CALYPSO': + text = """\ +boost_inc_dir = '/softs/local/boost/1.86.0/include' +""" + elif cluster == 'KRAKEN': + text = """\ boost_inc_dir = '/softs/local/boost/1.78.0_gcc112/include' """ f.write(text) @@ -92,9 +98,10 @@ def execute_with_live_display(command): subprocess.call('brew install gcc', shell=True) #subprocess.call('pip3 install numpy --no-use-pep517', shell=True) subprocess.call('pip3 install numpy', shell=True) - subprocess.call('pip3 install cython==3.1.1', shell=True) - subprocess.call('pip3 install packaging', shell=True) - subprocess.call('pip3 install scons==3.1.2', shell=True) + subprocess.call('pip3 install cython==3.1.1', shell=True) + subprocess.call('pip3 install packaging', shell=True) + # subprocess.call('pip3 install scons==3.1.2', shell=True) + subprocess.call('pip3 install scons', shell=True) subprocess.call('pip3 install wheel', shell=True) subprocess.call('pip3 install ruamel.yaml', shell=True) elif update_argument in ['no', 'n']: @@ -105,8 +112,26 @@ def execute_with_live_display(command): fill_cantera_conf(file_path, install_dir_path) error = subprocess.call('scons build && scons install', shell=True) else: + print("""To run cantera, the installation of: \n + - numpy, cython, scons, wheel and ruamel.yaml with pip command. \n + are required.""") + update_argument = input('Do you want to install/update those libraries ? (yes/no) ') + + if update_argument in ['yes', 'y']: + subprocess.call('pip3 install numpy', shell=True) + subprocess.call('pip3 install cython==3.1.1', shell=True) + subprocess.call('pip3 install packaging', shell=True) + subprocess.call('pip3 install scons', shell=True) + subprocess.call('pip3 install wheel', shell=True) + subprocess.call('pip3 install ruamel.yaml', shell=True) + elif update_argument in ['no', 'n']: + pass + else: + quit('Invalid answer ! \n Really ?! How could you fail a yes or no question ?') + + fill_cantera_conf(file_path, install_dir_path) - error = execute_with_live_display("./run_compil") + error = execute_with_live_display("./run_compil_" + cluster) #only print the following if the installation was successful diff --git a/run_compil b/run_compil deleted file mode 100755 index 64c909a8246..00000000000 --- a/run_compil +++ /dev/null @@ -1,5 +0,0 @@ -module purge -module load python/3.9.5 -module load compiler/gcc/11.2.0 -module list -scons build && scons install diff --git a/run_compil_CALYPSO b/run_compil_CALYPSO new file mode 100755 index 00000000000..6848df18d8b --- /dev/null +++ b/run_compil_CALYPSO @@ -0,0 +1,6 @@ +#!/bin/bash +module purge +#module load python/3.9.5 # Not needed if install is done in an python environment (already loaded to create the environment) +module load gcc/12.3.0 +# module list +scons build -j4 && scons install From 2e8dc24d2781ce80701b1f9e22516c1ae20aa86e Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 30 Jul 2025 11:54:53 +0200 Subject: [PATCH 40/98] Add load_cantera function for .bashrc MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Modifications qui seront validées : modifié : install_cantera.py --- install_cantera.py | 141 ++++++++++++++++++++++++++------------------- 1 file changed, 82 insertions(+), 59 deletions(-) diff --git a/install_cantera.py b/install_cantera.py index 98b6868b6c5..e5487c317dd 100644 --- a/install_cantera.py +++ b/install_cantera.py @@ -4,35 +4,6 @@ import os import subprocess -# Asking about the environment -if sys.version_info[0] < 3: - quit('You should compile cantera with python 3 ! Use module load python/3.9.5') - string_argument = raw_input('Are you installing Cantera on NFS machine ? (yes/no) ') - python_version = 2 -else: - string_argument = input('Are you installing Cantera on NFS machine ? (yes/no) ') - python_version = 3 - -if string_argument in ['yes', 'y']: - argument = 'NFS' - cluster = input('On which cluster are you installing Cantera ? (KRAKEN/CALYPSO) ') -elif string_argument in ['no', 'n']: - argument = 'local' -else: - quit('Invalid answer ! \n Really ?! How could you fail a yes or no question ?') - -dir_path = os.path.dirname(os.path.realpath(__file__)) - -install_dir_path = os.path.dirname(os.path.realpath(__file__)) + "/INSTALL_DIR" - -if not os.path.isdir(install_dir_path): - os.mkdir(install_dir_path) - -#create mech_lib folder in INSTALL_DIR -if not os.path.isdir(install_dir_path + "/mech_lib"): - os.mkdir(install_dir_path + "/mech_lib") - -file_path = dir_path + "/cantera.conf" def fill_cantera_conf(file_path, install_dir_path): f = open(file_path, 'w') @@ -63,6 +34,7 @@ def fill_cantera_conf(file_path, install_dir_path): f.close() + def execute_with_live_display(command): process = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True) @@ -84,6 +56,36 @@ def execute_with_live_display(command): return process.returncode +# Asking about the environment +if sys.version_info[0] < 3: + quit('You should compile cantera with python 3 ! Use module load python/3.9.5') + string_argument = raw_input('Are you installing Cantera on NFS machine ? (yes/no) ') + python_version = 2 +else: + string_argument = input('Are you installing Cantera on NFS machine ? (yes/no) ') + python_version = 3 + +if string_argument in ['yes', 'y']: + argument = 'NFS' + cluster = input('On which cluster are you installing Cantera ? (KRAKEN/CALYPSO) ') +elif string_argument in ['no', 'n']: + argument = 'local' +else: + quit('Invalid answer ! \n Really ?! How could you fail a yes or no question ?') + +dir_path = os.path.dirname(os.path.realpath(__file__)) + +install_dir_path = os.path.dirname(os.path.realpath(__file__)) + "/INSTALL_DIR" + +if not os.path.isdir(install_dir_path): + os.mkdir(install_dir_path) + +#create mech_lib folder in INSTALL_DIR +if not os.path.isdir(install_dir_path + "/mech_lib"): + os.mkdir(install_dir_path + "/mech_lib") + +file_path = dir_path + "/cantera.conf" + if argument == 'local': print("""To run cantera, the installation of: \n - python, boost and gcc with brew command. \n @@ -134,22 +136,22 @@ def execute_with_live_display(command): error = execute_with_live_display("./run_compil_" + cluster) -#only print the following if the installation was successful -if argument == 'NFS' and not error: - #add an alias to load necessary modules - print("We suggest to add the alias 'load_cantera_mod' to purge and load necessary modules in ~/.bashrc") - #ask user if he wants to add the alias to ~/.bashrc - add_alias = input('Do you want to add the alias to ~/.bashrc ? (yes/no) ') - if add_alias in ['yes', 'y']: - err = subprocess.call("echo 'alias load_cantera_mod=\"module purge && module load compiler/gcc/11.2.0\"' >> ~/.bashrc", shell=True) - if not err : - print("Alias load_cantera_mod added to ~/.bashrc") - else : - print("FAILED to add alias load_cantera_mod to ~/.bashrc, you can do it manually :\ - alias load_cantera_mod='module purge && module load compiler/gcc/11.2.0'") - else : - print("Alias load_cantera_mod NOT added to ~/.bashrc") - +##only print the following if the installation was successful +#if argument == 'NFS' and not error: + ##add an alias to load necessary modules + #print("We suggest to add the alias 'load_cantera_mod' to purge and load necessary modules in ~/.bashrc") + ##ask user if he wants to add the alias to ~/.bashrc + #add_alias = input('Do you want to add the alias to ~/.bashrc ? (yes/no) ') + # if add_alias in ['yes', 'y']: + # err = subprocess.call("echo 'alias load_cantera_mod=\"module purge && module load compiler/gcc/11.2.0\"' >> ~/.bashrc", shell=True) + # if not err : + # print("Alias load_cantera_mod added to ~/.bashrc") + # else : + # print("FAILED to add alias load_cantera_mod to ~/.bashrc, you can do it manually :\ + # alias load_cantera_mod='module purge && module load compiler/gcc/11.2.0'") + # else : + # print("Alias load_cantera_mod NOT added to ~/.bashrc") + if not error: print("*" * 80) print() @@ -157,23 +159,44 @@ def execute_with_live_display(command): print("To do so, you can add the following lines to your .bashrc (or equivalent):") text="""\ #cantera-avbp-3.1 -export PYTHONPATH={0}/lib/python{1}.{2}/site-packages:$PYTHONPATH -export PKG_CONFIG_PATH={0}/lib/pkgconfig:$PKG_CONFIG_PATH -export LD_LIBRARY_PATH={0}/lib:$LD_LIBRARY_PATH -export PATH={0}/bin:$PATH -export PYTHON_CMD={3} - -#Only if you dont already have a custom lib folder: -export CUSTOM_LIB={0}/mech_lib -export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH - -#Required for MacOS: -export DYLD_LIBRARY_PATH=$CUSTOM_LIB - """ +function load_cantera +{7} + source {4} + + {5} + + export PYTHONPATH={0}/lib/python{1}.{2}/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH={0}/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH={0}/lib:$LD_LIBRARY_PATH + export PATH={0}/bin:$PATH + export PYTHON_CMD={3} + + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB={0}/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + +{6} +{8} +""" #get the output of which python to get the path to the python executable + open_braket_string = "{" + close_bracket_strinc = "}" pythonpath = subprocess.check_output('which python3', shell=True).decode('utf-8').split('\n')[0] + source_venv = subprocess.check_output('echo $VIRTUAL_ENV', shell=True).decode('utf-8').split('\n')[0] + "/bin/activate" + if argument == 'NFS' and cluster == 'CALYPSO': + module_gcc = "module load gcc/12.3.0" + else: + module_gcc = "" + if argument == 'local': + dyld_path = """\ + #Required for MacOS: + export DYLD_LIBRARY_PATH=$CUSTOM_LIB +""" + else: + dyld_path = "" + print() - print(text.format(install_dir_path,str(python_version), str(sys.version_info[1]),pythonpath)) + print(text.format(install_dir_path,str(python_version), str(sys.version_info[1]),pythonpath,source_venv,module_gcc,dyld_path,open_braket_string,close_bracket_strinc)) print() print("DONT FORGET TO SOURCE YOUR .bashrc !") print() From 74ba61f2a4968c6e3669be364a793bfcf6711bbc Mon Sep 17 00:00:00 2001 From: pestre Date: Fri, 1 Aug 2025 11:10:25 +0200 Subject: [PATCH 41/98] Add install for KRAKEN Changes to be committed: modified: install_cantera.py new file: run_compil_KRAKEN deleted: run_compil_kraken --- install_cantera.py | 2 ++ run_compil_KRAKEN | 10 ++++++++++ run_compil_kraken | 9 --------- 3 files changed, 12 insertions(+), 9 deletions(-) create mode 100755 run_compil_KRAKEN delete mode 100755 run_compil_kraken diff --git a/install_cantera.py b/install_cantera.py index e5487c317dd..719bff9c143 100644 --- a/install_cantera.py +++ b/install_cantera.py @@ -185,6 +185,8 @@ def execute_with_live_display(command): source_venv = subprocess.check_output('echo $VIRTUAL_ENV', shell=True).decode('utf-8').split('\n')[0] + "/bin/activate" if argument == 'NFS' and cluster == 'CALYPSO': module_gcc = "module load gcc/12.3.0" + elif argument == 'NFS' and cluster == 'KRAKEN': + module_gcc = "module load compiler/gcc/11.2.0" else: module_gcc = "" if argument == 'local': diff --git a/run_compil_KRAKEN b/run_compil_KRAKEN new file mode 100755 index 00000000000..7752a79f2b7 --- /dev/null +++ b/run_compil_KRAKEN @@ -0,0 +1,10 @@ +#!/bin/bash +module purge +# module load python/3.9.5 +module load compiler/gcc/11.2.0 +#require the installation of ruamel.yaml +# scons build python2_package=n prefix=/softs/local/cantera-avbp/3.0 blas_lapack_libs=lapack,atlas debug_linker_flags='-L/usr/lib64/atlas' +# mv /softs/local/cantera-avbp/3.0 /softs/local/cantera-avbp/3.0-`date +%d%b%Y` +# scons install +scons build -j4 && scons install + diff --git a/run_compil_kraken b/run_compil_kraken deleted file mode 100755 index 2d82c92a262..00000000000 --- a/run_compil_kraken +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash -module purge -module load python/3.9.5 -module load compiler/gcc/11.2.0 -#require the installation of ruamel.yaml -scons build python2_package=n prefix=/softs/local/cantera-avbp/3.0 blas_lapack_libs=lapack,atlas debug_linker_flags='-L/usr/lib64/atlas' -mv /softs/local/cantera-avbp/3.0 /softs/local/cantera-avbp/3.0-`date +%d%b%Y` -scons install - From a9c12800872e323539c40a10a7b20c614a93946c Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Mon, 4 Aug 2025 14:15:31 +0200 Subject: [PATCH 42/98] Clean install_cantera.py + update doc for installation Changes to be committed: modified: README.rst modified: install_cantera.py --- README.rst | 214 ++++++++++++++++++++++++++++++++++----------- install_cantera.py | 19 ---- 2 files changed, 164 insertions(+), 69 deletions(-) diff --git a/README.rst b/README.rst index d82930acf87..822f940d325 100644 --- a/README.rst +++ b/README.rst @@ -30,7 +30,7 @@ using the following MyBinder link: .. image:: https://mybinder.org/badge.svg :target: https://mybinder.org/repo/cantera/cantera-jupyter -Installation +Local Installation (MAC) ============ To ensure a smooth installation, we highly recommend setting up Cantera within a virtual environment. @@ -47,98 +47,212 @@ Follow the steps below for a **local** installation: python3 -m venv env_cantera source ~/env_cantera/bin/activate -2. (optional) Create an alias to load ``env_cantera``:: - - echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.zshrc - source ~/.zshrc - -3. Navigate to the Cantera directory:: +2. Navigate to the Cantera directory:: cd /Users/$USER/Documents/cantera-avbp -4. Switch to the right branch and run the installation script:: +3. Run the installation script:: - git checkout dev_cantera-avbp - python3 install_cantera.py + python install_cantera.py +4. When prompted about NFS, answer ``no``. + +5. When prompted about package and libraries installations (boost, numpy, scons,...), answer ``yes``. -5. When prompted about NFS, answer ``no``. 6. Wait for the compilation and installation process to complete successfully. If everything goes well, you should see the following message:: - ******************************************************************************** - To use this newly installed Cantera version, update your environment variables - by adding the following lines to your.bashrc (or equivalent): +******************************************************************************** + +To use this brandnew Cantera installation, you must update some of your environment variables. +To do so, you can add the following lines to your .bashrc (or equivalent): + +#cantera-avbp-3.1 +function load_cantera +{ + source /Users/$USER/Documents/VENV/test/bin/activate - #cantera-avbp-3.1 - export PYTHONPATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH - export PKG_CONFIG_PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH - export LD_LIBRARY_PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH - export PATH=/Users/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH - export PYTHON_CMD=/Users/$USER/canavbp3/bin/python3 - #Only if you dont already have a custom lib folder: - export CUSTOM_LIB=/Users/$USER/cantera-avbp/INSTALL_DIR/mech_lib - export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH - #Required for MacOS: - export DYLD_LIBRARY_PATH=$CUSTOM_LIB + export PYTHONPATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH + export PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/bin:$PATH - DONT FORGET TO SOURCE YOUR .bashrc! + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH - ******************************************************************************** + #Required for MacOS: + export DYLD_LIBRARY_PATH=$CUSTOM_LIB +} + + +DONT FORGET TO SOURCE YOUR .bashrc ! + +******************************************************************************** Copy and paste the provided lines into your ``.zshrc`` or ``.bashrc`` file and **source it**. +7. To activate Cantera environment:: + + load_cantera + +8. Test if everything works using a sample script, for example:: + + python samples/python/AVBP/ARC.py + + +KRAKEN Installation +============ + For **KRAKEN** users, use the following commands to install Cantera: -1. Load the necessary modules:: +0. Load the necessary modules:: module purge && module load python/3.9.5 + +1. Create a virtual environment in your home folder and activate it:: + + cd $HOME + python3 -m venv env_cantera + source ~/env_cantera/bin/activate + +2. Clone the Cantera repository:: + + cd /scratch/cfd/$USER + git clone git@github.com:cerfacs/cantera-avbp.git + +3. Run the installation script:: + + cd cantera-avbp + python install_cantera.py + +4. When prompted about NFS, answer ``yes``. + +5. When prompted about cluster, answer ``KRAKEN``. + +6. When prompted about package installations (numpy, scons,...), answer ``yes``. + +7. Wait for the compilation and installation process to complete successfully. + +If everything goes well, you should see the following message:: + +******************************************************************************** + +To use this brandnew Cantera installation, you must update some of your environment variables. +To do so, you can add the following lines to your .bashrc (or equivalent): + +#cantera-avbp-3.1 +function load_cantera +{ + source /home/cfd/$USER/env_cantera/bin/activate + + module load compiler/gcc/11.2.0 + + export PYTHONPATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH + export PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH + + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + + +} + + +DONT FORGET TO SOURCE YOUR .bashrc ! + +******************************************************************************** + +Copy and paste the provided lines into your ``.zshrc`` or ``.bashrc`` file and **source it**. + +8. To activate Cantera environment:: -2. Install ``ruamel.yaml`` package (not installed by default on KRAKEN):: - - pip3 install --user ruamel.yaml + load_cantera + +9. Test if everything works using a sample script, for example:: + + python samples/python/AVBP/ARC.py + + +CALYPSO Installation +============ + +For **CALYPSO** users, use the following commands to install Cantera: -3. Create a virtual environment in your home folder and activate it:: +0. Load the necessary modules:: + + module purge && module load python/3.9.19 + +1. Create a virtual environment in your home folder and activate it:: cd $HOME - python3 -m venv --system-site-packages env_cantera + python3 -m venv env_cantera source ~/env_cantera/bin/activate -4. (optional) Create an alias to load ``env_cantera``:: +2. Clone the Cantera repository:: + + cd /scratch/cfd/$USER + git clone git@github.com:cerfacs/cantera-avbp.git + +3. Run the installation script:: + + cd cantera-avbp + python install_cantera.py + +4. When prompted about NFS, answer ``yes``. - echo "alias load_cantera_env='source ~/env_cantera/bin/activate'" >> ~/.bashrc - source ~/.bashrc +5. When prompted about cluster, answer ``CALYPSO``. -5. Clone cantera-avbp repository (e.g. in your ``/scratch``), navigate to it and run the installation script:: +6. When prompted about package installations (numpy, scons,...), answer ``yes``. - git clone https://nitrox.cerfacs.fr/cantera/cantera-avbp.git /scratch/cfd/$USER - cd /scratch/cfd/$USER/cantera-avbp - git checkout 3.0 - python3 install_cantera.py +7. Wait for the compilation and installation process to complete successfully. -When prompted about NFS, answer 'yes' and wait for the compilation and installation to finish. +If everything goes well, you should see the following message:: + +******************************************************************************** + +To use this brandnew Cantera installation, you must update some of your environment variables. +To do so, you can add the following lines to your .bashrc (or equivalent): + +#cantera-avbp-3.1 +function load_cantera +{ + source /gpfs-calypso/home/cfd/$USER/env_cantera/bin/activate -If everything goes well, you will see a similar message as above, but with an additional question:: + module load gcc/12.3.0 + export PYTHONPATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH + export PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH - We suggest adding the alias 'load_cantera' to purge and load necessary modules in ~/.bashrc - Do you want to add the alias to ~/.bashrc? (yes/no) + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH -Answer ``yes`` to this question, then copy and paste the environment variables you need into your ``.bashrc`` file and **source it**. +} -Finally, load Cantera with the following command:: - load_cantera +DONT FORGET TO SOURCE YOUR .bashrc ! +******************************************************************************** + +Copy and paste the provided lines into your ``.zshrc`` or ``.bashrc`` file and **source it**. + +8. To activate Cantera environment:: + + load_cantera -Test if everything works using a sample script, for example:: +9. Test if everything works using a sample script, for example:: - python3 samples/python/AVBP/ARC.py + python samples/python/AVBP/ARC.py Documentation diff --git a/install_cantera.py b/install_cantera.py index 719bff9c143..8ad1b706cbc 100644 --- a/install_cantera.py +++ b/install_cantera.py @@ -98,11 +98,9 @@ def execute_with_live_display(command): subprocess.call('/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"', shell=True) subprocess.call('brew install boost', shell=True) subprocess.call('brew install gcc', shell=True) - #subprocess.call('pip3 install numpy --no-use-pep517', shell=True) subprocess.call('pip3 install numpy', shell=True) subprocess.call('pip3 install cython==3.1.1', shell=True) subprocess.call('pip3 install packaging', shell=True) - # subprocess.call('pip3 install scons==3.1.2', shell=True) subprocess.call('pip3 install scons', shell=True) subprocess.call('pip3 install wheel', shell=True) subprocess.call('pip3 install ruamel.yaml', shell=True) @@ -136,22 +134,6 @@ def execute_with_live_display(command): error = execute_with_live_display("./run_compil_" + cluster) -##only print the following if the installation was successful -#if argument == 'NFS' and not error: - ##add an alias to load necessary modules - #print("We suggest to add the alias 'load_cantera_mod' to purge and load necessary modules in ~/.bashrc") - ##ask user if he wants to add the alias to ~/.bashrc - #add_alias = input('Do you want to add the alias to ~/.bashrc ? (yes/no) ') - # if add_alias in ['yes', 'y']: - # err = subprocess.call("echo 'alias load_cantera_mod=\"module purge && module load compiler/gcc/11.2.0\"' >> ~/.bashrc", shell=True) - # if not err : - # print("Alias load_cantera_mod added to ~/.bashrc") - # else : - # print("FAILED to add alias load_cantera_mod to ~/.bashrc, you can do it manually :\ - # alias load_cantera_mod='module purge && module load compiler/gcc/11.2.0'") - # else : - # print("Alias load_cantera_mod NOT added to ~/.bashrc") - if not error: print("*" * 80) print() @@ -169,7 +151,6 @@ def execute_with_live_display(command): export PKG_CONFIG_PATH={0}/lib/pkgconfig:$PKG_CONFIG_PATH export LD_LIBRARY_PATH={0}/lib:$LD_LIBRARY_PATH export PATH={0}/bin:$PATH - export PYTHON_CMD={3} #Only if you dont already have a custom lib folder: export CUSTOM_LIB={0}/mech_lib From 3d9272cc81075a9d9e00e5f6c61c71895ae89e37 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Mon, 4 Aug 2025 18:52:11 +0200 Subject: [PATCH 43/98] Display correction Changes to be committed: modified: README.rst --- README.rst | 110 ++++++++++++++++++++++++++--------------------------- 1 file changed, 55 insertions(+), 55 deletions(-) diff --git a/README.rst b/README.rst index 822f940d325..b6184bdcd23 100644 --- a/README.rst +++ b/README.rst @@ -63,36 +63,36 @@ Follow the steps below for a **local** installation: If everything goes well, you should see the following message:: -******************************************************************************** + ******************************************************************************** -To use this brandnew Cantera installation, you must update some of your environment variables. -To do so, you can add the following lines to your .bashrc (or equivalent): + To use this brandnew Cantera installation, you must update some of your environment variables. + To do so, you can add the following lines to your .bashrc (or equivalent): -#cantera-avbp-3.1 -function load_cantera -{ - source /Users/$USER/Documents/VENV/test/bin/activate + #cantera-avbp-3.1 + function load_cantera + { + source /Users/$USER/Documents/VENV/test/bin/activate - export PYTHONPATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH - export PKG_CONFIG_PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH - export LD_LIBRARY_PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH - export PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/bin:$PATH + export PYTHONPATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH + export PATH=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/bin:$PATH - #Only if you dont already have a custom lib folder: - export CUSTOM_LIB=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/mech_lib - export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB=/Users/$USER/Documents/cantera-avbp/INSTALL_DIR/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH - #Required for MacOS: - export DYLD_LIBRARY_PATH=$CUSTOM_LIB + #Required for MacOS: + export DYLD_LIBRARY_PATH=$CUSTOM_LIB -} + } -DONT FORGET TO SOURCE YOUR .bashrc ! + DONT FORGET TO SOURCE YOUR .bashrc ! -******************************************************************************** + ******************************************************************************** Copy and paste the provided lines into your ``.zshrc`` or ``.bashrc`` file and **source it**. @@ -140,34 +140,34 @@ For **KRAKEN** users, use the following commands to install Cantera: If everything goes well, you should see the following message:: -******************************************************************************** + ******************************************************************************** -To use this brandnew Cantera installation, you must update some of your environment variables. -To do so, you can add the following lines to your .bashrc (or equivalent): + To use this brandnew Cantera installation, you must update some of your environment variables. + To do so, you can add the following lines to your .bashrc (or equivalent): -#cantera-avbp-3.1 -function load_cantera -{ - source /home/cfd/$USER/env_cantera/bin/activate + #cantera-avbp-3.1 + function load_cantera + { + source /home/cfd/$USER/env_cantera/bin/activate - module load compiler/gcc/11.2.0 + module load compiler/gcc/11.2.0 - export PYTHONPATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH - export PKG_CONFIG_PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH - export LD_LIBRARY_PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH - export PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH + export PYTHONPATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRAR + export PATH=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH - #Only if you dont already have a custom lib folder: - export CUSTOM_LIB=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/mech_lib - export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB=/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH -} + } -DONT FORGET TO SOURCE YOUR .bashrc ! + DONT FORGET TO SOURCE YOUR .bashrc ! -******************************************************************************** + ******************************************************************************** Copy and paste the provided lines into your ``.zshrc`` or ``.bashrc`` file and **source it**. @@ -215,34 +215,34 @@ For **CALYPSO** users, use the following commands to install Cantera: If everything goes well, you should see the following message:: -******************************************************************************** + ******************************************************************************** -To use this brandnew Cantera installation, you must update some of your environment variables. -To do so, you can add the following lines to your .bashrc (or equivalent): + To use this brandnew Cantera installation, you must update some of your environment variables. + To do so, you can add the following lines to your .bashrc (or equivalent): -#cantera-avbp-3.1 -function load_cantera -{ - source /gpfs-calypso/home/cfd/$USER/env_cantera/bin/activate + #cantera-avbp-3.1 + function load_cantera + { + source /gpfs-calypso/home/cfd/$USER/env_cantera/bin/activate - module load gcc/12.3.0 + module load gcc/12.3.0 - export PYTHONPATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH - export PKG_CONFIG_PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH - export LD_LIBRARY_PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH - export PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH + export PYTHONPATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/python3.9/site-packages:$PYTHONPATH + export PKG_CONFIG_PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib/pkgconfig:$PKG_CONFIG_PATH + export LD_LIBRARY_PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/lib:$LD_LIBRARY_PATH + export PATH=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/bin:$PATH - #Only if you dont already have a custom lib folder: - export CUSTOM_LIB=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/mech_lib - export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH + #Only if you dont already have a custom lib folder: + export CUSTOM_LIB=/gpfs-calypso/scratch/cfd/$USER/cantera-avbp/INSTALL_DIR/mech_lib + export LD_LIBRARY_PATH=$CUSTOM_LIB:$LD_LIBRARY_PATH -} + } -DONT FORGET TO SOURCE YOUR .bashrc ! + DONT FORGET TO SOURCE YOUR .bashrc ! -******************************************************************************** + ******************************************************************************** Copy and paste the provided lines into your ``.zshrc`` or ``.bashrc`` file and **source it**. From 4efd8f919e1d0f611766acafe9e6e87cd6477ce8 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 26 Aug 2025 17:13:27 +0200 Subject: [PATCH 44/98] Deactivate automatic workflows from cantera without removing them On branch FEATURE/github_workflows Changes to be committed: modified: .github/workflows/linters.yml modified: .github/workflows/main.yml modified: .github/workflows/packaging.yml modified: .github/workflows/post-merge-tests.yml --- .github/workflows/linters.yml | 9 ++++---- .github/workflows/main.yml | 29 +++++++++++++------------- .github/workflows/packaging.yml | 14 ++++++------- .github/workflows/post-merge-tests.yml | 20 +++++++++--------- 4 files changed, 37 insertions(+), 35 deletions(-) diff --git a/.github/workflows/linters.yml b/.github/workflows/linters.yml index df7d0c6dc78..5e636d6de1d 100644 --- a/.github/workflows/linters.yml +++ b/.github/workflows/linters.yml @@ -1,10 +1,11 @@ name: Linters on: - pull_request: - # Build when a pull request targets main - branches: - - main +# pull_request: +# # Build when a pull request targets main +# branches: +# - main + workflow_dispatch: jobs: linter: diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index a61055c65e9..cd773e239d1 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -1,20 +1,21 @@ name: CI on: - push: - # Build on tags that look like releases - tags: - - v* - # Build when main, testing, or the maintenance branch is pushed to - branches: - - main - - testing - - "3.1" - pull_request: - # Build when a pull request targets main or the maintenance branch - branches: - - main - - "3.1" + workflow_dispatch: + # push: + # # Build on tags that look like releases + # tags: + # - v* + # # Build when main, testing, or the maintenance branch is pushed to + # branches: + # - main + # - testing + # - "3.1" + # pull_request: + # # Build when a pull request targets main or the maintenance branch + # branches: + # - main + # - "3.1" concurrency: group: ${{ github.workflow }}-${{ github.ref }} diff --git a/.github/workflows/packaging.yml b/.github/workflows/packaging.yml index d49e496e32e..cf275a26be5 100644 --- a/.github/workflows/packaging.yml +++ b/.github/workflows/packaging.yml @@ -10,13 +10,13 @@ on: description: "Try to upload wheels and sdist to PyPI after building" required: false default: "false" - push: - # Run on tags that look like releases - tags: - - v* - # Run when main is pushed to - branches: - - main + # push: + # # Run on tags that look like releases + # tags: + # - v* + # # Run when main is pushed to + # branches: + # - main jobs: build-packages: diff --git a/.github/workflows/post-merge-tests.yml b/.github/workflows/post-merge-tests.yml index 9fb985326c0..1d6e9895aa4 100644 --- a/.github/workflows/post-merge-tests.yml +++ b/.github/workflows/post-merge-tests.yml @@ -6,16 +6,16 @@ on: description: "The ref to be built. Can be a tag, commit hash, or branch name" required: true default: "main" - push: - # Run when the main branch is pushed to - branches: - - main - # Run on pull requests when this file is modified - pull_request: - branches: - - main - paths: - - .github/workflows/post-merge-tests.yml + # push: + # # Run when the main branch is pushed to + # branches: + # - main + # # Run on pull requests when this file is modified + # pull_request: + # branches: + # - main + # paths: + # - .github/workflows/post-merge-tests.yml env: PIP_EXTRA_INDEX_URL: https://pypi.anaconda.org/scientific-python-nightly-wheels/simple From 80c124fd868cea38d3670a7e8447a4a242eda2ae Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 26 Aug 2025 19:30:49 +0200 Subject: [PATCH 45/98] Add new workflow for python package generation On branch FEATURE/github_workflows Changes to be committed: new file: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 378 ++++++++++++++++++++++++ 1 file changed, 378 insertions(+) create mode 100644 .github/workflows/CERFACS_packaging.yml diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml new file mode 100644 index 00000000000..71e18d67d59 --- /dev/null +++ b/.github/workflows/CERFACS_packaging.yml @@ -0,0 +1,378 @@ +name: Build Python Package + +on: + workflow_dispatch: + inputs: + incoming_ref: + description: > + The ref from cerfacs/cantera-avbp to be built. Can be a tag, commit hash, + or branch name. + required: true + default: "dev_cantera-avbp" + upload: + description: Attempt to upload to PyPI + required: true + default: "false" + build_linux: + description: "Build wheels on Linux" + required: true + default: "true" + # build_windows: + # description: "Build wheels on Windows" + # required: true + # default: "false" + # build_macos: + # description: "Build wheels on MacOS" + # required: true + # default: "false" + +concurrency: + group: ${{ github.ref }}-${{ github.event.inputs.incoming_ref}} + cancel-in-progress: true + +env: + CIBW_BUILD_FRONTEND: build + CIBW_TEST_EXTRAS: pandas,units + CIBW_TEST_REQUIRES: pytest + ACTION_URL: "https://github.com/cerfacs/cantera-avbp/actions/runs/${{ github.run_id }}" + REPO_API_URL: "https://api.github.com/repos/cerfacs/cantera-avbp/tarball/${{ github.event.inputs.incoming_ref }}" + + +jobs: + dump: + name: Dump the input parameters for the workflow + runs-on: ubuntu-22.04 + steps: + - name: Dump Event Payload + run: jq . "$GITHUB_EVENT_PATH" + - name: Echo the input variables + run: | + echo "${{ github.event.inputs.incoming_ref }}" + echo "${{ github.event.inputs.upload }}" + post-pending-status: + name: Post a pending workflow status to cerfacs/cantera-avbp + runs-on: ubuntu-22.04 + env: + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + outputs: + incoming-sha: ${{ steps.get-incoming-sha.outputs.incoming-sha }} + tag-ref: ${{ steps.munge-incoming-ref.outputs.tag-ref }} + steps: + - uses: actions/setup-python@v5 + with: + python-version: '3.10' + - name: Munge the incoming ref + id: munge-incoming-ref + run: | + import os + import re + from pathlib import Path + INCOMING_REF = "${{ github.event.inputs.incoming_ref }}" + INCOMING_SHA = "" + if INCOMING_REF.startswith("refs/"): + INCOMING_REF = INCOMING_REF.replace("refs/", "") + elif re.match(r"^v\d\.\d\.\d.*$", INCOMING_REF) is not None: + INCOMING_REF = f"tags/{INCOMING_REF}" + elif re.match(r"^[a-f0-9]{6,40}", INCOMING_REF) is not None: + INCOMING_SHA = INCOMING_REF + else: + INCOMING_REF = f"heads/{INCOMING_REF}" + TAG_REF = "false" + if INCOMING_REF.startswith("tags"): + TAG_REF = "true" + Path(os.environ["GITHUB_ENV"]).write_text( + f"INCOMING_REF={INCOMING_REF}\n" + f"TAG_REF={TAG_REF}\n" + f"INCOMING_SHA={INCOMING_SHA}" + ) + Path(os.environ["GITHUB_OUTPUT"]).write_text( + f"tag-ref={TAG_REF}" + ) + shell: python + - name: Get the SHA associated with the incoming ref + id: get-incoming-sha + run: | + if [[ "${INCOMING_SHA}" == "" ]]; then + INCOMING_SHA=$(gh api repos/cerfacs/cantera-avbp/git/matching-refs/${INCOMING_REF} \ + -H "Accept: application/vnd.github.v3+json" --jq ".[0].object.sha") + echo "INCOMING_SHA=${INCOMING_SHA}" >> $GITHUB_ENV + fi + # This needs to be in this step to be output to other jobs. + echo "incoming-sha=${INCOMING_SHA}" >> $GITHUB_OUTPUT + - name: Post the status to the upstream commit + id: set-the-status + if: env.TAG_REF == 'false' + run: | + gh api repos/cerfacs/cantera-avbp/statuses/${INCOMING_SHA} \ + -H "Accept: application/vnd.github.v3+json" \ + --field state='pending' \ + --field target_url=$ACTION_URL \ + --field context='PyPI Package Build' \ + --field description="Pending build" \ + --silent + sdist: + name: Build the sdist + runs-on: ubuntu-22.04 + needs: + - "post-pending-status" + outputs: + job-status: ${{ job.status }} + steps: + - name: Install dependencies + run: | + sudo apt-get update + sudo apt-get install libboost-dev + - uses: actions/checkout@v4 + name: Checkout the repository + with: + repository: "joebarteam11/cantera-avbp-3.0.0" + submodules: recursive + ref: ${{ github.event.inputs.incoming_ref }} + - name: Set Up Python 3.12 + uses: actions/setup-python@v5 + with: + python-version: "3.12" + - name: Install dependencies + run: python3 -m pip install -U pip scons build + - name: Build the sdist + run: | + python3 `which scons` sdist f90_interface=n python_package='none' \ + system_blas_lapack=n system_sundials=n system_eigen=n system_fmt=n \ + system_yamlcpp=n googletest=none env_vars='CYTHON_FORCE_REGEN' + env: + CYTHON_FORCE_REGEN: "1" + - name: Archive the built sdist + uses: actions/upload-artifact@v4 + with: + path: ./build/python_sdist/dist/*.tar.gz + name: cibw-sdist + if-no-files-found: error + # Copied from https://github.com/hynek/build-and-inspect-python-package/ + - name: Show SDist contents hierarchically, including metadata. + shell: bash + run: | + mkdir -p /tmp/out/sdist + cp build/python_sdist/dist/*.tar.gz /tmp/ + cd /tmp + tar xf *.tar.gz -C out/sdist + echo -e '\n
SDist contents\n' >> $GITHUB_STEP_SUMMARY + (cd /tmp/out/sdist && tree -Da --timefmt="%Y-%m-%dT%H:%M:%SZ" * | sed 's/^/ /' | tee -a $GITHUB_STEP_SUMMARY) + echo -e '\n
\n' >> $GITHUB_STEP_SUMMARY + echo ----- Metadata Follows ----- + echo -e '\n
Metadata\n' >> $GITHUB_STEP_SUMMARY + cat out/sdist/*/PKG-INFO | sed 's/^/ /' | tee -a $GITHUB_STEP_SUMMARY + echo -e '\n
\n' >> $GITHUB_STEP_SUMMARY + echo ----- End of Metadata ----- + + linux-wheel: + if: ${{ github.event.inputs.build_linux == 'true' }} + # run only if "build_linux" is true: + name: Build ${{ matrix.libc }}linux_${{ matrix.arch }} for py${{ matrix.py }} + runs-on: ubuntu-20.04 + needs: ["sdist", "post-pending-status"] + outputs: + job-status: ${{ job.status }} + strategy: + matrix: + py: ["38", "39", "310", "311"] + arch: ["x86_64","i686"] + libc: ["many", "musl"] + include: + - py: "311" + arch: "aarch64" + libc: "many" + - py: "311" + arch: "ppc64le" + libc: "many" + - py: "311" + arch: "s390x" + libc: "many" + - py: "310" + arch: "aarch64" + libc: "many" + - py: "310" + arch: "ppc64le" + libc: "many" + - py: "310" + arch: "s390x" + libc: "many" + - py: "39" + arch: "aarch64" + libc: "many" + - py: "38" + arch: "aarch64" + libc: "many" + fail-fast: true + env: + BOOST_INCLUDE: include + BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z + GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GH_TARBALL_DL: ${{ secrets.GH_TARBALL_DL }} + steps: + - name: Install dependencies + run: | + sudo apt-get update + sudo apt-get install libboost-dev tree -y + - name: Download pre-built sdist + uses: actions/download-artifact@v4 + with: + name: cibw-sdist + - name: Extract the sdist tarball + run: tar -xvf *.tar.gz --strip-components=1 + - name: Restore Boost cache + uses: actions/cache@v3 + id: cache-boost + with: + path: ${{ env.BOOST_INCLUDE }}/boost + key: boost-${{env.BOOST_URL}} + - name: Install Boost Headers + if: steps.cache-boost.outputs.cache-hit != 'true' + run: | + mkdir -p $BOOST_INCLUDE + curl --progress-bar --location --output $BOOST_INCLUDE/download.7z $BOOST_URL + 7z -o$BOOST_INCLUDE x $BOOST_INCLUDE/download.7z -y -bd boost_1_78_0/boost + mv $BOOST_INCLUDE/boost_1_78_0/boost $BOOST_INCLUDE/boost + rm $BOOST_INCLUDE/download.7z + rm -r $BOOST_INCLUDE/boost_1_78_0 + - name: Set up QEMU + uses: docker/setup-qemu-action@v3 + with: + platforms: all + - name: Build wheels + uses: pypa/cibuildwheel@v2.17.0 + + env: + CIBW_ENVIRONMENT: BOOST_INCLUDE=${{ env.BOOST_INCLUDE }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + CIBW_BUILD: cp${{ matrix.py }}-${{ matrix.libc }}linux* + CIBW_ARCHS: ${{ matrix.arch }} + # CIBW_ENVIRONMENT_PASS_LINUX: CFLAGS + # CIBW_MANYLINUX_I686_IMAGE: + # CIBW_BEFORE_ALL_LINUX: yum groupinstall 'Development Tools' -y && which gcc && gcc --version + # yum-config-manager --enable rhel-server-rhscl-7-rpms \ + # && yum-config-manager --add-repo=https://copr.fedoraproject.org/coprs/rhscl/centos-release-scl/repo/epel-6/rhscl-centos-release-scl-epel-6.repo \ + # && yum-config-manager --add-repo=https://copr.fedoraproject.org/coprs/rhscl/centos-release-scl/repo/epel-7/rhscl-centos-release-scl-epel-7.repo \ + # && yum install centos-release-scl + # cibuildwheel on Linux uses a Docker container to run the build, so + # runner.temp is not available. cibuildwheel also uses the /tmp folder, so + # we should be pretty safe to also use that. + CIBW_TEST_COMMAND: pytest -vv --durations=100 /tmp/test/python + CIBW_BEFORE_TEST: | + curl -sL -H "Authorization: token $GH_TARBALL_DL" -o /tmp/cantera.tar.gz $REPO_API_URL \ + && tar -xzf /tmp/cantera.tar.gz --strip-components=1 -C /tmp "joebarteam11-cantera-avbp-3.0.0-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + # curl -sL "https://github.com/joebarteam11/cantera-avbp-3.0.0/archive/${{ needs.post-pending-status.outputs.incoming-sha }}.tar.gz" -o /tmp/cantera-avbp.tar.gz \ + # && tar -xzf /tmp/cantera-avbp.tar.gz --strip-components=1 -C /tmp "cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + # curl - + # NumPy is generally not available for these platforms so testing takes a + # while. This just skips the tests on these + # combinations, the wheels are still built and uploaded. + CIBW_TEST_SKIP: "*-manylinux_{i686,ppc64le,s390x} *musl*" + + - name: Archive the built wheels + uses: actions/upload-artifact@v3 + with: + path: ./wheelhouse/*.whl + name: wheels + + # windows-wheel: + # if: ${{ github.event.inputs.build_windows == 'true' }} + # name: Build Windows Wheels for py${{ matrix.py }} + # runs-on: windows-2019 + # needs: ["sdist", "post-pending-status"] + # outputs: + # job-status: ${{ job.status }} + # strategy: + # matrix: + # py: ["311"] #"38", "39", "310", + # arch: ["AMD64"] # , "x86"] + # fail-fast: true + # env: + # BOOST_ROOT: ${{ github.workspace }}/3rdparty/boost + # BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z + # steps: + # - name: Download pre-built sdist + # uses: actions/download-artifact@v4 + # with: + # name: cibw-sdist + # - name: Extract the sdist tarball + # run: tar -xvf *.tar.gz --strip-components=1 + # shell: bash + # - name: Restore Boost cache + # uses: actions/cache@v3 + # id: cache-boost + # with: + # path: ${{env.BOOST_ROOT}} + # key: boost-${{env.BOOST_URL}} + # - name: Install Boost Headers + # if: steps.cache-boost.outputs.cache-hit != 'true' + # run: | + # BOOST_ROOT=$(echo $BOOST_ROOT | sed 's/\\/\//g') + # mkdir -p $BOOST_ROOT + # curl --progress-bar --location --output $BOOST_ROOT/download.7z $BOOST_URL + # 7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_78_0/boost + # mv $BOOST_ROOT/boost_1_78_0/boost $BOOST_ROOT/boost + # rm $BOOST_ROOT/download.7z + # shell: bash + # - name: Build wheels + # uses: pypa/cibuildwheel@v2.19.1 + # env: + # CIBW_ENVIRONMENT: BOOST_INCLUDE=${BOOST_ROOT} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + # CIBW_ARCHS: ${{ matrix.arch }} + # CIBW_BUILD: cp${{ matrix.py }}-* + # CIBW_TEST_COMMAND: pytest -vv --durations=100 ${{ runner.temp }}/test/python + # CIBW_BEFORE_TEST: | + # curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ + # && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "joebarteam11-cantera-avbp-3.0.0-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + # - name: Archive the built wheels + # uses: actions/upload-artifact@v3 + # with: + # path: ./wheelhouse/*.whl + # name: cibw-wheels-windows-${{ strategy.job-index }} + + # macos-wheel: + # if: ${{ github.event.inputs.build_macos == 'true' }} + # name: Build ${{ matrix.arch }} macOS Wheels for py${{ matrix.py }} + # runs-on: macos-11 + # needs: ["sdist", "post-pending-status"] + # outputs: + # job-status: ${{ job.status }} + # strategy: + # matrix: + # py: ["39"] + # arch: ["arm64"] + # deployment_target: ["11.0"] + # include: + # - py: "38" + # deployment_target: "10.15" + # arch: "x86_64" + # - py: "38" + # deployment_target: "10.15" + # arch: "arm64" + # fail-fast: true + # env: + # MACOSX_DEPLOYMENT_TARGET: ${{ matrix.deployment_target }} + # steps: + # - name: Download pre-built sdist + # uses: actions/download-artifact@v4 + # with: + # name: cibw-sdist + # - name: Extract the sdist tarball + # run: tar -xvf *.tar.gz --strip-components=1 + # - name: Install Brew dependencies + # run: brew install boost + # - name: Build wheels + # uses: pypa/cibuildwheel@v2.17.0 + # env: + # CIBW_ENVIRONMENT: BOOST_INCLUDE="$(brew --prefix)/include" RUNNER_TEMP=${{ runner.temp }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + # CIBW_BUILD: cp${{ matrix.py }}-* + # CIBW_ARCHS_MACOS: ${{ matrix.arch }} + # # Testing won't be available for macOS ARM until native ARM runners are available. + # CIBW_TEST_SKIP: "*-macosx_arm64" + # CIBW_TEST_COMMAND: pytest -vv --durations=100 ${RUNNER_TEMP}/test/python + # CIBW_BEFORE_TEST: | + # curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ + # && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "joebarteam11-cantera-avbp-3.0.0-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + # - name: Archive the built wheels + # uses: actions/upload-artifact@v3 + # with: + # path: ./wheelhouse/*.whl + # name: wheels From e72b1277d0c0d5c2dbbc9371b071b53d807af22e Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 27 Aug 2025 14:11:22 +0200 Subject: [PATCH 46/98] Correction of cerfacs workflows (tested on local machine only) On branch FEATURE/github_workflows Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 229 ++++++++++++------------ 1 file changed, 116 insertions(+), 113 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 71e18d67d59..40b3fec8dc2 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -16,15 +16,15 @@ on: build_linux: description: "Build wheels on Linux" required: true - default: "true" - # build_windows: - # description: "Build wheels on Windows" - # required: true - # default: "false" - # build_macos: - # description: "Build wheels on MacOS" - # required: true - # default: "false" + default: "false" + build_windows: + description: "Build wheels on Windows" + required: true + default: "false" + build_macos: + description: "Build wheels on MacOS" + required: true + default: "false" concurrency: group: ${{ github.ref }}-${{ github.event.inputs.incoming_ref}} @@ -59,6 +59,7 @@ jobs: tag-ref: ${{ steps.munge-incoming-ref.outputs.tag-ref }} steps: - uses: actions/setup-python@v5 + # if: ${{ !env.ACT }} # Si act est utilisé (workflow local) on ne fait pas l'install de python with: python-version: '3.10' - name: Munge the incoming ref @@ -125,11 +126,12 @@ jobs: - uses: actions/checkout@v4 name: Checkout the repository with: - repository: "joebarteam11/cantera-avbp-3.0.0" + repository: "cerfacs/cantera-avbp" submodules: recursive ref: ${{ github.event.inputs.incoming_ref }} - name: Set Up Python 3.12 uses: actions/setup-python@v5 + if: ${{ !env.ACT }} # Si act est utilisé (workflow local) on ne fait pas l'install de python with: python-version: "3.12" - name: Install dependencies @@ -143,6 +145,7 @@ jobs: CYTHON_FORCE_REGEN: "1" - name: Archive the built sdist uses: actions/upload-artifact@v4 + if: ${{ !env.ACT }} with: path: ./build/python_sdist/dist/*.tar.gz name: cibw-sdist @@ -258,7 +261,7 @@ jobs: CIBW_TEST_COMMAND: pytest -vv --durations=100 /tmp/test/python CIBW_BEFORE_TEST: | curl -sL -H "Authorization: token $GH_TARBALL_DL" -o /tmp/cantera.tar.gz $REPO_API_URL \ - && tar -xzf /tmp/cantera.tar.gz --strip-components=1 -C /tmp "joebarteam11-cantera-avbp-3.0.0-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + && tar -xzf /tmp/cantera.tar.gz --strip-components=1 -C /tmp "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" # curl -sL "https://github.com/joebarteam11/cantera-avbp-3.0.0/archive/${{ needs.post-pending-status.outputs.incoming-sha }}.tar.gz" -o /tmp/cantera-avbp.tar.gz \ # && tar -xzf /tmp/cantera-avbp.tar.gz --strip-components=1 -C /tmp "cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" # curl - @@ -273,106 +276,106 @@ jobs: path: ./wheelhouse/*.whl name: wheels - # windows-wheel: - # if: ${{ github.event.inputs.build_windows == 'true' }} - # name: Build Windows Wheels for py${{ matrix.py }} - # runs-on: windows-2019 - # needs: ["sdist", "post-pending-status"] - # outputs: - # job-status: ${{ job.status }} - # strategy: - # matrix: - # py: ["311"] #"38", "39", "310", - # arch: ["AMD64"] # , "x86"] - # fail-fast: true - # env: - # BOOST_ROOT: ${{ github.workspace }}/3rdparty/boost - # BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z - # steps: - # - name: Download pre-built sdist - # uses: actions/download-artifact@v4 - # with: - # name: cibw-sdist - # - name: Extract the sdist tarball - # run: tar -xvf *.tar.gz --strip-components=1 - # shell: bash - # - name: Restore Boost cache - # uses: actions/cache@v3 - # id: cache-boost - # with: - # path: ${{env.BOOST_ROOT}} - # key: boost-${{env.BOOST_URL}} - # - name: Install Boost Headers - # if: steps.cache-boost.outputs.cache-hit != 'true' - # run: | - # BOOST_ROOT=$(echo $BOOST_ROOT | sed 's/\\/\//g') - # mkdir -p $BOOST_ROOT - # curl --progress-bar --location --output $BOOST_ROOT/download.7z $BOOST_URL - # 7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_78_0/boost - # mv $BOOST_ROOT/boost_1_78_0/boost $BOOST_ROOT/boost - # rm $BOOST_ROOT/download.7z - # shell: bash - # - name: Build wheels - # uses: pypa/cibuildwheel@v2.19.1 - # env: - # CIBW_ENVIRONMENT: BOOST_INCLUDE=${BOOST_ROOT} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - # CIBW_ARCHS: ${{ matrix.arch }} - # CIBW_BUILD: cp${{ matrix.py }}-* - # CIBW_TEST_COMMAND: pytest -vv --durations=100 ${{ runner.temp }}/test/python - # CIBW_BEFORE_TEST: | - # curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ - # && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "joebarteam11-cantera-avbp-3.0.0-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - # - name: Archive the built wheels - # uses: actions/upload-artifact@v3 - # with: - # path: ./wheelhouse/*.whl - # name: cibw-wheels-windows-${{ strategy.job-index }} + windows-wheel: + if: ${{ github.event.inputs.build_windows == 'true' }} + name: Build Windows Wheels for py${{ matrix.py }} + runs-on: windows-2019 + needs: ["sdist", "post-pending-status"] + outputs: + job-status: ${{ job.status }} + strategy: + matrix: + py: ["311"] #"38", "39", "310", + arch: ["AMD64"] # , "x86"] + fail-fast: true + env: + BOOST_ROOT: ${{ github.workspace }}/3rdparty/boost + BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z + steps: + - name: Download pre-built sdist + uses: actions/download-artifact@v4 + with: + name: cibw-sdist + - name: Extract the sdist tarball + run: tar -xvf *.tar.gz --strip-components=1 + shell: bash + - name: Restore Boost cache + uses: actions/cache@v3 + id: cache-boost + with: + path: ${{env.BOOST_ROOT}} + key: boost-${{env.BOOST_URL}} + - name: Install Boost Headers + if: steps.cache-boost.outputs.cache-hit != 'true' + run: | + BOOST_ROOT=$(echo $BOOST_ROOT | sed 's/\\/\//g') + mkdir -p $BOOST_ROOT + curl --progress-bar --location --output $BOOST_ROOT/download.7z $BOOST_URL + 7z -o$BOOST_ROOT x $BOOST_ROOT/download.7z -y -bd boost_1_78_0/boost + mv $BOOST_ROOT/boost_1_78_0/boost $BOOST_ROOT/boost + rm $BOOST_ROOT/download.7z + shell: bash + - name: Build wheels + uses: pypa/cibuildwheel@v2.19.1 + env: + CIBW_ENVIRONMENT: BOOST_INCLUDE=${BOOST_ROOT} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + CIBW_ARCHS: ${{ matrix.arch }} + CIBW_BUILD: cp${{ matrix.py }}-* + CIBW_TEST_COMMAND: pytest -vv --durations=100 ${{ runner.temp }}/test/python + CIBW_BEFORE_TEST: | + curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ + && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "joebarteam11-cantera-avbp-3.0.0-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + - name: Archive the built wheels + uses: actions/upload-artifact@v3 + with: + path: ./wheelhouse/*.whl + name: cibw-wheels-windows-${{ strategy.job-index }} - # macos-wheel: - # if: ${{ github.event.inputs.build_macos == 'true' }} - # name: Build ${{ matrix.arch }} macOS Wheels for py${{ matrix.py }} - # runs-on: macos-11 - # needs: ["sdist", "post-pending-status"] - # outputs: - # job-status: ${{ job.status }} - # strategy: - # matrix: - # py: ["39"] - # arch: ["arm64"] - # deployment_target: ["11.0"] - # include: - # - py: "38" - # deployment_target: "10.15" - # arch: "x86_64" - # - py: "38" - # deployment_target: "10.15" - # arch: "arm64" - # fail-fast: true - # env: - # MACOSX_DEPLOYMENT_TARGET: ${{ matrix.deployment_target }} - # steps: - # - name: Download pre-built sdist - # uses: actions/download-artifact@v4 - # with: - # name: cibw-sdist - # - name: Extract the sdist tarball - # run: tar -xvf *.tar.gz --strip-components=1 - # - name: Install Brew dependencies - # run: brew install boost - # - name: Build wheels - # uses: pypa/cibuildwheel@v2.17.0 - # env: - # CIBW_ENVIRONMENT: BOOST_INCLUDE="$(brew --prefix)/include" RUNNER_TEMP=${{ runner.temp }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - # CIBW_BUILD: cp${{ matrix.py }}-* - # CIBW_ARCHS_MACOS: ${{ matrix.arch }} - # # Testing won't be available for macOS ARM until native ARM runners are available. - # CIBW_TEST_SKIP: "*-macosx_arm64" - # CIBW_TEST_COMMAND: pytest -vv --durations=100 ${RUNNER_TEMP}/test/python - # CIBW_BEFORE_TEST: | - # curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ - # && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "joebarteam11-cantera-avbp-3.0.0-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - # - name: Archive the built wheels - # uses: actions/upload-artifact@v3 - # with: - # path: ./wheelhouse/*.whl - # name: wheels + macos-wheel: + if: ${{ github.event.inputs.build_macos == 'true' }} + name: Build ${{ matrix.arch }} macOS Wheels for py${{ matrix.py }} + runs-on: macos-11 + needs: ["sdist", "post-pending-status"] + outputs: + job-status: ${{ job.status }} + strategy: + matrix: + py: ["39"] + arch: ["arm64"] + deployment_target: ["11.0"] + # include: + # - py: "38" + # deployment_target: "10.15" + # arch: "x86_64" + # - py: "38" + # deployment_target: "10.15" + # arch: "arm64" + fail-fast: true + env: + MACOSX_DEPLOYMENT_TARGET: ${{ matrix.deployment_target }} + steps: + - name: Download pre-built sdist + uses: actions/download-artifact@v4 + with: + name: cibw-sdist + - name: Extract the sdist tarball + run: tar -xvf *.tar.gz --strip-components=1 + - name: Install Brew dependencies + run: brew install boost + - name: Build wheels + uses: pypa/cibuildwheel@v2.17.0 + env: + CIBW_ENVIRONMENT: BOOST_INCLUDE="$(brew --prefix)/include" RUNNER_TEMP=${{ runner.temp }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + CIBW_BUILD: cp${{ matrix.py }}-* + CIBW_ARCHS_MACOS: ${{ matrix.arch }} + # Testing won't be available for macOS ARM until native ARM runners are available. + CIBW_TEST_SKIP: "*-macosx_arm64" + CIBW_TEST_COMMAND: pytest -vv --durations=100 ${RUNNER_TEMP}/test/python + CIBW_BEFORE_TEST: | + curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ + && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + - name: Archive the built wheels + uses: actions/upload-artifact@v3 + with: + path: ./wheelhouse/*.whl + name: wheels From 804fd4032c1a0cb9036f7dfbe20966259899cf19 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 27 Aug 2025 15:51:07 +0200 Subject: [PATCH 47/98] Modify secret token name On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 40b3fec8dc2..2f3cd1296c3 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -53,7 +53,7 @@ jobs: name: Post a pending workflow status to cerfacs/cantera-avbp runs-on: ubuntu-22.04 env: - GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GH_TOKEN: ${{ secrets.GHT }} outputs: incoming-sha: ${{ steps.get-incoming-sha.outputs.incoming-sha }} tag-ref: ${{ steps.munge-incoming-ref.outputs.tag-ref }} @@ -209,7 +209,7 @@ jobs: env: BOOST_INCLUDE: include BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z - GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} + GH_TOKEN: ${{ secrets.GHT }} GH_TARBALL_DL: ${{ secrets.GH_TARBALL_DL }} steps: - name: Install dependencies From e558dc544c708f7f48bddb70654133df7b730dc5 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 27 Aug 2025 16:28:33 +0200 Subject: [PATCH 48/98] Update github secret with personal acces token On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 2f3cd1296c3..8621989963d 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -53,7 +53,7 @@ jobs: name: Post a pending workflow status to cerfacs/cantera-avbp runs-on: ubuntu-22.04 env: - GH_TOKEN: ${{ secrets.GHT }} + GH_TOKEN: ${{ secrets.PAT }} outputs: incoming-sha: ${{ steps.get-incoming-sha.outputs.incoming-sha }} tag-ref: ${{ steps.munge-incoming-ref.outputs.tag-ref }} @@ -209,7 +209,7 @@ jobs: env: BOOST_INCLUDE: include BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z - GH_TOKEN: ${{ secrets.GHT }} + GH_TOKEN: ${{ secrets.PAT }} GH_TARBALL_DL: ${{ secrets.GH_TARBALL_DL }} steps: - name: Install dependencies From 0cd27a497ace2795797331e070aeb49c59ff0549 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 14:04:12 +0200 Subject: [PATCH 49/98] Change macOS version to macos-13 for macos-wheel workflow On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 8621989963d..55751d98f0f 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -334,7 +334,7 @@ jobs: macos-wheel: if: ${{ github.event.inputs.build_macos == 'true' }} name: Build ${{ matrix.arch }} macOS Wheels for py${{ matrix.py }} - runs-on: macos-11 + runs-on: macos-13 needs: ["sdist", "post-pending-status"] outputs: job-status: ${{ job.status }} @@ -342,7 +342,7 @@ jobs: matrix: py: ["39"] arch: ["arm64"] - deployment_target: ["11.0"] + deployment_target: ["13.0"] # include: # - py: "38" # deployment_target: "10.15" From 03dc3051ce3678f67c85f8545428ef82dcf5c5e1 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 14:11:24 +0200 Subject: [PATCH 50/98] Update upload-artifact version to v4 On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 55751d98f0f..0471f3cdec8 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -375,7 +375,7 @@ jobs: curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - name: Archive the built wheels - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: path: ./wheelhouse/*.whl name: wheels From a851692e7ca36f2303639abfdebb49c5bbeba903 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 14:58:52 +0200 Subject: [PATCH 51/98] Add libomp hdf5 and doxygen to brew install On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 0471f3cdec8..2c24f87e08b 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -333,14 +333,14 @@ jobs: macos-wheel: if: ${{ github.event.inputs.build_macos == 'true' }} - name: Build ${{ matrix.arch }} macOS Wheels for py${{ matrix.py }} + name: Build ${{ matrix.arch }} macOS Wheels for Python ${{ matrix.python-version }} runs-on: macos-13 needs: ["sdist", "post-pending-status"] outputs: job-status: ${{ job.status }} strategy: matrix: - py: ["39"] + python-version: ["39"] arch: ["arm64"] deployment_target: ["13.0"] # include: @@ -360,13 +360,22 @@ jobs: name: cibw-sdist - name: Extract the sdist tarball run: tar -xvf *.tar.gz --strip-components=1 + # - name: Write dependencies to a file for caching # added from cantera + # run: | + # echo "scons ruamel.yaml numpy cython!=3.1.2 pandas pytest pytest-xdist pytest-github-actions-annotate-failures pint graphviz Jinja2" | tr " " "\n" > requirements.txt + # - name: Set up Python + # uses: actions/setup-python@v5 + # with: + # python-version: ${{ matrix.python-version }} + # cache: pip + # cache-dependency-path: requirements.txt - name: Install Brew dependencies - run: brew install boost + run: brew install --display-times boost libomp hdf5 doxygen - name: Build wheels uses: pypa/cibuildwheel@v2.17.0 env: CIBW_ENVIRONMENT: BOOST_INCLUDE="$(brew --prefix)/include" RUNNER_TEMP=${{ runner.temp }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - CIBW_BUILD: cp${{ matrix.py }}-* + CIBW_BUILD: cp${{ matrix.python-version }}-* CIBW_ARCHS_MACOS: ${{ matrix.arch }} # Testing won't be available for macOS ARM until native ARM runners are available. CIBW_TEST_SKIP: "*-macosx_arm64" From 3f3bcd4b5b23b8e36b7c58e1fccc46694546b4e5 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 15:37:45 +0200 Subject: [PATCH 52/98] Force hdf5 static library for wheel creation On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 2c24f87e08b..403ecb9b7f2 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -370,11 +370,21 @@ jobs: # cache: pip # cache-dependency-path: requirements.txt - name: Install Brew dependencies - run: brew install --display-times boost libomp hdf5 doxygen + # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine + run: | + brew install --display-times boost libomp doxygen + brew install hdf5 --build-from-source --force-bottle - name: Build wheels uses: pypa/cibuildwheel@v2.17.0 env: - CIBW_ENVIRONMENT: BOOST_INCLUDE="$(brew --prefix)/include" RUNNER_TEMP=${{ runner.temp }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + CIBW_ENVIRONMENT: | + BOOST_INCLUDE="$(brew --prefix)/include" + RUNNER_TEMP=${{ runner.temp }} + CT_SKIP_SLOW=1 + REPO_API_URL=${{ env.REPO_API_URL }} + GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + HDF5_ROOT="$(brew --prefix hdf5)" + HDF5_STATIC=1 CIBW_BUILD: cp${{ matrix.python-version }}-* CIBW_ARCHS_MACOS: ${{ matrix.arch }} # Testing won't be available for macOS ARM until native ARM runners are available. From 13f88f77f07efbcecac7054db2261838d531b4ee Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 15:44:51 +0200 Subject: [PATCH 53/98] Bugfix incompatible options On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 403ecb9b7f2..829f2832b6b 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -373,7 +373,7 @@ jobs: # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine run: | brew install --display-times boost libomp doxygen - brew install hdf5 --build-from-source --force-bottle + brew install hdf5 --build-from-source - name: Build wheels uses: pypa/cibuildwheel@v2.17.0 env: From 6f73cb6596e90c066acef019976495d77a451137 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 16:10:15 +0200 Subject: [PATCH 54/98] bugfix in CIBW_ENVIRONMENT declarations (only the first line was read if | is used instead of > On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 829f2832b6b..16fd7e24441 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -377,7 +377,7 @@ jobs: - name: Build wheels uses: pypa/cibuildwheel@v2.17.0 env: - CIBW_ENVIRONMENT: | + CIBW_ENVIRONMENT: > BOOST_INCLUDE="$(brew --prefix)/include" RUNNER_TEMP=${{ runner.temp }} CT_SKIP_SLOW=1 From 029ad39ce2d24e666b201c810264716e68eaf564 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 16:59:57 +0200 Subject: [PATCH 55/98] Try to force HDF5 lib in CIBW On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 16fd7e24441..ea67a2d8890 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -372,8 +372,9 @@ jobs: - name: Install Brew dependencies # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine run: | - brew install --display-times boost libomp doxygen - brew install hdf5 --build-from-source + brew install --display-times boost libomp doxygen hdf5 + # brew install cmake@3.31.6 + # brew install hdf5 --build-from-source - name: Build wheels uses: pypa/cibuildwheel@v2.17.0 env: @@ -383,8 +384,9 @@ jobs: CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + HDF5_DIR="$(brew --prefix hdf5)" HDF5_ROOT="$(brew --prefix hdf5)" - HDF5_STATIC=1 + # HDF5_STATIC=1 CIBW_BUILD: cp${{ matrix.python-version }}-* CIBW_ARCHS_MACOS: ${{ matrix.arch }} # Testing won't be available for macOS ARM until native ARM runners are available. From 2ba8aed4eaf6daadc9a015d3780b25f9eba7e10a Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 17:33:21 +0200 Subject: [PATCH 56/98] Test imposing CMake3.31.6 version On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 24 +++++++++++++++++++----- 1 file changed, 19 insertions(+), 5 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index ea67a2d8890..2deb89feba5 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -372,21 +372,29 @@ jobs: - name: Install Brew dependencies # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine run: | - brew install --display-times boost libomp doxygen hdf5 - # brew install cmake@3.31.6 - # brew install hdf5 --build-from-source + brew install --display-times boost libomp doxygen + # brew install --display-times boost libomp doxygen hdf5 + brew install cmake@3.31.6 + brew install hdf5 --build-from-source - name: Build wheels uses: pypa/cibuildwheel@v2.17.0 env: + # CIBW_ENVIRONMENT: > + # BOOST_INCLUDE="$(brew --prefix)/include" + # RUNNER_TEMP=${{ runner.temp }} + # CT_SKIP_SLOW=1 + # REPO_API_URL=${{ env.REPO_API_URL }} + # GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + # HDF5_DIR="$(brew --prefix hdf5)" + # HDF5_ROOT="$(brew --prefix hdf5)" CIBW_ENVIRONMENT: > BOOST_INCLUDE="$(brew --prefix)/include" RUNNER_TEMP=${{ runner.temp }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - HDF5_DIR="$(brew --prefix hdf5)" HDF5_ROOT="$(brew --prefix hdf5)" - # HDF5_STATIC=1 + HDF5_STATIC=1 CIBW_BUILD: cp${{ matrix.python-version }}-* CIBW_ARCHS_MACOS: ${{ matrix.arch }} # Testing won't be available for macOS ARM until native ARM runners are available. @@ -395,6 +403,12 @@ jobs: CIBW_BEFORE_TEST: | curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + - name: print info + run: | + pwd + ls + ls ${{ runner.temp }} + cat ${{ runner.temp }}/cantera.conf - name: Archive the built wheels uses: actions/upload-artifact@v4 with: From d4402f5acc7a48a27ef8526802413e7e8e8fde93 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 18:00:44 +0200 Subject: [PATCH 57/98] Test On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 2deb89feba5..b737353b514 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -374,7 +374,7 @@ jobs: run: | brew install --display-times boost libomp doxygen # brew install --display-times boost libomp doxygen hdf5 - brew install cmake@3.31.6 + # brew install cmake@3.31.6 brew install hdf5 --build-from-source - name: Build wheels uses: pypa/cibuildwheel@v2.17.0 @@ -395,6 +395,7 @@ jobs: GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} HDF5_ROOT="$(brew --prefix hdf5)" HDF5_STATIC=1 + CANTERA_USE_SYSTEM_HDF5=y CIBW_BUILD: cp${{ matrix.python-version }}-* CIBW_ARCHS_MACOS: ${{ matrix.arch }} # Testing won't be available for macOS ARM until native ARM runners are available. From f4613fae0cce5aef4a29ec500972df03abdbc9e2 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 18:22:12 +0200 Subject: [PATCH 58/98] test On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 27 +++++++++++++------------ 1 file changed, 14 insertions(+), 13 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index b737353b514..2e12f4ef16c 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -372,30 +372,31 @@ jobs: - name: Install Brew dependencies # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine run: | - brew install --display-times boost libomp doxygen - # brew install --display-times boost libomp doxygen hdf5 + # brew install --display-times boost libomp doxygen + brew install --display-times boost libomp doxygen hdf5 # brew install cmake@3.31.6 - brew install hdf5 --build-from-source + # brew install hdf5 --build-from-source - name: Build wheels uses: pypa/cibuildwheel@v2.17.0 env: - # CIBW_ENVIRONMENT: > - # BOOST_INCLUDE="$(brew --prefix)/include" - # RUNNER_TEMP=${{ runner.temp }} - # CT_SKIP_SLOW=1 - # REPO_API_URL=${{ env.REPO_API_URL }} - # GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - # HDF5_DIR="$(brew --prefix hdf5)" - # HDF5_ROOT="$(brew --prefix hdf5)" CIBW_ENVIRONMENT: > BOOST_INCLUDE="$(brew --prefix)/include" RUNNER_TEMP=${{ runner.temp }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + # HDF5_DIR="$(brew --prefix hdf5)" HDF5_ROOT="$(brew --prefix hdf5)" - HDF5_STATIC=1 - CANTERA_USE_SYSTEM_HDF5=y + HDF5_USE_STATIC_LIBS=ON + # CIBW_ENVIRONMENT: > + # BOOST_INCLUDE="$(brew --prefix)/include" + # RUNNER_TEMP=${{ runner.temp }} + # CT_SKIP_SLOW=1 + # REPO_API_URL=${{ env.REPO_API_URL }} + # GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + # HDF5_ROOT="$(brew --prefix hdf5)" + # HDF5_STATIC=1 + # CANTERA_USE_SYSTEM_HDF5=y CIBW_BUILD: cp${{ matrix.python-version }}-* CIBW_ARCHS_MACOS: ${{ matrix.arch }} # Testing won't be available for macOS ARM until native ARM runners are available. From 4bf6c61c03c13840cac30702a93735f7f9822c60 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 18:28:10 +0200 Subject: [PATCH 59/98] Bugfix in CIBW_ENVIRONMENT On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 2e12f4ef16c..80d5fd3fe7e 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -385,7 +385,6 @@ jobs: CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - # HDF5_DIR="$(brew --prefix hdf5)" HDF5_ROOT="$(brew --prefix hdf5)" HDF5_USE_STATIC_LIBS=ON # CIBW_ENVIRONMENT: > From 7bd40396ec8c2f9f573d860cf0cbffd3216a4ed9 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 29 Aug 2025 18:48:34 +0200 Subject: [PATCH 60/98] Comment print info job --- .github/workflows/CERFACS_packaging.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 80d5fd3fe7e..883e9095ffe 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -404,12 +404,12 @@ jobs: CIBW_BEFORE_TEST: | curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - - name: print info - run: | - pwd - ls - ls ${{ runner.temp }} - cat ${{ runner.temp }}/cantera.conf + # - name: print info + # run: | + # ls + # pwd + # ls ${{ runner.temp }} + # cat ${{ runner.temp }}/cantera.conf - name: Archive the built wheels uses: actions/upload-artifact@v4 with: From c9b264e03d099e47ce96c10cbee8abf7846b3cb5 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Thu, 4 Sep 2025 17:28:08 +0200 Subject: [PATCH 61/98] Adapted MACOS wheel workflow from cantera official wheel generator (https://github.com/cantera/pypi-packages) On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: new file: .github/build_dependencies.sh new file: .github/cibw_before_all_macos.sh new file: .github/dependencies.sh modified: .github/workflows/CERFACS_packaging.yml --- .github/build_dependencies.sh | 88 +++++++++++++ .github/cibw_before_all_macos.sh | 95 ++++++++++++++ .github/dependencies.sh | 6 + .github/workflows/CERFACS_packaging.yml | 167 +++++++++++++++++------- 4 files changed, 308 insertions(+), 48 deletions(-) create mode 100644 .github/build_dependencies.sh create mode 100644 .github/cibw_before_all_macos.sh create mode 100644 .github/dependencies.sh diff --git a/.github/build_dependencies.sh b/.github/build_dependencies.sh new file mode 100644 index 00000000000..3fc66717909 --- /dev/null +++ b/.github/build_dependencies.sh @@ -0,0 +1,88 @@ +#!/bin/bash +pushd ${RUNNER_TEMP} + +curl -fsSLO "https://github.com/HDFGroup/hdf5/releases/download/hdf5_${HDF5_VERSION}/hdf5-${HDF5_VERSION}.tar.gz" +tar -xzf hdf5-${HDF5_VERSION}.tar.gz +mkdir -p hdf5-${HDF5_VERSION}/build +pushd hdf5-${HDF5_VERSION}/build + +cmake -G "$GENERATOR" \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${HDF5_DIR}" \ + -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON \ + -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON \ + -DHDF5_BUILD_EXAMPLES:BOOL=OFF \ + -DHDF5_BUILD_TOOLS:BOOL=OFF \ + -DBUILD_TESTING:BOOL=OFF \ + -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ \ + -DZLIB_PACKAGE_NAME:STRING=zlib \ + -DZLIB_TGZ_NAME:STRING=zlib-${ZLIB_VERSION}.tar.gz \ + -DZLIB_TGZ_ORIGPATH:STRING=https://github.com/madler/zlib/releases/download/v${ZLIB_VERSION} \ + -DZLIB_USE_LOCALCONTENT:BOOL=OFF \ + -DLIBAEC_PACKAGE_NAME:STRING=libaec \ + -DLIBAEC_TGZ_NAME:STRING=libaec-${LIBAEC_VERSION}.tar.gz \ + -DLIBAEC_TGZ_ORIGPATH:STRING=https://github.com/MathisRosenhauer/libaec/releases/download/v${LIBAEC_VERSION} \ + -DLIBAEC_USE_LOCALCONTENT:BOOL=OFF \ + -DHDF_PACKAGE_NAMESPACE:STRING=ct_ \ + .. + +cmake --build . --target install --config Release +popd + +curl -fsSLO https://github.com/BlueBrain/HighFive/archive/refs/tags/v${HIGHFIVE_VERSION}.tar.gz +tar -xzf v${HIGHFIVE_VERSION}.tar.gz +mkdir -p HighFive-${HIGHFIVE_VERSION}/build +pushd HighFive-${HIGHFIVE_VERSION}/build + +cmake -G "$GENERATOR" \ + -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \ + -DCMAKE_BUILD_TYPE=Release \ + -DHDF5_ROOT="${HDF5_DIR}" \ + -DCMAKE_INSTALL_PREFIX="${HIGHFIVE_DIR}" \ + -DHIGHFIVE_USE_BOOST:BOOL=OFF \ + -DHIGHFIVE_UNIT_TESTS:BOOL=OFF \ + -DHIGHFIVE_EXAMPLES:BOOL=OFF \ + -DHIGHFIVE_BUILD_DOCS:BOOL=OFF \ + .. + +cmake --build . --target install --config Release +popd + +curl -fsSLO https://github.com/LLNL/sundials/releases/download/v${SUNDIALS_VERSION}/sundials-${SUNDIALS_VERSION}.tar.gz +tar -xzf sundials-${SUNDIALS_VERSION}.tar.gz +mkdir -p sundials-${SUNDIALS_VERSION}/build +pushd sundials-${SUNDIALS_VERSION}/build + +cmake -G "$GENERATOR" \ + -DCMAKE_BUILD_TYPE=Release \ + -DCMAKE_INSTALL_PREFIX="${SUNDIALS_DIR}" \ + -DEXAMPLES_INSTALL=OFF \ + -DEXAMPLES_ENABLE_C=OFF \ + -DBUILD_ARKODE=OFF \ + -DBUILD_CVODE=OFF \ + -DBUILD_IDA=OFF \ + -DBUILD_KINSOL=OFF \ + -DBUILD_CPODES=OFF \ + -DBUILD_FORTRAN_MODULE_INTERFACE=OFF \ + "${SUNDIALS_BUILD_OPTIONS[@]}" \ + .. + +cmake --build . --target install --config Release +popd + +curl -fsSLO https://github.com/jbeder/yaml-cpp/archive/refs/tags/${YAML_CPP_VERSION}.tar.gz +tar -xzf ${YAML_CPP_VERSION}.tar.gz +mkdir -p yaml-cpp-${YAML_CPP_VERSION}/build +pushd yaml-cpp-${YAML_CPP_VERSION}/build +cmake -G "$GENERATOR" \ + -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \ + -DCMAKE_INSTALL_PREFIX="${YAML_CPP_DIR}" \ + -DCMAKE_BUILD_TYPE:STRING=Release \ + -DCMAKE_INSTALL_LIBDIR:STRING=lib \ + -DYAML_CPP_FORMAT_SOURCE:BOOL=OFF \ + -DBUILD_TESTING:BOOL=OFF \ + -DBUILD_SHARED_LIBS:BOOL=ON \ + .. + +cmake --build . --target install --config Release +popd \ No newline at end of file diff --git a/.github/cibw_before_all_macos.sh b/.github/cibw_before_all_macos.sh new file mode 100644 index 00000000000..1e4a949ed46 --- /dev/null +++ b/.github/cibw_before_all_macos.sh @@ -0,0 +1,95 @@ +#!/bin/bash +# Adapted from h5py. Licensed under the BSD 3-Clause license. +# Copyright (c) 2008 Andrew Collette and contributors +# All rights reserved. + +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions are +# met: + +# 1. Redistributions of source code must retain the above copyright +# notice, this list of conditions and the following disclaimer. + +# 2. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the +# distribution. + +# 3. Neither the name of the copyright holder nor the names of its +# contributors may be used to endorse or promote products derived from +# this software without specific prior written permission. + +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +# HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +set -eo pipefail # Option pour que le script exit si une erreur est détecté dans l'un des pipeline +set +x # set -x correspond au mode debug qui permet de print les commende avant de les exécuter, set -x permet d'éviter ça (utile pour éviter que les token github apparaissent dans les log) + +function setup_github_env { + echo "HDF5_ROOT=${HDF5_DIR}" | tee -a $GITHUB_ENV + echo "HighFive_ROOT=${HIGHFIVE_DIR}" | tee -a $GITHUB_ENV + echo "SUNDIALS_ROOT=${SUNDIALS_DIR}" | tee -a $GITHUB_ENV + echo "MACOSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}" | tee -a $GITHUB_ENV + echo "DYLD_FALLBACK_LIBRARY_PATH=${HDF5_DIR}/lib:${YAML_CPP_DIR}/lib" | tee -a $GITHUB_ENV + echo "yaml-cpp_ROOT=${YAML_CPP_DIR}" | tee -a $GITHUB_ENV +} + +# Check if the current script ($0) is called with the correct option ($1) which should correspond to the project path +if [[ "$1" == "" ]] ; then + echo "Usage: $0 " + exit 1 +fi + +PROJECT_PATH="$1" +ARCH=$(uname -m) # Récupère l'architecture du système (arm64 / x86_64 ...) +GENERATOR="Ninja" +SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd ) + +source "${SCRIPT_DIR}/dependencies.sh" + +HDF5_DIR="${PROJECT_PATH}/cache/hdf5/${HDF5_VERSION}-${ARCH}" +HIGHFIVE_DIR="${PROJECT_PATH}/cache/highfive/${HIGHFIVE_VERSION}-${ARCH}" +SUNDIALS_DIR="${PROJECT_PATH}/cache/sundials/${SUNDIALS_VERSION}-${ARCH}" +SUNDIALS_BUILD_OPTIONS=( + "-DENABLE_LAPACK=ON" + "-DBLA_VENDOR=Apple" + "-DSUNDIALS_LAPACK_CASE=LOWER" + "-DSUNDIALS_LAPACK_UNDERSCORES=NONE" +) +YAML_CPP_DIR="${PROJECT_PATH}/cache/yaml-cpp/${YAML_CPP_VERSION}-${ARCH}" + +# When compiling HDF5, we should use the minimum across all Python versions for a given +# arch, for versions see for example a more updated version of the following: +# https://github.com/pypa/cibuildwheel/blob/9c75ea15c2f31a77e6043b80b1b7081372319d85/cibuildwheel/macos.py#L302-L315 +if [[ "${ARCH}" == "arm64" ]]; then + export MACOSX_DEPLOYMENT_TARGET="11.0" +else + # This is the minimum version for Cantera + export MACOSX_DEPLOYMENT_TARGET="10.15" +fi + +lib_name=libhdf5.dylib +inc_name=highfive.hpp + +if [ -f ${HDF5_DIR}/lib/${lib_name} ] && [ -f ${HIGHFIVE_DIR}/include/highfive/${inc_name} ]; then + echo "using cached build" + setup_github_env + exit 0 +else + echo "building dependencies" +fi + +brew install ninja cmake --formula + +source "${SCRIPT_DIR}/build_dependencies.sh" # Build here hdf5, highFive, sundials, yaml_cpp + +setup_github_env \ No newline at end of file diff --git a/.github/dependencies.sh b/.github/dependencies.sh new file mode 100644 index 00000000000..e940953234f --- /dev/null +++ b/.github/dependencies.sh @@ -0,0 +1,6 @@ +export HDF5_VERSION="1.14.5" +export LIBAEC_VERSION="1.1.3" +export ZLIB_VERSION="1.3.1" +export HIGHFIVE_VERSION="2.10.0" +export SUNDIALS_VERSION="7.1.1" +export YAML_CPP_VERSION="0.8.0" \ No newline at end of file diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 883e9095ffe..14cf40a77e8 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -340,26 +340,80 @@ jobs: job-status: ${{ job.status }} strategy: matrix: - python-version: ["39"] - arch: ["arm64"] - deployment_target: ["13.0"] - # include: - # - py: "38" - # deployment_target: "10.15" - # arch: "x86_64" - # - py: "38" - # deployment_target: "10.15" - # arch: "arm64" - fail-fast: true - env: - MACOSX_DEPLOYMENT_TARGET: ${{ matrix.deployment_target }} + # python-version: ["39"] + # arch: ["arm64"] + # deployment_target: ["13.0"] + include: + - py: "38" + # deployment_target: "10.15" + boost-arch: aarch64 + boost-toolset: clang + boost-platform-version: "13" + boost-version: "1.86.0" + arch: "arm64" + fail-fast: true # Si plusieurs configs dans la matrice et fail-fast = False permet de continuer le workflow pour les autre config. + # env: + # MACOSX_DEPLOYMENT_TARGET: ${{ matrix.deployment_target }} steps: + # - uses: actions/checkout@v5 ## Pas sur que cette étape soit nécéssaire car on a déja récupéré la bonne branche lors de la création de la sdist. + # name: Checkout the repository + # with: + # repository: "cerfacs/cantera-avbp" + # submodules: recursive + # ref: ${{ github.event.inputs.incoming_ref }} - name: Download pre-built sdist - uses: actions/download-artifact@v4 + uses: actions/download-artifact@v5 with: name: cibw-sdist - name: Extract the sdist tarball run: tar -xvf *.tar.gz --strip-components=1 + shell: bash + - name: Set test file download destination + id: download-test-files + run: | + mkdir -p "${RUNNER_TEMP}/ct-test-dir" + echo "test-root=${RUNNER_TEMP}/ct-test-dir" >> $GITHUB_OUTPUT + shell: bash + # - name: Download and unpack the tarball ## Pas sur que ce step fonctionne car le lien est invalide, et la sdist à déja été récupéré avant donc je voit pas à quoi ça pourrait servir + # run: | + # curl -fsSL "https://github.com/cantera/cantera/archive/${INCOMING_SHA}.tar.gz" -o cantera.tar.gz + # tar -xzf cantera.tar.gz --strip-components=1 "cantera-${INCOMING_SHA}/test" + # rm cantera.tar.gz + # shell: bash + # working-directory: "${{ steps.download-test-files.outputs.test-root }}" + # env: + # INCOMING_SHA: ${{ needs.post-pending-status.outputs.incoming-sha }} + - name: Install boost + uses: MarkusJx/install-boost@b1f0ee8b87cf60236b72440c72d0085d002770c5 # v2.5.0 + id: install-boost + with: + # REQUIRED: Specify the required boost version + # A list of supported versions can be found here: + # https://github.com/MarkusJx/prebuilt-boost/blob/main/versions-manifest.json + boost_version: ${{ matrix.boost-version }} + # OPTIONAL: Specify a custon install location + boost_install_dir: ${{ runner.temp }} + toolset: ${{ matrix.boost-toolset }} + platform_version: ${{ matrix.boost-platform-version }} + arch: ${{ matrix.boost-arch }} + # - name: Restore the cached built libraries ## This step is usesfull if several architechures are build. This enable to load lib instead of re-install them each time. This first time there are no cache directory thus this step is ignored (return cache-hit = 'false') + # id: restore-built-libraries + # # Our custom manylinux images already have all our dependencies installed + # uses: actions/cache/restore@v4 + # with: + # key: ${{ matrix.os }}-${{ matrix.arch }}-${{ hashFiles('dependencies.sh') }}-1 + # path: ${{ github.workspace }}/cache + - name: Build required libraries + run: bash ./cibw_before_all_macos.sh "${{ github.workspace }}" + # if: runner.os == 'macOS' + + - name: Set up CIBW environment + run: | + echo "Boost_ROOT=$BOOST_ROOT" >> $GITHUB_ENV + # if: runner.os == 'macOS' + env: + BOOST_ROOT: ${{ steps.install-boost.outputs.BOOST_ROOT }} + # - name: Write dependencies to a file for caching # added from cantera # run: | # echo "scons ruamel.yaml numpy cython!=3.1.2 pandas pytest pytest-xdist pytest-github-actions-annotate-failures pint graphviz Jinja2" | tr " " "\n" > requirements.txt @@ -369,41 +423,58 @@ jobs: # python-version: ${{ matrix.python-version }} # cache: pip # cache-dependency-path: requirements.txt - - name: Install Brew dependencies - # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine - run: | - # brew install --display-times boost libomp doxygen - brew install --display-times boost libomp doxygen hdf5 - # brew install cmake@3.31.6 - # brew install hdf5 --build-from-source + # - name: Save the cache # This step is usefull when multiple architectures are build. It enable to save in caches the installed libs that will be loaded in the following build by "Restore the cached built libraries" step. + # uses: actions/cache/save@v4 + # if: always() && runner.os != 'Linux' && steps.restore-built-libraries.outputs.cache-hit != 'true' + # with: + # path: ${{ github.workspace }}/cache + # key: ${{ steps.restore-built-libraries.outputs.cache-primary-key }} - name: Build wheels - uses: pypa/cibuildwheel@v2.17.0 + uses: pypa/cibuildwheel@c923d83ad9c1bc00211c5041d0c3f73294ff88f6 # 3.1.4 env: - CIBW_ENVIRONMENT: > - BOOST_INCLUDE="$(brew --prefix)/include" - RUNNER_TEMP=${{ runner.temp }} - CT_SKIP_SLOW=1 - REPO_API_URL=${{ env.REPO_API_URL }} - GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - HDF5_ROOT="$(brew --prefix hdf5)" - HDF5_USE_STATIC_LIBS=ON - # CIBW_ENVIRONMENT: > - # BOOST_INCLUDE="$(brew --prefix)/include" - # RUNNER_TEMP=${{ runner.temp }} - # CT_SKIP_SLOW=1 - # REPO_API_URL=${{ env.REPO_API_URL }} - # GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - # HDF5_ROOT="$(brew --prefix hdf5)" - # HDF5_STATIC=1 - # CANTERA_USE_SYSTEM_HDF5=y - CIBW_BUILD: cp${{ matrix.python-version }}-* - CIBW_ARCHS_MACOS: ${{ matrix.arch }} - # Testing won't be available for macOS ARM until native ARM runners are available. - CIBW_TEST_SKIP: "*-macosx_arm64" - CIBW_TEST_COMMAND: pytest -vv --durations=100 ${RUNNER_TEMP}/test/python - CIBW_BEFORE_TEST: | - curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ - && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + CANTERA_TEST_DIR: ${{ steps.download-test-files.outputs.test-root }} + # CIBW_ENVIRONMENT_LINUX: CT_SKIP_SLOW=1 CANTERA_TEST_DIR=/host${{ steps.download-test-files.outputs.test-root }} + # CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4 + # CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: delvewheel repair --add-path %HDF5_LIB_DIR%;%SUNDIALS_LIB_DIR%;%YAML_CPP_LIB_DIR% -w {dest_dir} {wheel} + CIBW_ENVIRONMNET_MACOS: CT_SKIP_SLOW=1 + CIBW_BUILD: "cp*-*" + CIBW_ARCHS: ${{ matrix.arch }} + + # - name: Install Brew dependencies + # # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine + # run: | + # # brew install --display-times boost libomp doxygen + # brew install --display-times boost libomp doxygen hdf5 + # # brew install cmake@3.31.6 + # # brew install hdf5 --build-from-source + # - name: Build wheels + # uses: pypa/cibuildwheel@v2.17.0 + # env: + # CIBW_ENVIRONMENT: > + # BOOST_INCLUDE="$(brew --prefix)/include" + # RUNNER_TEMP=${{ runner.temp }} + # CT_SKIP_SLOW=1 + # REPO_API_URL=${{ env.REPO_API_URL }} + # GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + # HDF5_ROOT="$(brew --prefix hdf5)" + # HDF5_USE_STATIC_LIBS=ON + # # CIBW_ENVIRONMENT: > + # # BOOST_INCLUDE="$(brew --prefix)/include" + # # RUNNER_TEMP=${{ runner.temp }} + # # CT_SKIP_SLOW=1 + # # REPO_API_URL=${{ env.REPO_API_URL }} + # # GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + # # HDF5_ROOT="$(brew --prefix hdf5)" + # # HDF5_STATIC=1 + # # CANTERA_USE_SYSTEM_HDF5=y + # CIBW_BUILD: cp${{ matrix.python-version }}-* + # CIBW_ARCHS_MACOS: ${{ matrix.arch }} + # # Testing won't be available for macOS ARM until native ARM runners are available. + # CIBW_TEST_SKIP: "*-macosx_arm64" + # CIBW_TEST_COMMAND: pytest -vv --durations=100 ${RUNNER_TEMP}/test/python + # CIBW_BEFORE_TEST: | + # curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ + # && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" # - name: print info # run: | # ls @@ -414,4 +485,4 @@ jobs: uses: actions/upload-artifact@v4 with: path: ./wheelhouse/*.whl - name: wheels + name: cibw-wheels-${{ runner.os }}-${{ strategy.job-index }} From 5c4a50a4718ce7b51a2d5cc76e50e3eb9cb28d19 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Thu, 4 Sep 2025 17:48:12 +0200 Subject: [PATCH 62/98] Boost lib not available for MACOS13 and arm34 architecture -> switched to MACOS14 On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 14cf40a77e8..dcf57c9464f 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -334,7 +334,7 @@ jobs: macos-wheel: if: ${{ github.event.inputs.build_macos == 'true' }} name: Build ${{ matrix.arch }} macOS Wheels for Python ${{ matrix.python-version }} - runs-on: macos-13 + runs-on: macos-14 needs: ["sdist", "post-pending-status"] outputs: job-status: ${{ job.status }} @@ -344,11 +344,11 @@ jobs: # arch: ["arm64"] # deployment_target: ["13.0"] include: - - py: "38" + - # py: "38" # deployment_target: "10.15" boost-arch: aarch64 boost-toolset: clang - boost-platform-version: "13" + boost-platform-version: "14" boost-version: "1.86.0" arch: "arm64" fail-fast: true # Si plusieurs configs dans la matrice et fail-fast = False permet de continuer le workflow pour les autre config. From 9ab56fca5af354d4d1cd0e485d2e3c1db1d949b0 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 16:13:07 +0200 Subject: [PATCH 63/98] Trying to find *.sh in my repo On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index dcf57c9464f..8d5cafa70b8 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -404,7 +404,7 @@ jobs: # key: ${{ matrix.os }}-${{ matrix.arch }}-${{ hashFiles('dependencies.sh') }}-1 # path: ${{ github.workspace }}/cache - name: Build required libraries - run: bash ./cibw_before_all_macos.sh "${{ github.workspace }}" + run: bash .github/cibw_before_all_macos.sh "${{ github.workspace }}" # if: runner.os == 'macOS' - name: Set up CIBW environment From 5dfd512d64e1b73eb3d7947c242fbd549b281dbb Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 16:19:25 +0200 Subject: [PATCH 64/98] Add debug step to get more info where .sh files are On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 8d5cafa70b8..7d263a78c81 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -403,6 +403,14 @@ jobs: # with: # key: ${{ matrix.os }}-${{ matrix.arch }}-${{ hashFiles('dependencies.sh') }}-1 # path: ${{ github.workspace }}/cache + - name: Debug repo content + run: | + echo "=== Liste du contenu à la racine ===" + ls -alh + echo "=== Liste du contenu de .github ===" + ls -alh .github || echo ".github n'existe pas" + echo "=== Liste récursive de .github ===" + ls -R .github || echo ".github n'existe pas" - name: Build required libraries run: bash .github/cibw_before_all_macos.sh "${{ github.workspace }}" # if: runner.os == 'macOS' From e9acd2c08ef0b319aef1a1cc2844d271ce691f70 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 16:51:39 +0200 Subject: [PATCH 65/98] Add a new job to save .sh scripts to artifacts On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 55 +++++++++++++++++++++++++ 1 file changed, 55 insertions(+) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 7d263a78c81..620b126da70 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -166,6 +166,61 @@ jobs: cat out/sdist/*/PKG-INFO | sed 's/^/ /' | tee -a $GITHUB_STEP_SUMMARY echo -e '\n\n' >> $GITHUB_STEP_SUMMARY echo ----- End of Metadata ----- + + upload-sh-scripts: + name: Upload the *.sh scripts required for installation + runs-on: ubuntu-latest + needs: + - "post-pending-status" + outputs: + job-status: ${{ job.status }} + steps: + # - name: Install dependencies + # run: | + # sudo apt-get update + # sudo apt-get install libboost-dev + - uses: actions/checkout@v5 + name: Checkout the repository + with: + repository: "cerfacs/cantera-avbp" + submodules: recursive + ref: ${{ github.event.inputs.incoming_ref }} + # - name: Set Up Python 3.12 + # uses: actions/setup-python@v5 + # if: ${{ !env.ACT }} # Si act est utilisé (workflow local) on ne fait pas l'install de python + # with: + # python-version: "3.12" + # - name: Install dependencies + # run: python3 -m pip install -U pip scons build + # - name: Build the sdist + # run: | + # python3 `which scons` sdist f90_interface=n python_package='none' \ + # system_blas_lapack=n system_sundials=n system_eigen=n system_fmt=n \ + # system_yamlcpp=n googletest=none env_vars='CYTHON_FORCE_REGEN' + # env: + # CYTHON_FORCE_REGEN: "1" + - name: Archive the *.sh scripts + uses: actions/upload-artifact@v4 + with: + path: ./github/*.sh + name: sh-scripts + if-no-files-found: error + # # Copied from https://github.com/hynek/build-and-inspect-python-package/ + # - name: Show SDist contents hierarchically, including metadata. + # shell: bash + # run: | + # mkdir -p /tmp/out/sdist + # cp build/python_sdist/dist/*.tar.gz /tmp/ + # cd /tmp + # tar xf *.tar.gz -C out/sdist + # echo -e '\n
SDist contents\n' >> $GITHUB_STEP_SUMMARY + # (cd /tmp/out/sdist && tree -Da --timefmt="%Y-%m-%dT%H:%M:%SZ" * | sed 's/^/ /' | tee -a $GITHUB_STEP_SUMMARY) + # echo -e '\n
\n' >> $GITHUB_STEP_SUMMARY + # echo ----- Metadata Follows ----- + # echo -e '\n
Metadata\n' >> $GITHUB_STEP_SUMMARY + # cat out/sdist/*/PKG-INFO | sed 's/^/ /' | tee -a $GITHUB_STEP_SUMMARY + # echo -e '\n
\n' >> $GITHUB_STEP_SUMMARY + # echo ----- End of Metadata ----- linux-wheel: if: ${{ github.event.inputs.build_linux == 'true' }} From b4cef6c79d2145a0c228af92e271f6da724ec749 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 16:57:26 +0200 Subject: [PATCH 66/98] Print info for debug On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 620b126da70..6fb751a3b1a 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -183,7 +183,7 @@ jobs: name: Checkout the repository with: repository: "cerfacs/cantera-avbp" - submodules: recursive + # submodules: recursive ref: ${{ github.event.inputs.incoming_ref }} # - name: Set Up Python 3.12 # uses: actions/setup-python@v5 @@ -199,6 +199,14 @@ jobs: # system_yamlcpp=n googletest=none env_vars='CYTHON_FORCE_REGEN' # env: # CYTHON_FORCE_REGEN: "1" + - name: Debug repo content + run: | + echo "=== Liste du contenu à la racine ===" + ls -alh + echo "=== Liste du contenu de .github ===" + ls -alh .github || echo ".github n'existe pas" + echo "=== Liste récursive de .github ===" + ls -R .github || echo ".github n'existe pas" - name: Archive the *.sh scripts uses: actions/upload-artifact@v4 with: From 1d817c8b89c09248596998346ce7197d6cef1bdb Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 16:59:49 +0200 Subject: [PATCH 67/98] Bugfix path for .sh scripts On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 6fb751a3b1a..60cab5f7955 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -199,18 +199,18 @@ jobs: # system_yamlcpp=n googletest=none env_vars='CYTHON_FORCE_REGEN' # env: # CYTHON_FORCE_REGEN: "1" - - name: Debug repo content - run: | - echo "=== Liste du contenu à la racine ===" - ls -alh - echo "=== Liste du contenu de .github ===" - ls -alh .github || echo ".github n'existe pas" - echo "=== Liste récursive de .github ===" - ls -R .github || echo ".github n'existe pas" + # - name: Debug repo content + # run: | + # echo "=== Liste du contenu à la racine ===" + # ls -alh + # echo "=== Liste du contenu de .github ===" + # ls -alh .github || echo ".github n'existe pas" + # echo "=== Liste récursive de .github ===" + # ls -R .github || echo ".github n'existe pas" - name: Archive the *.sh scripts uses: actions/upload-artifact@v4 with: - path: ./github/*.sh + path: .github/*.sh name: sh-scripts if-no-files-found: error # # Copied from https://github.com/hynek/build-and-inspect-python-package/ From da72fc52d6b28f67ab9964d617db9285019b476c Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 17:07:20 +0200 Subject: [PATCH 68/98] Give explicitetly the name of the .sh On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 60cab5f7955..c99141ce2a7 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -210,7 +210,10 @@ jobs: - name: Archive the *.sh scripts uses: actions/upload-artifact@v4 with: - path: .github/*.sh + path: | + .github/build_dependencies.sh + .github/cibw_before_all_macos.sh + .github/dependencies.sh name: sh-scripts if-no-files-found: error # # Copied from https://github.com/hynek/build-and-inspect-python-package/ From 8c476ed69037a97d6223a3fd6231a88d42285bf3 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 17:17:47 +0200 Subject: [PATCH 69/98] Add download step to get .sh from artifacts On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 48 +++---------------------- 1 file changed, 5 insertions(+), 43 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index c99141ce2a7..f9c7afbc234 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -175,38 +175,12 @@ jobs: outputs: job-status: ${{ job.status }} steps: - # - name: Install dependencies - # run: | - # sudo apt-get update - # sudo apt-get install libboost-dev - uses: actions/checkout@v5 name: Checkout the repository with: repository: "cerfacs/cantera-avbp" # submodules: recursive ref: ${{ github.event.inputs.incoming_ref }} - # - name: Set Up Python 3.12 - # uses: actions/setup-python@v5 - # if: ${{ !env.ACT }} # Si act est utilisé (workflow local) on ne fait pas l'install de python - # with: - # python-version: "3.12" - # - name: Install dependencies - # run: python3 -m pip install -U pip scons build - # - name: Build the sdist - # run: | - # python3 `which scons` sdist f90_interface=n python_package='none' \ - # system_blas_lapack=n system_sundials=n system_eigen=n system_fmt=n \ - # system_yamlcpp=n googletest=none env_vars='CYTHON_FORCE_REGEN' - # env: - # CYTHON_FORCE_REGEN: "1" - # - name: Debug repo content - # run: | - # echo "=== Liste du contenu à la racine ===" - # ls -alh - # echo "=== Liste du contenu de .github ===" - # ls -alh .github || echo ".github n'existe pas" - # echo "=== Liste récursive de .github ===" - # ls -R .github || echo ".github n'existe pas" - name: Archive the *.sh scripts uses: actions/upload-artifact@v4 with: @@ -216,22 +190,6 @@ jobs: .github/dependencies.sh name: sh-scripts if-no-files-found: error - # # Copied from https://github.com/hynek/build-and-inspect-python-package/ - # - name: Show SDist contents hierarchically, including metadata. - # shell: bash - # run: | - # mkdir -p /tmp/out/sdist - # cp build/python_sdist/dist/*.tar.gz /tmp/ - # cd /tmp - # tar xf *.tar.gz -C out/sdist - # echo -e '\n
SDist contents\n' >> $GITHUB_STEP_SUMMARY - # (cd /tmp/out/sdist && tree -Da --timefmt="%Y-%m-%dT%H:%M:%SZ" * | sed 's/^/ /' | tee -a $GITHUB_STEP_SUMMARY) - # echo -e '\n
\n' >> $GITHUB_STEP_SUMMARY - # echo ----- Metadata Follows ----- - # echo -e '\n
Metadata\n' >> $GITHUB_STEP_SUMMARY - # cat out/sdist/*/PKG-INFO | sed 's/^/ /' | tee -a $GITHUB_STEP_SUMMARY - # echo -e '\n
\n' >> $GITHUB_STEP_SUMMARY - # echo ----- End of Metadata ----- linux-wheel: if: ${{ github.event.inputs.build_linux == 'true' }} @@ -401,7 +359,7 @@ jobs: if: ${{ github.event.inputs.build_macos == 'true' }} name: Build ${{ matrix.arch }} macOS Wheels for Python ${{ matrix.python-version }} runs-on: macos-14 - needs: ["sdist", "post-pending-status"] + needs: ["sdist","upload-sh-scripts", "post-pending-status"] outputs: job-status: ${{ job.status }} strategy: @@ -427,6 +385,10 @@ jobs: # repository: "cerfacs/cantera-avbp" # submodules: recursive # ref: ${{ github.event.inputs.incoming_ref }} + - name: Download shell scripts required to set-up environments and install libraries + uses: actions/download-artifact@v5 + with: + name: sh-scripts - name: Download pre-built sdist uses: actions/download-artifact@v5 with: From cf86cf00fb13b7de141e8cafbda2dcc5eb420a5a Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 17:25:06 +0200 Subject: [PATCH 70/98] Bugfix: wrong path On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index f9c7afbc234..1d9cfa880cb 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -431,16 +431,16 @@ jobs: # with: # key: ${{ matrix.os }}-${{ matrix.arch }}-${{ hashFiles('dependencies.sh') }}-1 # path: ${{ github.workspace }}/cache - - name: Debug repo content - run: | - echo "=== Liste du contenu à la racine ===" - ls -alh - echo "=== Liste du contenu de .github ===" - ls -alh .github || echo ".github n'existe pas" - echo "=== Liste récursive de .github ===" - ls -R .github || echo ".github n'existe pas" + # - name: Debug repo content + # run: | + # echo "=== Liste du contenu à la racine ===" + # ls -alh + # echo "=== Liste du contenu de .github ===" + # ls -alh .github || echo ".github n'existe pas" + # echo "=== Liste récursive de .github ===" + # ls -R .github || echo ".github n'existe pas" - name: Build required libraries - run: bash .github/cibw_before_all_macos.sh "${{ github.workspace }}" + run: bash cibw_before_all_macos.sh "${{ github.workspace }}" # if: runner.os == 'macOS' - name: Set up CIBW environment From 72953a7b9898d741aa1d3805538fbc48f691dd8e Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 17:32:06 +0200 Subject: [PATCH 71/98] Need to uninstall cmake before installing brew cmake version On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/cibw_before_all_macos.sh --- .github/cibw_before_all_macos.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/cibw_before_all_macos.sh b/.github/cibw_before_all_macos.sh index 1e4a949ed46..921722e8109 100644 --- a/.github/cibw_before_all_macos.sh +++ b/.github/cibw_before_all_macos.sh @@ -88,6 +88,8 @@ else echo "building dependencies" fi +brew uninstall cmake + brew install ninja cmake --formula source "${SCRIPT_DIR}/build_dependencies.sh" # Build here hdf5, highFive, sundials, yaml_cpp From 667583002dd295677a4e3ca560f5cab8cf3f1e6a Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 17:59:27 +0200 Subject: [PATCH 72/98] Try to force cython version to 3.1.1 On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 1d9cfa880cb..b9af9f37a27 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -473,6 +473,7 @@ jobs: # CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4 # CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: delvewheel repair --add-path %HDF5_LIB_DIR%;%SUNDIALS_LIB_DIR%;%YAML_CPP_LIB_DIR% -w {dest_dir} {wheel} CIBW_ENVIRONMNET_MACOS: CT_SKIP_SLOW=1 + CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install cython==3.1.1'" # Force cython version CIBW_BUILD: "cp*-*" CIBW_ARCHS: ${{ matrix.arch }} From 60b6dd0073a50f2f6fbe2ab6bf6f9380b4b93758 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 18:37:10 +0200 Subject: [PATCH 73/98] Set cython version directly into cantera sources On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml modified: SConstruct modified: interfaces/cython/pyproject.toml --- .github/workflows/CERFACS_packaging.yml | 4 ++-- SConstruct | 2 +- interfaces/cython/pyproject.toml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index b9af9f37a27..e361cb934b1 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -357,7 +357,7 @@ jobs: macos-wheel: if: ${{ github.event.inputs.build_macos == 'true' }} - name: Build ${{ matrix.arch }} macOS Wheels for Python ${{ matrix.python-version }} + name: Build ${{ matrix.arch }} macOS Wheels #for Python ${{ matrix.python-version }} runs-on: macos-14 needs: ["sdist","upload-sh-scripts", "post-pending-status"] outputs: @@ -473,7 +473,7 @@ jobs: # CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4 # CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: delvewheel repair --add-path %HDF5_LIB_DIR%;%SUNDIALS_LIB_DIR%;%YAML_CPP_LIB_DIR% -w {dest_dir} {wheel} CIBW_ENVIRONMNET_MACOS: CT_SKIP_SLOW=1 - CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install cython==3.1.1'" # Force cython version + # CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install cython==3.1.1'" # Force cython version CIBW_BUILD: "cp*-*" CIBW_ARCHS: ${{ matrix.arch }} diff --git a/SConstruct b/SConstruct index bb2196ac7c4..97429e3f47c 100644 --- a/SConstruct +++ b/SConstruct @@ -1660,7 +1660,7 @@ elif env['python_package'] == 'none': env["python_min_version"] = python_min_version env["python_max_version"] = python_max_version env["py_requires_ver_str"] = py_requires_ver_str -env["cython_version_spec"] = SpecifierSet(">=0.29.31", prereleases=True) +env["cython_version_spec"] = SpecifierSet(">=0.29.31,!=3.1.2", prereleases=True) env["numpy_version_spec"] = SpecifierSet(">=1.12.0,<3", prereleases=True) env["cython_version_spec_str"] = str(env["cython_version_spec"]) env["numpy_version_spec_str"] = str(env["numpy_version_spec"]) diff --git a/interfaces/cython/pyproject.toml b/interfaces/cython/pyproject.toml index cb092f63ec4..643c60a5ad2 100644 --- a/interfaces/cython/pyproject.toml +++ b/interfaces/cython/pyproject.toml @@ -1,3 +1,3 @@ [build-system] -requires = ["setuptools>=43.0.0", "wheel", "Cython>=0.29.12"] +requires = ["setuptools>=43.0.0", "wheel", "Cython>=0.29.12,!=3.1.2"] build-backend = "setuptools.build_meta" From 2d14bba98d0bc07fba712fd9cfb2a6ca3875b29f Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 19:18:21 +0200 Subject: [PATCH 74/98] Add cython version into the pyproject.toml.in of python_sdist directory On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: interfaces/python_sdist/pyproject.toml.in --- interfaces/python_sdist/pyproject.toml.in | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/interfaces/python_sdist/pyproject.toml.in b/interfaces/python_sdist/pyproject.toml.in index e4f5f2a1f0b..911eec1a0be 100644 --- a/interfaces/python_sdist/pyproject.toml.in +++ b/interfaces/python_sdist/pyproject.toml.in @@ -1,5 +1,5 @@ [build-system] -requires = ["scikit-build-core", "cython", "numpy>=2.0; python_version >= '3.9'", "oldest-supported-numpy; python_version == '3.8'"] +requires = ["scikit-build-core", "cython!=3.1.2", "numpy>=2.0; python_version >= '3.9'", "oldest-supported-numpy; python_version == '3.8'"] build-backend = "scikit_build_core.build" [project] @@ -35,6 +35,7 @@ requires-python = "@py_requires_ver_str@" dependencies = [ "numpy >= 1.12.0,<3", "ruamel.yaml >= 0.15.34", + "cython !