├── .gitignore ├── LICENSE ├── README.md ├── __init__.py ├── conda_build_config.yaml ├── examples ├── gvl_reactions │ ├── README │ └── gvl.json ├── pentyl_pes │ ├── README │ └── pentyl.json ├── propanol_homolytic_scissions │ ├── README │ └── propanol.json └── propanol_radical_ME │ ├── README │ └── propanoyl.json ├── graphics └── kinbot_logo_V2.png ├── kinbot ├── __init__.py ├── ase_modules │ ├── __init__.py │ ├── calculators │ │ ├── __init__.py │ │ ├── gaussian.py │ │ ├── nn_pes.py │ │ └── qchem.py │ ├── constraints.py │ └── io │ │ ├── __init__.py │ │ ├── formats.py │ │ ├── gaussian.py │ │ └── zmatrix.py ├── bfgs.py ├── bond_combinations.py ├── cheminfo.py ├── config_log.py ├── conformers.py ├── constants.py ├── exceptions.py ├── find_motif.py ├── fragments.py ├── frequencies.py ├── geometry.py ├── hindered_rotors.py ├── irc.py ├── kb.py ├── license_message.py ├── mesmer.py ├── mess.py ├── modify_geom.py ├── molpro.py ├── optimize.py ├── orca.py ├── parameters.py ├── pes.py ├── postprocess.py ├── pp_settings.py ├── pp_tables.py ├── qc.py ├── reac_General.py ├── reac_family.py ├── reaction_finder.py ├── reaction_finder_bimol.py ├── reaction_generator.py ├── reactions │ ├── __init__.py │ ├── reac_12_shift_S_F.py │ ├── reac_12_shift_S_R.py │ ├── reac_Cyclic_Ether_Formation.py │ ├── reac_Diels_alder_addition.py │ ├── reac_HO2_Elimination_from_PeroxyRadical.py │ ├── reac_Intra_Diels_alder_R.py │ ├── reac_Intra_RH_Add_Endocyclic_F.py │ ├── reac_Intra_RH_Add_Endocyclic_R.py │ ├── reac_Intra_RH_Add_Exocyclic_F.py │ ├── reac_Intra_RH_Add_Exocyclic_R.py │ ├── reac_Intra_R_Add_Endocyclic_F.py │ ├── reac_Intra_R_Add_ExoTetCyclic_F.py │ ├── reac_Intra_R_Add_Exocyclic_F.py │ ├── reac_Intra_disproportionation_F.py │ ├── reac_Intra_disproportionation_R.py │ ├── reac_Korcek_step2.py │ ├── reac_Korcek_step2_even.py │ ├── reac_Korcek_step2_odd.py │ ├── reac_R_Addition_COm3_R.py │ ├── reac_R_Addition_CSm_R.py │ ├── reac_R_Addition_MultipleBond.py │ ├── reac_Retro_Ene.py │ ├── reac_abstraction.py │ ├── reac_barrierless_saddle.py │ ├── reac_beta_delta.py │ ├── reac_bimol_disproportionation_R.py │ ├── reac_birad_recombination_F.py │ ├── reac_birad_recombination_R.py │ ├── reac_combinatorial.py │ ├── reac_cpd_H_migration.py │ ├── reac_h2_elim.py │ ├── reac_homolytic_scission.py │ ├── reac_intra_H_migration.py │ ├── reac_intra_H_migration_suprafacial.py │ ├── reac_intra_OH_migration.py │ ├── reac_intra_OH_migration_Exocyclic_F.py │ ├── reac_intra_R_migration.py │ ├── reac_ketoenol.py │ ├── reac_r12_cycloaddition.py │ ├── reac_r12_insertion_R.py │ ├── reac_r13_insertion_CO2.py │ ├── reac_r13_insertion_ROR.py │ ├── reac_r13_insertion_RSR.py │ ├── reac_r14_birad_scission.py │ ├── reac_r14_cyclic_birad_scission_R.py │ └── reac_r22_cycloaddition.py ├── reader_gauss.py ├── reader_qchem.py ├── stationary_pt.py ├── symmetry.py ├── thread_kinbot.py ├── tpl │ ├── __init__.py │ ├── arrow.png │ ├── ase_gauss_hir.tpl.py │ ├── ase_gauss_irc.tpl.py │ ├── ase_gauss_opt_well.tpl.py │ ├── ase_gauss_ring_conf.tpl.py │ ├── ase_gauss_ts_end.tpl.py │ ├── ase_gauss_ts_search.tpl.py │ ├── ase_gauss_vts.tpl.py │ ├── ase_nwchem_freq_well.tpl.py │ ├── ase_nwchem_irc.tpl.py │ ├── ase_nwchem_opt_well.tpl.py │ ├── ase_nwchem_ts_end.tpl.py │ ├── ase_nwchem_ts_search.tpl.py │ ├── ase_nwchem_ts_search_ase_constraints.tpl.py │ ├── ase_qchem_hir.tpl.py │ ├── ase_qchem_irc.tpl.py │ ├── ase_qchem_opt_well.tpl.py │ ├── ase_qchem_ts_end.tpl.py │ ├── ase_qchem_ts_search.tpl.py │ ├── ase_sella_hir.tpl.py │ ├── ase_sella_irc.tpl.py │ ├── ase_sella_opt_well.tpl.py │ ├── ase_sella_ring_conf.tpl.py │ ├── ase_sella_ts_end.tpl.py │ ├── ase_sella_ts_search.tpl.py │ ├── ase_sella_vts.tpl.py │ ├── local_molpro.tpl │ ├── mess_2tst.tpl │ ├── mess_atom.tpl │ ├── mess_barrier.tpl │ ├── mess_barrier_union.tpl │ ├── mess_barrierless.tpl │ ├── mess_bimol.tpl │ ├── mess_bimol_union.tpl │ ├── mess_core_rr.tpl │ ├── mess_dummy.tpl │ ├── mess_fragment.tpl │ ├── mess_fragment_OH.tpl │ ├── mess_freerotor.tpl │ ├── mess_header.tpl │ ├── mess_hinderedrotor.tpl │ ├── mess_hinderedrotorgeom.tpl │ ├── mess_outerrrho.tpl │ ├── mess_pst.tpl │ ├── mess_pstfragment.tpl │ ├── mess_rrho.tpl │ ├── mess_termol.tpl │ ├── mess_ts.tpl │ ├── mess_tunneling.tpl │ ├── mess_variational.tpl │ ├── mess_well.tpl │ ├── mess_well_union.tpl │ ├── molpro.tpl │ ├── molpro_ts_search.tpl.py │ ├── molpro_vts.tpl │ ├── pbs.tpl │ ├── pbs_mesmer.tpl │ ├── pbs_mess.tpl │ ├── pbs_mess_uq.tpl │ ├── pbs_molpro.tpl │ ├── pbs_python.tpl │ ├── pesviewer.inp.tpl │ ├── readme.txt │ ├── rotdPy.tpl │ ├── rotdPy_1d_corr.tpl │ ├── rotdPy_calc.tpl │ ├── rotdPy_frag.tpl │ ├── rotdPy_surf.tpl │ ├── slurm.tpl │ ├── slurm_mesmer.tpl │ ├── slurm_mess.tpl │ ├── slurm_mess_uq.tpl │ ├── slurm_molpro.tpl │ ├── slurm_orca.tpl │ └── slurm_python.tpl ├── uncertaintyAnalysis.py ├── utils.py ├── vrc_tst_scan.py ├── vrc_tst_surfaces.py └── zmatrix.py ├── meta.yaml ├── pyproject.toml └── tests ├── __init__.py ├── bfgs.py ├── cheminfo.py ├── dihedrals.py ├── find_motif.py ├── frequencies.py ├── geometry.py ├── input └── cheminfo_xyz.xyz ├── modify_geom.py ├── multimolecular.py ├── multimolecular_data.json ├── resonance.py ├── symmetry.py ├── symmetry_data.json ├── test_kinbot.dat └── test_kinbot.py /.gitignore: -------------------------------------------------------------------------------- 1 | *pyc 2 | build 3 | .idea 4 | *egg* 5 | dist 6 | .vscode 7 | *.ipynb 8 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/README.md -------------------------------------------------------------------------------- /__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/__init__.py -------------------------------------------------------------------------------- /conda_build_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/conda_build_config.yaml -------------------------------------------------------------------------------- /examples/gvl_reactions/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/examples/gvl_reactions/README -------------------------------------------------------------------------------- /examples/gvl_reactions/gvl.