Added a module for working with RMG reaction families #754

alongd · 2024-07-02T09:15:19Z

Now we can identify for each ARC reaction all possible pathways between the reactants and products according to reaction families supported by RMG.
Also added dummy ARC families (w/o kinetics) to assist in identifying reaction templates.
Tests added.

arc/reaction/family_test.py

arc/reaction/family.py

arc/mapping/engine.py

arc/mapping/engine_test.py

arc/mapping/driver.py

arc/mapping/engine.py

arc/reaction/family.py

arc/reaction/reaction.py

arc/family/family.py

+
+if TYPE_CHECKING:
+    from arc.species import ARCSpecies
+    from arc.reaction.reaction import ARCReaction


arc/family/family.py

arc/mapping/engine.py

arc/reaction/reaction.py

 from arc.common import get_logger
 from arc.exceptions import ReactionError, InputError
+from arc.family.family import ReactionFamily, get_reaction_family_products


arc/reaction/reaction.py

 from arc.common import get_logger
 from arc.exceptions import ReactionError, InputError
+from arc.family.family import ReactionFamily, get_reaction_family_products


arc/checks/ts_test.py

+    # def test_check_normal_mode_displacement(self):
+    #     """Test the check_normal_mode_displacement() function."""
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS_intra_H_migration_CBS-QB3.out')
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertTrue(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #
+    #     self.rxn_2b.ts_species.populate_ts_checks()
+    #     self.assertFalse(self.rxn_2b.ts_species.ts_checks['NMD'])
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2b, job=self.job1)
+    #     self.assertFalse(self.rxn_2b.ts_species.ts_checks['NMD'])
+    #
+    #     # Wrong TS for intra H migration [CH2]CC <=> C[CH]C
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS_C3_intraH_1.out')  # A wrong TS.
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS_C3_intraH_2.out')  # A wrong TS.
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS_C3_intraH_3.out')  # ** The correct TS. **
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertTrue(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS_C3_intraH_4.out')  # A wrong TS.
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS_C3_intraH_5.out')  # A wrong TS.
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS_C3_intraH_6.out')  # A wrong TS.
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS_C3_intraH_7.out')  # A wrong TS.
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'freq',
+    #                                                        'TS_C3_intraH_8.out')  # Correct TS (freq run, not composite).
+    #     self.rxn_2a.ts_species.populate_ts_checks()
+    #     self.assertFalse(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_2a, job=self.job1)
+    #     self.assertTrue(self.rxn_2a.ts_species.ts_checks['NMD'])
+    #
+    #     # CCO[O] + CC <=> CCOO + [CH2]C, incorrect TS:
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS0_composite_2043.out')
+    #     self.rxn_4.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_4, job=self.job1)
+    #     self.assertFalse(self.rxn_4.ts_species.ts_checks['NMD'])
+    #
+    #     # CCO[O] + CC <=> CCOO + [CH2]C, correct TS:
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS0_composite_2102.out')
+    #     self.rxn_4.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_4, job=self.job1)
+    #     self.assertTrue(self.rxn_4.ts_species.ts_checks['NMD'])
+    #
+    #     # NCC + H <=> CH3CHNH2 + H2, correct TS:
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'composite',
+    #                                                        'TS0_composite_2044.out')
+    #     self.rxn_5.ts_species.populate_ts_checks()
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_5, job=self.job1)
+    #     self.assertTrue(self.rxn_5.ts_species.ts_checks['NMD'])
+    #
+    #     # NH2 + N2H3 <=> NH + N2H4:
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'freq', 'TS_NH2+N2H3.out')
+    #     rxn_6 = ARCReaction(r_species=[ARCSpecies(label='NH2', xyz="""N       0.00000000   -0.00000000    0.14115400


arc/checks/ts_test.py

+    # def test_check_normal_mode_displacement_wip(self):
+    #     """Test the check_normal_mode_displacement() function."""
+    #     self.job1.local_path_to_output_file = os.path.join(ts.ARC_PATH, 'arc', 'testing', 'freq',
+    #                                                        'TS_NH3+H=NH2+H2.out')  # NH3 + H <=> NH2 + H2
+    #     self.rxn_3.ts_species.populate_ts_checks()
+    #     self.assertFalse(self.rxn_3.ts_species.ts_checks['NMD'])
+    #     ts.check_normal_mode_displacement(reaction=self.rxn_3, job=self.job1)
+    #     self.assertTrue(self.rxn_3.ts_species.ts_checks['NMD'])


