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introduction.html
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<li class="toctree-l1 current"><a class="current reference internal" href="#">Introduction</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#description">Description</a></li>
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<section id="introduction">
<h1>Introduction<a class="headerlink" href="#introduction" title="Link to this heading"></a></h1>
<img alt="_images/pymm.gif" src="_images/pymm.gif" />
<p>This documentation describes the <strong>pymm</strong> tool hosted in <a class="reference external" href="https://github.com/cssr-tools/pymm">https://github.com/cssr-tools/pymm</a>.</p>
<section id="description">
<h2>Description<a class="headerlink" href="#description" title="Link to this heading"></a></h2>
<p>The <strong>pymm</strong> tool relies on Python packages (e.g., <a class="reference external" href="https://porespy.org">porespy</a> and
<a class="reference external" href="https://scikit-image.org">skimage</a>) to generate the spatial domains for the simulations from
the microsystem images, and <a class="reference external" href="https://gmsh.info">Gmsh</a> as a mesh generator.
The numerical simulations for the water flow and tracer are performed using
the <a class="reference external" href="https://www.openfoam.com">OpenFOAM</a> simulator. This framework could be applied to general images and
the current implementation could be (‘easily’) extended to consider further
geometry of devices and solvers in OpenFOAM.</p>
</section>
<section id="overview">
<h2>Overview<a class="headerlink" href="#overview" title="Link to this heading"></a></h2>
<p>The current implementation supports the following executable with the argument options:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pymm<span class="w"> </span>-i<span class="w"> </span>image.png<span class="w"> </span>-p<span class="w"> </span>parameters.toml<span class="w"> </span>-o<span class="w"> </span>output<span class="w"> </span>-m<span class="w"> </span>image<span class="w"> </span>-t<span class="w"> </span>all<span class="w"> </span>-g<span class="w"> </span>gmsh
</pre></div>
</div>
<p>where</p>
<ul class="simple">
<li><p>-i, -image: The base name of the image (‘microsystem.png’ by default).</p></li>
<li><p>-p, -parameters: The base name of the <a class="reference internal" href="configuration_file.html"><span class="doc">configuration file</span></a> (‘parameters.toml’ by default).</p></li>
<li><p>-m, -mode: The configuration of the microsystem, currently only image and device supported (‘image’ by default).</p></li>
<li><p>-t, -type: Run the whole framework (‘all’), only the generation of the PNG figures, with the segmentation to grains, voids, and boundary (‘pngs’), the mesh files for Gmsh (‘mesh’), keep the current mesh and only simulate the flow velocity field (‘flow’), mesh and flow (‘mesh_flow’), flow and tracer (‘flow_tracer’), or only tracer simulations (‘tracer’) (‘mesh’ by default).</p></li>
<li><p>-o, -output: The base name of the <a class="reference internal" href="output_folder.html"><span class="doc">output folder</span></a> (‘output’ by default).</p></li>
<li><p>-g, -gmsh: The full path to the Gmsh executable or simple ‘gmsh’ if it runs from the terminal (‘gmsh’ by default).</p></li>
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