├── .DS_Store ├── .github └── workflows │ └── python-test.yml ├── .gitignore ├── .ipynb_checkpoints ├── enumeration_tutorial-checkpoint.ipynb └── tutorial-checkpoint.ipynb ├── .pysisyphusrc ├── LICENSE.md ├── MR └── YARPrun.log ├── Makefile ├── README.md ├── __MACOSX └── classy-YARP │ ├── ._.DS_Store │ ├── docs │ └── ._.DS_Store │ └── yarp │ └── ._test.pdf ├── _build ├── doctrees │ ├── environment.pickle │ ├── index.doctree │ └── yarp_docs.doctree └── html │ ├── .buildinfo │ ├── _sources │ ├── index.rst.txt │ └── yarp_docs.rst.txt │ ├── _static │ ├── _sphinx_javascript_frameworks_compat.js │ ├── alabaster.css │ ├── basic.css │ ├── custom.css │ ├── doctools.js │ ├── documentation_options.js │ ├── file.png │ ├── jquery-3.6.0.js │ ├── jquery.js │ ├── language_data.js │ ├── minus.png │ ├── plus.png │ ├── pygments.css │ ├── searchtools.js │ ├── underscore-1.13.1.js │ └── underscore.js │ ├── genindex.html │ ├── index.html │ ├── objects.inv │ ├── search.html │ ├── searchindex.js │ └── yarp_docs.html ├── crest-test ├── .CHRG ├── .UHF ├── .history.xyz ├── HGCIXCUEYOPUTN.xyz ├── coord ├── coord.original ├── cre_members ├── cregen_0.tmp ├── cregen_1.tmp ├── crest.energies ├── crest_best.xyz ├── crest_conformers.xyz ├── crest_rotamers.xyz ├── gfnff_adjacency ├── gfnff_charges ├── gfnff_topo ├── struc.xyz └── wbo ├── docs ├── .DS_Store ├── Makefile ├── conf.py ├── index.rst ├── make.bat └── source │ ├── conf.py │ ├── enum.rst │ ├── find_lewis.rst │ ├── hashes.rst │ ├── index.rst │ ├── input_parsers.rst │ ├── installation.rst │ ├── properties.rst │ ├── sieve.rst │ ├── taffi_functions.rst │ ├── usage.rst │ └── yarpecule.rst ├── env.yaml ├── env_linux.yaml ├── env_mac.yaml ├── examples ├── FeCO5.xyz ├── b1.pdf ├── b1f1.pdf ├── b2.pdf ├── b2f1.pdf ├── b2f2_0-49.pdf ├── benzene.pdf ├── f1.pdf ├── f2.pdf ├── reactant.pdf ├── reaction.py └── test_examples.py ├── meta.yaml ├── pyTEST_Example ├── Class-Refinement-Example │ ├── 10025_2 │ │ ├── 10025_2-TS.xyz │ │ ├── 10025_2-TSOPT.in │ │ ├── 10025_2-TSOPT.out │ │ ├── 10025_2-TSOPT.xyz │ │ ├── 10025_2-TSOPT_trj.xyz │ │ └── 10025_2.xyz │ ├── 105772_0 │ │ ├── 105772_0-TSOPT.in │ │ ├── 105772_0-TSOPT.out │ │ ├── 105772_0-TSOPT.xyz │ │ ├── 105772_0-TSOPT_trj.xyz │ │ └── 105772_0.xyz │ ├── 586_0 │ │ ├── 586_0-TSOPT.in │ │ └── 586_0.xyz │ ├── 70099_1 │ │ ├── 70099_1-TSOPT.in │ │ ├── 70099_1-TSOPT.out │ │ ├── 70099_1-TSOPT.xyz │ │ └── 70099_1.xyz │ ├── SINGLE_RXN.p │ ├── job_test.submit │ ├── parameters.yaml │ ├── reaction_xyz │ │ ├── 10025_2.xyz │ │ ├── 105772_0.xyz │ │ ├── 112_0.xyz │ │ ├── 586_0.xyz │ │ ├── 70099_1.xyz │ │ ├── 70635_0.xyz │ │ └── 75482_0.xyz │ └── readme.md ├── DFT_class.py ├── GSM │ └── template.yaml ├── ML.py ├── RESULT │ └── YARPrun.log ├── TS_refinement.py ├── analyze_functions.py ├── bin │ ├── DFT_models │ │ ├── Delta2_model_1.jpt │ │ ├── Delta2_model_2.jpt │ │ ├── Delta2_model_3.jpt │ │ ├── Delta2_model_4.jpt │ │ ├── Delta2_model_5.jpt │ │ ├── Delta2_model_6.jpt │ │ ├── Delta2_model_7.jpt │ │ └── Delta2_model_8.jpt │ ├── G4_models │ │ ├── G4_model_1.jpt │ │ ├── G4_model_2.jpt │ │ ├── G4_model_3.jpt │ │ ├── G4_model_4.jpt │ │ └── G4_model_5.jpt │ ├── IRC_model.json │ ├── gsm.orca │ ├── inpfileq │ ├── poor_model.sav │ ├── rich_model.sav │ └── ssm_inpfileq ├── calculator.py ├── class_main_dft.py ├── class_refinement.py ├── conf.py ├── constants.py ├── crc_at_nd │ └── TS_refine.py ├── initialize.py ├── irc.py ├── job_mapping.py ├── job_submission.py ├── main_dft.py ├── main_xtb.py ├── model_reaction.py ├── opt.py ├── parameters.yaml ├── qc_jobs.py ├── reaction_xyz │ └── DA.xyz ├── read_yarp_reaction.py ├── readme.md ├── scripts │ ├── ard │ │ ├── create_gsm_jobs.py │ │ ├── create_prod_optfreq_jobs.py │ │ ├── create_ts_optfreq_jobs.py │ │ ├── extract_reactions.py │ │ ├── filter_reactants.py │ │ ├── gsm_job_stats.py │ │ ├── make_opt_jobs.py │ │ ├── make_opt_jobs_rad.py │ │ ├── parse_qm9.py │ │ ├── refine_products_and_ts.py │ │ └── refine_reactants.py │ ├── auto3D.py │ ├── gscreate │ ├── ograd │ ├── ograd_xtb │ ├── qend │ ├── qstart │ └── tm2orca.py ├── template.yaml ├── test_rxn.py ├── tsopt.py ├── utils.py └── wrappers │ ├── crest.py │ ├── gaussian.py │ ├── gsm.py │ ├── model_reaction.py │ ├── orca.py │ ├── pysis.py │ ├── reaction.py │ └── xtb.py ├── pyproject.toml ├── pytest_requirements.txt ├── reaction ├── .ipynb_checkpoints │ └── joint_opt_tutorial-checkpoint.ipynb ├── .job_dft.submit.swp ├── .opt.xtboptok ├── .xtboptok ├── DA.p ├── DA │ ├── IRC-record.txt │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0 │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-TS.xyz │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-TSguess.xyz │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-irc.