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/examples/gvl_reactions/gvl.json -------------------------------------------------------------------------------- /examples/pentyl_pes/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/examples/pentyl_pes/README -------------------------------------------------------------------------------- /examples/pentyl_pes/pentyl.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/examples/pentyl_pes/pentyl.json -------------------------------------------------------------------------------- /examples/propanol_homolytic_scissions/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/examples/propanol_homolytic_scissions/README -------------------------------------------------------------------------------- /examples/propanol_homolytic_scissions/propanol.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/examples/propanol_homolytic_scissions/propanol.json -------------------------------------------------------------------------------- /examples/propanol_radical_ME/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/examples/propanol_radical_ME/README -------------------------------------------------------------------------------- /examples/propanol_radical_ME/propanoyl.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/examples/propanol_radical_ME/propanoyl.json -------------------------------------------------------------------------------- /graphics/kinbot_logo_V2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/graphics/kinbot_logo_V2.png -------------------------------------------------------------------------------- /kinbot/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/__init__.py -------------------------------------------------------------------------------- /kinbot/ase_modules/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /kinbot/ase_modules/calculators/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /kinbot/ase_modules/calculators/gaussian.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/ase_modules/calculators/gaussian.py -------------------------------------------------------------------------------- /kinbot/ase_modules/calculators/nn_pes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/ase_modules/calculators/nn_pes.py -------------------------------------------------------------------------------- /kinbot/ase_modules/calculators/qchem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/ase_modules/calculators/qchem.py -------------------------------------------------------------------------------- /kinbot/ase_modules/constraints.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/ase_modules/constraints.py -------------------------------------------------------------------------------- /kinbot/ase_modules/io/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /kinbot/ase_modules/io/formats.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/ase_modules/io/formats.py -------------------------------------------------------------------------------- /kinbot/ase_modules/io/gaussian.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/ase_modules/io/gaussian.py -------------------------------------------------------------------------------- /kinbot/ase_modules/io/zmatrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/ase_modules/io/zmatrix.py -------------------------------------------------------------------------------- /kinbot/bfgs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/bfgs.py -------------------------------------------------------------------------------- /kinbot/bond_combinations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/bond_combinations.py -------------------------------------------------------------------------------- /kinbot/cheminfo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/cheminfo.py -------------------------------------------------------------------------------- /kinbot/config_log.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/config_log.py -------------------------------------------------------------------------------- /kinbot/conformers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/conformers.py -------------------------------------------------------------------------------- /kinbot/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/constants.py -------------------------------------------------------------------------------- /kinbot/exceptions.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/exceptions.py -------------------------------------------------------------------------------- /kinbot/find_motif.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/find_motif.py -------------------------------------------------------------------------------- /kinbot/fragments.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/fragments.py -------------------------------------------------------------------------------- /kinbot/frequencies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/frequencies.py -------------------------------------------------------------------------------- /kinbot/geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/geometry.py -------------------------------------------------------------------------------- /kinbot/hindered_rotors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/hindered_rotors.py -------------------------------------------------------------------------------- /kinbot/irc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/irc.py -------------------------------------------------------------------------------- /kinbot/kb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/kb.py -------------------------------------------------------------------------------- /kinbot/license_message.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/license_message.py -------------------------------------------------------------------------------- /kinbot/mesmer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/mesmer.py -------------------------------------------------------------------------------- /kinbot/mess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/mess.py -------------------------------------------------------------------------------- /kinbot/modify_geom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/modify_geom.py -------------------------------------------------------------------------------- /kinbot/molpro.