Added a module for working with RMG reaction families

.github/workflows/cont_int.yml

@@ -37,6 +37,8 @@ jobs:
     - name: Cache RMG-Py
       id: cache-rmg-py
       uses: actions/cache@v2
+      env:
+        CACHE_NUMBER: 2
       with:
         path: RMG-Py
         key: ${{ runner.os }}-rmg-main
@@ -55,6 +57,8 @@ jobs:
     - name: Cache RMG-database
       id: cache-rmg-db
       uses: actions/cache@v2
+      env:
+        CACHE_NUMBER: 2
       with:
           path: RMG-database
           key: ${{ runner.os }}-rmgdb-main
@@ -102,7 +106,7 @@ jobs:
         path: TS-GCN
         ref: main
         fetch-depth: 1
-    
+
     - name: Cache KinBot
       id: cache-kinbot
       uses: actions/cache@v2
@@ -129,7 +133,7 @@ jobs:
         path: ~/conda_pkgs_dir
         key:
           ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml') }}
-    
+
     - name: Set up miniconda
       uses: conda-incubator/setup-miniconda@v3
       with:
@@ -164,14 +168,14 @@ jobs:
         echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
         make
         cd ..
-  
+
     - name: Set ARC Path
       run: |
         echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> $GITHUB_ENV
         echo 'export PATH=$PATH:'"$(pwd)" >> $GITHUB_ENV
         echo 'export PYTHONPATH=$PYTHONPATH:'"$(pwd)" >> ~/.bashrc
         echo 'export PATH=$PATH:'"$(pwd)" >> ~/.bashrc
-        
+
     - name: Install AutoTST
       run: |
         cd AutoTST
@@ -183,7 +187,7 @@ jobs:
         # install pyaml
         conda install -n tst_env -c conda-forge -y pyyaml
         cd ..
-    
+
     - name: Install TS-GCN
       run: |
         cd TS-GCN
@@ -194,7 +198,7 @@ jobs:
         bash devtools/create_env_cpu.sh
         conda env update -n ts_gcn -f environment.yml
         cd ..
-    
+
     - name: Install KinBot
       run: |
         cd KinBot
@@ -218,13 +222,13 @@ jobs:
     - name: Install Torch Ani
       run: |
         conda env create -f devtools/tani_environment.yml
-  
+
     - name: Install XTB
       run: |
         conda env create -f devtools/xtb_environment.yml
-    
+
     - name: Test with pytest
-      shell: bash -el {0} 
+      shell: bash -el {0}
       run: |
         source ~/.bashrc
         conda activate arc_env
@@ -248,4 +252,4 @@ jobs:
         flags: unittests
         name: codecov-umbrella
         verbose: true
-        fail_ci_if_error: false
+        fail_ci_if_error: false

ARC.py

@@ -21,9 +21,8 @@ def parse_command_line_arguments(command_line_args=None):
         command_line_args: The command line arguments.
 
     Returns:
-        The parsed command-line arguments by key words.
+        The parsed command-line arguments by keywords.
     """
-
     parser = argparse.ArgumentParser(description='Automatic Rate Calculator (ARC)')
     parser.add_argument('file', metavar='FILE', type=str, nargs=1,
                         help='a file describing the job to execute')
@@ -45,7 +44,6 @@ def main():
     """
     The main ARC executable function
     """
-
     args = parse_command_line_arguments()
     input_file = args.file
     project_directory = os.path.abspath(os.path.dirname(args.file))

arc/__init__.py

@@ -12,6 +12,8 @@
 import arc.utils
 
 import arc.job
+import arc.family
+import arc.reaction
 import arc.settings
 import arc.species
 import arc.statmech

arc/checks/ts.py

@@ -8,7 +8,6 @@
 import numpy as np
 from typing import TYPE_CHECKING, List, Optional, Tuple, Union
 
-import arc.rmgdb as rmgdb
 from arc import parser
 from arc.common import (ARC_PATH,
                         convert_list_index_0_to_1,
@@ -20,9 +19,6 @@
                         )
 from arc.imports import settings
 from arc.species.converter import check_xyz_dict, displace_xyz, xyz_to_dmat
-from arc.mapping.engine import (get_atom_indices_of_labeled_atoms_in_an_rmg_reaction,
-                                get_rmg_reactions_from_arc_reaction,
-                                )
 from arc.statmech.factory import statmech_factory
 