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-tsopt.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0_input.yaml │ │ ├── P.xyz │ │ ├── R.xyz │ │ ├── RUN.yaml │ │ ├── backward_end_initial.xyz │ │ ├── backward_end_opt.xyz │ │ ├── backward_end_optimization.trj │ │ ├── backward_first.xyz │ │ ├── backward_irc.trj │ │ ├── backward_irc_data.h5 │ │ ├── backward_last.xyz │ │ ├── calculator.log │ │ ├── finished_first.xyz │ │ ├── finished_irc.trj │ │ ├── finished_irc_data.h5 │ │ ├── finished_last.xyz │ │ ├── forward_end_initial.xyz │ │ ├── forward_end_opt.xyz │ │ ├── forward_end_optimization.trj │ │ ├── forward_first.xyz │ │ ├── forward_irc.trj │ │ ├── forward_irc_data.h5 │ │ ├── forward_last.xyz │ │ ├── internal_coords.log │ │ ├── irc.log │ │ ├── left_ts_right_geoms.trj │ │ ├── optimization.h5 │ │ ├── optimizer.log │ │ ├── pysisyphus.log │ │ ├── ts_final_geometry.xyz │ │ ├── ts_final_hessian.h5 │ │ ├── ts_hess_calc_cyc_0.h5 │ │ ├── ts_hess_calc_cyc_1.h5 │ │ ├── ts_hess_calc_cyc_2.h5 │ │ ├── ts_hess_calc_cyc_3.h5 │ │ ├── ts_imaginary_mode_000.trj │ │ ├── ts_opt.xyz │ │ └── ts_optimization.trj │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_1 │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_1-TSguess.xyz │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_1-tsopt.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_1_input.yaml │ │ ├── P.xyz │ │ ├── R.xyz │ │ ├── RUN.yaml │ │ ├── calculator.log │ │ ├── optimization.h5 │ │ ├── optimizer.log │ │ ├── ts_final_geometry.xyz │ │ ├── ts_final_hessian.h5 │ │ ├── ts_hess_calc_cyc_0.h5 │ │ ├── ts_hess_calc_cyc_1.h5 │ │ ├── ts_hess_calc_cyc_2.h5 │ │ ├── ts_hess_calc_cyc_3.h5 │ │ ├── ts_imaginary_mode_000.trj │ │ ├── ts_opt.xyz │ │ └── ts_optimization.trj │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_2 │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-string.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0_input.yaml │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_1-string.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_1_input.yaml │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_2-TSguess.xyz │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_2-string.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_2-tsopt.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_2_input.yaml │ │ ├── P.xyz │ │ ├── R.xyz │ │ ├── RUN.yaml │ │ ├── calculator.log │ │ ├── cos.log │ │ ├── cos_hei.trj │ │ ├── current_geometries.trj │ │ ├── cycle_000.trj │ │ ├── cycle_001.trj │ │ ├── cycle_002.trj │ │ ├── cycle_003.trj │ │ ├── cycle_004.trj │ │ ├── cycle_005.trj │ │ ├── cycle_006.trj │ │ ├── cycle_007.trj │ │ ├── cycle_008.trj │ │ ├── cycle_009.trj │ │ ├── cycle_010.trj │ │ ├── cycle_011.trj │ │ ├── cycle_012.trj │ │ ├── cycle_013.trj │ │ ├── cycle_014.trj │ │ ├── cycle_015.trj │ │ ├── cycle_016.trj │ │ ├── cycle_017.trj │ │ ├── cycle_018.trj │ │ ├── cycle_019.trj │ │ ├── cycle_020.trj │ │ ├── cycle_021.trj │ │ ├── cycle_022.trj │ │ ├── cycle_023.trj │ │ ├── cycle_024.trj │ │ ├── cycle_025.trj │ │ ├── cycle_026.trj │ │ ├── final_geometries.trj │ │ ├── image_000.trj │ │ ├── image_001.trj │ │ ├── image_002.trj │ │ ├── image_003.trj │ │ ├── image_004.trj │ │ ├── image_005.trj │ │ ├── image_006.trj │ │ ├── image_007.trj │ │ ├── image_008.trj │ │ ├── image_009.trj │ │ ├── image_010.trj │ │ ├── optimization.h5 │ │ ├── optimization.trj │ │ ├── optimizer.log │ │ ├── splined_hei.xyz │ │ ├── too_similar.trj │ │ ├── ts_final_geometry.xyz │ │ ├── ts_final_hessian.h5 │ │ ├── ts_hess_calc_cyc_0.h5 │ │ ├── ts_hess_calc_cyc_1.h5 │ │ ├── ts_hess_calc_cyc_2.h5 │ │ ├── ts_hess_calc_cyc_3.h5 │ │ ├── ts_imaginary_mode_000.trj │ │ ├── ts_opt.xyz │ │ └── ts_optimization.trj │ ├── YARPrun.log │ ├── conformer │ │ ├── HGCIXCUEYOPUTN │ │ │ ├── .CHRG │ │ │ ├── .UHF │ │ │ ├── .history.xyz │ │ │ ├── HGCIXCUEYOPUTN-crest.out │ │ │ ├── HGCIXCUEYOPUTN.xyz │ │ │ ├── coord │ │ │ ├── coord.original │ │ │ ├── cre_members │ │ │ ├── cregen_0.tmp │ │ │ ├── cregen_1.tmp │ │ │ ├── crest.energies │ │ │ ├── crest_best.xyz │ │ │ ├── crest_conformers.xyz │ │ │ ├── crest_rotamers.xyz │ │ │ ├── gfnff_adjacency │ │ │ ├── gfnff_charges │ │ │ ├── gfnff_topo │ │ │ ├── struc.xyz │ │ │ └── wbo │ │ └── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO │ │ │ ├── .CHRG │ │ │ ├── .UHF │ │ │ ├── .history.xyz │ │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO-crest.out │ │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO.xyz │ │ │ ├── coord │ │ │ ├── coord.original │ │ │ ├── cre_members │ │ │ ├── cregen_0.tmp │ │ │ ├── cregen_1.tmp │ │ │ ├── crest.energies │ │ │ ├── crest_best.xyz │ │ │ ├── crest_conformers.xyz │ │ │ ├── crest_rotamers.xyz │ │ │ ├── gfnff_adjacency │ │ │ ├── gfnff_charges │ │ │ ├── gfnff_topo │ │ │ ├── struc.xyz │ │ │ └── wbo │ ├── rxn_conf │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0.xyz │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_1.xyz │ │ └── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_2.xyz │ └── xtb_run │ │ ├── HGCIXCUEYOPUTN │ │ ├── HGCIXCUEYOPUTN-init.xyz │ │ ├── HGCIXCUEYOPUTN-opt.out │ │ ├── HGCIXCUEYOPUTN_input.yaml │ │ ├── RUN.yaml │ │ ├── calculator.log │ │ ├── final_geometry.xyz │ │ ├── final_hessian.h5 │ │ ├── hess_calc_cyc_1.h5 │ │ ├── hess_calc_cyc_2.h5 │ │ ├── hess_calc_cyc_3.h5 │ │ ├── hess_calc_cyc_4.h5 │ │ ├── hess_calc_cyc_5.h5 │ │ ├── hess_calc_cyc_6.h5 │ │ ├── hess_calc_cyc_7.h5 │ │ ├── optimization.h5 │ │ ├── optimization.trj │ │ └── optimizer.log │ │ └── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO-init.xyz │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO-opt.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_input.yaml │ │ ├── RUN.yaml │ │ ├── calculator.log │ │ ├── final_geometry.xyz │ │ ├── final_hessian.h5 │ │ ├── hess_calc_cyc_1.h5 │ │ ├── hess_calc_cyc_2.h5 │ │ ├── hess_calc_cyc_3.h5 │ │ ├── hess_calc_cyc_4.h5 │ │ ├── hess_calc_cyc_5.h5 │ │ ├── hess_calc_cyc_6.h5 │ │ ├── hess_calc_cyc_7.h5 │ │ ├── optimization.h5 │ │ ├── optimization.trj │ │ └── optimizer.log ├── ML.py ├── TS_refinement.py ├── YARPrun.log ├── analyze_functions.py ├── bin │ ├── DFT_models │ │ ├── Delta2_model_1.jpt │ │ ├── Delta2_model_2.jpt │ │ ├── Delta2_model_3.jpt │ │ ├── Delta2_model_4.jpt │ │ ├── Delta2_model_5.jpt │ │ ├── Delta2_model_6.jpt │ │ ├── Delta2_model_7.jpt │ │ └── Delta2_model_8.jpt │ ├── G4_models │ │ ├── G4_model_1.jpt │ │ ├── G4_model_2.jpt │ │ ├── G4_model_3.jpt │ │ ├── G4_model_4.jpt │ │ └── G4_model_5.jpt │ ├── IRC_model.json │ ├── gsm.orca │ ├── inpfileq │ ├── poor_model.sav │ └── rich_model.sav ├── charges ├── conf.py ├── conformer │ ├── HGCIXCUEYOPUTN │ │ ├── .CHRG │ │ ├── .UHF │ │ ├── .history.xyz │ │ ├── HGCIXCUEYOPUTN-crest.out │ │ ├── HGCIXCUEYOPUTN.xyz │ │ ├── coord │ │ ├── coord.original │ │ ├── cre_members │ │ ├── cregen_0.tmp │ │ ├── cregen_1.tmp │ │ ├── crest.energies │ │ ├── crest_best.xyz │ │ ├── crest_conformers.xyz │ │ ├── crest_rotamers.xyz │ │ ├── gfnff_adjacency │ │ ├── gfnff_charges │ │ ├── gfnff_topo │ │ ├── struc.xyz │ │ └── wbo │ └── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO │ │ ├── .CHRG │ │ ├── .UHF │ │ ├── .history.xyz │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO-crest.