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/molpro.py -------------------------------------------------------------------------------- /kinbot/optimize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/optimize.py -------------------------------------------------------------------------------- /kinbot/orca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/orca.py -------------------------------------------------------------------------------- /kinbot/parameters.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/parameters.py -------------------------------------------------------------------------------- /kinbot/pes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/pes.py -------------------------------------------------------------------------------- /kinbot/postprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/postprocess.py -------------------------------------------------------------------------------- /kinbot/pp_settings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/pp_settings.py -------------------------------------------------------------------------------- /kinbot/pp_tables.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/pp_tables.py -------------------------------------------------------------------------------- /kinbot/qc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/qc.py -------------------------------------------------------------------------------- /kinbot/reac_General.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reac_General.py -------------------------------------------------------------------------------- /kinbot/reac_family.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reac_family.py -------------------------------------------------------------------------------- /kinbot/reaction_finder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reaction_finder.py -------------------------------------------------------------------------------- /kinbot/reaction_finder_bimol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reaction_finder_bimol.py -------------------------------------------------------------------------------- /kinbot/reaction_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reaction_generator.py -------------------------------------------------------------------------------- /kinbot/reactions/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/__init__.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_12_shift_S_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_12_shift_S_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_12_shift_S_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_12_shift_S_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Cyclic_Ether_Formation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Cyclic_Ether_Formation.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Diels_alder_addition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Diels_alder_addition.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_HO2_Elimination_from_PeroxyRadical.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_HO2_Elimination_from_PeroxyRadical.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_Diels_alder_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_Diels_alder_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_RH_Add_Endocyclic_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_RH_Add_Endocyclic_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_RH_Add_Endocyclic_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_RH_Add_Endocyclic_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_RH_Add_Exocyclic_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_RH_Add_Exocyclic_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_RH_Add_Exocyclic_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_RH_Add_Exocyclic_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_R_Add_Endocyclic_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_R_Add_Endocyclic_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_R_Add_ExoTetCyclic_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_R_Add_ExoTetCyclic_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_R_Add_Exocyclic_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_R_Add_Exocyclic_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_disproportionation_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_disproportionation_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Intra_disproportionation_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Intra_disproportionation_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Korcek_step2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Korcek_step2.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Korcek_step2_even.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Korcek_step2_even.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Korcek_step2_odd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Korcek_step2_odd.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_R_Addition_COm3_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_R_Addition_COm3_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_R_Addition_CSm_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_R_Addition_CSm_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_R_Addition_MultipleBond.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_R_Addition_MultipleBond.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_Retro_Ene.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_Retro_Ene.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_abstraction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_abstraction.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_barrierless_saddle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_barrierless_saddle.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_beta_delta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_beta_delta.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_bimol_disproportionation_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_bimol_disproportionation_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_birad_recombination_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_birad_recombination_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_birad_recombination_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_birad_recombination_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_combinatorial.