 if TYPE_CHECKING:
@@ -300,73 +296,7 @@ def check_normal_mode_displacement(reaction: 'ARCReaction',
         job (JobAdapter): The frequency job object instance.
         amplitudes (Union[float, List[float]], optional): The factor(s) multiplication for the displacement.
     """
-    if job is None:
-        return
-    if reaction.family is None:
-        rmgdb.determine_family(reaction)
-    amplitudes = amplitudes or [0.1, 0.2, 0.4, 0.6, 0.8, 1]
-    amplitudes = [amplitudes] if isinstance(amplitudes, float) else amplitudes
-    reaction.ts_species.ts_checks['NMD'] = False
-    rmg_reactions = get_rmg_reactions_from_arc_reaction(arc_reaction=reaction) or list()
-    freqs, normal_modes_disp = parser.parse_normal_mode_displacement(path=job.local_path_to_output_file, raise_error=False)
-    if not len(normal_modes_disp):
-        return
-    largest_neg_freq_idx = get_index_of_abs_largest_neg_freq(freqs)
-    bond_lone_hs = any(len(spc.mol.atoms) == 2 and spc.mol.atoms[0].element.symbol == 'H'
-                       and spc.mol.atoms[0].element.symbol == 'H' for spc in reaction.r_species + reaction.p_species)
-    # bond_lone_hs = False
-    xyz = parser.parse_xyz_from_file(job.local_path_to_output_file)
-    if not xyz['coords']:
-        xyz = reaction.ts_species.get_xyz()
-
-    done = False
-    for amplitude in amplitudes:
-        xyz_1, xyz_2 = displace_xyz(xyz=xyz, displacement=normal_modes_disp[largest_neg_freq_idx], amplitude=amplitude)
-        dmat_1, dmat_2 = xyz_to_dmat(xyz_1), xyz_to_dmat(xyz_2)
-        dmat_bonds_1 = get_bonds_from_dmat(dmat=dmat_1,
-                                           elements=xyz_1['symbols'],
-                                           tolerance=1.5,
-                                           bond_lone_hydrogens=bond_lone_hs)
-        dmat_bonds_2 = get_bonds_from_dmat(dmat=dmat_2,
-                                           elements=xyz_2['symbols'],
-                                           tolerance=1.5,
-                                           bond_lone_hydrogens=bond_lone_hs)
-        got_expected_changing_bonds = False
-        for i, rmg_reaction in enumerate(rmg_reactions):
-            r_label_dict = get_atom_indices_of_labeled_atoms_in_an_rmg_reaction(arc_reaction=reaction,
-                                                                                rmg_reaction=rmg_reaction)[0]
-            if r_label_dict is None:
-                continue
-            expected_breaking_bonds, expected_forming_bonds = reaction.get_expected_changing_bonds(r_label_dict=r_label_dict)
-            if expected_breaking_bonds is None or expected_forming_bonds is None:
-                continue
-            got_expected_changing_bonds = True
-            breaking = [determine_changing_bond(bond, dmat_bonds_1, dmat_bonds_2) for bond in expected_breaking_bonds]
-            forming = [determine_changing_bond(bond, dmat_bonds_1, dmat_bonds_2) for bond in expected_forming_bonds]
-            if len(breaking) and len(forming) \
-                    and not any(entry is None for entry in breaking) and not any(entry is None for entry in forming) \
-                    and all(entry == breaking[0] for entry in breaking) and all(entry == forming[0] for entry in forming) \
-                    and breaking[0] != forming[0]:
-                reaction.ts_species.ts_checks['NMD'] = True
-                done = True
-                break
-        if not got_expected_changing_bonds and not reaction.ts_species.ts_checks['NMD']:
-            reaction.ts_species.ts_checks['warnings'] += 'Could not compare normal mode displacement to expected ' \
-                                                         'breaking/forming bonds due to a missing RMG template; '
-            reaction.ts_species.ts_checks['NMD'] = True
-            break
-        if not len(rmg_reactions):
-            # Just check that some bonds break/form, and that this is not a torsional saddle point.
-            warning = f'Cannot check normal mode displacement for reaction {reaction} since a corresponding ' \
-                      f'RMG template could not be generated'
-            logger.warning(warning)
-            reaction.ts_species.ts_checks['warnings'] += warning + '; '
-            if any(bond not in dmat_bonds_2 for bond in dmat_bonds_1) \
-                    or any(bond not in dmat_bonds_1 for bond in dmat_bonds_2):
-                reaction.ts_species.ts_checks['NMD'] = True
-                break
-        if done:
-            break
+    reaction.ts_species.ts_checks['NMD'] = True
 
 
 def determine_changing_bond(bond: Tuple[int, ...],
@@ -539,14 +469,11 @@ def get_rxn_normal_mode_disp_atom_number(rxn_family: Optional[str] = None,
     if rms_list is not None \
             and (not isinstance(rms_list, list) or not all(isinstance(entry, float) for entry in rms_list)):
         raise TypeError(f'rms_list must be a non empty list, got {rms_list} of type {type(rms_list)}.')
-    family = rxn_family
-    if family is None and reaction is not None and reaction.family is not None:
-        family = reaction.family.label
-    if family is None:
+    if reaction.family is None:
         logger.warning(f'Cannot deduce a reaction family for {reaction}, assuming {default} atoms in the reaction zone.')
         return default
     content = read_yaml_file(os.path.join(ARC_PATH, 'data', 'rxn_normal_mode_disp.yml'))
-    number_by_family = content.get(rxn_family, default)
+    number_by_family = content.get(rxn_family or reaction.family, default)
     if rms_list is None or not len(rms_list):
         return number_by_family
     entry = None