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO.xyz │ │ ├── coord │ │ ├── coord.original │ │ ├── cre_members │ │ ├── cregen_0.tmp │ │ ├── cregen_1.tmp │ │ ├── crest.energies │ │ ├── crest_best.xyz │ │ ├── crest_conformers.xyz │ │ ├── crest_rotamers.xyz │ │ ├── gfnff_adjacency │ │ ├── gfnff_charges │ │ ├── gfnff_topo │ │ ├── struc.xyz │ │ └── wbo ├── constants.py ├── job_dft.submit ├── job_mapping.py ├── job_submission.py ├── job_xtb.submit ├── main_dft.py ├── main_xtb.py ├── model_reaction.py ├── parameters.yaml ├── qc_jobs.py ├── radicals.p ├── reaction_xyz │ └── DA.xyz ├── read_yarp_reaction.py ├── rxn_conf │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_1.xyz │ └── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_2.xyz ├── scripts │ ├── ard │ │ ├── create_gsm_jobs.py │ │ ├── create_prod_optfreq_jobs.py │ │ ├── create_ts_optfreq_jobs.py │ │ ├── extract_reactions.py │ │ ├── filter_reactants.py │ │ ├── gsm_job_stats.py │ │ ├── make_opt_jobs.py │ │ ├── make_opt_jobs_rad.py │ │ ├── parse_qm9.py │ │ ├── refine_products_and_ts.py │ │ └── refine_reactants.py │ ├── auto3D.py │ ├── gscreate │ ├── ograd │ ├── ograd_xtb │ ├── qend │ ├── qstart │ └── tm2orca.py ├── tst.xyz ├── utils.py ├── wrappers │ ├── .reaction.py.swp │ ├── crest.py │ ├── gaussian.py │ ├── gsm.py │ ├── model_reaction.py │ ├── orca.py │ ├── pysis.py │ ├── reaction.py │ └── xtb.py ├── xtb_run │ ├── HGCIXCUEYOPUTN │ │ ├── HGCIXCUEYOPUTN-init.xyz │ │ ├── HGCIXCUEYOPUTN-opt.out │ │ ├── HGCIXCUEYOPUTN_input.yaml │ │ ├── RUN.yaml │ │ ├── calculator.log │ │ ├── final_geometry.xyz │ │ ├── final_hessian.h5 │ │ ├── hess_calc_cyc_1.h5 │ │ ├── hess_calc_cyc_2.h5 │ │ ├── hess_calc_cyc_3.h5 │ │ ├── hess_calc_cyc_4.h5 │ │ ├── hess_calc_cyc_5.h5 │ │ ├── hess_calc_cyc_6.h5 │ │ ├── hess_calc_cyc_7.h5 │ │ ├── optimization.h5 │ │ ├── optimization.trj │ │ └── optimizer.log │ └── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO-init.xyz │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO-opt.out │ │ ├── KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_input.yaml │ │ ├── RUN.yaml │ │ ├── calculator.log │ │ ├── final_geometry.xyz │ │ ├── final_hessian.h5 │ │ ├── hess_calc_cyc_1.h5 │ │ ├── hess_calc_cyc_2.h5 │ │ ├── hess_calc_cyc_3.h5 │ │ ├── hess_calc_cyc_4.h5 │ │ ├── hess_calc_cyc_5.h5 │ │ ├── hess_calc_cyc_6.h5 │ │ ├── hess_calc_cyc_7.h5 │ │ ├── optimization.h5 │ │ ├── optimization.trj │ │ └── optimizer.log └── xyz_test │ └── 0.xyz ├── setup.cfg ├── tutorial.ipynb ├── tutorial ├── .ipynb_checkpoints │ ├── enumeration_tutorial-checkpoint.ipynb │ └── joint_opt_tutorial-checkpoint.ipynb ├── butylacid.pdf ├── butylacid.xyz ├── cyclopentene_H2.xyz ├── cyclopetene_H2.pdf ├── enumeration_tutorial.ipynb ├── enumeration_tutorial.py ├── ethanol.xyz ├── ethanol_form_all.pdf ├── ethanol_form_n.pdf ├── n-hexane.pdf ├── n_hex.pdf ├── n_hex.xyz ├── reactant.pdf ├── reactant2.pdf ├── test.xyz └── test2.xyz └── yarp ├── __init__.py ├── constants.py ├── enum.py ├── find_lewis.py ├── hashes.py ├── input_parsers.py ├── misc.py ├── properties.py ├── sieve.py ├── smiles.py ├── taffi_functions.py ├── test.pdf └── yarpecule.py /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/.DS_Store -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | # Byte-compiled / optimized / DLL files 2 | __pycache__/ 3 | *.py[cod] 4 | *$py.class 5 | *.*~ 6 | 7 | # C extensions 8 | *.so 9 | 10 | # Distribution / packaging 11 | .Python 12 | build/ 13 | develop-eggs/ 14 | dev/ 15 | dist/ 16 | downloads/ 17 | eggs/ 18 | .eggs/ 19 | lib/ 20 | lib64/ 21 | parts/ 22 | sdist/ 23 | var/ 24 | wheels/ 25 | share/python-wheels/ 26 | *.egg-info/ 27 | .installed.cfg 28 | *.egg 29 | MANIFEST 30 | 31 | # Installer logs 32 | pip-log.txt 33 | pip-delete-this-directory.txt 34 | 35 | # Unit test / coverage reports 36 | htmlcov/ 37 | .tox/ 38 | .nox/ 39 | .coverage 40 | .coverage.* 41 | .cache 42 | nosetests.xml 43 | coverage.xml 44 | *.cover 45 | *.py,cover 46 | .hypothesis/ 47 | .pytest_cache/ 48 | cover/ 49 | RESULT/ 50 | #*.p 51 | 52 | # Sphinx documentation 53 | docs/_build/ 54 | 55 | -------------------------------------------------------------------------------- /.pysisyphusrc: -------------------------------------------------------------------------------- 1 | [orca] 2 | # ORCA needs the full path to its binary, so please provide the full path. 3 | #cmd=/sw/pkgs/lsa/orca/5.0.3/bin/orca 4 | 5 | [psi4] 6 | # As the Psi4 installation without conda is, to put it slightly, tricky it was 7 | # decided to allow the installation of Psi4 into a separate conda environment. 8 | # pysisyphus then creates a Psi4 input and sends it to the (bash)-script given below 9 | # that accepts/expects one argument. It is the responsibility of the scrip to activate 10 | # the appropriate conda environment and submit the Psi4 input. An example runpsi4.sh 11 | # script is given below. 