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_combinatorial.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_cpd_H_migration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_cpd_H_migration.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_h2_elim.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_h2_elim.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_homolytic_scission.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_homolytic_scission.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_intra_H_migration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_intra_H_migration.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_intra_H_migration_suprafacial.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_intra_H_migration_suprafacial.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_intra_OH_migration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_intra_OH_migration.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_intra_OH_migration_Exocyclic_F.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_intra_OH_migration_Exocyclic_F.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_intra_R_migration.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_intra_R_migration.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_ketoenol.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_ketoenol.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_r12_cycloaddition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_r12_cycloaddition.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_r12_insertion_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_r12_insertion_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_r13_insertion_CO2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_r13_insertion_CO2.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_r13_insertion_ROR.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_r13_insertion_ROR.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_r13_insertion_RSR.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_r13_insertion_RSR.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_r14_birad_scission.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_r14_birad_scission.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_r14_cyclic_birad_scission_R.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_r14_cyclic_birad_scission_R.py -------------------------------------------------------------------------------- /kinbot/reactions/reac_r22_cycloaddition.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reactions/reac_r22_cycloaddition.py -------------------------------------------------------------------------------- /kinbot/reader_gauss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reader_gauss.py -------------------------------------------------------------------------------- /kinbot/reader_qchem.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/reader_qchem.py -------------------------------------------------------------------------------- /kinbot/stationary_pt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/stationary_pt.py -------------------------------------------------------------------------------- /kinbot/symmetry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/symmetry.py -------------------------------------------------------------------------------- /kinbot/thread_kinbot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/thread_kinbot.py -------------------------------------------------------------------------------- /kinbot/tpl/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/__init__.py -------------------------------------------------------------------------------- /kinbot/tpl/arrow.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/arrow.png -------------------------------------------------------------------------------- /kinbot/tpl/ase_gauss_hir.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_gauss_hir.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_gauss_irc.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_gauss_irc.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_gauss_opt_well.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_gauss_opt_well.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_gauss_ring_conf.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_gauss_ring_conf.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_gauss_ts_end.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_gauss_ts_end.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_gauss_ts_search.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_gauss_ts_search.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_gauss_vts.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_gauss_vts.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_nwchem_freq_well.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_nwchem_freq_well.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_nwchem_irc.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_nwchem_irc.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_nwchem_opt_well.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_nwchem_opt_well.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_nwchem_ts_end.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_nwchem_ts_end.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_nwchem_ts_search.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_nwchem_ts_search.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_nwchem_ts_search_ase_constraints.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_nwchem_ts_search_ase_constraints.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_qchem_hir.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_qchem_hir.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_qchem_irc.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_qchem_irc.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_qchem_opt_well.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_qchem_opt_well.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_qchem_ts_end.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_qchem_ts_end.