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Added a Linear TS search job adapter #695

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f58ba89
Added Reaction.is_unimolecular()
alongd Aug 21, 2023
2855751
Tests: Reaction.is_unimolecular()
alongd May 15, 2024
52e1c2b
Added an atom_order arg to xyz_to_zmat()
alongd Aug 21, 2023
4931623
Tests: xyz_to_zmat()
alongd Aug 21, 2023
6f1b2f0
Added 'linear' to ts_adapters_by_rmg_family
alongd Aug 21, 2023
712ff65
Added check_ordered_zmats()
alongd Aug 21, 2023
8fe9165
Tests: check_ordered_zmats()
alongd Aug 21, 2023
b3dd557
Added linear to JobEnum
alongd Aug 21, 2023
ace4fe8
Added the Linear TS search job adapter
alongd May 15, 2024
73badaf
Tests: Linear TS Job Adapter
alongd May 15, 2024
7a5f247
Added order_xyz_by_atom_map to converter
alongd May 26, 2024
91b3a10
Tests: converter order_xyz_by_atom_map()
alongd May 26, 2024
aa2ad9e
Added update_zmat_by_xyz() to zmat
alongd May 26, 2024
4232f1e
Tests: zmat update_zmat_by_xyz()
alongd May 26, 2024
6eccc9a
Tests: added many isomerization families
alongd May 28, 2024
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3 changes: 2 additions & 1 deletion arc/job/adapter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,9 +96,10 @@ class JobEnum(str, Enum):

# TS search methods
autotst = 'autotst' # AutoTST, 10.1021/acs.jpca.7b07361, 10.26434/chemrxiv.13277870.v2
gcn = 'gcn' # Graph neural network for isomerization, https://doi.org/10.1021/acs.jpclett.0c00500
heuristics = 'heuristics' # ARC's heuristics
kinbot = 'kinbot' # KinBot, 10.1016/j.cpc.2019.106947
gcn = 'gcn' # Graph neural network for isomerization, https://doi.org/10.1021/acs.jpclett.0c00500
linear = 'linear' # ARC's linear TS search
user = 'user' # user guesses
xtb_gsm = 'xtb_gsm' # Double ended growing string method (DE-GSM), [10.1021/ct400319w, 10.1063/1.4804162] via xTB

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86 changes: 46 additions & 40 deletions arc/job/adapters/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,48 +27,54 @@
settings['default_job_settings'], settings['global_ess_settings'], settings['rotor_scan_resolution']