12 | #cmd=/user/johannes/bin/runpsi4.sh 13 | 14 | [xtb] 15 | # Cmd to execute. Please ensure that xtb is on your $PATH. 16 | cmd=CONDA_ENV/bin/xtb 17 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | BSD 4-Clause License (Year 2023) 2 | -------------------------------- 3 | 4 | Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 5 | 6 | 1. Redistributions of source code must retain the above copyright notice, this list of conditions, and the following disclaimer. 7 | 8 | 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions, and the following disclaimer in the documentation and/or other materials provided with the distribution. 9 | 10 | 3. Neither the name of the Savoie Research Group nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. 11 | 12 | 4. This software or any derivative works based on it must not be used for commercial purposes without the explicit permission of the Savoie Research Group. 13 | 14 | THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 15 | -------------------------------------------------------------------------------- /MR/YARPrun.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/MR/YARPrun.log -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = . 9 | BUILDDIR = _build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /__MACOSX/classy-YARP/._.DS_Store: -------------------------------------------------------------------------------- 1 | Mac OS X  2Fx @ATTRxx -------------------------------------------------------------------------------- /__MACOSX/classy-YARP/docs/._.DS_Store: -------------------------------------------------------------------------------- 1 | Mac OS X  2Fx @ATTRxx -------------------------------------------------------------------------------- /__MACOSX/classy-YARP/yarp/._test.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/__MACOSX/classy-YARP/yarp/._test.pdf -------------------------------------------------------------------------------- /_build/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/_build/doctrees/environment.pickle -------------------------------------------------------------------------------- /_build/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/_build/doctrees/index.doctree -------------------------------------------------------------------------------- /_build/doctrees/yarp_docs.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/_build/doctrees/yarp_docs.doctree -------------------------------------------------------------------------------- /_build/html/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: 5a5a79e336c6f5ab4d0802d5989379f1 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /_build/html/_sources/index.rst.txt: -------------------------------------------------------------------------------- 1 | .. yarp documentation master file, created by 2 | sphinx-quickstart on Tue Aug 1 17:37:31 2023. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to yarp's documentation! 7 | ================================ 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | :caption: Table of Contents: 12 | 13 | yarp/enum 14 | yarp/find_lewis 15 | yarp/yarpecule 16 | yarp/properties 17 | yarp/sieve 18 | yarp/taffi_functions 19 | yarp/hashes 20 | 21 | Indices and tables 22 | ================== 23 | 24 | * :ref:`genindex` 25 | * :ref:`modindex` 26 | * :ref:`search` 27 | -------------------------------------------------------------------------------- /_build/html/_sources/yarp_docs.rst.txt: -------------------------------------------------------------------------------- 1 | YARP Documentation 2 | ================== 3 | 4 | .. toctree:: 5 | :maxdepth: 2 6 | :caption: Contents: 7 | 8 | yarp/enum 9 | yarp/find_lewis 10 | yarp/yarpecule 11 | yarp/properties 12 | yarp/sieve 13 | yarp/taffi_functions 14 | yarp/hashes 15 | 16 | 17 | -------------------------------------------------------------------------------- /_build/html/_static/custom.css: -------------------------------------------------------------------------------- 1 | /* This file intentionally left blank. */ 2 | -------------------------------------------------------------------------------- /_build/html/_static/documentation_options.js: -------------------------------------------------------------------------------- 1 | var DOCUMENTATION_OPTIONS = { 2 | URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'), 3 | VERSION: '0.0.1', 4 | LANGUAGE: 'en', 5 | COLLAPSE_INDEX: false, 6 | BUILDER: 'html', 7 | FILE_SUFFIX: '.html', 8 | LINK_SUFFIX: '.html', 9 | HAS_SOURCE: true, 10 | SOURCELINK_SUFFIX: '.txt', 11 | NAVIGATION_WITH_KEYS: false, 12 | SHOW_SEARCH_SUMMARY: true, 13 | ENABLE_SEARCH_SHORTCUTS: false, 14 | }; -------------------------------------------------------------------------------- /_build/html/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/_build/html/_static/file.png -------------------------------------------------------------------------------- /_build/html/_static/minus.png: -------------------------------------------------------------------------------- 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["index"], "filenames": ["index.rst"], "titles": ["Welcome to yarp\u2019s documentation!"], "terms": {"index": 0, "modul": 0, "search": 0, "page": 0}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"welcom": 0, "yarp": 0, "s": 0, "document": 0, "tabl": 0, "content": [], "indic": 0}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx": 56}}) -------------------------------------------------------------------------------- /crest-test/.CHRG: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /crest-test/.UHF: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /crest-test/HGCIXCUEYOPUTN.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.9956591 1.11365923 0.1813245 4 | C -1.27606981 2.60235503 0.00621401 5 | H -1.87015336 0.60701239 0.59652452 6 | H -0.7812413 0.6721264 -0.79519026 7 | H -1.41873999 3.05865194 0.98976411 8 | H -2.19153548 2.75281318 -0.57214871 9 | C -0.0976857 3.27066793 -0.69802489 10 | C 1.20712102 2.85883263 -0.08807867 11 | C 1.34217747 1.81494158 0.71224008 12 | C 0.20657607 0.91889617 1.10162547 13 | H -0.19651844 4.35903197 -0.65048292 14 | H -0.09394222 2.99564592 -1.75944204 15 | H 2.06428799 3.46565932 -0.34755613 16 | H 2.30699362 1.56935897 1.13582647 17 | H 0.53724803 -0.12289727 1.07602732 18 | H -0.07794548 1.13896956 2.13677416 19 | -------------------------------------------------------------------------------- /crest-test/coord: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.295088226202 -2.263800091107 -0.634138661590 c 3 | -1.292088281533 -2.265464712524 0.634056332466 c 4 | 2.322904944744 -3.994206989544 -0.179205698862 h 5 | 1.044698769369 -2.190078486933 -2.681447286114 h 6 | -1.041768043094 -2.192337658840 2.681333359449 h 7 | -2.317586628534 -3.996976997084 0.178400298607 h 8 | -2.803553791597 0.034691577261 -0.229383129388 c 9 | -1.246578273224 2.395528184261 -0.103747756470 c 10 | 1.243471645777 2.397054551059 0.103660870272 c 11 | 2.803431564312 0.038209819334 0.229608709754 c 12 | -4.494116553686 0.258513698982 0.936970921237 h 13 | -3.445831312177 -0.237935087196 -2.178959122695 h 14 | -2.279000343666 4.156608892075 -0.212022732609 h 15 | 2.273534947061 4.159552882526 0.212137646278 h 16 | 4.493564022762 0.264200629483 -0.936890142823 h 17 | 3.446328084846 -0.234018483334 2.179011061435 h 18 | $end 19 | -------------------------------------------------------------------------------- /crest-test/coord.original: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.28992982557468 -2.26746589704554 -0.63329407795591 c 3 | -1.29832788035191 -2.26284726941081 0.63200755473820 c 4 | 2.31317584212588 -4.00001664354289 -0.17693925998668 h 5 | 1.04148077821211 -2.19472988954586 -2.68058402820615 h 6 | -1.04993140807258 -2.19263119367580 2.67917637414379 h 7 | -2.32816364887465 -3.99108482495238 0.17497116152461 h 8 | -2.80358096380565 0.04176413999782 -0.22900267675224 c 9 | -1.24055488180125 2.39844941057478 -0.10403502758791 c 10 | 1.24948216750331 2.39380839251654 0.10314975789265 c 11 | 2.80353819538852 0.03111785740424 0.22991930963453 c 12 | -4.49274888695266 0.26949066979136 0.93810152204698 h 13 | -3.44821794912227 -0.22901190285445 -2.17769177975425 h 14 | -2.26857148600712 4.16207672047857 -0.21254318991131 h 15 | 2.28400273513809 4.15354321839493 0.21174364596438 h 16 | 4.49482647358172 0.25248342009207 -0.93561964546874 h 17 | 3.44474088562378 -0.24231285527158 2.17955270306003 h 18 | $end 19 | -------------------------------------------------------------------------------- /crest-test/cre_members: -------------------------------------------------------------------------------- 1 | 3 2 | 2 1 2 3 | 2 3 4 4 | 1 5 5 5 | -------------------------------------------------------------------------------- /crest-test/cregen_0.