=3.1.2", ] [project.readme] From dde15bef67db49920733e7bdfbcb023f44d9b0cb Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 19:33:47 +0200 Subject: [PATCH 75/98] Imposing cython==3.1.1 On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: interfaces/python_sdist/pyproject.toml.in --- interfaces/python_sdist/pyproject.toml.in | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/interfaces/python_sdist/pyproject.toml.in b/interfaces/python_sdist/pyproject.toml.in index 911eec1a0be..eb325801c63 100644 --- a/interfaces/python_sdist/pyproject.toml.in +++ b/interfaces/python_sdist/pyproject.toml.in @@ -1,5 +1,5 @@ [build-system] -requires = ["scikit-build-core", "cython!=3.1.2", "numpy>=2.0; python_version >= '3.9'", "oldest-supported-numpy; python_version == '3.8'"] +requires = ["scikit-build-core", "cython==3.1.1", "numpy>=2.0; python_version >= '3.9'", "oldest-supported-numpy; python_version == '3.8'"] build-backend = "scikit_build_core.build" [project] @@ -35,7 +35,7 @@ requires-python = "@py_requires_ver_str@" dependencies = [ "numpy >= 1.12.0,<3", "ruamel.yaml >= 0.15.34", - "cython !=3.1.2", + "cython ==3.1.1", ] [project.readme] From c711aeebd716baca5596577e7ce9e35067f16dbf Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 19:52:05 +0200 Subject: [PATCH 76/98] derniers test en rajoutant CIBW_BEFORE_BUILD --- .github/workflows/CERFACS_packaging.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index e361cb934b1..170f71a1058 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -34,6 +34,7 @@ env: CIBW_BUILD_FRONTEND: build CIBW_TEST_EXTRAS: pandas,units CIBW_TEST_REQUIRES: pytest + CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 ACTION_URL: "https://github.com/cerfacs/cantera-avbp/actions/runs/${{ github.run_id }}" REPO_API_URL: "https://api.github.com/repos/cerfacs/cantera-avbp/tarball/${{ github.event.inputs.incoming_ref }}" From d6b8a136001f4a0b479c7dd752ae2cd9a3c8bac8 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 9 Sep 2025 20:03:31 +0200 Subject: [PATCH 77/98] test On branch FEATURE/github_workflows Your branch is ahead of 'origin/FEATURE/github_workflows' by 1 commit. (use "git push" to publish your local commits) Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 170f71a1058..71a815e814c 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -474,7 +474,8 @@ jobs: # CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4 # CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: delvewheel repair --add-path %HDF5_LIB_DIR%;%SUNDIALS_LIB_DIR%;%YAML_CPP_LIB_DIR% -w {dest_dir} {wheel} CIBW_ENVIRONMNET_MACOS: CT_SKIP_SLOW=1 - # CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install cython==3.1.1'" # Force cython version + CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 + CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install Cython==3.1.1 numpy>=2.0" # Force cython version CIBW_BUILD: "cp*-*" CIBW_ARCHS: ${{ matrix.arch }} From 22eda0f8142a7950cbf608fe2264a73eb8499a11 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 10 Sep 2025 10:01:07 +0200 Subject: [PATCH 78/98] Bugfix CIBW_BEFORE_BUILD On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 71a815e814c..5a4d416ac6d 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -474,8 +474,11 @@ jobs: # CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4 # CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: delvewheel repair --add-path %HDF5_LIB_DIR%;%SUNDIALS_LIB_DIR%;%YAML_CPP_LIB_DIR% -w {dest_dir} {wheel} CIBW_ENVIRONMNET_MACOS: CT_SKIP_SLOW=1 - CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 - CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install Cython==3.1.1 numpy>=2.0" # Force cython version + # CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 + CIBW_BEFORE_BUILD: | + python -m pip install --upgrade pip + python -m pip install Cython==3.1.1 numpy>=2.0 + # CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install Cython==3.1.1 numpy>=2.0" # Force cython version CIBW_BUILD: "cp*-*" CIBW_ARCHS: ${{ matrix.arch }} From 536511ec144568755af49ba3afd02c4b7f772188 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 10 Sep 2025 14:59:30 +0200 Subject: [PATCH 79/98] Forcing clang compiler and correction on CIBW_ENVIRONMENT_MACOS On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 5a4d416ac6d..c8d49570560 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -469,11 +469,13 @@ jobs: - name: Build wheels uses: pypa/cibuildwheel@c923d83ad9c1bc00211c5041d0c3f73294ff88f6 # 3.1.4 env: + CC: clang + CXX: clang++ CANTERA_TEST_DIR: ${{ steps.download-test-files.outputs.test-root }} # CIBW_ENVIRONMENT_LINUX: CT_SKIP_SLOW=1 CANTERA_TEST_DIR=/host${{ steps.download-test-files.outputs.test-root }} # CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4 # CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: delvewheel repair --add-path %HDF5_LIB_DIR%;%SUNDIALS_LIB_DIR%;%YAML_CPP_LIB_DIR% -w {dest_dir} {wheel} - CIBW_ENVIRONMNET_MACOS: CT_SKIP_SLOW=1 + CIBW_ENVIRONMENT_MACOS: CT_SKIP_SLOW=1 # CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 CIBW_BEFORE_BUILD: | python -m pip install --upgrade pip From 2178e2e103843502e49b17c0a63f4671d7ec7958 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 10 Sep 2025 15:17:19 +0200 Subject: [PATCH 80/98] Add SDKROOT env On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index c8d49570560..f5e0b30bd82 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -471,6 +471,7 @@ jobs: env: CC: clang CXX: clang++ + SDKROOT: /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk CANTERA_TEST_DIR: ${{ steps.download-test-files.outputs.test-root }} # CIBW_ENVIRONMENT_LINUX: CT_SKIP_SLOW=1 CANTERA_TEST_DIR=/host${{ steps.download-test-files.outputs.test-root }} # CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4 From b680bbcd2d65ac0e4ad460160bf0c8a384bd0204 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 10 Sep 2025 16:39:43 +0200 Subject: [PATCH 81/98] Change python minimal version to 3.9 On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml modified: SConstruct modified: interfaces/python_sdist/pyproject.toml.in --- .github/workflows/CERFACS_packaging.yml | 8 ++++---- SConstruct | 4 ++-- interfaces/python_sdist/pyproject.toml.in | 3 +-- 3 files changed, 7 insertions(+), 8 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index f5e0b30bd82..9ac0a177f79 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -31,10 +31,10 @@ concurrency: cancel-in-progress: true env: - CIBW_BUILD_FRONTEND: build - CIBW_TEST_EXTRAS: pandas,units - CIBW_TEST_REQUIRES: pytest - CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 + # CIBW_BUILD_FRONTEND: build + # CIBW_TEST_EXTRAS: pandas,units + # CIBW_TEST_REQUIRES: pytest + # CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 ACTION_URL: "https://github.com/cerfacs/cantera-avbp/actions/runs/${{ github.run_id }}" REPO_API_URL: "https://api.github.com/repos/cerfacs/cantera-avbp/tarball/${{ github.event.inputs.incoming_ref }}" diff --git a/SConstruct b/SConstruct index 97429e3f47c..be255a70bc5 100644 --- a/SConstruct +++ b/SConstruct @@ -99,7 +99,7 @@ from buildutils import (Option, PathOption, BoolOption, EnumOption, Configuratio config_error, run_preprocessor, make_relative_path_absolute) # ensure that Python and SCons versions are sufficient for the build process -EnsurePythonVersion(3, 7) +EnsurePythonVersion(3, 9) EnsureSConsVersion(3, 0, 0) if not COMMAND_LINE_TARGETS: @@ -180,7 +180,7 @@ else: # Python Package Settings -python_min_version = parse_version("3.8") +python_min_version = parse_version("3.9") # Newest Python version not supported/tested by Cantera python_max_version = parse_version("3.14") # The string is used to set python_requires in setup.cfg.in diff --git a/interfaces/python_sdist/pyproject.toml.in b/interfaces/python_sdist/pyproject.toml.in index eb325801c63..cc90069b0b6 100644 --- a/interfaces/python_sdist/pyproject.toml.in +++ b/interfaces/python_sdist/pyproject.toml.in @@ -1,5 +1,5 @@ [build-system] -requires = ["scikit-build-core", "cython==3.1.1", "numpy>=2.0; python_version >= '3.9'", "oldest-supported-numpy; python_version == '3.8'"] +requires = ["scikit-build-core", "cython==3.1.1", "numpy>=2.0; python_version >= '3.9'", "oldest-supported-numpy; python_version == '3.9'"] build-backend = "scikit_build_core.build" [project] @@ -22,7 +22,6 @@ classifiers = [ "Programming Language :: Cython", "Programming Language :: Fortran", "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", From 77be1645295b5bd1fe572c66bce3ce33450a075a Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Wed, 10 Sep 2025 17:16:06 +0200 Subject: [PATCH 82/98] Deactivate pytest after wheel creation by CIBW On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 9ac0a177f79..93cbc0b30d7 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -403,7 +403,7 @@ jobs: mkdir -p "${RUNNER_TEMP}/ct-test-dir" echo "test-root=${RUNNER_TEMP}/ct-test-dir" >> $GITHUB_OUTPUT shell: bash - # - name: Download and unpack the tarball ## Pas sur que ce step fonctionne car le lien est invalide, et la sdist à déja été récupéré avant donc je voit pas à quoi ça pourrait servir + # - name: Download and unpack the tarball ## Ce step sert a télécharger les sources pour que les pytest tests puissent être exec après la génération de la wheel. # run: | # curl -fsSL "https://github.com/cantera/cantera/archive/${INCOMING_SHA}.tar.gz" -o cantera.tar.gz # tar -xzf cantera.tar.gz --strip-components=1 "cantera-${INCOMING_SHA}/test" @@ -482,8 +482,9 @@ jobs: python -m pip install --upgrade pip python -m pip install Cython==3.1.1 numpy>=2.0 # CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install Cython==3.1.1 numpy>=2.0" # Force cython version - CIBW_BUILD: "cp*-*" + CIBW_BUILD: "cp39-macosx_arm64" #"cp*-*" CIBW_ARCHS: ${{ matrix.arch }} + CIBW_TEST_SKIP: "*" # Enable to deactivate the automatic pytest after building the wheel # - name: Install Brew dependencies # # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine From 9dcaa41b2e4c461352d909fb44dfb24cf7f66945 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Thu, 18 Sep 2025 17:42:22 +0200 Subject: [PATCH 83/98] Cleaning Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 92 +++---------------------- 1 file changed, 11 insertions(+), 81 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 93cbc0b30d7..e750dc86315 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -31,10 +31,6 @@ concurrency: cancel-in-progress: true env: - # CIBW_BUILD_FRONTEND: build - # CIBW_TEST_EXTRAS: pandas,units - # CIBW_TEST_REQUIRES: pytest - # CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 ACTION_URL: "https://github.com/cerfacs/cantera-avbp/actions/runs/${{ github.run_id }}" REPO_API_URL: "https://api.github.com/repos/cerfacs/cantera-avbp/tarball/${{ github.event.inputs.incoming_ref }}" @@ -60,7 +56,6 @@ jobs: tag-ref: ${{ steps.munge-incoming-ref.outputs.tag-ref }} steps: - uses: actions/setup-python@v5 - # if: ${{ !env.ACT }} # Si act est utilisé (workflow local) on ne fait pas l'install de python with: python-version: '3.10' - name: Munge the incoming ref @@ -132,7 +127,6 @@ jobs: ref: ${{ github.event.inputs.incoming_ref }} - name: Set Up Python 3.12 uses: actions/setup-python@v5 - if: ${{ !env.ACT }} # Si act est utilisé (workflow local) on ne fait pas l'install de python with: python-version: "3.12" - name: Install dependencies @@ -146,7 +140,6 @@ jobs: CYTHON_FORCE_REGEN: "1" - name: Archive the built sdist uses: actions/upload-artifact@v4 - if: ${{ !env.ACT }} with: path: ./build/python_sdist/dist/*.tar.gz name: cibw-sdist @@ -360,7 +353,7 @@ jobs: if: ${{ github.event.inputs.build_macos == 'true' }} name: Build ${{ matrix.arch }} macOS Wheels #for Python ${{ matrix.python-version }} runs-on: macos-14 - needs: ["sdist","upload-sh-scripts", "post-pending-status"] + needs: ["sdist", "upload-sh-scripts", "post-pending-status"] outputs: job-status: ${{ job.status }} strategy: @@ -377,41 +370,29 @@ jobs: boost-version: "1.86.0" arch: "arm64" fail-fast: true # Si plusieurs configs dans la matrice et fail-fast = False permet de continuer le workflow pour les autre config. - # env: - # MACOSX_DEPLOYMENT_TARGET: ${{ matrix.deployment_target }} + steps: - # - uses: actions/checkout@v5 ## Pas sur que cette étape soit nécéssaire car on a déja récupéré la bonne branche lors de la création de la sdist. - # name: Checkout the repository - # with: - # repository: "cerfacs/cantera-avbp" - # submodules: recursive - # ref: ${{ github.event.inputs.incoming_ref }} - name: Download shell scripts required to set-up environments and install libraries uses: actions/download-artifact@v5 with: name: sh-scripts + - name: Download pre-built sdist uses: actions/download-artifact@v5 with: name: cibw-sdist + - name: Extract the sdist tarball run: tar -xvf *.tar.gz --strip-components=1 shell: bash + - name: Set test file download destination id: download-test-files run: | mkdir -p "${RUNNER_TEMP}/ct-test-dir" echo "test-root=${RUNNER_TEMP}/ct-test-dir" >> $GITHUB_OUTPUT shell: bash - # - name: Download and unpack the tarball ## Ce step sert a télécharger les sources pour que les pytest tests puissent être exec après la génération de la wheel. - # run: | - # curl -fsSL "https://github.com/cantera/cantera/archive/${INCOMING_SHA}.tar.gz" -o cantera.tar.gz - # tar -xzf cantera.tar.gz --strip-components=1 "cantera-${INCOMING_SHA}/test" - # rm cantera.tar.gz - # shell: bash - # working-directory: "${{ steps.download-test-files.outputs.test-root }}" - # env: - # INCOMING_SHA: ${{ needs.post-pending-status.outputs.incoming-sha }} + - name: Install boost uses: MarkusJx/install-boost@b1f0ee8b87cf60236b72440c72d0085d002770c5 # v2.5.0 id: install-boost @@ -425,6 +406,7 @@ jobs: toolset: ${{ matrix.boost-toolset }} platform_version: ${{ matrix.boost-platform-version }} arch: ${{ matrix.boost-arch }} + # - name: Restore the cached built libraries ## This step is usesfull if several architechures are build. This enable to load lib instead of re-install them each time. This first time there are no cache directory thus this step is ignored (return cache-hit = 'false') # id: restore-built-libraries # # Our custom manylinux images already have all our dependencies installed @@ -432,40 +414,34 @@ jobs: # with: # key: ${{ matrix.os }}-${{ matrix.arch }}-${{ hashFiles('dependencies.sh') }}-1 # path: ${{ github.workspace }}/cache - # - name: Debug repo content - # run: | - # echo "=== Liste du contenu à la racine ===" - # ls -alh - # echo "=== Liste du contenu de .github ===" - # ls -alh .github || echo ".github n'existe pas" - # echo "=== Liste récursive de .github ===" - # ls -R .github || echo ".github n'existe pas" + - name: Build required libraries run: bash cibw_before_all_macos.sh "${{ github.workspace }}" - # if: runner.os == 'macOS' - name: Set up CIBW environment run: | echo "Boost_ROOT=$BOOST_ROOT" >> $GITHUB_ENV - # if: runner.os == 'macOS' env: BOOST_ROOT: ${{ steps.install-boost.outputs.BOOST_ROOT }} # - name: Write dependencies to a file for caching # added from cantera # run: | # echo "scons ruamel.yaml numpy cython!=3.1.2 pandas pytest pytest-xdist pytest-github-actions-annotate-failures pint graphviz Jinja2" | tr " " "\n" > requirements.txt + # - name: Set up Python # uses: actions/setup-python@v5 # with: # python-version: ${{ matrix.python-version }} # cache: pip # cache-dependency-path: requirements.txt + # - name: Save the cache # This step is usefull when multiple architectures are build. It enable to save in caches the installed libs that will be loaded in the following build by "Restore the cached built libraries" step. # uses: actions/cache/save@v4 # if: always() && runner.os != 'Linux' && steps.restore-built-libraries.outputs.cache-hit != 'true' # with: # path: ${{ github.workspace }}/cache # key: ${{ steps.restore-built-libraries.outputs.cache-primary-key }} + - name: Build wheels uses: pypa/cibuildwheel@c923d83ad9c1bc00211c5041d0c3f73294ff88f6 # 3.1.4 env: @@ -473,60 +449,14 @@ jobs: CXX: clang++ SDKROOT: /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk CANTERA_TEST_DIR: ${{ steps.download-test-files.outputs.test-root }} - # CIBW_ENVIRONMENT_LINUX: CT_SKIP_SLOW=1 CANTERA_TEST_DIR=/host${{ steps.download-test-files.outputs.test-root }} - # CIBW_ENVIRONMENT_WINDOWS: CT_SKIP_SLOW=1 CMAKE_BUILD_PARALLEL_LEVEL=4 - # CIBW_REPAIR_WHEEL_COMMAND_WINDOWS: delvewheel repair --add-path %HDF5_LIB_DIR%;%SUNDIALS_LIB_DIR%;%YAML_CPP_LIB_DIR% -w {dest_dir} {wheel} CIBW_ENVIRONMENT_MACOS: CT_SKIP_SLOW=1 - # CIBW_BEFORE_BUILD: python -m pip install Cython==3.1.1 numpy>=2.0 CIBW_BEFORE_BUILD: | python -m pip install --upgrade pip python -m pip install Cython==3.1.1 numpy>=2.0 - # CIBW_ENVIRONMENT: "CIBW_BEFORE_BUILD='python -m pip install Cython==3.1.1 numpy>=2.0" # Force cython version CIBW_BUILD: "cp39-macosx_arm64" #"cp*-*" CIBW_ARCHS: ${{ matrix.arch }} CIBW_TEST_SKIP: "*" # Enable to deactivate the automatic pytest after building the wheel - # - name: Install Brew dependencies - # # Force installation of hdf5 on static lib (--build-from-source) so that wheel use this library instead of available ones on target machine - # run: | - # # brew install --display-times boost libomp doxygen - # brew install --display-times boost libomp doxygen hdf5 - # # brew install cmake@3.31.6 - # # brew install hdf5 --build-from-source - # - name: Build wheels - # uses: pypa/cibuildwheel@v2.17.0 - # env: - # CIBW_ENVIRONMENT: > - # BOOST_INCLUDE="$(brew --prefix)/include" - # RUNNER_TEMP=${{ runner.temp }} - # CT_SKIP_SLOW=1 - # REPO_API_URL=${{ env.REPO_API_URL }} - # GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - # HDF5_ROOT="$(brew --prefix hdf5)" - # HDF5_USE_STATIC_LIBS=ON - # # CIBW_ENVIRONMENT: > - # # BOOST_INCLUDE="$(brew --prefix)/include" - # # RUNNER_TEMP=${{ runner.temp }} - # # CT_SKIP_SLOW=1 - # # REPO_API_URL=${{ env.REPO_API_URL }} - # # GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - # # HDF5_ROOT="$(brew --prefix hdf5)" - # # HDF5_STATIC=1 - # # CANTERA_USE_SYSTEM_HDF5=y - # CIBW_BUILD: cp${{ matrix.python-version }}-* - # CIBW_ARCHS_MACOS: ${{ matrix.arch }} - # # Testing won't be available for macOS ARM until native ARM runners are available. - # CIBW_TEST_SKIP: "*-macosx_arm64" - # CIBW_TEST_COMMAND: pytest -vv --durations=100 ${RUNNER_TEMP}/test/python - # CIBW_BEFORE_TEST: | - # curl -sL -H "Authorization: token $GH_TARBALL_DL" -o ${{ runner.temp }}/cantera.tar.gz $REPO_API_URL \ - # && tar -xzf ${{ runner.temp }}/cantera.tar.gz --strip-components=1 -C ${{ runner.temp }} "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - # - name: print info - # run: | - # ls - # pwd - # ls ${{ runner.temp }} - # cat ${{ runner.temp }}/cantera.conf - name: Archive the built wheels uses: actions/upload-artifact@v4 with: From 278892c0296f8f6c5a1e8af029aa4929e1c0705f Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Thu, 18 Sep 2025 19:00:13 +0200 Subject: [PATCH 84/98] Add linux wheels workflow (not tested) On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 322 ++++++++++++++++-------- 1 file changed, 216 insertions(+), 106 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index e750dc86315..94ba22dd190 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -185,114 +185,114 @@ jobs: name: sh-scripts if-no-files-found: error - linux-wheel: - if: ${{ github.event.inputs.build_linux == 'true' }} - # run only if "build_linux" is true: - name: Build ${{ matrix.libc }}linux_${{ matrix.arch }} for py${{ matrix.py }} - runs-on: ubuntu-20.04 - needs: ["sdist", "post-pending-status"] - outputs: - job-status: ${{ job.status }} - strategy: - matrix: - py: ["38", "39", "310", "311"] - arch: ["x86_64","i686"] - libc: ["many", "musl"] - include: - - py: "311" - arch: "aarch64" - libc: "many" - - py: "311" - arch: "ppc64le" - libc: "many" - - py: "311" - arch: "s390x" - libc: "many" - - py: "310" - arch: "aarch64" - libc: "many" - - py: "310" - arch: "ppc64le" - libc: "many" - - py: "310" - arch: "s390x" - libc: "many" - - py: "39" - arch: "aarch64" - libc: "many" - - py: "38" - arch: "aarch64" - libc: "many" - fail-fast: true - env: - BOOST_INCLUDE: include - BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z - GH_TOKEN: ${{ secrets.PAT }} - GH_TARBALL_DL: ${{ secrets.GH_TARBALL_DL }} - steps: - - name: Install dependencies - run: | - sudo apt-get update - sudo apt-get install libboost-dev tree -y - - name: Download pre-built sdist - uses: actions/download-artifact@v4 - with: - name: cibw-sdist - - name: Extract the sdist tarball - run: tar -xvf *.tar.gz --strip-components=1 - - name: Restore Boost cache - uses: actions/cache@v3 - id: cache-boost - with: - path: ${{ env.BOOST_INCLUDE }}/boost - key: boost-${{env.BOOST_URL}} - - name: Install Boost Headers - if: steps.cache-boost.outputs.cache-hit != 'true' - run: | - mkdir -p $BOOST_INCLUDE - curl --progress-bar --location --output $BOOST_INCLUDE/download.7z $BOOST_URL - 7z -o$BOOST_INCLUDE x $BOOST_INCLUDE/download.7z -y -bd boost_1_78_0/boost - mv $BOOST_INCLUDE/boost_1_78_0/boost $BOOST_INCLUDE/boost - rm $BOOST_INCLUDE/download.7z - rm -r $BOOST_INCLUDE/boost_1_78_0 - - name: Set up QEMU - uses: docker/setup-qemu-action@v3 - with: - platforms: all - - name: Build wheels - uses: pypa/cibuildwheel@v2.17.0 + # linux-wheel: + # if: ${{ github.event.inputs.build_linux == 'true' }} + # # run only if "build_linux" is true: + # name: Build ${{ matrix.libc }}linux_${{ matrix.arch }} for py${{ matrix.py }} + # runs-on: ubuntu-20.04 + # needs: ["sdist", "post-pending-status"] + # outputs: + # job-status: ${{ job.status }} + # strategy: + # matrix: + # py: ["38", "39", "310", "311"] + # arch: ["x86_64","i686"] + # libc: ["many", "musl"] + # include: + # - py: "311" + # arch: "aarch64" + # libc: "many" + # - py: "311" + # arch: "ppc64le" + # libc: "many" + # - py: "311" + # arch: "s390x" + # libc: "many" + # - py: "310" + # arch: "aarch64" + # libc: "many" + # - py: "310" + # arch: "ppc64le" + # libc: "many" + # - py: "310" + # arch: "s390x" + # libc: "many" + # - py: "39" + # arch: "aarch64" + # libc: "many" + # - py: "38" + # arch: "aarch64" + # libc: "many" + # fail-fast: true + # env: + # BOOST_INCLUDE: include + # BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z + # GH_TOKEN: ${{ secrets.PAT }} + # GH_TARBALL_DL: ${{ secrets.GH_TARBALL_DL }} + # steps: + # - name: Install dependencies + # run: | + # sudo apt-get update + # sudo apt-get install libboost-dev tree -y + # - name: Download pre-built sdist + # uses: actions/download-artifact@v4 + # with: + # name: cibw-sdist + # - name: Extract the sdist tarball + # run: tar -xvf *.tar.gz --strip-components=1 + # - name: Restore Boost cache + # uses: actions/cache@v3 + # id: cache-boost + # with: + # path: ${{ env.BOOST_INCLUDE }}/boost + # key: boost-${{env.BOOST_URL}} + # - name: Install Boost Headers + # if: steps.cache-boost.outputs.cache-hit != 'true' + # run: | + # mkdir -p $BOOST_INCLUDE + # curl --progress-bar --location --output $BOOST_INCLUDE/download.7z $BOOST_URL + # 7z -o$BOOST_INCLUDE x $BOOST_INCLUDE/download.7z -y -bd boost_1_78_0/boost + # mv $BOOST_INCLUDE/boost_1_78_0/boost $BOOST_INCLUDE/boost + # rm $BOOST_INCLUDE/download.7z + # rm -r $BOOST_INCLUDE/boost_1_78_0 + # - name: Set up QEMU + # uses: docker/setup-qemu-action@v3 + # with: + # platforms: all + # - name: Build wheels + # uses: pypa/cibuildwheel@v2.17.0 - env: - CIBW_ENVIRONMENT: BOOST_INCLUDE=${{ env.BOOST_INCLUDE }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - CIBW_BUILD: cp${{ matrix.py }}-${{ matrix.libc }}linux* - CIBW_ARCHS: ${{ matrix.arch }} - # CIBW_ENVIRONMENT_PASS_LINUX: CFLAGS - # CIBW_MANYLINUX_I686_IMAGE: - # CIBW_BEFORE_ALL_LINUX: yum groupinstall 'Development Tools' -y && which gcc && gcc --version - # yum-config-manager --enable rhel-server-rhscl-7-rpms \ - # && yum-config-manager --add-repo=https://copr.fedoraproject.org/coprs/rhscl/centos-release-scl/repo/epel-6/rhscl-centos-release-scl-epel-6.repo \ - # && yum-config-manager --add-repo=https://copr.fedoraproject.org/coprs/rhscl/centos-release-scl/repo/epel-7/rhscl-centos-release-scl-epel-7.repo \ - # && yum install centos-release-scl - # cibuildwheel on Linux uses a Docker container to run the build, so - # runner.temp is not available. cibuildwheel also uses the /tmp folder, so - # we should be pretty safe to also use that. - CIBW_TEST_COMMAND: pytest -vv --durations=100 /tmp/test/python - CIBW_BEFORE_TEST: | - curl -sL -H "Authorization: token $GH_TARBALL_DL" -o /tmp/cantera.tar.gz $REPO_API_URL \ - && tar -xzf /tmp/cantera.tar.gz --strip-components=1 -C /tmp "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - # curl -sL "https://github.com/joebarteam11/cantera-avbp-3.0.0/archive/${{ needs.post-pending-status.outputs.incoming-sha }}.tar.gz" -o /tmp/cantera-avbp.tar.gz \ - # && tar -xzf /tmp/cantera-avbp.tar.gz --strip-components=1 -C /tmp "cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - # curl - - # NumPy is generally not available for these platforms so testing takes a - # while. This just skips the tests on these - # combinations, the wheels are still built and uploaded. - CIBW_TEST_SKIP: "*-manylinux_{i686,ppc64le,s390x} *musl*" + # env: + # CIBW_ENVIRONMENT: BOOST_INCLUDE=${{ env.BOOST_INCLUDE }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} + # CIBW_BUILD: cp${{ matrix.py }}-${{ matrix.libc }}linux* + # CIBW_ARCHS: ${{ matrix.arch }} + # # CIBW_ENVIRONMENT_PASS_LINUX: CFLAGS + # # CIBW_MANYLINUX_I686_IMAGE: + # # CIBW_BEFORE_ALL_LINUX: yum groupinstall 'Development Tools' -y && which gcc && gcc --version + # # yum-config-manager --enable rhel-server-rhscl-7-rpms \ + # # && yum-config-manager --add-repo=https://copr.fedoraproject.org/coprs/rhscl/centos-release-scl/repo/epel-6/rhscl-centos-release-scl-epel-6.repo \ + # # && yum-config-manager --add-repo=https://copr.fedoraproject.org/coprs/rhscl/centos-release-scl/repo/epel-7/rhscl-centos-release-scl-epel-7.repo \ + # # && yum install centos-release-scl + # # cibuildwheel on Linux uses a Docker container to run the build, so + # # runner.temp is not available. cibuildwheel also uses the /tmp folder, so + # # we should be