Added a module for working with RMG reaction families #754
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Module: Main
Module: Mapping
Module: rmgdb
Module: Scheduler
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| if TYPE_CHECKING: | ||
| from arc.species import ARCSpecies | ||
| from arc.reaction.reaction import ARCReaction |
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Module-level cyclic import Error
| from arc.common import get_logger | ||
| from arc.exceptions import ReactionError, InputError | ||
| from arc.family.family import ReactionFamily, get_reaction_family_products |
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Module-level cyclic import Error
| from arc.common import get_logger | ||
| from arc.exceptions import ReactionError, InputError | ||
| from arc.family.family import ReactionFamily, get_reaction_family_products |
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Module-level cyclic import Error
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| # 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 |
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| # 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']) |
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| # 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) | ||
|
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| # 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) |
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| xyz_1, xyz_2 = None, None | ||
| try: | ||
| xyz_1 = new_spc.get_xyz() | ||
| except: |
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| xyz_1, xyz_2 = None, None | ||
| try: | ||
| xyz_1 = new_spc.get_xyz() | ||
| except: |
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Except block handles 'BaseException' Note
| pass | ||
| try: | ||
| xyz_2 = spc.get_xyz() | ||
| except: |
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| pass | ||
| try: | ||
| xyz_2 = spc.get_xyz() | ||
| except: |
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Except block handles 'BaseException' Note
It is obsolete now
Currently the rmgdb module is only used by processor which will be dealt with in a different PR
It is no longer an object, no need to call family.label No need to call determine_family() since family is now a property of reaction
f! ts check (? replaced this function?)
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
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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.