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 43 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 43 12 | reference state Etot : -17.931438889999999 13 | number of doubles removed by rot/RMSD : 38 14 | total number unique points considered further : 5 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -17.93144 0.49935 0.99869 1 2 mtd4 17 | 2 0.000 -17.93144 0.49934 mtd9 18 | 3 4.144 -17.92484 0.00046 0.00092 2 2 mtd2 19 | 4 4.145 -17.92483 0.00046 mtd10 20 | 5 4.249 -17.92467 0.00039 0.00039 3 1 mtd6 21 | T /K : 298.15 22 | E lowest : -17.93144 23 | ensemble average energy (kcal) : 0.005 24 | ensemble entropy (J/mol K, cal/mol K) : 5.851 1.398 25 | ensemble free energy (kcal/mol) : -0.417 26 | population of lowest in % : 99.869 27 | number of unique conformers for further calc 3 28 | list of relative energies saved as "crest.energies" 29 | -------------------------------------------------------------------------------- /crest-test/cregen_1.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 42 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 42 12 | reference state Etot : -17.931438889999999 13 | number of doubles removed by rot/RMSD : 38 14 | total number unique points considered further : 4 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -17.93144 0.49954 0.99908 1 2 input 17 | 2 0.000 -17.93144 0.49954 mtd2 18 | 3 4.143 -17.92484 0.00046 0.00092 2 2 mtd6 19 | 4 4.143 -17.92484 0.00046 mtd10 20 | T /K : 298.15 21 | E lowest : -17.93144 22 | ensemble average energy (kcal) : 0.004 23 | ensemble entropy (J/mol K, cal/mol K) : 5.825 1.392 24 | ensemble free energy (kcal/mol) : -0.415 25 | population of lowest in % : 99.908 26 | number of unique conformers for further calc 2 27 | list of relative energies saved as "crest.energies" 28 | -------------------------------------------------------------------------------- /crest-test/crest.energies: -------------------------------------------------------------------------------- 1 | 1 0.000 2 | 2 4.143 3 | 3 4.249 4 | -------------------------------------------------------------------------------- /crest-test/crest_best.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -17.93143890 3 | C 0.6852104290 -1.1980200447 0.3355910795 4 | C -0.6838194098 -1.1986894336 -0.3355950715 5 | H 0.5527387282 -1.1591291370 1.4189731350 6 | H 1.2290809701 -2.1136974366 0.0947258845 7 | H -1.2266308176 -2.1150627075 -0.0951113980 8 | H -0.5512673011 -1.1592462686 -1.4188961559 9 | C -1.4836105169 0.0184153130 0.1214608912 10 | C -0.6595764605 1.2676743380 0.0549325562 11 | C 0.6581184954 1.2684407217 -0.0549030869 12 | C 1.4835561842 0.0200832026 -0.1214564933 13 | H -1.8235543173 -0.1260952609 1.1529625188 14 | H -2.3780466489 0.1369564570 -0.4958399858 15 | H -1.2058225870 2.1996225066 0.1122803734 16 | H 1.2032753860 2.2010072619 -0.1122808781 17 | H 1.8237535817 -0.1239851359 -1.1530108776 18 | H 2.3779182634 0.1395720671 0.4958413644 19 | -------------------------------------------------------------------------------- /crest-test/gfnff_adjacency: -------------------------------------------------------------------------------- 1 | # indices of neighbouring atoms (max seven) 2 | 2 3 4 10 3 | 1 5 6 7 4 | 1 5 | 1 6 | 2 7 | 2 8 | 2 8 11 12 9 | 7 9 13 10 | 8 10 14 11 | 1 9 15 16 12 | 7 13 | 7 14 | 8 15 | 9 16 | 10 17 | 10 18 | -------------------------------------------------------------------------------- /crest-test/gfnff_charges: -------------------------------------------------------------------------------- 1 | -0.04920891 2 | -0.04921297 3 | 0.02442185 4 | 0.03058669 5 | 0.03058188 6 | 0.02442383 7 | -0.04703062 8 | -0.04311763 9 | -0.04311976 10 | -0.04702738 11 | 0.02607117 12 | 0.02828606 13 | 0.02999329 14 | 0.02999599 15 | 0.02606952 16 | 0.02828701 17 | -------------------------------------------------------------------------------- /crest-test/gfnff_topo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/crest-test/gfnff_topo -------------------------------------------------------------------------------- /crest-test/struc.