pretty safe to also use that. + # CIBW_TEST_COMMAND: pytest -vv --durations=100 /tmp/test/python + # CIBW_BEFORE_TEST: | + # curl -sL -H "Authorization: token $GH_TARBALL_DL" -o /tmp/cantera.tar.gz $REPO_API_URL \ + # && tar -xzf /tmp/cantera.tar.gz --strip-components=1 -C /tmp "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + # # curl -sL "https://github.com/joebarteam11/cantera-avbp-3.0.0/archive/${{ needs.post-pending-status.outputs.incoming-sha }}.tar.gz" -o /tmp/cantera-avbp.tar.gz \ + # # && tar -xzf /tmp/cantera-avbp.tar.gz --strip-components=1 -C /tmp "cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" + # # curl - + # # NumPy is generally not available for these platforms so testing takes a + # # while. This just skips the tests on these + # # combinations, the wheels are still built and uploaded. + # CIBW_TEST_SKIP: "*-manylinux_{i686,ppc64le,s390x} *musl*" - - name: Archive the built wheels - uses: actions/upload-artifact@v3 - with: - path: ./wheelhouse/*.whl - name: wheels + # - name: Archive the built wheels + # uses: actions/upload-artifact@v3 + # with: + # path: ./wheelhouse/*.whl + # name: wheels windows-wheel: if: ${{ github.event.inputs.build_windows == 'true' }} @@ -462,3 +462,113 @@ jobs: with: path: ./wheelhouse/*.whl name: cibw-wheels-${{ runner.os }}-${{ strategy.job-index }} + + linux-wheel: + if: ${{ github.event.inputs.build_linux == 'true' }} + name: Build ${{ matrix.arch }} linux Wheels #for Python ${{ matrix.python-version }} + runs-on: ubuntu-24.04-arm + needs: ["sdist", "post-pending-status"] + outputs: + job-status: ${{ job.status }} + strategy: + matrix: + # python-version: ["39"] + # arch: ["arm64"] + # deployment_target: ["13.0"] + include: + - # py: "38" + arch: aarch64 + fail-fast: true # Si plusieurs configs dans la matrice et fail-fast = False permet de continuer le workflow pour les autre config. + + steps: + # - name: Download shell scripts required to set-up environments and install libraries + # uses: actions/download-artifact@v5 + # with: + # name: sh-scripts + + - name: Download pre-built sdist + uses: actions/download-artifact@v5 + with: + name: cibw-sdist + + - name: Extract the sdist tarball + run: tar -xvf *.tar.gz --strip-components=1 + shell: bash + + - name: Set test file download destination + id: download-test-files + run: | + mkdir -p "${RUNNER_TEMP}/ct-test-dir" + echo "test-root=${RUNNER_TEMP}/ct-test-dir" >> $GITHUB_OUTPUT + shell: bash + + # - name: Install boost + # uses: MarkusJx/install-boost@b1f0ee8b87cf60236b72440c72d0085d002770c5 # v2.5.0 + # id: install-boost + # with: + # # REQUIRED: Specify the required boost version + # # A list of supported versions can be found here: + # # https://github.com/MarkusJx/prebuilt-boost/blob/main/versions-manifest.json + # boost_version: ${{ matrix.boost-version }} + # # OPTIONAL: Specify a custon install location + # boost_install_dir: ${{ runner.temp }} + # toolset: ${{ matrix.boost-toolset }} + # platform_version: ${{ matrix.boost-platform-version }} + # arch: ${{ matrix.boost-arch }} + + # - name: Restore the cached built libraries ## This step is usesfull if several architechures are build. This enable to load lib instead of re-install them each time. This first time there are no cache directory thus this step is ignored (return cache-hit = 'false') + # id: restore-built-libraries + # # Our custom manylinux images already have all our dependencies installed + # uses: actions/cache/restore@v4 + # with: + # key: ${{ matrix.os }}-${{ matrix.arch }}-${{ hashFiles('dependencies.sh') }}-1 + # path: ${{ github.workspace }}/cache + + # - name: Build required libraries + # run: bash cibw_before_all_macos.sh "${{ github.workspace }}" + + # - name: Set up CIBW environment + # run: | + # echo "Boost_ROOT=$BOOST_ROOT" >> $GITHUB_ENV + # env: + # BOOST_ROOT: ${{ steps.install-boost.outputs.BOOST_ROOT }} + + # - name: Write dependencies to a file for caching # added from cantera + # run: | + # echo "scons ruamel.yaml numpy cython!=3.1.2 pandas pytest pytest-xdist pytest-github-actions-annotate-failures pint graphviz Jinja2" | tr " " "\n" > requirements.txt + + # - name: Set up Python + # uses: actions/setup-python@v5 + # with: + # python-version: ${{ matrix.python-version }} + # cache: pip + # cache-dependency-path: requirements.txt + + # - name: Save the cache # This step is usefull when multiple architectures are build. It enable to save in caches the installed libs that will be loaded in the following build by "Restore the cached built libraries" step. + # uses: actions/cache/save@v4 + # if: always() && runner.os != 'Linux' && steps.restore-built-libraries.outputs.cache-hit != 'true' + # with: + # path: ${{ github.workspace }}/cache + # key: ${{ steps.restore-built-libraries.outputs.cache-primary-key }} + + - name: Build wheels + uses: pypa/cibuildwheel@c923d83ad9c1bc00211c5041d0c3f73294ff88f6 # 3.1.4 + env: + # CC: clang + # CXX: clang++ + # SDKROOT: /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk + # CANTERA_TEST_DIR: ${{ steps.download-test-files.outputs.test-root }} + CIBW_ENVIRONMENT_LINUX: CT_SKIP_SLOW=1 CANTERA_TEST_DIR=/host${{ steps.download-test-files.outputs.test-root }} + CIBW_BEFORE_BUILD: | + python -m pip install --upgrade pip + python -m pip install Cython==3.1.1 numpy>=2.0 + CIBW_BUILD: "cp39-manylinux_aarch64" #"cp*-*" "cp39-manylinux_x86_64" + CIBW_ARCHS: ${{ matrix.arch }} + CIBW_TEST_SKIP: "*" # Enable to deactivate the automatic pytest after building the wheel + CIBW_MANYLINUX_AARCH64_IMAGE: ghcr.io/cantera/manylinux_2_28_aarch64-hdf5-boost:latest + + - name: Archive the built wheels + uses: actions/upload-artifact@v4 + with: + path: ./wheelhouse/*.whl + name: cibw-wheels-${{ runner.os }}-${{ strategy.job-index }} From 275e9792b686bb560433a06709caa8a1a0c23cb6 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 23 Sep 2025 17:38:44 +0200 Subject: [PATCH 85/98] Switch to x86 architecture On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 94ba22dd190..1000c0edaef 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -477,7 +477,7 @@ jobs: # deployment_target: ["13.0"] include: - # py: "38" - arch: aarch64 + arch: x86_64 #aarch64 fail-fast: true # Si plusieurs configs dans la matrice et fail-fast = False permet de continuer le workflow pour les autre config. steps: @@ -562,10 +562,10 @@ jobs: CIBW_BEFORE_BUILD: | python -m pip install --upgrade pip python -m pip install Cython==3.1.1 numpy>=2.0 - CIBW_BUILD: "cp39-manylinux_aarch64" #"cp*-*" "cp39-manylinux_x86_64" - CIBW_ARCHS: ${{ matrix.arch }} + CIBW_BUILD: "cp39-manylinux_x86_64" #"cp39-manylinux_aarch64" #"cp*-*" "cp39-manylinux_x86_64" + # CIBW_ARCHS: ${{ matrix.arch }} CIBW_TEST_SKIP: "*" # Enable to deactivate the automatic pytest after building the wheel - CIBW_MANYLINUX_AARCH64_IMAGE: ghcr.io/cantera/manylinux_2_28_aarch64-hdf5-boost:latest + # CIBW_MANYLINUX_AARCH64_IMAGE: ghcr.io/cantera/manylinux_2_28_aarch64-hdf5-boost:latest - name: Archive the built wheels uses: actions/upload-artifact@v4 From 1e233b98a55314903fa42eb9f9a21c5003a7416f Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 23 Sep 2025 17:55:09 +0200 Subject: [PATCH 86/98] Set ubuntu-24.04 for job runner --- .github/workflows/CERFACS_packaging.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 1000c0edaef..1a0844170b0 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -466,7 +466,7 @@ jobs: linux-wheel: if: ${{ github.event.inputs.build_linux == 'true' }} name: Build ${{ matrix.arch }} linux Wheels #for Python ${{ matrix.python-version }} - runs-on: ubuntu-24.04-arm + runs-on: ubuntu-24.04 needs: ["sdist", "post-pending-status"] outputs: job-status: ${{ job.status }} From b7ebe438868eb9e344085fe457677099b3f9d25f Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 23 Sep 2025 18:09:37 +0200 Subject: [PATCH 87/98] Test on python 3.12 --- .github/workflows/CERFACS_packaging.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index 1a0844170b0..d1092a80037 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -562,7 +562,7 @@ jobs: CIBW_BEFORE_BUILD: | python -m pip install --upgrade pip python -m pip install Cython==3.1.1 numpy>=2.0 - CIBW_BUILD: "cp39-manylinux_x86_64" #"cp39-manylinux_aarch64" #"cp*-*" "cp39-manylinux_x86_64" + CIBW_BUILD: "cp312-manylinux_x86_64" #"cp39-manylinux_aarch64" #"cp*-*" "cp39-manylinux_x86_64" # CIBW_ARCHS: ${{ matrix.arch }} CIBW_TEST_SKIP: "*" # Enable to deactivate the automatic pytest after building the wheel # CIBW_MANYLINUX_AARCH64_IMAGE: ghcr.io/cantera/manylinux_2_28_aarch64-hdf5-boost:latest From b825a8ab4be1a08e66aab3d3f952d26e72810f1e Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 23 Sep 2025 18:40:35 +0200 Subject: [PATCH 88/98] Update pyproject.toml.in with CIBW setup --- interfaces/python_sdist/pyproject.toml.in | 16 +++++++++------- 1 file changed, 9 insertions(+), 7 deletions(-) diff --git a/interfaces/python_sdist/pyproject.toml.in b/interfaces/python_sdist/pyproject.toml.in index cc90069b0b6..16016d8811b 100644 --- a/interfaces/python_sdist/pyproject.toml.in +++ b/interfaces/python_sdist/pyproject.toml.in @@ -1,5 +1,5 @@ [build-system] -requires = ["scikit-build-core", "cython==3.1.1", "numpy>=2.0; python_version >= '3.9'", "oldest-supported-numpy; python_version == '3.9'"] +requires = ["scikit-build-core", "cython==3.1.1", "numpy>=2.0; python_version >= '3.9'"] build-backend = "scikit_build_core.build" [project] @@ -8,12 +8,12 @@ version = "@cantera_version@" description = "Cantera is an open-source suite of tools for problems involving chemical kinetics, thermodynamics, and transport processes." authors = [{name = "Cantera Developers", email = "developers@cantera.org"}] keywords = ["chemistry physics"] -license = { file = "License.txt" } +license = "BSD-3-Clause" +license-files = ["License.txt"] classifiers = [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Education", "Intended Audience :: Science/Research", - "License :: OSI Approved :: BSD License", "Operating System :: MacOS :: MacOS X", "Operating System :: Microsoft :: Windows", "Operating System :: POSIX :: Linux", @@ -26,6 +26,8 @@ classifiers = [ "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: 3.14", "Programming Language :: Python :: Implementation :: CPython", "Topic :: Scientific/Engineering :: Chemistry", "Topic :: Scientific/Engineering :: Physics", @@ -68,8 +70,7 @@ build.verbose = true version = ">=3.27" [tool.scikit-build.ninja] -# As of 01-DEC-2024, Ninja 1.12 is not available on PyPI -version = ">=1.11" +version = ">=1.13" make-fallback = false [tool.scikit-build.cmake.define] @@ -84,8 +85,9 @@ exclude = ["pyproject.toml.in", "cantera/with_units/solution.py.in"] exclude = ["include", "lib", "share", "**.pyx", "cantera/CMakeLists.txt"] [tool.cibuildwheel] -build-frontend = { name="build", args=["-vv"] } -skip = "pp* *musllinux*" +build-frontend = { name="build[uv]", args=["-vv"] } +archs = "auto64" +skip = ["*musllinux*", "cp3??t-win*"] test-extras = ["pandas", "units", "graphviz"] test-requires = ["pytest"] manylinux-x86_64-image = "ghcr.io/cantera/cantera-base-manylinux_2_28-x86_64" From 7b4c3a56f199b2472a569f940dd02fe8e392f1ac Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 23 Sep 2025 19:13:24 +0200 Subject: [PATCH 89/98] Add cstring and algorithm includes in Parser.cpp to enable compilation on github workflow On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: src/base/Parser.cpp --- src/base/Parser.cpp | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/base/Parser.cpp b/src/base/Parser.cpp index bbee10b6160..2e3567e5dce 100644 --- a/src/base/Parser.cpp +++ b/src/base/Parser.cpp @@ -5,6 +5,8 @@ #include #include #include +#include +#include void Param::print() { cout << m_name; From 00f0fc2e00f77506a1d0129ccad1081597b1a77e Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Mon, 13 Oct 2025 14:54:42 +0200 Subject: [PATCH 90/98] Clean CERFACS github workflows On branch FEATURE/github_workflows Your branch is up to date with 'origin/FEATURE/github_workflows'. Changes to be committed: modified: .github/workflows/CERFACS_packaging.yml --- .github/workflows/CERFACS_packaging.yml | 174 +----------------------- 1 file changed, 4 insertions(+), 170 deletions(-) diff --git a/.github/workflows/CERFACS_packaging.yml b/.github/workflows/CERFACS_packaging.yml index d1092a80037..9e4311a464b 100644 --- a/.github/workflows/CERFACS_packaging.yml +++ b/.github/workflows/CERFACS_packaging.yml @@ -46,6 +46,7 @@ jobs: run: | echo "${{ github.event.inputs.incoming_ref }}" echo "${{ github.event.inputs.upload }}" + post-pending-status: name: Post a pending workflow status to cerfacs/cantera-avbp runs-on: ubuntu-22.04 @@ -107,6 +108,7 @@ jobs: --field context='PyPI Package Build' \ --field description="Pending build" \ --silent + sdist: name: Build the sdist runs-on: ubuntu-22.04 @@ -162,6 +164,7 @@ jobs: echo ----- End of Metadata ----- upload-sh-scripts: + if: ${{ github.event.inputs.build_macos == 'true' }} name: Upload the *.sh scripts required for installation runs-on: ubuntu-latest needs: @@ -184,115 +187,6 @@ jobs: .github/dependencies.sh name: sh-scripts if-no-files-found: error - - # linux-wheel: - # if: ${{ github.event.inputs.build_linux == 'true' }} - # # run only if "build_linux" is true: - # name: Build ${{ matrix.libc }}linux_${{ matrix.arch }} for py${{ matrix.py }} - # runs-on: ubuntu-20.04 - # needs: ["sdist", "post-pending-status"] - # outputs: - # job-status: ${{ job.status }} - # strategy: - # matrix: - # py: ["38", "39", "310", "311"] - # arch: ["x86_64","i686"] - # libc: ["many", "musl"] - # include: - # - py: "311" - # arch: "aarch64" - # libc: "many" - # - py: "311" - # arch: "ppc64le" - # libc: "many" - # - py: "311" - # arch: "s390x" - # libc: "many" - # - py: "310" - # arch: "aarch64" - # libc: "many" - # - py: "310" - # arch: "ppc64le" - # libc: "many" - # - py: "310" - # arch: "s390x" - # libc: "many" - # - py: "39" - # arch: "aarch64" - # libc: "many" - # - py: "38" - # arch: "aarch64" - # libc: "many" - # fail-fast: true - # env: - # BOOST_INCLUDE: include - # BOOST_URL: https://boostorg.jfrog.io/artifactory/main/release/1.78.0/source/boost_1_78_0.7z - # GH_TOKEN: ${{ secrets.PAT }} - # GH_TARBALL_DL: ${{ secrets.GH_TARBALL_DL }} - # steps: - # - name: Install dependencies - # run: | - # sudo apt-get update - # sudo apt-get install libboost-dev tree -y - # - name: Download pre-built sdist - # uses: actions/download-artifact@v4 - # with: - # name: cibw-sdist - # - name: Extract the sdist tarball - # run: tar -xvf *.tar.gz --strip-components=1 - # - name: Restore Boost cache - # uses: actions/cache@v3 - # id: cache-boost - # with: - # path: ${{ env.BOOST_INCLUDE }}/boost - # key: boost-${{env.BOOST_URL}} - # - name: Install Boost Headers - # if: steps.cache-boost.outputs.cache-hit != 'true' - # run: | - # mkdir -p $BOOST_INCLUDE - # curl --progress-bar --location --output $BOOST_INCLUDE/download.7z $BOOST_URL - # 7z -o$BOOST_INCLUDE x $BOOST_INCLUDE/download.7z -y -bd boost_1_78_0/boost - # mv $BOOST_INCLUDE/boost_1_78_0/boost $BOOST_INCLUDE/boost - # rm $BOOST_INCLUDE/download.7z - # rm -r $BOOST_INCLUDE/boost_1_78_0 - # - name: Set up QEMU - # uses: docker/setup-qemu-action@v3 - # with: - # platforms: all - # - name: Build wheels - # uses: pypa/cibuildwheel@v2.17.0 - - # env: - # CIBW_ENVIRONMENT: BOOST_INCLUDE=${{ env.BOOST_INCLUDE }} CT_SKIP_SLOW=1 REPO_API_URL=${{ env.REPO_API_URL }} GH_TARBALL_DL=${{ env.GH_TARBALL_DL }} - # CIBW_BUILD: cp${{ matrix.py }}-${{ matrix.libc }}linux* - # CIBW_ARCHS: ${{ matrix.arch }} - # # CIBW_ENVIRONMENT_PASS_LINUX: CFLAGS - # # CIBW_MANYLINUX_I686_IMAGE: - # # CIBW_BEFORE_ALL_LINUX: yum groupinstall 'Development Tools' -y && which gcc && gcc --version - # # yum-config-manager --enable rhel-server-rhscl-7-rpms \ - # # && yum-config-manager --add-repo=https://copr.fedoraproject.org/coprs/rhscl/centos-release-scl/repo/epel-6/rhscl-centos-release-scl-epel-6.repo \ - # # && yum-config-manager --add-repo=https://copr.fedoraproject.org/coprs/rhscl/centos-release-scl/repo/epel-7/rhscl-centos-release-scl-epel-7.repo \ - # # && yum install centos-release-scl - # # cibuildwheel on Linux uses a Docker container to run the build, so - # # runner.temp is not available. cibuildwheel also uses the /tmp folder, so - # # we should be pretty safe to also use that. - # CIBW_TEST_COMMAND: pytest -vv --durations=100 /tmp/test/python - # CIBW_BEFORE_TEST: | - # curl -sL -H "Authorization: token $GH_TARBALL_DL" -o /tmp/cantera.tar.gz $REPO_API_URL \ - # && tar -xzf /tmp/cantera.tar.gz --strip-components=1 -C /tmp "cerfacs-cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - # # curl -sL "https://github.com/joebarteam11/cantera-avbp-3.0.0/archive/${{ needs.post-pending-status.outputs.incoming-sha }}.tar.gz" -o /tmp/cantera-avbp.tar.gz \ - # # && tar -xzf /tmp/cantera-avbp.tar.gz --strip-components=1 -C /tmp "cantera-avbp-${{ needs.post-pending-status.outputs.incoming-sha }}/test" - # # curl - - # # NumPy is generally not available for these platforms so testing takes a - # # while. This just skips the tests on these - # # combinations, the wheels are still built and uploaded. - # CIBW_TEST_SKIP: "*-manylinux_{i686,ppc64le,s390x} *musl*" - - # - name: Archive the built wheels - # uses: actions/upload-artifact@v3 - # with: - # path: ./wheelhouse/*.whl - # name: wheels windows-wheel: if: ${{ github.event.inputs.build_windows == 'true' }} @@ -481,11 +375,6 @@ jobs: fail-fast: true # Si plusieurs configs dans la matrice et fail-fast = False permet de continuer le workflow pour les autre config. steps: - # - name: Download shell scripts required to set-up environments and install libraries - # uses: actions/download-artifact@v5 - # with: - # name: sh-scripts - - name: Download pre-built sdist uses: actions/download-artifact@v5 with: @@ -502,70 +391,15 @@ jobs: echo "test-root=${RUNNER_TEMP}/ct-test-dir" >> $GITHUB_OUTPUT shell: bash - # - name: Install boost - # uses: MarkusJx/install-boost@b1f0ee8b87cf60236b72440c72d0085d002770c5 # v2.5.0 - # id: install-boost - # with: - # # REQUIRED: Specify the required boost version - # # A list of supported versions can be found here: - # # https://github.com/MarkusJx/prebuilt-boost/blob/main/versions-manifest.json - # boost_version: ${{ matrix.boost-version }} - # # OPTIONAL: Specify a custon install location - # boost_install_dir: ${{ runner.temp }} - # toolset: ${{ matrix.boost-toolset }} - # platform_version: ${{ matrix.boost-platform-version }} - # arch: ${{ matrix.boost-arch }} - - # - name: Restore the cached built libraries ## This step is usesfull if several architechures are build. This enable to load lib instead of re-install them each time. This first time there are no cache directory thus this step is ignored (return cache-hit = 'false') - # id: restore-built-libraries - # # Our custom manylinux images already have all our dependencies installed - # uses: actions/cache/restore@v4 - # with: - # key: ${{ matrix.os }}-${{ matrix.arch }}-${{ hashFiles('dependencies.sh') }}-1 - # path: ${{ github.workspace }}/cache - - # - name: Build required libraries - # run: bash cibw_before_all_macos.sh "${{ github.workspace }}" - - # - name: Set up CIBW environment - # run: | - # echo "Boost_ROOT=$BOOST_ROOT" >> $GITHUB_ENV - # env: - # BOOST_ROOT: ${{ steps.install-boost.outputs.BOOST_ROOT }} - - # - name: Write dependencies to a file for caching # added from cantera - # run: | - # echo "scons ruamel.yaml numpy cython!=3.1.2 pandas pytest pytest-xdist pytest-github-actions-annotate-failures pint graphviz Jinja2" | tr " " "\n" > requirements.txt - - # - name: Set up Python - # uses: actions/setup-python@v5 - # with: - # python-version: ${{ matrix.python-version }} - # cache: pip - # cache-dependency-path: requirements.txt - - # - name: Save the cache # This step is usefull when multiple architectures are build. It enable to save in caches the installed libs that will be loaded in the following build by "Restore the cached built libraries" step. - # uses: actions/cache/save@v4 - # if: always() && runner.os != 'Linux' && steps.restore-built-libraries.outputs.cache-hit != 'true' - # with: - # path: ${{ github.workspace }}/cache - # key: ${{ steps.restore-built-libraries.outputs.cache-primary-key }} - - name: Build wheels uses: pypa/cibuildwheel@c923d83ad9c1bc00211c5041d0c3f73294ff88f6 # 3.1.4 env: - # CC: clang - # CXX: clang++ - # SDKROOT: /Applications/Xcode_15.4.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX14.5.sdk - # CANTERA_TEST_DIR: ${{ steps.download-test-files.outputs.test-root }} CIBW_ENVIRONMENT_LINUX: CT_SKIP_SLOW=1 CANTERA_TEST_DIR=/host${{ steps.download-test-files.outputs.test-root }} CIBW_BEFORE_BUILD: | python -m pip install --upgrade pip python -m pip install Cython==3.1.1 numpy>=2.0 - CIBW_BUILD: "cp312-manylinux_x86_64" #"cp39-manylinux_aarch64" #"cp*-*" "cp39-manylinux_x86_64" - # CIBW_ARCHS: ${{ matrix.arch }} + CIBW_BUILD: "cp312-manylinux_x86_64" #"cp39-manylinux_aarch64" #"cp*-*" CIBW_TEST_SKIP: "*" # Enable to deactivate the automatic pytest after building the wheel - # CIBW_MANYLINUX_AARCH64_IMAGE: ghcr.io/cantera/manylinux_2_28_aarch64-hdf5-boost:latest - name: Archive the built wheels uses: actions/upload-artifact@v4 From a0577952edbdbcd6991c57aa26972c03b5d80918 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Fri, 17 Oct 2025 15:42:57 +0200 Subject: [PATCH 91/98] Move getDistributionOrdre0 into evalSoot The the soot distribution q[k] is local and is erased for each new position (not a 2D array) thus it cannot be computed for all point before evalSoot On branch BUGFIX/Soot_computation Changes to be committed: modified: src/oneD/Flow1D.cpp --- src/oneD/Flow1D.cpp | 45 ++++++++++++++++++++++++++++++++++++++------- 1 file changed, 38 insertions(+), 7 deletions(-) diff --git a/src/oneD/Flow1D.cpp b/src/oneD/Flow1D.cpp index 37158e376a7..8e2ecb24b1e 100644 --- a/src/oneD/Flow1D.cpp +++ b/src/oneD/Flow1D.cpp @@ -417,9 +417,9 @@ void Flow1D::eval(size_t jGlobal, double* xGlobal, double* rsdGlobal, computeRadiation(x, jmin, jmax); } for (size_t j = jmin; j <= jmax; j++) { - if (m_nsoot > 0){ - getDistributionOrdre0(x,j); - } + // if (m_nsoot > 0){ + // getDistributionOrdre0(x,j); + // } AVBPcompute_local_thick(x,j); } @@ -427,6 +427,19 @@ void Flow1D::eval(size_t jGlobal, double* xGlobal, double* rsdGlobal, evalContinuity(x, rsd, diag, rdt, jmin, jmax); evalMomentum(x, rsd, diag, rdt, jmin, jmax); evalSoot(x, rsd, diag, rdt, jmin, jmax); + // cout< 0){ - updateSootDiffFluxes(x, j0, j1); - } + if (m_nsoot > 0){ + updateSootDiffFluxes(x, j0, j1); + } } void Flow1D::updateTransport(double* x, size_t j0, size_t j1) @@ -896,7 +909,10 @@ void Flow1D::evalElectricField(double* x, double* rsd, int* diag, void Flow1D::evalSoot(double* x, double* rsd, int* diag, double rdt, size_t jmin, size_t jmax) { + // cout<<"print c_offset_S"< 0){ + if (jmin == 0) { // left boundary for (size_t k = 0; k < m_nsoot; k++){ rsd[index(c_offset_S + k, jmin)] = - (m_soot_diff(k,jmin) @@ -915,6 +931,7 @@ void Flow1D::evalSoot(double* x, double* rsd, int* diag, size_t j0 = std::max(jmin, 1); size_t j1 = std::min(jmax, m_points-2); for (size_t j = j0; j <= j1; j++) { // interior points + getDistributionOrdre0(x,j); sootSource(x,j); for (size_t k = 0; k < m_nsoot; k++){ // Convection @@ -929,6 +946,10 @@ void Flow1D::evalSoot(double* x, double* rsd, int* diag, double soot_source = 0; soot_source += (k == 0 ? m_qdotNucleation[j] : 0.0); soot_source += (m_do_condensation ? m_qdotCondensation(k,j) : 0.0); + // cout<<"print m_qdotNucleation"<setActive(c_offset_S+k, false); - setBounds(c_offset_S + k, -1.0e-5, 1e5); + setBounds(c_offset_S + k, -1.0e+5, 1e5); } } @@ -1902,6 +1923,11 @@ void Flow1D::sootCondensation(const double* x, size_t j){ if ( k>0 ){ m_qdotCondensation(k-1,j) -= term3; } + // cout<<"in sootCondensation"< Date: Fri, 17 Oct 2025 20:32:05 +0200 Subject: [PATCH 92/98] Fuck, I want to kill myself... I forgot to reset bounds for soot and spend the whole day trying to debug a bug that doesn't exist ! ==> At least soots are working now :') On branch BUGFIX/Soot_computation Changes to be committed: modified: ../../../src/oneD/Flow1D.cpp --- src/oneD/Flow1D.cpp | 26 +++++++++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/src/oneD/Flow1D.cpp b/src/oneD/Flow1D.cpp index 8e2ecb24b1e..932856d529f 100644 --- a/src/oneD/Flow1D.cpp +++ b/src/oneD/Flow1D.cpp @@ -441,6 +441,7 @@ void Flow1D::eval(size_t jGlobal, double* xGlobal, double* rsdGlobal, // exit(0); evalSpecies(x, rsd, diag, rdt, jmin, jmax); + // exit(0); evalEnergy(x, rsd, diag, rdt, jmin, jmax); evalLambda(x, rsd, diag, rdt, jmin, jmax); evalElectricField(x, rsd, diag, rdt, jmin, jmax); @@ -527,6 +528,7 @@ void Flow1D::updateTransport(double* x, size_t j0, size_t j1) void Flow1D::updateDiffFluxes(const double* x, size_t j0, size_t j1) { if (m_do_multicomponent) { + // cout<<"multicomponent"< 0 && m_do_retroaction){ m_wdot(k,j) -= sootConsumption(k,j); + // if (j==2){ + // cout<<"in evalSpecies"<setActive(c_offset_S+k, false); - setBounds(c_offset_S + k, -1.0e+5, 1e5); + setBounds(c_offset_S + k, -1.0e-5, 1e5); } } From 7fb4687d8a6f9866a9a1b1eaa72cbd705070e720 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Mon, 20 Oct 2025 09:13:32 +0200 Subject: [PATCH 93/98] Cleanning On branch BUGFIX/Soot_computation Changes to be committed: modified: src/oneD/Flow1D.cpp --- src/oneD/Flow1D.cpp | 70 ++++++--------------------------------------- 1 file changed, 9 insertions(+), 61 deletions(-) diff --git a/src/oneD/Flow1D.cpp b/src/oneD/Flow1D.cpp index 932856d529f..9c5a37c95f9 100644 --- a/src/oneD/Flow1D.cpp +++ b/src/oneD/Flow1D.cpp @@ -417,9 +417,6 @@ void Flow1D::eval(size_t jGlobal, double* xGlobal, double* rsdGlobal, computeRadiation(x, jmin, jmax); } for (size_t j = jmin; j <= jmax; j++) { - // if (m_nsoot > 0){ - // getDistributionOrdre0(x,j); - // } AVBPcompute_local_thick(x,j); } @@ -427,21 +424,7 @@ void Flow1D::eval(size_t jGlobal, double* xGlobal, double* rsdGlobal, evalContinuity(x, rsd, diag, rdt, jmin, jmax); evalMomentum(x, rsd, diag, rdt, jmin, jmax); evalSoot(x, rsd, diag, rdt, jmin, jmax); - // cout<(jmin, 1); size_t j1 = std::min(jmax, m_points-2); for (size_t j = j0; j <= j1; j++) { + getWdot(x,j); for (size_t k = 0; k < m_nsp; k++) { - if (m_nsoot > 0 && m_do_retroaction){ m_wdot(k,j) -= sootConsumption(k,j); - // if (j==2){ - // cout<<"in evalSpecies"< 0){ if (jmin == 0) { // left boundary @@ -955,8 +914,10 @@ void Flow1D::evalSoot(double* x, double* rsd, int* diag, size_t j0 = std::max(jmin, 1); size_t j1 = std::min(jmax, m_points-2); for (size_t j = j0; j <= j1; j++) { // interior points + getDistributionOrdre0(x,j); sootSource(x,j); + for (size_t k = 0; k < m_nsoot; k++){ // Convection double soot_convec = rho_u(x,j)*dYsdz(x,k,j); @@ -966,21 +927,18 @@ void Flow1D::evalSoot(double* x, double* rsd, int* diag, // Thermophoresis double soot_soret = 2.0 * (m_soot_soret(k,j) - m_soot_soret(k,j-1)) / (z(j+1) - z(j-1)); + // Source terms [m3/kg/s] double soot_source = 0; soot_source += (k == 0 ? m_qdotNucleation[j] : 0.0); soot_source += (m_do_condensation ? m_qdotCondensation(k,j) : 0.0); - // cout<<"print m_qdotNucleation"<0 ){ m_qdotCondensation(k-1,j) -= term3; } - // cout<<"in sootCondensation"< Date: Fri, 7 Nov 2025 15:30:22 +0100 Subject: [PATCH 94/98] Added fictive as in AVBP. Works on a 1D premixed flame using San Diego chemistry. A fictive species is put with the source term of a real species and both mass fractions works. Now to be checked on counterflow diff flames. Examples are being sets to play with fictives. --- include/cantera/oneD/Domain1D.h | 2 +- include/cantera/oneD/DomainFactory.h | 6 +- include/cantera/oneD/Flow1D.h | 105 ++++++++++++++- interfaces/cython/cantera/_onedim.pxd | 13 +- interfaces/cython/cantera/_onedim.pyx | 85 +++++++++++- interfaces/cython/cantera/onedim.py | 72 ++++++---- src/oneD/Domain1D.cpp | 4 +- src/oneD/DomainFactory.cpp | 36 ++--- src/oneD/Flow1D.cpp | 186 ++++++++++++++++++++++++-- 9 files changed, 444 insertions(+), 65 deletions(-) diff --git a/include/cantera/oneD/Domain1D.h b/include/cantera/oneD/Domain1D.h index 01d5aa8c30e..b8bba461cb5 100644 --- a/include/cantera/oneD/Domain1D.h +++ b/include/cantera/oneD/Domain1D.h @@ -34,7 +34,7 @@ class Domain1D * @param points Number of grid points. * @param time (unused) */ - Domain1D(size_t nv=1, size_t points=1, double time=0.0, size_t nsoot=0, size_t neq=0); + Domain1D(size_t nv=1, size_t points=1, double time=0.0, size_t nsoot=0, size_t nfic=0, size_t neq=0); virtual ~Domain1D(); Domain1D(const Domain1D&) = delete; diff --git a/include/cantera/oneD/DomainFactory.h b/include/cantera/oneD/DomainFactory.h index 0b5211979cf..cff9c0ef75f 100644 --- a/include/cantera/oneD/DomainFactory.h +++ b/include/cantera/oneD/DomainFactory.h @@ -19,7 +19,7 @@ namespace Cantera //! ```cpp //! shared_ptr d1 = newDomain("Inlet", sol, "reactants"); //! ``` -class DomainFactory : public Factory, const string&, const size_t&> +class DomainFactory : public Factory, const string&, const size_t&, const size_t&> { public: /** @@ -51,7 +51,7 @@ class DomainFactory : public Factory, const strin //! @ingroup onedGroup template shared_ptr newDomain( - const string& domainType, shared_ptr solution, const string& id="", const size_t& sections=0) + const string& domainType, shared_ptr solution, const string& id="", const size_t& sections=0, const size_t& fictives=0) { string id_ = id; if (id_ == "") { @@ -59,7 +59,7 @@ shared_ptr newDomain( } auto ret = std::dynamic_pointer_cast( shared_ptr( - DomainFactory::factory()->create(domainType, solution, id_, sections))); + DomainFactory::factory()->create(domainType, solution, id_, sections, fictives))); if (!ret) { throw CanteraError("newDomain", "Invalid cast: unable to access 'Domain1D' as '{}'.", demangle(typeid(T))); diff --git a/include/cantera/oneD/Flow1D.h b/include/cantera/oneD/Flow1D.h index 7f48ff2cafe..a22d96d7112 100644 --- a/include/cantera/oneD/Flow1D.h +++ b/include/cantera/oneD/Flow1D.h @@ -62,17 +62,17 @@ class Flow1D : public Domain1D //! @param nsp Number of species. //! @param points Initial number of grid points //! @param n_eq Number of non-species equations (default = 6 for spatial resolution) - Flow1D(ThermoPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); + Flow1D(ThermoPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t nfic = 0, size_t neq = c_offset_Y, size_t points = 1); //! Delegating constructor - Flow1D(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Y, size_t points = 1); + Flow1D(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t nfic = 0, size_t neq = c_offset_Y, size_t points = 1); //! Create a new flow domain. //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and //! transport properties //! @param id name of flow domain //! @param points initial number of grid points - Flow1D(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Y, size_t points=1); + Flow1D(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t nfic = 0, size_t neq = c_offset_Y, size_t points=1); virtual ~Flow1D(); // virtual kw required for derived class destructors (flamelet) @@ -322,6 +322,59 @@ class Flow1D : public Domain1D return m_epsilon_right; } + // Turn fictive species on / off. + + const size_t getFictives() const { + return m_nfic; + } + + void setFictives(size_t nFic) { + m_nfic = nFic; + } + + void initFictive(); + + // Returns fictive name + std::string fictiveName(size_t n) const { + return m_fictive_name[n]; + } + + // Fictive transport properties + void setFictiveSchmidt(std::vector fictive_schmidt) { + m_fictive_schmidt = fictive_schmidt; + } + const doublereal getFictiveSchmidt(size_t k) const { + return m_fictive_schmidt[k]; + } + + // Fictive fuel and oxidizer inlet conditions + void setFictive_fuel_inlet_Y(std::vector fictive_fuel_inlet_Y) { + m_fictive_fuel_inlet_Y = fictive_fuel_inlet_Y; + } + + const doublereal getFictive_fuel_inlet_Y(size_t k) const { + return m_fictive_fuel_inlet_Y[k]; + } + void setFictive_oxidizer_inlet_Y(std::vector fictive_oxidizer_inlet_Y) { + m_fictive_oxidizer_inlet_Y = fictive_oxidizer_inlet_Y; + } + const doublereal getFictive_oxidizer_inlet_Y(size_t k) const { + return m_fictive_oxidizer_inlet_Y[k]; + } + + // Fictive source term + void setFictiveSourceTermProfile(const std::string& name, vector& zfixed, vector& omegafixed) { + for (size_t k = 0; k < m_nfic; k++) { + if (m_fictive_name[k] == name) { + for (size_t i = 0; i < m_points; i++) { + m_fictive_source_term(k, i) = omegafixed[i]; + } + } + } + } + + + // Turn soot formation on / off. // setSections const size_t getSections() const{ @@ -1159,10 +1212,14 @@ class Flow1D : public Domain1D virtual void evalElectricField(double* x, double* rsd, int* diag, double rdt, size_t jmin, size_t jmax); - // Evaluate the species equations' residuals. + // Evaluate the soot sections equations' residuals. virtual void evalSoot(double* x, double* rsd, int* diag, double rdt, size_t jmin, size_t jmax); + // Evaluate the fictive species equations' residuals. + virtual void evalFictives(double* x, double* rsd, int* diag, + double rdt, size_t jmin, size_t jmax); + //! @} End of Governing Equations /** @@ -1265,6 +1322,19 @@ class Flow1D : public Domain1D double Ys_prev(size_t k, size_t j) const { return prevSoln(c_offset_S + k, j); } + + //Fictive species + double Yfic(const double* x, size_t k, size_t j) const { + return x[index(c_offset_F+k, j)]; + } + + double& Yfic(double* x, size_t k, size_t j) { + return x[index(c_offset_F+k, j)]; + } + + double Yfic_prev(size_t k, size_t j) const { + return prevSoln(c_offset_F + k, j); + } //---- //! Get the mole fraction of species `k` at point `j` from the local state vector @@ -1333,6 +1403,12 @@ class Flow1D : public Domain1D return (Ys(x,k,jloc) - Ys(x,k,jloc-1))/m_dz[jloc-1]; } + // Fictive species + double dYficdz(const double* x, size_t k, size_t j) const { + size_t jloc = (u(x,j) > 0.0 ? j : j + 1); + return (Yfic(x,k,jloc) - Yfic(x,k,jloc-1))/m_dz[jloc-1]; + } + /** * Calculates the spatial derivative of temperature T with respect to z at point * j using upwind differencing. @@ -1412,6 +1488,9 @@ class Flow1D : public Domain1D //! Update the soot diffusive mass fluxes. virtual void updateSootDiffFluxes(const double* x, size_t j0, size_t j1); + //! Update the fictive species diffusive mass fluxes. + virtual void updateFictiveDiffFluxes(const double* x, size_t j0, size_t j1); + /** * Compute the spatial derivative of species specific molar enthalpies using upwind * differencing. Updates all species molar enthalpies for all species at point j. @@ -1482,7 +1561,9 @@ class Flow1D : public Domain1D size_t m_nsp; //!< Number of species in the mechanism size_t m_neq; //!< Number of non-species equations - size_t m_nsoot; + size_t m_nsoot; //!< Number of soot sections + size_t m_nfic; //!< Number of fictive species equations + std::string m_fuel; //! Phase object used for calculating thermodynamic properties @@ -1566,6 +1647,20 @@ class Flow1D : public Domain1D //! radiative heat loss vector vector m_qdotRadiation; + // ---------------------- + // FICTIVE SPECIES RELATED VARIABLES + // ---------------------- + size_t fictive_loglevel=1; + std::vector m_fictive_name; + Array2D m_fic_diff ; + Array2D m_fic_soret ; + Array2D m_fictive_source_term; + size_t c_offset_F = 7; // CAC + vector m_fictive_schmidt; + vector m_fictive_fuel_inlet_Y; + vector m_fictive_oxidizer_inlet_Y; + + // ---------------------- // SOOT RELATED VARIABLES // ---------------------- diff --git a/interfaces/cython/cantera/_onedim.pxd b/interfaces/cython/cantera/_onedim.pxd index c37c24977c8..b4b0b1b8566 100644 --- a/interfaces/cython/cantera/_onedim.pxd +++ b/interfaces/cython/cantera/_onedim.pxd @@ -13,7 +13,7 @@ from .thermo cimport * cdef extern from "cantera/oneD/DomainFactory.h" namespace "Cantera": cdef shared_ptr[CxxDomain1D] CxxNewDomain1D "newDomain" ( - string, shared_ptr[CxxSolution], string, size_t) except +translate_exception + string, shared_ptr[CxxSolution], string, size_t, size_t) except +translate_exception cdef extern from "cantera/oneD/Domain1D.h": @@ -105,6 +105,17 @@ cdef extern from "cantera/oneD/Flow1D.h": void setRightControlPointTemperature(double) except +translate_exception void setSections(size_t) size_t getSections() + + void setFictives(size_t) + size_t getFictives() + double getFictiveSchmidt(size_t) + void setFictiveSchmidt(vector[double]&) + double getFictive_fuel_inlet_Y(size_t) + void setFictive_fuel_inlet_Y(vector[double]&) + double getFictive_oxidizer_inlet_Y(size_t) + void setFictive_oxidizer_inlet_Y(vector[double]&) + void setFictiveSourceTermProfile(string, vector[double]&, vector[double]&) + void setFlameletFlow() diff --git a/interfaces/cython/cantera/_onedim.pyx b/interfaces/cython/cantera/_onedim.pyx index e064dc20f9e..718476884ef 100644 --- a/interfaces/cython/cantera/_onedim.pyx +++ b/interfaces/cython/cantera/_onedim.pyx @@ -308,7 +308,10 @@ cdef class Boundary1D(Domain1D): self._domain = CxxNewDomain1D( stringify(self._domain_type), phase._base, stringify(name), #add kwargs if kwargs provided - kwargs['sections'] if 'sections' in kwargs else 0, + # Get 'sections' from kwargs, defaulting to 0 if not provided + kwargs.get('sections', 0), + # Get 'fictives' from kwargs, defaulting to 0 if not provided + kwargs.get('fictives', 0), ) self.domain = self._domain.get() self.boundary = self.domain @@ -452,7 +455,10 @@ cdef class FlowBase(Domain1D): self._domain = CxxNewDomain1D( stringify(self._domain_type), phase._base, stringify(name), #add kwargs if kwargs provided - kwargs['sections'] if 'sections' in kwargs else 0, + # Get 'sections' from kwargs, defaulting to 0 if not provided + kwargs.get('sections', 0), + # Get 'fictives' from kwargs, defaulting to 0 if not provided + kwargs.get('fictives', 0), ) self.domain = self._domain.get() self.flow = self.domain @@ -597,6 +603,81 @@ cdef class FlowBase(Domain1D): data[j] = self.flow.radiativeHeatLoss(j) return data + # BEGIN of fictive species API + + property fictive_equations: + """ + Returns number of fictive equations. + + :param None + + :return int : + Number of fictive equations + """ + def __set__(self, nFic): + #self.flow.setFictives(nFic) + raise KeyError ('/!\ FICTIVE SPECIES ERROR : You cannot set equations number this way !') + def __get__(self): + return self.flow.getFictives() + + property fictive_schmidt : + """ + Gets / sets flame Schmidt number of the fictive species + + : param adiabatic_temperature = double : + adiabatic temperature (K) + + : return double : + adiabatic temperature (K) + """ + def __set__(self, fictive_schmidt): + self.flow.setFictiveSchmidt(fictive_schmidt) + + property fictive_fuel_inlet_Y : + """ + Gets / sets flame temperature used as reference for Kazakov's surface reactions model + + : param adiabatic_temperature = double : + adiabatic temperature (K) + + : return double : + adiabatic temperature (K) + """ + def __set__(self, fictive_fuel_inlet_Y): + self.flow.setFictive_fuel_inlet_Y(fictive_fuel_inlet_Y) + + property fictive_oxidizer_inlet_Y : + """ + Gets / sets flame temperature used as reference for Kazakov's surface reactions model + + : param adiabatic_temperature = double : + adiabatic temperature (K) + + : return double : + adiabatic temperature (K) + """ + def __set__(self, fictive_oxidizer_inlet_Y): + self.flow.setFictive_oxidizer_inlet_Y(fictive_oxidizer_inlet_Y) + + def set_fictive_source_term_profile(self, name, pos, Omegas): + """Set the fixed temperature profile. This profile is used + whenever the energy equation is disabled. + + :param pos: + arrray of relative positions from 0 to 1 + :param temp: + array of temperature values + + >>> d.set_fixed_temp_profile(array([0.0, 0.5, 1.0]), + ... array([500.0, 1500.0, 2000.0]) + """ + cdef vector[double] x, y + for p in pos: + x.push_back(p) + for value in Omegas: + y.push_back(value) + self.flow.setFictiveSourceTermProfile(stringify(name) ,x, y) + # BEGIN of soot API property soot_loglevel: diff --git a/interfaces/cython/cantera/onedim.py b/interfaces/cython/cantera/onedim.py index 0f181ed876c..a7836e07aa2 100644 --- a/interfaces/cython/cantera/onedim.py +++ b/interfaces/cython/cantera/onedim.py @@ -288,6 +288,32 @@ def boundary_emissivities(self, epsilon): if len(epsilon) != 2: raise ValueError("Boundary emissivities must both be set at the same time.") self.flame.boundary_emissivities = epsilon[0], epsilon[1] + + + @property + def fic_Y(self): + """ + Gets fictive mass fraction. + + : param None + + : return (fictives equations x points) numpy array : + fictive mass fraction for each equations at each point + """ + data = np.empty((self.flame.fictive_equations, self.flame.n_points)) + ns = self.flame.fictive_equations + for k in range(ns): + data[k,:] = self.profile(self.flame, 'Yfic_'+str(k)) + + return data + + # BEGIN of fictive species API + def add_fic(self, fictive_schmidt=[0], fictive_fuel_inlet_Y = [0], fictive_oxidizer_inlet_Y=[0] ): + if self.flame.fictive_equations == 0: + raise CanteraError('/!\ FICTIVES SPECIES ERROR : cannot set fictive equations') + self.flame.fictive_schmidt = fictive_schmidt + self.flame.fictive_fuel_inlet_Y = fictive_fuel_inlet_Y + self.flame.fictive_oxidizer_inlet_Y = fictive_oxidizer_inlet_Y # BEGIN of soot API @@ -1198,7 +1224,7 @@ class FreeFlame(FlameBase): """A freely-propagating flat flame.""" __slots__ = ('inlet', 'flame', 'outlet') - def __init__(self, gas, grid=None, width=None, sections=0): + def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): """ A domain of type `FreeFlow` named 'flame' will be created to represent the flame. The three domains comprising the stack are stored as ``self.inlet``, @@ -1214,15 +1240,15 @@ def __init__(self, gas, grid=None, width=None, sections=0): """ #: `Inlet1D` at the left of the domain representing premixed reactants - self.inlet = Inlet1D(name='reactants', phase=gas, sections=sections) + self.inlet = Inlet1D(name='reactants', phase=gas, sections=sections, fictives=fictives) #: `Outlet1D` at the right of the domain representing the burned products - self.outlet = Outlet1D(name='products', phase=gas, sections=sections) + self.outlet = Outlet1D(name='products', phase=gas, sections=sections, fictives=fictives) if not hasattr(self, 'flame'): # Create flame domain if not already instantiated by a child class #: `FreeFlow` domain representing the flame - self.flame = FreeFlow(gas, name='flame', sections=sections) + self.flame = FreeFlow(gas, name='flame', sections=sections, fictives=fictives) if width is not None: if grid is not None: @@ -1393,7 +1419,7 @@ class BurnerFlame(FlameBase): """A burner-stabilized flat flame.""" __slots__ = ('burner', 'flame', 'outlet') - def __init__(self, gas, grid=None, width=None, sections=0): + def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1412,15 +1438,15 @@ def __init__(self, gas, grid=None, width=None, sections=0): """ #: `Inlet1D` at the left of the domain representing the burner surface through #: which reactants flow - self.burner = Inlet1D(name='burner', phase=gas, sections=sections) + self.burner = Inlet1D(name='burner', phase=gas, sections=sections, fictives=fictives) #: `Outlet1D` at the right of the domain representing the burned gas - self.outlet = Outlet1D(name='outlet', phase=gas, sections=sections) + self.outlet = Outlet1D(name='outlet', phase=gas, sections=sections, fictives=fictives) if not hasattr(self, 'flame'): # Create flame domain if not already instantiated by a child class #: `UnstrainedFlow` domain representing the flame - self.flame = UnstrainedFlow(gas, name='flame', sections=sections) + self.flame = UnstrainedFlow(gas, name='flame', sections=sections, fictives=fictives) if width is not None: if grid is not None: @@ -1531,7 +1557,7 @@ class CounterflowDiffusionFlame(FlameBase): """ A counterflow diffusion flame """ __slots__ = ('fuel_inlet', 'flame', 'oxidizer_inlet') - def __init__(self, gas, grid=None, width=None, sections=0): + def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1550,15 +1576,15 @@ def __init__(self, gas, grid=None, width=None, sections=0): """ #: `Inlet1D` at the left of the domain representing the fuel mixture - self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas, sections=sections) + self.fuel_inlet = Inlet1D(name='fuel_inlet', phase=gas, sections=sections, fictives=fictives) self.fuel_inlet.T = gas.T #: `Inlet1D` at the right of the domain representing the oxidizer mixture - self.oxidizer_inlet = Inlet1D(name='oxidizer_inlet', phase=gas, sections=sections) + self.oxidizer_inlet = Inlet1D(name='oxidizer_inlet', phase=gas, sections=sections, fictives=fictives) self.oxidizer_inlet.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) if width is not None: if grid is not None: @@ -1850,7 +1876,7 @@ class ImpingingJet(FlameBase): """An axisymmetric flow impinging on a surface at normal incidence.""" __slots__ = ('inlet', 'flame', 'surface') - def __init__(self, gas, grid=None, width=None, surface=None, sections=0): + def __init__(self, gas, grid=None, width=None, surface=None, sections=0, fictives=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1871,10 +1897,10 @@ def __init__(self, gas, grid=None, width=None, surface=None, sections=0): """ #: `Inlet1D` at the left of the domain representing the incoming reactants - self.inlet = Inlet1D(name='inlet', phase=gas, sections=sections) + self.inlet = Inlet1D(name='inlet', phase=gas, sections=sections, fictives=fictives) #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) self.flame.set_axisymmetric_flow() if width is not None: @@ -1940,7 +1966,7 @@ class CounterflowPremixedFlame(FlameBase): """ A premixed counterflow flame """ __slots__ = ('reactants', 'flame', 'products') - def __init__(self, gas, grid=None, width=None, sections=0): + def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -1958,15 +1984,15 @@ def __init__(self, gas, grid=None, width=None, sections=0): """ #: `Inlet1D` at the left of the domain representing premixed reactants - self.reactants = Inlet1D(name='reactants', phase=gas, sections=sections) + self.reactants = Inlet1D(name='reactants', phase=gas, sections=sections, fictives=fictives) self.reactants.T = gas.T #: `Inlet1D` at the right of the domain representing burned products - self.products = Inlet1D(name='products', phase=gas, sections=sections) + self.products = Inlet1D(name='products', phase=gas, sections=sections, fictives=fictives) self.products.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) if width is not None: if grid is not None: @@ -2047,7 +2073,7 @@ class CounterflowTwinPremixedFlame(FlameBase): """ __slots__ = ('reactants', 'flame', 'products') - def __init__(self, gas, grid=None, width=None, sections=0): + def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): """ :param gas: `Solution` (using the IdealGas thermodynamic model) used to @@ -2063,14 +2089,14 @@ def __init__(self, gas, grid=None, width=None, sections=0): represent the flame. The three domains comprising the stack are stored as ``self.reactants``, ``self.flame``, and ``self.products``. """ - self.reactants = Inlet1D(name='reactants', phase=gas, sections=sections) + self.reactants = Inlet1D(name='reactants', phase=gas, sections=sections, fictives=fictives) self.reactants.T = gas.T #: `AxisymmetricFlow` domain representing the flame - self.flame = AxisymmetricFlow(gas, name='flame', sections=sections) + self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) #The right boundary is a symmetry plane - self.products = SymmetryPlane1D(name='products', phase=gas, sections=sections) + self.products = SymmetryPlane1D(name='products', phase=gas, sections=sections, fictives=fictives) if width is not None: if grid is not None: diff --git a/src/oneD/Domain1D.cpp b/src/oneD/Domain1D.cpp index f0a87500bab..61bd1f1c338 100644 --- a/src/oneD/Domain1D.cpp +++ b/src/oneD/Domain1D.cpp @@ -16,9 +16,9 @@ namespace Cantera { -Domain1D::Domain1D(size_t nv, size_t points, double time, size_t nsoot, size_t neq) +Domain1D::Domain1D(size_t nv, size_t points, double time, size_t nsoot, size_t nfic, size_t neq) { - resize(nv+nsoot+neq, points); + resize(nv+nsoot+nfic+neq, points); } Domain1D::~Domain1D() diff --git a/src/oneD/DomainFactory.cpp b/src/oneD/DomainFactory.cpp index 6ed0e7519f0..29a81e9626a 100644 --- a/src/oneD/DomainFactory.cpp +++ b/src/oneD/DomainFactory.cpp @@ -18,72 +18,72 @@ std::mutex DomainFactory::domain_mutex; DomainFactory::DomainFactory() { - reg("inlet", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("inlet", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new Inlet1D(solution, id); }); - reg("empty", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("empty", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new Empty1D(solution, id); }); - reg("symmetry-plane", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("symmetry-plane", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new Symm1D(solution, id); }); - reg("outlet", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("outlet", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new Outlet1D(solution, id); }); - reg("outlet-reservoir", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("outlet-reservoir", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new OutletRes1D(solution, id); }); - reg("surface", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("surface", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new Surf1D(solution, id); }); - reg("reacting-surface", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("reacting-surface", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new ReactingSurf1D(solution, id); }); - reg("gas-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("gas-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new Flow1D(solution, id, sections); }); - reg("legacy-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("legacy-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new Flow1D(solution, id, sections); }); - reg("ion-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("ion-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new IonFlow(solution, id); }); - reg("free-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("free-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { Flow1D* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new Flow1D(solution, id, sections); + ret = new Flow1D(solution, id, sections, fictives); } ret->setFreeFlow(); return ret; }); - reg("axisymmetric-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("axisymmetric-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0 , const size_t& fictives = 0) { Flow1D* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new Flow1D(solution, id, sections); + ret = new Flow1D(solution, id, sections, fictives); } ret->setAxisymmetricFlow(); return ret; }); - reg("unstrained-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("unstrained-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { Flow1D* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new Flow1D(solution, id, sections); + ret = new Flow1D(solution, id, sections, fictives); } ret->setUnstrainedFlow(); return ret; }); - reg("flamelet-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0) { + reg("flamelet-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { Flow1D* ret; if (solution->transport()->transportModel() == "ionized-gas") { ret = new IonFlow(solution, id); } else { - ret = new Flamelet(solution, id, sections); // neq = 1 for flamelet + ret = new Flamelet(solution, id, sections, fictives); // neq = 1 for flamelet } ret->setFlameletFlow(); return ret; diff --git a/src/oneD/Flow1D.cpp b/src/oneD/Flow1D.cpp index 9c5a37c95f9..9bad1355491 100644 --- a/src/oneD/Flow1D.cpp +++ b/src/oneD/Flow1D.cpp @@ -18,11 +18,12 @@ using namespace std; namespace Cantera { -Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : - Domain1D(nsp, points, 0.0, nsoot, neq), // CERFACS : c_offset_Y is not added like in the official cantera release because in Domain1D.cpp we resize with nsoot and neq. +Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t nfic, size_t neq, size_t points) : + Domain1D(nsp, points, 0.0, nsoot, nfic, neq), // CERFACS : c_offset_Y is not added like in the official cantera release because in Domain1D.cpp we resize with nsoot and neq. m_nsp(nsp), m_neq(neq), - m_nsoot(nsoot) + m_nsoot(nsoot), + m_nfic(nfic) { m_points = points; @@ -32,10 +33,10 @@ Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t