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_qchem_ts_search.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_qchem_ts_search.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_sella_hir.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_sella_hir.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_sella_irc.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_sella_irc.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_sella_opt_well.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_sella_opt_well.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_sella_ring_conf.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_sella_ring_conf.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_sella_ts_end.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_sella_ts_end.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_sella_ts_search.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_sella_ts_search.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/ase_sella_vts.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/ase_sella_vts.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/local_molpro.tpl: -------------------------------------------------------------------------------- 1 | {command} {name}.inp 2 | 3 | -------------------------------------------------------------------------------- /kinbot/tpl/mess_2tst.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_2tst.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_atom.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_atom.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_barrier.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_barrier.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_barrier_union.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_barrier_union.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_barrierless.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_barrierless.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_bimol.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_bimol.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_bimol_union.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_bimol_union.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_core_rr.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_core_rr.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_dummy.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_dummy.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_fragment.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_fragment.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_fragment_OH.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_fragment_OH.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_freerotor.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_freerotor.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_header.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_header.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_hinderedrotor.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_hinderedrotor.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_hinderedrotorgeom.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_hinderedrotorgeom.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_outerrrho.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_outerrrho.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_pst.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_pst.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_pstfragment.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_pstfragment.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_rrho.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_rrho.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_termol.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_termol.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_ts.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_ts.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_tunneling.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_tunneling.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_variational.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_variational.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_well.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_well.tpl -------------------------------------------------------------------------------- /kinbot/tpl/mess_well_union.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/mess_well_union.tpl -------------------------------------------------------------------------------- /kinbot/tpl/molpro.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/molpro.tpl -------------------------------------------------------------------------------- /kinbot/tpl/molpro_ts_search.tpl.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/molpro_ts_search.tpl.py -------------------------------------------------------------------------------- /kinbot/tpl/molpro_vts.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/molpro_vts.tpl -------------------------------------------------------------------------------- /kinbot/tpl/pbs.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/pbs.tpl -------------------------------------------------------------------------------- /kinbot/tpl/pbs_mesmer.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/pbs_mesmer.tpl -------------------------------------------------------------------------------- /kinbot/tpl/pbs_mess.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/pbs_mess.tpl -------------------------------------------------------------------------------- /kinbot/tpl/pbs_mess_uq.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/pbs_mess_uq.tpl -------------------------------------------------------------------------------- /kinbot/tpl/pbs_molpro.tpl: -------------------------------------------------------------------------------- 1 | {command} molpro/{name}.inp 2 | 3 | -------------------------------------------------------------------------------- /kinbot/tpl/pbs_python.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/pbs_python.tpl -------------------------------------------------------------------------------- /kinbot/tpl/pesviewer.inp.