├── .coveragerc ├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.md │ ├── feature_request.md │ └── question.md ├── labeler.yml └── workflows │ ├── ci.yml │ ├── codeql.yml │ ├── docker_build.yml │ ├── gh-pages.yml │ ├── labeler.yml │ └── update-cache.yml ├── .gitignore ├── ARC.py ├── CODE_OF_CONDUCT.md ├── Dockerfile ├── LICENSE ├── Makefile ├── README.md ├── _config.yml ├── arc ├── __init__.py ├── checks │ ├── __init__.py │ ├── common.py │ ├── common_test.py │ ├── nmd.py │ ├── nmd_test.py │ ├── ts.py │ └── ts_test.py ├── common.py ├── common_test.py ├── constants.pxd ├── constants.py ├── exceptions.py ├── family │ ├── __init__.py │ ├── family.py │ └── family_test.py ├── imports.py ├── job │ ├── __init__.py │ ├── adapter.py │ ├── adapter_test.py │ ├── adapters │ │ ├── __init__.py │ │ ├── cfour.py │ │ ├── cfour_test.py │ │ ├── common.py │ │ ├── common_test.py │ │ ├── gaussian.py │ │ ├── gaussian_test.py │ │ ├── mockter.py │ │ ├── mockter_test.py │ │ ├── molpro.py │ │ ├── molpro_test.py │ │ ├── obabel.py │ │ ├── obabel_test.py │ │ ├── orca.py │ │ ├── orca_test.py │ │ ├── psi_4.py │ │ ├── qchem.py │ │ ├── scripts │ │ │ ├── autotst_script.py │ │ │ ├── gcn_script.py │ │ │ ├── ob_script.py │ │ │ ├── tani_script.py │ │ │ └── xtb_gsm │ │ │ │ ├── gsm.orca │ │ │ │ ├── ograd │ │ │ │ └── tm2orca.py │ │ ├── terachem.py │ │ ├── torch_ani.py │ │ ├── torch_ani_test.py │ │ ├── ts │ │ │ ├── __init__.py │ │ │ ├── autotst_ts.py │ │ │ ├── gcn_test.py │ │ │ ├── gcn_ts.py │ │ │ ├── heuristics.py │ │ │ ├── heuristics_test.py │ │ │ ├── kinbot_test.py │ │ │ ├── kinbot_ts.py │ │ │ ├── xtb_gsm.py │ │ │ └── xtbgsm_test.py │ │ ├── xtb_adapter.py │ │ └── xtb_test.py │ ├── factory.py │ ├── local.py │ ├── local_test.py │ ├── ssh.py │ ├── ssh_test.py │ ├── trsh.py │ └── trsh_test.py ├── level.py ├── level_test.py ├── main.py ├── main_test.py ├── mapping │ ├── __init__.py │ ├── driver.py │ ├── driver_test.py │ ├── engine.py │ └── engine_test.py ├── molecule │ ├── __init__.py │ ├── adjlist.py │ ├── adjlist_test.py │ ├── atomtype.pxd │ ├── atomtype.py │ ├── atomtype_test.py │ ├── atomtypedatabase.py │ ├── converter.pxd │ ├── converter.py │ ├── converter_test.py │ ├── draw.py │ ├── draw_test.py │ ├── element.pxd │ ├── element.py │ ├── element_test.py │ ├── filtration.py │ ├── filtration_test.py │ ├── graph.pxd │ ├── graph.pyx │ ├── graph_test.py │ ├── group.pxd │ ├── group.py │ ├── group_test.py │ ├── inchi.pxd │ ├── inchi.py │ ├── inchi_test.py │ ├── kekulize.pyx │ ├── kekulize_test.py │ ├── molecule.pxd │ ├── molecule.py │ ├── molecule_test.py │ ├── pathfinder.pxd │ ├── pathfinder.py │ ├── pathfinder_test.py │ ├── resonance.pxd │ ├── resonance.py │ ├── resonance_test.py │ ├── symmetry.pxd │ ├── symmetry.py │ ├── symmetry_test.py │ ├── translator.pxd │ ├── translator.py │ ├── translator_test.py │ ├── util.py │ ├── util_test.py │ ├── vf2.pxd │ ├── vf2.pyx │ └── vf2_test.py ├── parser │ ├── __init__.py │ ├── adapter.py │ ├── adapters │ │ ├── __init__.py │ │ ├── cfour.py │ │ ├── gaussian.py │ │ ├── molpro.py │ │ ├── orca.py │ │ ├── psi_4.py │ │ ├── qchem.py │ │ ├── terachem.py │ │ ├── xtb.py │ │ └── yaml.py │ ├── factory.py │ ├── parser.py │ └── parser_test.py ├── plotter.py ├── plotter_test.py ├── processor.py ├── processor_test.py ├── reaction │ ├── __init__.py │ ├── reaction.py │ └── reaction_test.py ├── scheduler.py ├── scheduler_test.py ├── scripts │ ├── __init__.py │ ├── common.py │ ├── libraries.yaml │ ├── rmg_kinetics.py │ ├── rmg_thermo.py │ └── save_arkane_thermo.py ├── settings │ ├── __init__.py │ ├── inputs.py │ ├── settings.py │ ├── submit.py │ └── submit_test.py ├── species │ ├── __init__.py │ ├── conformers.py │ ├── conformers_test.py │ ├── converter.py │ ├── converter_test.py │ ├── perceive.py │ ├── perceive_test.py │ ├── species.py │ ├── species_test.py │ ├── vectors.py │ ├── vectors_test.py │ ├── xyz_to_smiles.py │ ├── zmat.py │ └── zmat_test.py ├── statmech │ ├── __init__.py │ ├── adapter.py │ ├── arkane.py │ ├── arkane_test.py │ └── factory.py ├── testing │ ├── N2H4_opt_QChem.out │ ├── NH3_oneDMin.dat │ ├── TS_confs │ │ ├── TS0_conf_0.out │ │ ├── TS0_conf_0_input.gjf │ │ ├── TS0_conf_1.out │ │ ├── TS0_conf_10.out │ │ ├── TS0_conf_10_input.gjf │ │ ├── TS0_conf_11.out │ │ ├── TS0_conf_11_input.gjf │ │ ├── TS0_conf_1_input.gjf │ │ ├── TS0_conf_2.out │ │ ├── TS0_conf_2_input.gjf │ │ ├── TS0_conf_3.out │ │ ├── TS0_conf_3_input.gjf │ │ ├── TS0_conf_4.out │ │ ├── TS0_conf_4_input.gjf │ │ ├── TS0_conf_5.out │ │ ├── TS0_conf_5_input.gjf │ │ ├── TS0_conf_6.out │ │ ├── TS0_conf_6_input.gjf │ │ ├── TS0_conf_7.out │ │ ├── TS0_conf_7_input.gjf │ │ ├── TS0_conf_8.out │ │ ├── TS0_conf_8_input.gjf │ │ ├── TS0_conf_9.out │ │ └── TS0_conf_9_input.gjf │ ├── composite │ │ ├── C2H5NO2__C2H5ONO.out │ │ ├── C3H7 │ │ │ ├── TS1.log │ │ │ ├── TS2.log │ │ │ ├── TS3.log │ │ │ ├── TS4.log │ │ │ ├── TS5.log │ │ │ ├── TS6.log │ │ │ ├── TS7.log │ │ │ ├── iC3H7.gjf │ │ │ └── nC3H7.gjf │ │ ├── SO2OO_CBS-QB3.log │ │ ├── TS0_composite_2043.out │ │ ├── TS0_composite_2044.out │ │ ├── TS0_composite_2102.out │ │ ├── TS1_composite_695.out │ │ ├── TS_butylene_intra_H_migration.out │ │ └── TS_intra_H_migration_CBS-QB3.out │ ├── freq │ │ ├── C2H6_freq_QChem.out │ │ ├── C3H7_intra_h_TS.out │ │ ├── CH2O_freq_molpro.out │ │ ├── CH2O_freq_terachem.dat │ │ ├── CH3OO_freq_gaussian.out │ │ ├── CHO_neg_freq.out │ │ ├── CO2_xtb.out │ │ ├── Gaussian_neg_freq.out │ │ ├── HO2+N2H4_H2O2+N2H3_freq.out │ │ ├── NO3_freq_QChem_fails_on_cclib.out │ │ ├── TS_C3_intraH_8.out │ │ ├── TS_CH4_OH.log │ │ ├── TS_NH2+N2H3.out │ │ ├── TS_NH2+N2H3_xtb.out │ │ ├── TS_NH3+H=NH2+H2.out │ │ ├── TS_nC3H7-iC3H7.out │ │ ├── dual_freq_output.out │ │ ├── ethylamine_freq_terachem_output.out │ │ ├── formaldehyde_freq_terachem_output.out │ │ ├── iC3H7.out │ │ ├── nC3H7.out │ │ ├── orca_example_freq.log │ │ ├── output.yml │ │ └── vibspectrum │ ├── irc │ │ ├── cyano_irc_1.out │ │ ├── irc_failed.out │ │ ├── rxn_1_irc_1.out │ │ └── rxn_1_irc_2.out │ ├── job_log │ │ ├── memory_exceeded.log │ │ ├── no_issues.log │ │ └── using_to_few.log │ ├── methylamine_conformer_0.out │ ├── methylamine_conformer_1.out │ ├── mltspc_output.out │ ├── mockter.yml │ ├── normal_mode │ │ ├── HO2 │ │ │ ├── g98.out │ │ │ └── output.out │ │ └── TS_0 │ │ │ ├── g98.out │ │ │ └── output.out │ ├── opt │ │ ├── TS_nC3H7-iC3H7.out │ │ ├── iC3H7.out │ │ ├── nC3H7.out │ │ ├── xtb_opt_1.out │ │ └── xtb_opt_2.out │ ├── orca_example_opt.log │ ├── reactions │ │ └── methanoate_hydrolysis │ │ │ ├── TS1.gjf │ │ │ ├── TS2.gjf │ │ │ ├── input_1.yml │ │ │ └── input_2.yml │ ├── restart │ │ ├── 1_restart_thermo │ │ │ ├── calcs │ │ │ │ ├── freq_a19031.out │ │ │ │ ├── freq_a19038.out │ │ │ │ ├── freq_a19046.out │ │ │ │ ├── scan_a19034.out │ │ │ │ ├── scan_a19040.out │ │ │ │ ├── scan_a19049.out │ │ │ │ ├── sp_a19014.out │ │ │ │ ├── sp_a19032.out │ │ │ │ ├── sp_a19039.out │ │ │ │ └── sp_a19047.out │ │ │ └── restart.yml │ │ ├── 2_restart_rate │ │ │ ├── calcs │ │ │ │ ├── Species │ │ │ │ │ ├── N2H3_freq.out │ │ │ │ │ ├── N2H3_opt.out │ │ │ │ │ ├── N2H4_freq.out │ │ │ │ │ ├── N2H4_opt.out │ │ │ │ │ ├── NH2_freq.out │ │ │ │ │ ├── NH2_opt.out │ │ │ │ │ ├── NH_freq.out │ │ │ │ │ └── NH_opt.out │ │ │ │ └── TSs │ │ │ │ │ ├── TS_freq.out │ │ │ │ │ └── TS_opt.out │ │ │ └── restart.yml │ │ ├── 3_restart_bde │ │ │ ├── calcs │ │ │ │ └── Species │ │ │ │ │ ├── H │ │ │ │ │ └── sp_a4339 │ │ │ │ │ │ └── output.out │ │ │ │ │ ├── anilino_radical │ │ │ │ │ ├── freq_a4345 │ │ │ │ │ │ └── output.out │ │ │ │ │ ├── opt_a4344 │ │ │ │ │ │ └── output.out │ │ │ │ │ └── scan_a4346 │ │ │ │ │ │ └── output.out │ │ │ │ │ ├── anilino_radical_BDE_1_9_A │ │ │ │ │ ├── freq_a4387 │ │ │ │ │ │ └── output.out │ │ │ │ │ └── opt_a4382 │ │ │ │ │ │ └── output.out │ │ │ │ │ ├── anilino_radical_BDE_3_4_A │ │ │ │ │ ├── freq_a4388 │ │ │ │ │ │ └── output.out │ │ │ │ │ └── opt_a4381 │ │ │ │ │ │ └── output.out │ │ │ │ │ ├── anilino_radical_BDE_5_10_A │ │ │ │ │ ├── freq_a4389 │ │ │ │ │ │ └── output.out │ │ │ │ │ └── opt_a4383 │ │ │ │ │ │ └── output.out │ │ │ │ │ ├── anilino_radical_BDE_6_11_A │ │ │ │ │ ├── freq_a4390 │ │ │ │ │ │ └── output.out │ │ │ │ │ └── opt_a4384 │ │ │ │ │ │ └── output.out │ │ │ │ │ ├── anilino_radical_BDE_7_12_A │ │ │ │ │ ├── freq_a4391 │ │ │ │ │ │ └── output.out │ │ │ │ │ └── opt_a4386 │ │ │ │ │ │ └── output.out │ │ │ │ │ └── anilino_radical_BDE_8_13_A │ │ │ │ │ ├── freq_a4392 │ │ │ │ │ └── output.out │ │ │ │ │ └── opt_a4385 │ │ │ │ │ └── output.out │ │ │ └── restart.yml │ │ ├── 4_globalized_paths │ │ │ ├── calcs │ │ │ │ └── Species │ │ │ │ │ └── HCN │ │ │ │ │ └── freq_a38229 │ │ │ │ │ └── output.out │ │ │ └── restart_paths.yml │ │ └── 5_TS1 │ │ │ ├── freq_a7002 │ │ │ ├── input.gjf │ │ │ └── output.out │ │ │ ├── restart.yml │ │ │ └── sp_a7003 │ │ │ ├── input.in │ │ │ └── output.out │ ├── rotor_scans │ │ ├── CH2OOH.out │ │ ├── CH3C(O)O_FreeRotor.out │ │ ├── COCCOO.out │ │ ├── H2O2.out │ │ ├── N2O3.out │ │ ├── OOC1CCOCO1.out │ │ ├── TS_errored.out │ │ ├── TS_scan.out │ │ ├── l103_err.out │ │ ├── orca │ │ │ ├── cc.txt │ │ │ └── dft.txt │ │ ├── sBuOH.out │ │ ├── scan_1d_curvilinear_error.out │ │ ├── scan_2D_N3H5.out │ │ ├── scan_2D_relaxed_OCdOO.log │ │ └── xtb_1 │ │ │ ├── output.out │ │ │ └── xtbscan.log │ ├── sp │ │ ├── NCC_xTB.out │ │ ├── formaldehyde_sp_terachem_output.out │ │ ├── formaldehyde_sp_terachem_results.dat │ │ ├── mehylamine_CCSD(T).out │ │ ├── output.yml │ │ └── psi4_mrcc.dat │ ├── statmech │ │ └── iC3H7_xtb │ │ │ ├── freq_a1597 │ │ │ └── output.out │ │ │ └── opt_a1596 │ │ │ └── output.out │ ├── stringfile.xyz0000 │ ├── tani_output.yml │ ├── test_JobAdapter_ServerTimeLimit │ │ └── calcs │ │ │ └── Species │ │ │ └── spc1 │ │ │ └── spc1 │ │ │ ├── err.txt │ │ │ ├── input.gjf │ │ │ └── submit.sub │ ├── trsh │ │ ├── gaussian │ │ │ ├── atomic_number_out_of_range.out │ │ │ ├── converged.out │ │ │ ├── inaccurate_quadrature.out │ │ │ ├── l123_deltax.out │ │ │ ├── l301.out │ │ │ ├── l301_checkfile.out │ │ │ ├── l401.out │ │ │ ├── l913.out │ │ │ ├── l9999.out │ │ │ ├── maxsteps.out │ │ │ └── syntax.out │ │ ├── molpro │ │ │ ├── insufficient_memory.out │ │ │ ├── insufficient_memory_2.out │ │ │ ├── insufficient_memory_3.out │ │ │ └── unrecognized_basis_set.out │ │ ├── orca │ │ │ ├── orca_GTOInt_error.log │ │ │ ├── orca_basis_error.log │ │ │ ├── orca_input_error.log │ │ │ ├── orca_mdci_error.log │ │ │ ├── orca_mdci_error_2.log │ │ │ ├── orca_mdci_error_3.log │ │ │ ├── orca_mdci_memory_error.log │ │ │ ├── orca_multiplicity_error.log │ │ │ ├── orca_scf_blow_up_error.log │ │ │ ├── orca_scf_memory_error.log │ │ │ ├── orca_successful_sp.log │ │ │ ├── orca_successful_sp_scf.log │ │ │ ├── orca_too_many_cores.log │ │ │ └── orca_wavefunction_not_converge_error.log │ │ └── qchem │ │ │ └── H2_opt.out │ ├── xyz │ │ ├── AIBN.gjf │ │ ├── CH3C(O)O.gjf │ │ ├── CH3C(O)O.xyz │ │ ├── Gaussian_large.log │ │ ├── TS.gjf │ │ ├── conformers_after_optimization.txt │ │ ├── conformers_before_optimization.txt │ │ ├── conformers_file.txt │ │ ├── ethane_minimize_terachem_output.out │ │ ├── formaldehyde_coords.xyz │ │ ├── molpro.in │ │ ├── optim_traj_terachem.xyz │ │ ├── qchem.in │ │ ├── qchem_output.out │ │ └── scan_optim.xyz │ └── yml_testing │ │ ├── C3_1.yml │ │ ├── C3_2.yml │ │ ├── HNNO+NH3O=H2NO+NH2NO │ │ ├── H2NO.yml │ │ ├── HNNO.yml │ │ ├── NH2NO.yml │ │ └── NH3O.yml │ │ └── N4H6.yml └── utils │ ├── __init__.py │ ├── delete.py │ ├── scale.py │ ├── scale_test.py │ └── wip.py ├── data ├── AEC.yml ├── elements.yml ├── ess_methods.yml ├── families │ └── hydrolysis.py ├── freq_scale_factors.yml └── rxn_normal_mode_disp.yml ├── devtools ├── clean.sh ├── compile.sh ├── delete.sh ├── gcn_environment.yml ├── install_all.sh ├── install_arc.sh ├── install_autotst.sh ├── install_gcn.sh ├── install_gcn_cpu.sh ├── install_kinbot.sh ├── install_ob.sh ├── install_pyrdl.sh ├── install_rmg.sh ├── install_sella.sh ├── install_torchani.sh ├── install_xtb.sh ├── lite.sh ├── ob_environment.yml ├── sella_environment.yml ├── tani_environment.yml └── xtb_environment.yml ├── docker-compose.yml ├── dockerfiles ├── aliases.sh ├── aliases_print.sh ├── docker_tests │ └── test_docker_smoke.py └── entrywrapper.sh ├── docs ├── Makefile └── source │ ├── advanced.rst │ ├── api │ ├── common.rst │ ├── conformers.rst │ ├── converter.rst │ ├── index.rst │ ├── job.rst │ ├── level.rst │ ├── local.rst │ ├── main.rst │ ├── parser.rst │ ├── plotter.rst │ ├── processor.rst │ ├── reaction.rst │ ├── rmgdb.rst │ ├── scale.rst │ ├── scheduler.rst │ ├── species.rst │ ├── ssh.rst │ ├── trsh.rst │ ├── vectors.rst │ └── zmat.rst │ ├── arc.png │ ├── cite.rst │ ├── conf.py │ ├── contribute.rst │ ├── credits.rst │ ├── examples.rst │ ├── index.rst │ ├── installation.rst │ ├── licence.rst │ ├── links.txt │ ├── media.rst │ ├── output.rst │ ├── release.rst │ ├── running.rst │ └── tools.rst ├── environment.yml ├── examples ├── TS │ └── input.yml ├── bde │ └── input.yml ├── minimal │ └── input.yml ├── mockter │ └── input.yml ├── rates_demo │ └── input.yml └── thermo_demo │ └── input.yml ├── functional ├── functional_test.py ├── restart_test.py └── ts_guess.xyz ├── ipython ├── Demo │ ├── ARC rxn demo using YAML.ipynb │ ├── ARC thermo demo.ipynb │ └── yml │ │ ├── H2O.yml │ │ ├── OH.yml │ │ ├── ethanol + OH = o_ethanol_rad + H2O.yml │ │ ├── ethanol.yml │ │ └── o_ethanol_rad.yml └── Tools │ ├── ARC ESS diagnostics.ipynb │ ├── ARC_example.ipynb │ ├── Determine harmonic frequencies scaling factor.ipynb │ ├── External symmetry and optical isomers.ipynb │ ├── OneDMin script.ipynb │ ├── Perceive_xyz_(xyz_to_smiles).ipynb │ ├── Plot xyz.ipynb │ ├── TS Guesses.ipynb │ ├── Visualize 1D Torsion scan.ipynb │ ├── Visualize 2D Torsion scan.ipynb │ ├── conformers.ipynb │ ├── confs │ ├── conformer torsions 0.png │ ├── conformer torsions 1.png │ ├── conformer torsions 2.png │ ├── conformer torsions 3.png │ ├── conformer torsions 4.png │ ├── conformer torsions 5.png │ ├── conformer torsions 6.png │ ├── conformer torsions 7.png │ └── conformer torsions 8.png │ 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