arc/checks/ts_test.py

+    # def test_get_expected_num_atoms_with_largest_normal_mode_disp(self):
+    #     """Test the get_expected_num_atoms_with_largest_normal_mode_disp() function"""
+    #     normal_disp_mode_rms = [0.01414213562373095, 0.05, 0.04, 0.5632938842203065, 0.7993122043357026,
+    #                             0.08944271909999159, 0.10677078252031312, 0.09000000000000001, 0.05, 0.09433981132056604]
+    #     num_of_atoms = ts.get_expected_num_atoms_with_largest_normal_mode_disp(normal_mode_disp_rms=normal_disp_mode_rms,
+    #                                                                            ts_guesses=self.ts_1.ts_guesses)
+    #     self.assertEqual(num_of_atoms, 4)
+
+    # def test_get_rxn_normal_mode_disp_atom_number(self):
+    #     """Test the get_rxn_normal_mode_disp_atom_number() function."""
+    #     with self.assertRaises(TypeError):
+    #         ts.get_rxn_normal_mode_disp_atom_number('family', rms_list='family')
+    #     with self.assertRaises(TypeError):
+    #         ts.get_rxn_normal_mode_disp_atom_number('family', rms_list=['family'])
+    #     with self.assertRaises(TypeError):
+    #         ts.get_rxn_normal_mode_disp_atom_number('family', rms_list=15.215)
+    #     self.assertEqual(ts.get_rxn_normal_mode_disp_atom_number(), 3)
+    #     self.assertEqual(ts.get_rxn_normal_mode_disp_atom_number('default'), 3)
+    #     self.assertEqual(ts.get_rxn_normal_mode_disp_atom_number('intra_H_migration'), 3)
+    #     self.assertEqual(ts.get_rxn_normal_mode_disp_atom_number('intra_H_migration', rms_list=self.rms_list_1), 4)


arc/family/family.py

arc/family/family_test.py

arc/job/adapters/ts/heuristics.py

arc/job/adapters/ts/heuristics_test.py

arc/mapping/engine_test.py

arc/family/__init__.py

arc/mapping/driver.py

arc/mapping/engine_test.py

arc/family/__init__.py

arc/mapping/engine.py

+        xyz_1, xyz_2 = None, None
+        try:
+            xyz_1 = new_spc.get_xyz()
+        except:


arc/mapping/engine.py

+        xyz_1, xyz_2 = None, None
+        try:
+            xyz_1 = new_spc.get_xyz()
+        except:


arc/mapping/engine.py

+            pass
+        try:
+            xyz_2 = spc.get_xyz()
+        except:


arc/mapping/engine.py

+            pass
+        try:
+            xyz_2 = spc.get_xyz()
+        except:


f driver

to run RMG as standalone in its own env to get thermo and kinetics for comparisons

when comparing RMG's thermo and kinetics to ARC's computations

and from KinBot tests

arc/plotter.py

@@ -2,6 +2,7 @@
 A module for plotting and saving output files such as RMG libraries.
 """

+import math


arc/processor.py

@@ -2,21 +2,25 @@
 Processor module for computing thermodynamic properties and rate coefficients using statistical mechanics.
 """

+import math


arc/processor.py

arc/reaction/reaction.py

+        # for spc in r_species + p_species:
+        #     if not isinstance(spc, ARCSpecies):
+        #         raise InputError(f'All reactants and products must be ARCSpecies objects. Got {spc} which is a '
+        #                          f'{type(spc)} object.')


arc/scripts/rmg_kinetics.py

+from common import parse_command_line_arguments, read_yaml_file, save_yaml_file
+
+from rmgpy.data.kinetics.common import find_degenerate_reactions
+from rmgpy.data.kinetics.family import KineticsFamily, TemplateReaction


arc/scripts/rmg_kinetics.py

+from rmgpy.data.rmg import RMGDatabase
+from rmgpy import settings as rmg_settings
+from rmgpy.reaction import same_species_lists, Reaction
+from rmgpy.rmg.model import get_family_library_object


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Minor: CI style modifications

d5e7a93

alongd added 11 commits January 5, 2025 09:26

Tests: Modifications to mapping engine tests

0f4ca27

Modifications to mapping driver

6b6482d

f driver

Tests: Modifications to mapping driver tests

919609b

Tests: Modifications to reaction tests

b28b729

Added check_molecule_list_order() to species converter

6ae8171

Added RMG thermo and kinetics scripts

956aae3

to run RMG as standalone in its own env to get thermo and kinetics for comparisons

Modified the trype of the species rmg_thermo attribute

0c0dde9

Modified the type of the Reaction rmg_kinetics attribute

a54aa17

Updated processor to use RMG's scripts instead of RMG's API

e7ebf28

when comparing RMG's thermo and kinetics to ARC's computations

Updated plotter for RMG's parsed data

03e6bd4

Tests: Updated H atomtype in common tests to H0

3d65d5e

alongd force-pushed the reaction_families branch from 64a7b7e to 3d65d5e Compare January 5, 2025 07:29

alongd added 6 commits January 5, 2025 20:42

Removed rmg_reaction from reaction

b74718b

Tests: Removed rmg_reaction from reaction tests

001d1a1

and from KinBot tests

Tests: Minor: Fix isotope SMILES in conformers tests

7264cd1

Removed utilization of .rmg_reaction from ARC's modules

80d3798

Todo: fix plotter

4ec241a

tmp cache

01f3727

alongd force-pushed the reaction_families branch from a0888cd to 01f3727 Compare January 5, 2025 19:06

alongd added 8 commits January 8, 2025 08:59

f autotst ts

5a46e58

tmp cache

dceeddb

f kinbot tst

1e15036

Check species type in Reaction

66bb36d

f scripts

fdc608a

Added calculate_arrhenius_rate_coefficient() to common

26b73ea

Tests: calculate_arrhenius_rate_coefficient

ff5aca8

TMP

cfddb72

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Added a module for working with RMG reaction families #754

Added a module for working with RMG reaction families #754

alongd commented Jul 2, 2024

Added a module for working with RMG reaction families #754

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Added a module for working with RMG reaction families #754

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alongd commented Jul 2, 2024