ts_adapters_by_rmg_family = {'1+2_Cycloaddition': ['kinbot'],
'1,2_Insertion_CO': ['kinbot'],
'1,2_Insertion_carbene': ['kinbot'],
'1,2_shiftC': ['gcn', 'xtb_gsm'],
'1,2_shiftS': ['gcn', 'kinbot', 'xtb_gsm'],
'1,3_Insertion_CO2': ['kinbot'],
'1,3_Insertion_ROR': ['kinbot'],
'1,3_Insertion_RSR': ['kinbot'],
'1,4_Cyclic_birad_scission': ['gcn', 'xtb_gsm'],
'2+2_cycloaddition': ['kinbot'],
'6_membered_central_C-C_shift': ['gcn', 'xtb_gsm'],
'Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH': ['gcn', 'xtb_gsm'],
'Cyclic_Ether_Formation': ['kinbot'],
'Cyclopentadiene_scission': ['gcn', 'xtb_gsm'],
'Diels_alder_addition': ['kinbot'],
ts_adapters_by_rmg_family = {'1+2_Cycloaddition': ['kinbot', 'linear'],
'1,2_Insertion_CO': ['kinbot', 'linear'],
'1,2_Insertion_carbene': ['kinbot', 'linear'],
'1,2_shiftC': ['gcn', 'xtb_gsm', 'linear'],
'1,2_shiftS': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'1,3_Insertion_CO2': ['kinbot', 'linear'],
'1,3_Insertion_ROR': ['kinbot', 'linear'],
'1,3_Insertion_RSR': ['kinbot', 'linear'],
'1,3_NH3_elimination': ['linear'],
'1,3_sigmatropic_rearrangement': ['linear'],
'1,4_Cyclic_birad_scission': ['gcn', 'xtb_gsm', 'linear'],
'1,4_Linear_birad_scission': ['linear'],
'2+2_cycloaddition': ['kinbot', 'linear'],
'6_membered_central_C-C_shift': ['gcn', 'xtb_gsm', 'linear'],
'Birad_recombination': ['linear'],
'Concerted_Intra_Diels_alder_monocyclic_1,2_shiftH': ['gcn', 'xtb_gsm', 'linear'],
'Cyclic_Ether_Formation': ['kinbot', 'linear'],
'Cyclic_Thioether_Formation': ['linear'],
'Cyclopentadiene_scission': ['gcn', 'xtb_gsm', 'linear'],
'Diels_alder_addition': ['kinbot', 'linear'],
'H_Abstraction': ['heuristics', 'autotst'],
'HO2_Elimination_from_PeroxyRadical': ['kinbot'],
'Intra_2+2_cycloaddition_Cd': ['gcn', 'xtb_gsm'],
'Intra_5_membered_conjugated_C=C_C=C_addition': ['gcn', 'xtb_gsm'],
'Intra_Diels_alder_monocyclic': ['gcn', 'kinbot', 'xtb_gsm'],
'Intra_Disproportionation': ['gcn', 'xtb_gsm'],
'Intra_ene_reaction': ['gcn', 'kinbot', 'xtb_gsm'],
'intra_H_migration': ['autotst', 'gcn', 'kinbot', 'xtb_gsm'],
'intra_NO2_ONO_conversion': ['gcn', 'xtb_gsm'],
'intra_OH_migration': ['gcn', 'kinbot', 'xtb_gsm'],
'Intra_RH_Add_Endocyclic': ['gcn', 'kinbot', 'xtb_gsm'],
'Intra_RH_Add_Exocyclic': ['gcn', 'kinbot', 'xtb_gsm'],
'Intra_R_Add_Endocyclic': ['gcn', 'kinbot', 'xtb_gsm'],
'Intra_R_Add_Exo_scission': ['gcn', 'xtb_gsm'],
'Intra_R_Add_Exocyclic': ['gcn', 'kinbot', 'xtb_gsm'],
'Intra_R_Add_ExoTetCyclic': ['kinbot'],
'Intra_Retro_Diels_alder_bicyclic': ['kinbot'],
'intra_substitutionCS_isomerization': ['gcn', 'xtb_gsm'],
'intra_substitutionS_isomerization': ['gcn', 'xtb_gsm'],
'Ketoenol': ['gcn', 'kinbot', 'xtb_gsm'],
'Korcek_step1': ['gcn', 'xtb_gsm'],
'Korcek_step2': ['kinbot'],
'R_Addition_COm': ['kinbot'],
'R_Addition_CSm': ['kinbot'],
'R_Addition_MultipleBond': ['autotst', 'kinbot'],
'HO2_Elimination_from_PeroxyRadical': ['kinbot', 'linear'],
'Intra_2+2_cycloaddition_Cd': ['gcn', 'xtb_gsm', 'linear'],
'Intra_5_membered_conjugated_C=C_C=C_addition': ['gcn', 'xtb_gsm', 'linear'],
'Intra_Diels_alder_monocyclic': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'Intra_Disproportionation': ['gcn', 'xtb_gsm', 'linear'],
'Intra_ene_reaction': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'intra_H_migration': ['autotst', 'gcn', 'kinbot', 'xtb_gsm', 'linear'],
'intra_NO2_ONO_conversion': ['gcn', 'xtb_gsm', 'linear'],
'intra_OH_migration': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'Intra_RH_Add_Endocyclic': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'Intra_RH_Add_Exocyclic': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'Intra_R_Add_Endocyclic': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'Intra_R_Add_Exo_scission': ['gcn', 'xtb_gsm', 'linear'],
'Intra_R_Add_Exocyclic': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'Intra_R_Add_ExoTetCyclic': ['kinbot', 'linear'],
'Intra_Retro_Diels_alder_bicyclic': ['kinbot', 'linear'],
'intra_substitutionCS_cyclization': ['linear'],
'intra_substitutionS_cyclization': ['linear'],
'intra_substitutionS_isomerization': ['gcn', 'xtb_gsm', 'linear'],
'Ketoenol': ['gcn', 'kinbot', 'xtb_gsm', 'linear'],
'Korcek_step1': ['gcn', 'xtb_gsm', 'linear'],
'Korcek_step2': ['kinbot', 'linear'],
'R_Addition_COm': ['kinbot', 'linear'],
'R_Addition_CSm': ['kinbot', 'linear'],
'R_Addition_MultipleBond': ['autotst', 'kinbot', 'linear'],
'Retroene': ['kinbot'],
'Singlet_Carbene_Intra_Disproportionation': ['gcn', 'xtb_gsm'],
'Singlet_Carbene_Intra_Disproportionation': ['gcn', 'xtb_gsm', 'linear'],
}

all_families_ts_adapters = []
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