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/pesviewer.inp.tpl -------------------------------------------------------------------------------- /kinbot/tpl/readme.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/readme.txt -------------------------------------------------------------------------------- /kinbot/tpl/rotdPy.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/rotdPy.tpl -------------------------------------------------------------------------------- /kinbot/tpl/rotdPy_1d_corr.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/rotdPy_1d_corr.tpl -------------------------------------------------------------------------------- /kinbot/tpl/rotdPy_calc.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/rotdPy_calc.tpl -------------------------------------------------------------------------------- /kinbot/tpl/rotdPy_frag.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/rotdPy_frag.tpl -------------------------------------------------------------------------------- /kinbot/tpl/rotdPy_surf.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/rotdPy_surf.tpl -------------------------------------------------------------------------------- /kinbot/tpl/slurm.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/slurm.tpl -------------------------------------------------------------------------------- /kinbot/tpl/slurm_mesmer.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/slurm_mesmer.tpl -------------------------------------------------------------------------------- /kinbot/tpl/slurm_mess.tpl: -------------------------------------------------------------------------------- 1 | mess me/mess.inp 2 | 3 | -------------------------------------------------------------------------------- /kinbot/tpl/slurm_mess_uq.tpl: -------------------------------------------------------------------------------- 1 | mess me/mess_{n}.inp 2 | 3 | -------------------------------------------------------------------------------- /kinbot/tpl/slurm_molpro.tpl: -------------------------------------------------------------------------------- 1 | module load molpro 2 | {command} {name}.inp 3 | 4 | -------------------------------------------------------------------------------- /kinbot/tpl/slurm_orca.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/slurm_orca.tpl -------------------------------------------------------------------------------- /kinbot/tpl/slurm_python.tpl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/tpl/slurm_python.tpl -------------------------------------------------------------------------------- /kinbot/uncertaintyAnalysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/uncertaintyAnalysis.py -------------------------------------------------------------------------------- /kinbot/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/utils.py -------------------------------------------------------------------------------- /kinbot/vrc_tst_scan.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/vrc_tst_scan.py -------------------------------------------------------------------------------- /kinbot/vrc_tst_surfaces.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/vrc_tst_surfaces.py -------------------------------------------------------------------------------- /kinbot/zmatrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/kinbot/zmatrix.py -------------------------------------------------------------------------------- /meta.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/meta.yaml -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/pyproject.toml -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/__init__.py -------------------------------------------------------------------------------- /tests/bfgs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/bfgs.py -------------------------------------------------------------------------------- /tests/cheminfo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/cheminfo.py -------------------------------------------------------------------------------- /tests/dihedrals.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/dihedrals.py -------------------------------------------------------------------------------- /tests/find_motif.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/find_motif.py -------------------------------------------------------------------------------- /tests/frequencies.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/frequencies.py -------------------------------------------------------------------------------- /tests/geometry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/geometry.py -------------------------------------------------------------------------------- /tests/input/cheminfo_xyz.xyz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/input/cheminfo_xyz.xyz -------------------------------------------------------------------------------- /tests/modify_geom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/modify_geom.py -------------------------------------------------------------------------------- /tests/multimolecular.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/multimolecular.py -------------------------------------------------------------------------------- /tests/multimolecular_data.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/multimolecular_data.json -------------------------------------------------------------------------------- /tests/resonance.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/resonance.py -------------------------------------------------------------------------------- /tests/symmetry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/symmetry.py -------------------------------------------------------------------------------- /tests/symmetry_data.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/symmetry_data.json -------------------------------------------------------------------------------- /tests/test_kinbot.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/test_kinbot.dat -------------------------------------------------------------------------------- /tests/test_kinbot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/zadorlab/KinBot/HEAD/tests/test_kinbot.py --------------------------------------------------------------------------------