poi m_thermo = ph; size_t nsp2 = m_thermo->nSpecies(); - m_nv = m_neq + m_nsp + m_nsoot; // CERFACS the number of variable is number of equations + number of species + number of soot sections (soot sections are placed after the species.) + m_nv = m_neq + m_nsp + m_nsoot + m_nfic; // CERFACS the number of variable is number of equations + number of species + number of soot sections (soot sections are placed after the species.) + number of fictive species // CERFACS : I don't understand why do we do that ? nsp2 will always be different than nsp if we have soots. And even if we have soots, the domain size should already have the correct size. - if (nsp2 + m_nsoot != m_nsp) { + if (nsp2 + m_nsoot + m_nfic != m_nsp) { m_nsp = nsp2; Domain1D::resize(m_nv, points); } @@ -109,18 +110,24 @@ Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t poi if (m_nsoot > 0){ initSoot(); } + // A. Coudray + //---------------------Fictive initialisation----------- + + if (m_nfic > 0){ + initFictive(); + } } -Flow1D::Flow1D(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) - : Flow1D(th.get(), nsp, nsoot, neq, points) +Flow1D::Flow1D(shared_ptr th, size_t nsp, size_t nsoot, size_t nfic, size_t neq, size_t points) + : Flow1D(th.get(), nsp, nsoot, nfic, neq, points) { auto sol = Solution::create(); sol->setThermo(th); setSolution(sol); } -Flow1D::Flow1D(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) - : Flow1D(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) +Flow1D::Flow1D(shared_ptr sol, const string& id, size_t nsoot, size_t nfic, size_t neq, size_t points) + : Flow1D(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, nfic, neq, points) { setSolution(sol); m_id = id; @@ -222,6 +229,17 @@ void Flow1D::resize(size_t ncomponents, size_t points) m_qdotSg.resize(m_nsoot, m_points, 0.0); m_qdotOxidation.resize(m_nsoot, m_points, 0.0); } + + // Fictive species + if (m_nfic != 0){ + m_fic_diff.resize(m_nfic, m_points, 0.0); + m_fic_soret.resize(m_nfic, m_points, 0.0); + m_fictive_source_term.resize(m_nfic,m_points, 0.0); + m_fictive_oxidizer_inlet_Y.resize(m_nfic); + m_fictive_fuel_inlet_Y.resize(m_nfic); + m_fictive_schmidt.resize(m_nfic); + } + } void Flow1D::setupGrid(size_t n, const double* z) @@ -424,6 +442,7 @@ void Flow1D::eval(size_t jGlobal, double* xGlobal, double* rsdGlobal, evalContinuity(x, rsd, diag, rdt, jmin, jmax); evalMomentum(x, rsd, diag, rdt, jmin, jmax); evalSoot(x, rsd, diag, rdt, jmin, jmax); + evalFictives(x, rsd, diag, rdt, jmin, jmax); evalSpecies(x, rsd, diag, rdt, jmin, jmax); evalEnergy(x, rsd, diag, rdt, jmin, jmax); evalLambda(x, rsd, diag, rdt, jmin, jmax); @@ -458,6 +477,10 @@ void Flow1D::updateProperties(size_t jg, double* x, size_t jmin, size_t jmax) if (m_nsoot > 0){ updateSootDiffFluxes(x, j0, j1); } + if (m_nfic > 0){ + updateFictiveDiffFluxes(x, j0, j1); + } + } void Flow1D::updateTransport(double* x, size_t j0, size_t j1) @@ -949,6 +972,51 @@ void Flow1D::evalSoot(double* x, double* rsd, int* diag, } } +void Flow1D::evalFictives(double* x, double* rsd, int* diag, + double rdt, size_t jmin, size_t jmax) +{ + if (m_nfic > 0){ + + if (jmin == 0) { // left boundary + for (size_t k = 0; k < m_nfic; k++){ + rsd[index(c_offset_F + k, jmin)] = Yfic(x,k,0)-m_fictive_fuel_inlet_Y[k]; + diag[index(c_offset_F + k, jmin)] = 0; + } + } + if (jmax == m_points - 1) { // right boundary + for (size_t k = 0; k < m_nfic; k++){ //right boundary + rsd[index(c_offset_F + k, jmax)] = m_fic_diff(k,jmax-1) + rho_u(x,jmax)*Yfic(x,k,jmax); + diag[index(c_offset_F + k, jmax)] = 0; + } + } + // j0 and j1 are constrained to only interior points + size_t j0 = std::max(jmin, 1); + size_t j1 = std::min(jmax, m_points-2); + for (size_t j = j0; j <= j1; j++) { // interior points + + for (size_t k = 0; k < m_nfic; k++){ + // Convection + double fic_convec = rho_u(x,j)*dYficdz(x,k,j); + // Diffusion + double fic_diffus = 2.0 * (m_fic_diff(k,j) - m_fic_diff(k,j-1)) + / (z(j+1) - z(j-1)); + // Thermophoresis + double fic_soret = 2.0 * (m_fic_soret(k,j) - m_fic_soret(k,j-1)) + / (z(j+1) - z(j-1)); + + // Source terms [m3/kg/s] + double fic_source = m_fictive_source_term(k,j); // m_wt[5]*m_wdot(5, j); // + + // Residual + rsd[index(c_offset_F + k, j)] = + (fic_source - fic_convec + fic_diffus + fic_soret) / m_rho[j] + - rdt * (Yfic(x,k,j) - Yfic_prev(k,j)); + diag[index(c_offset_F + k, j)] = 1; + } + } + } +} + void Flow1D::show(const double* x) { writelog(" Pressure: {:10.4g} Pa\n", m_press); @@ -986,6 +1054,8 @@ string Flow1D::componentName(size_t n) const return m_thermo->speciesName(n - c_offset_Y); } else if (n >= c_offset_S && n < (c_offset_S + m_nsoot)) { return sectionName(n-c_offset_S); + } else if (n >= c_offset_F && n < (c_offset_F + m_nfic)) { + return fictiveName(n-c_offset_F); } else { return ""; } @@ -1008,6 +1078,8 @@ size_t Flow1D::componentIndex(const string& name) const return c_offset_Uo; } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()) { return stoi(name.substr(2))+c_offset_S; // offset not required in previous version, why? + } else if (find(m_fictive_name.begin(), m_fictive_name.end(), name) != m_fictive_name.end()) { + return stoi(name.substr(5))+c_offset_F; // CAC } else { for (size_t n=c_offset_Y; npressure(); vector did_section(m_nsoot,false); + vector did_fictive(m_nfic,false); bool wrote_header = false; const auto grid = arr.getComponent("grid").as>(); @@ -1145,16 +1218,28 @@ void Flow1D::fromArray(SolutionArray& arr, double* soln) did_section[n]=true; writelog("Adding soot section to soln "+name+"\n"); } + else if (find(m_fictive_name.begin(), m_fictive_name.end(), name) != m_fictive_name.end()){ + size_t n = stoi(name.substr(5)); + did_fictive[n]=true; + writelog("Adding fictive equation to soln "+name+"\n"); + } for (size_t j = 0; j < nPoints(); j++) { soln[index(i,j)] = data[j]; } } else if (find(m_section_name.begin(), m_section_name.end(), name) != m_section_name.end()){ - size_t n = stoi(name.substr(2)); + size_t n = stoi(name.substr(2)); did_section[n]=true; writelog("Creating soot section in soln "+name+"\n"); for (size_t j = 0; j < nPoints(); j++) { soln[index(n+c_offset_S,j)] = 0.0; } + } else if (find(m_fictive_name.begin(), m_fictive_name.end(), name) != m_fictive_name.end()){ + size_t n = stoi(name.substr(5)); + did_fictive[n]=true; + writelog("Creating fictive equation in soln "+name+"\n"); + for (size_t j = 0; j < nPoints(); j++) { + soln[index(n+c_offset_F,j)] = 0.0; + } } else { warn_user("Flow1D::fromArray", "Saved state does not contain values for " "component '{}' in domain '{}'.", name, id()); @@ -1175,6 +1260,21 @@ void Flow1D::fromArray(SolutionArray& arr, double* soln) } } + if (m_nfic != 0) { + wrote_header = false; + for (size_t ks = 0; ks < m_nfic; ks++) { + if (did_fictive[ks] == false) { + if (!wrote_header) { + writelog("\n\n"); + writelog("Missing data for fictives species:\n"); + wrote_header = true; + } + writelog(m_fictive_name[ks]+" "); + } + } + } + + updateProperties(npos, soln + loc(), 0, m_points - 1); } @@ -1456,6 +1556,72 @@ void Flow1D::AVBPcompute_local_thick(double* x,size_t j){ avbp_thick[j] = avbp_fthick; } +//---------------------------------// +// Fictive SPECIES RELATED MTEHODS // +//---------------------------------// + +void Flow1D:: initFictive(){ + //---------------------------------------------------- + // Initializes fictives computation + //---------------------------------------------------- + + // Sets offset of fictives equations in solution array + // Resizes necessay arrays + // Sets fictives names "Yfic_X", disables refinement on fictives and sets clipping + + // Offset definition + c_offset_F = c_offset_Y + m_nsp; + // Array allocation + m_fictive_name.resize(m_nfic); + m_fic_diff.resize(m_nfic, m_points, 0.0); + m_fic_soret.resize(m_nfic, m_points, 0.0); + m_fictive_source_term.resize(m_nfic,m_points, 0.0); + m_fictive_oxidizer_inlet_Y.resize(m_nfic); + m_fictive_fuel_inlet_Y.resize(m_nfic); + m_fictive_schmidt.resize(m_nfic); + // Fictive equations setup + for (size_t k = 0; k < m_nfic; k++) { + std::string string_k = std::to_string(k); + m_fictive_name[k] = "Yfic_" + string_k; + m_refiner->setActive(c_offset_F+k, false); + setBounds(c_offset_F + k, -1.0e-5, 1e5); + + } +} + + +void Flow1D::updateFictiveDiffFluxes(const doublereal* x, size_t j0, size_t j1){ + //---------------------------------------------------- + // Computes fictive species molecular and thermal diffusion fluxes + //---------------------------------------------------- + for (size_t j = j0; j < j1; j++) { + // Evaluate gas at midpoints : j->j+1/2 + setGasAtMidpoint(x,j); + + doublereal rho = m_thermo->density(); + doublereal visco = m_trans->viscosity(); + doublereal lambda_th = m_trans->thermalConductivity(); + + doublereal dz = z(j+1) - z(j); + // Evaluate viscosity + for (size_t k = 0; k < m_nfic; k++){ + // Evaluate fictive mass fraction at j+1/2 + doublereal Yficmid = 0.5 * (Yfic(x,k,j)+Yfic(x,k,j+1)); + // Evaluate centered differencies at j+1/2 + doublereal dYfic = Yfic(x,k,j+1) - Yfic(x,k,j); + //Evaluate diffusion coefficient at j+1/2 + doublereal Dfic = visco / rho / m_fictive_schmidt[k]; + // Evaluate fictive mass diffusion flux at j+1/2 + m_fic_diff(k,j) = rho * Dfic * dYfic/dz; + } + } +} + +//--------------------------------------// +// END FICITVE SPECIES RELATED MTEHODS // +//---------------------------------// + + //----------------------// // SOOT RELATED MTEHODS // //----------------------// From 19d9175a4feef45d9ea395562a18dda29e956d92 Mon Sep 17 00:00:00 2001 From: Alexandre Coudray Date: Wed, 12 Nov 2025 09:16:17 +0100 Subject: [PATCH 95/98] Added an example script to run fictive species on premixed flames All seems to work ! --- samples/python/AVBP/fictive_species.py | 102 +++++++++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 samples/python/AVBP/fictive_species.py diff --git a/samples/python/AVBP/fictive_species.py b/samples/python/AVBP/fictive_species.py new file mode 100644 index 00000000000..9b12e317db6 --- /dev/null +++ b/samples/python/AVBP/fictive_species.py @@ -0,0 +1,102 @@ +# This script exists to show to use fictive species in Cantera. +# The implementation makes it's use similar to AVBP/ +# Note: only constant Schmidt number per species is possible + + +import cantera as ct +import numpy as np +import matplotlib.pyplot as plt +import os +os.chdir(os.path.dirname(os.path.abspath(__file__))) + +loglevel = 0 # For clarity + +# Setting the mechanism name +mech = 'BISETTI' +P, T = 1e5, 300 +# Creating gas object +#if cantera version is 2.5.0 or higher, use the following line instead +if ct.__version__ >= '2.5.0': + gas = ct.Solution('./inputs/%s.yaml' % mech) +else: + gas = ct.Solution('./inputs/%s.cti' % mech) + +phi = 2.0 # equivalence ratio +fuel = {'C2H4': 1} # Ethylene composition +oxidizer = {'O2': 1, 'N2': 3.76} # Oxygen composition + +print("First flame: a rich premixed ethylene/air flame !") + +gas.TP = T, P +gas.set_equivalence_ratio(phi, fuel, oxidizer) + +# -------------- First, a flame without fictive species ------------------ # + +f = ct.FreeFlame(gas, width=0.02) # Create the free laminar premixed flame specifying the width of the grid +f.inlet.X = gas.X # Inlet condition on mass fraction +f.inlet.T = gas.T # Inlet condition on temperature + + +f.energy_enabled = True +tol_ss = [1.0e-5, 1.0e-9] # [rtol atol] for steady-state problem +tol_ts = [1.0e-5, 1.0e-9] # [rtol atol] for time stepping +f.flame.set_steady_tolerances(default=tol_ss) +f.flame.set_transient_tolerances(default=tol_ts) +f.set_max_jac_age(50, 50) +f.set_time_step(1.0e-5, [2, 5, 10, 20, 80]) # s + +f.set_refine_criteria(ratio=2.0, slope=0.05, curve=0.05) + +print("Solving flame without fictive") +f.solve(loglevel=1, refine_grid='refine') +if ct.__version__ >= '2.5.0': + f.save('./RESULTS/%s.yaml' % mech,'without_fic',overwrite=True) +else: + f.save('./RESULTS/%s.xml' % mech,'without_fic') + +# For the purpose of showing the fictive species, we store the source term of the soot precursor. +Omega_fic = np.zeros(f.flame.n_points,'d') +for n in range(f.flame.n_points): + f.set_gas_state(n) + Omega_fic[n] = gas.net_production_rates[gas.species_index('A2')] * gas.molecular_weights[gas.species_index('A2')] +grid = f.flame.grid + +# ------------- Second, fictive species are declared and the previosu flame is restored -------------------- # +f = ct.FreeFlame(gas, width=0.02, fictives=1) + +if ct.__version__ >= '2.5.0': + f.restore('./RESULTS/%s.yaml' % mech, 'without_fic') +else: + f.restore('./RESULTS/%s.xml' % mech, 'without_fic') + +# Fictive species properties are set like this (remember the order !) +# Note: the Schmidt of A2 is not the real one but sounds close.. +f.add_fic( + fictive_schmidt = [2.0], + fictive_fuel_inlet_Y = [0.0], + fictive_oxidizer_inlet_Y = [0.0] +) + + +# Add source term to the ficitve species (here, this is the "real" source term of A2) +f.flame.set_fictive_source_term_profile('Yfic_0', grid, Omega_fic) +print("Solving flame with fictive") +f.solve(loglevel=1, refine_grid='disabled') # Grid refinement must be deactivated ! +if ct.__version__ >= '2.5.0': + f.save('./RESULTS/%s.yaml' % mech,'with_fic',overwrite=True) +else: + f.save('./RESULTS/%s.xml' % mech,'with_fic') + +# Retrieve data +fictive_data = f.fic_Y +Y_A2_fic = fictive_data[0,:] + +Y_A2 = np.zeros(f.flame.n_points,'d') +for n in range(f.flame.n_points): + f.set_gas_state(n) + Y_A2[n]=gas.Y[gas.species_index('A2')] +plt.figure() +plt.plot(f.grid, Y_A2_fic, marker="*", label='A2-Fictive') +plt.plot(f.grid, Y_A2, label='A2-Real') +plt.legend() +plt.savefig('plot_premixed_with_fictive.png', dpi=500) \ No newline at end of file From 5e05a1e7383bbb7c14a7244ace484afb3a1fd034 Mon Sep 17 00:00:00 2001 From: Antoine Pestre Date: Tue, 2 Dec 2025 10:41:37 +0100 Subject: [PATCH 96/98] Several bugfixes - Add nfic to Flamelet class to be able to add nfic in Flow1D call - typo in _onedim.pyx - Display plot instead of saving picture in sample fictive_species.py - Add fictive parameter in construction of gas-flow and legacy-flow. Not really necessary but done as sections param for consistency - Add missing argument of Flow1D call in IonFlow.cpp On branch FEATURE/Fictive_species Changes to be committed: modified: include/cantera/oneD/Flamelet.h modified: interfaces/cython/cantera/_onedim.pyx modified: samples/python/AVBP/fictive_species.py modified: src/oneD/DomainFactory.cpp modified: src/oneD/Flamelet.cpp modified: src/oneD/IonFlow.cpp --- include/cantera/oneD/Flamelet.h | 6 +++--- interfaces/cython/cantera/_onedim.pyx | 2 +- samples/python/AVBP/fictive_species.py | 3 ++- src/oneD/DomainFactory.cpp | 4 ++-- src/oneD/Flamelet.cpp | 12 ++++++------ src/oneD/IonFlow.cpp | 2 +- 6 files changed, 15 insertions(+), 14 deletions(-) diff --git a/include/cantera/oneD/Flamelet.h b/include/cantera/oneD/Flamelet.h index be52f1a64cd..fa922aee8bc 100644 --- a/include/cantera/oneD/Flamelet.h +++ b/include/cantera/oneD/Flamelet.h @@ -23,17 +23,17 @@ namespace Cantera class Flamelet : public Flow1D { public: - Flamelet(IdealGasPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); + Flamelet(IdealGasPhase* ph = 0, size_t nsp = 1, size_t nsoot = 0, size_t nfic = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); //! Delegating constructor - Flamelet(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); + Flamelet(shared_ptr th, size_t nsp = 1, size_t nsoot = 0, size_t nfic = 0, size_t neq = c_offset_Yflamelet, size_t points = 1); //! Create a new flow domain. //! @param sol Solution object used to evaluate all thermodynamic, kinetic, and //! transport properties //! @param id name of flow domain //! @param points initial number of grid points - Flamelet(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t neq = c_offset_Yflamelet, size_t points=1); + Flamelet(shared_ptr sol, const string& id="", size_t nsoot = 0, size_t nfic = 0, size_t neq = c_offset_Yflamelet, size_t points=1); virtual ~Flamelet(); diff --git a/interfaces/cython/cantera/_onedim.pyx b/interfaces/cython/cantera/_onedim.pyx index 718476884ef..88c07af2c0a 100644 --- a/interfaces/cython/cantera/_onedim.pyx +++ b/interfaces/cython/cantera/_onedim.pyx @@ -669,7 +669,7 @@ cdef class FlowBase(Domain1D): array of temperature values >>> d.set_fixed_temp_profile(array([0.0, 0.5, 1.0]), - ... array([500.0, 1500.0, 2000.0]) + ... array([500.0, 1500.0, 2000.0])) """ cdef vector[double] x, y for p in pos: diff --git a/samples/python/AVBP/fictive_species.py b/samples/python/AVBP/fictive_species.py index 9b12e317db6..1e62e048705 100644 --- a/samples/python/AVBP/fictive_species.py +++ b/samples/python/AVBP/fictive_species.py @@ -99,4 +99,5 @@ plt.plot(f.grid, Y_A2_fic, marker="*", label='A2-Fictive') plt.plot(f.grid, Y_A2, label='A2-Real') plt.legend() -plt.savefig('plot_premixed_with_fictive.png', dpi=500) \ No newline at end of file +# plt.savefig('plot_premixed_with_fictive.png', dpi=500) +plt.show() \ No newline at end of file diff --git a/src/oneD/DomainFactory.cpp b/src/oneD/DomainFactory.cpp index 29a81e9626a..bdc60ea4e15 100644 --- a/src/oneD/DomainFactory.cpp +++ b/src/oneD/DomainFactory.cpp @@ -40,10 +40,10 @@ DomainFactory::DomainFactory() return new ReactingSurf1D(solution, id); }); reg("gas-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { - return new Flow1D(solution, id, sections); + return new Flow1D(solution, id, sections, fictives); }); reg("legacy-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { - return new Flow1D(solution, id, sections); + return new Flow1D(solution, id, sections, fictives); }); reg("ion-flow", [](shared_ptr solution, const string& id, const size_t& sections = 0, const size_t& fictives = 0) { return new IonFlow(solution, id); diff --git a/src/oneD/Flamelet.cpp b/src/oneD/Flamelet.cpp index abe1a311b8d..7791032ff18 100644 --- a/src/oneD/Flamelet.cpp +++ b/src/oneD/Flamelet.cpp @@ -19,21 +19,21 @@ using namespace std; namespace Cantera { -Flamelet::Flamelet(IdealGasPhase* ph, size_t nsp, size_t nsoot, size_t neq, size_t points) : - Flow1D(ph, nsp, nsoot, neq, points) { +Flamelet::Flamelet(IdealGasPhase* ph, size_t nsp, size_t nsoot, size_t nfic, size_t neq, size_t points) : + Flow1D(ph, nsp, nsoot, nfic, neq, points) { m_dovisc = true; m_updateChi = true; m_do_unityLewisNumber = true; } -Flamelet::Flamelet(shared_ptr th, size_t nsp, size_t nsoot, size_t neq, size_t points) - : Flow1D(th.get(), nsp, nsoot, neq, points) { +Flamelet::Flamelet(shared_ptr th, size_t nsp, size_t nsoot, size_t nfic, size_t neq, size_t points) + : Flow1D(th.get(), nsp, nsoot, nfic, neq, points) { m_solution = Solution::create(); m_solution->setThermo(th); } -Flamelet::Flamelet(shared_ptr sol, const string& id, size_t nsoot, size_t neq, size_t points) - : Flow1D(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, neq, points) { +Flamelet::Flamelet(shared_ptr sol, const string& id, size_t nsoot, size_t nfic, size_t neq, size_t points) + : Flow1D(sol->thermo().get(), sol->thermo()->nSpecies(), nsoot, nfic, neq, points) { m_solution = sol; m_id = id; m_kin = m_solution->kinetics().get(); diff --git a/src/oneD/IonFlow.cpp b/src/oneD/IonFlow.cpp index 87a77c75576..3d2cac4a38c 100644 --- a/src/oneD/IonFlow.cpp +++ b/src/oneD/IonFlow.cpp @@ -16,7 +16,7 @@ namespace Cantera { IonFlow::IonFlow(ThermoPhase* ph, size_t nsp, size_t points) : - Flow1D(ph, nsp, 0, c_offset_Y, points) + Flow1D(ph, nsp, 0, 0, c_offset_Y, points) //CERFACS 0,0 are set here because it correspond to nsoot=0 and nfic = 0, that have been added in Flow1D { // make a local copy of species charge for (size_t k = 0; k < m_nsp; k++) { From dad83d04afad9aa544ae8f523afe9b777b92bd4f Mon Sep 17 00:00:00 2001 From: Alexandre Coudray Date: Wed, 3 Dec 2025 09:09:48 +0100 Subject: [PATCH 97/98] Added an error if one wants to use both fictive species and soot at the same time. Should be possible if playing with offset_F --- interfaces/cython/cantera/onedim.py | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/interfaces/cython/cantera/onedim.py b/interfaces/cython/cantera/onedim.py index a7836e07aa2..7afb1e15ebe 100644 --- a/interfaces/cython/cantera/onedim.py +++ b/interfaces/cython/cantera/onedim.py @@ -1250,6 +1250,9 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): #: `FreeFlow` domain representing the flame self.flame = FreeFlow(gas, name='flame', sections=sections, fictives=fictives) + if sections and fictives: + raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") + if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") @@ -1447,6 +1450,10 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): # Create flame domain if not already instantiated by a child class #: `UnstrainedFlow` domain representing the flame self.flame = UnstrainedFlow(gas, name='flame', sections=sections, fictives=fictives) + + # Cannot used both fictive and soot at the same time + if sections and fictives: + raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") if width is not None: if grid is not None: @@ -1586,6 +1593,10 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): #: `AxisymmetricFlow` domain representing the flame self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) + # Cannot used both fictive and soot at the same time + if sections and fictives: + raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") + if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") @@ -1903,6 +1914,10 @@ def __init__(self, gas, grid=None, width=None, surface=None, sections=0, fictive self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) self.flame.set_axisymmetric_flow() + # Cannot used both fictive and soot at the same time + if sections and fictives: + raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") + if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") @@ -1994,6 +2009,10 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): #: `AxisymmetricFlow` domain representing the flame self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) + # Cannot used both fictive and soot at the same time + if sections and fictives: + raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") + if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") @@ -2098,6 +2117,10 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): #The right boundary is a symmetry plane self.products = SymmetryPlane1D(name='products', phase=gas, sections=sections, fictives=fictives) + # Cannot used both fictive and soot at the same time + if sections and fictives: + raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") + if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") From b11d9681f0b86a4b1467433e97678d0974b02d25 Mon Sep 17 00:00:00 2001 From: Alexandre Coudray Date: Wed, 3 Dec 2025 10:00:54 +0100 Subject: [PATCH 98/98] remove warnign fictive+soots in onedim.py and moved to Flow1D.cpp --- interfaces/cython/cantera/onedim.py | 23 ----------------------- src/oneD/Flow1D.cpp | 5 +++++ 2 files changed, 5 insertions(+), 23 deletions(-) diff --git a/interfaces/cython/cantera/onedim.py b/interfaces/cython/cantera/onedim.py index 7afb1e15ebe..a7836e07aa2 100644 --- a/interfaces/cython/cantera/onedim.py +++ b/interfaces/cython/cantera/onedim.py @@ -1250,9 +1250,6 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): #: `FreeFlow` domain representing the flame self.flame = FreeFlow(gas, name='flame', sections=sections, fictives=fictives) - if sections and fictives: - raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") - if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") @@ -1450,10 +1447,6 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): # Create flame domain if not already instantiated by a child class #: `UnstrainedFlow` domain representing the flame self.flame = UnstrainedFlow(gas, name='flame', sections=sections, fictives=fictives) - - # Cannot used both fictive and soot at the same time - if sections and fictives: - raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") if width is not None: if grid is not None: @@ -1593,10 +1586,6 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): #: `AxisymmetricFlow` domain representing the flame self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) - # Cannot used both fictive and soot at the same time - if sections and fictives: - raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") - if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") @@ -1914,10 +1903,6 @@ def __init__(self, gas, grid=None, width=None, surface=None, sections=0, fictive self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) self.flame.set_axisymmetric_flow() - # Cannot used both fictive and soot at the same time - if sections and fictives: - raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") - if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") @@ -2009,10 +1994,6 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): #: `AxisymmetricFlow` domain representing the flame self.flame = AxisymmetricFlow(gas, name='flame', sections=sections, fictives=fictives) - # Cannot used both fictive and soot at the same time - if sections and fictives: - raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") - if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") @@ -2117,10 +2098,6 @@ def __init__(self, gas, grid=None, width=None, sections=0, fictives=0): #The right boundary is a symmetry plane self.products = SymmetryPlane1D(name='products', phase=gas, sections=sections, fictives=fictives) - # Cannot used both fictive and soot at the same time - if sections and fictives: - raise ValueError("'sections' and 'fictives' arguments are mutually exclusive") - if width is not None: if grid is not None: raise ValueError("'grid' and 'width' arguments are mutually exclusive") diff --git a/src/oneD/Flow1D.cpp b/src/oneD/Flow1D.cpp index 9bad1355491..d3fca653076 100644 --- a/src/oneD/Flow1D.cpp +++ b/src/oneD/Flow1D.cpp @@ -105,6 +105,11 @@ Flow1D::Flow1D(ThermoPhase* ph, size_t nsp, size_t nsoot, size_t nfic, size_t ne //---------------------AVBP thickening initialisation------------ AVBPReadInputChem(); + if ( m_nsoot > 0 & m_nfic > 0 ){ + throw CanteraError("Flow1D::Flow1D", + "Cannot use both fictive species and soot sections at the same time"); + } + // E. Lameloise //---------------------Soot computation initialisation----------- if (m_nsoot > 0){