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.9956591000 1.1136592300 0.1813245000 4 | C -1.2760698100 2.6023550300 0.0062140100 5 | H -1.8701533600 0.6070123900 0.5965245200 6 | H -0.7812413000 0.6721264000 -0.7951902600 7 | H -1.4187399900 3.0586519400 0.9897641100 8 | H -2.1915354800 2.7528131800 -0.5721487100 9 | C -0.0976857000 3.2706679300 -0.6980248900 10 | C 1.2071210200 2.8588326300 -0.0880786700 11 | C 1.3421774700 1.8149415800 0.7122400800 12 | C 0.2065760700 0.9188961700 1.1016254700 13 | H -0.1965184400 4.3590319700 -0.6504829200 14 | H -0.0939422200 2.9956459200 -1.7594420400 15 | H 2.0642879900 3.4656593200 -0.3475561300 16 | H 2.3069936200 1.5693589700 1.1358264700 17 | H 0.5372480300 -0.1228972700 1.0760273200 18 | H -0.0779454800 1.1389695600 2.1367741600 19 | -------------------------------------------------------------------------------- /crest-test/wbo: -------------------------------------------------------------------------------- 1 | 1 2 1.0089739664674109 2 | 1 3 0.97869920995253179 3 | 1 4 0.97856020766418528 4 | 2 5 0.97856192982996038 5 | 2 6 0.97869731003715965 6 | 2 7 1.0067487346514603 7 | 7 8 1.0239128406394697 8 | 8 9 1.9287010741107977 9 | 1 10 1.0067391023459167 10 | 9 10 1.0238819138627508 11 | 7 11 0.96826183118890075 12 | 7 12 0.95921256777824049 13 | 8 13 0.96803568655112293 14 | 9 14 0.96804328552257812 15 | 10 15 0.96830079136139424 16 | 10 16 0.95921010478615099 17 | -------------------------------------------------------------------------------- /docs/.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/docs/.DS_Store -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line, and also 5 | # from the environment for the first two. 6 | SPHINXOPTS ?= 7 | SPHINXBUILD ?= sphinx-build 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /docs/index.rst: -------------------------------------------------------------------------------- 1 | Welcome to yarp documentation! 2 | ====================================== 3 | 4 | `yarp` is a python package with classes and functions that implement the yarp reaction exploration 5 | methodology. The core classes are built for workflows that involve enumerating potential reactions, 6 | performing pattern matching on molecules, conducting transition state searches, managing calculations, 7 | analyzing the outcomes of transition state searches, analyzing networks, and digesting large amounts 8 | of reaction data. 9 | 10 | 11 | Given the generality of these capabilities, we have refactored the original `yarp` workflows into the 12 | object-oriented package that you are reading the docs for, so that other researchers can leverage these 13 | algorithms in their own custom chemical workflows. 14 | 15 | **This software is still work in progress. Use at your own risk. Also take a look at the _license** 16 | 17 | .. _license: https://github.com/bsavoie/yarp/blob/master/LICENSE 18 | .. _issue: https://github.com/bsavoie/yarp/issues 19 | 20 | .. toctree:: 21 | :maxdepth: 4 22 | :numbered: 23 | :caption: Contents: 24 | 25 | overview.rst 26 | installation.rst 27 | yarpecule.rst 28 | ts.rst 29 | net.rst 30 | sieve.rst 31 | worked_examples.rst 32 | api/modules.rst 33 | 34 | Indices and tables 35 | ================== 36 | 37 | .. * :ref:`genindex` 38 | * :ref:`search` 39 | -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=source 11 | set BUILDDIR=build 12 | 13 | %SPHINXBUILD% >NUL 2>NUL 14 | if errorlevel 9009 ( 15 | echo. 16 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 17 | echo.installed, then set the SPHINXBUILD environment variable to point 18 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 19 | echo.may add the Sphinx directory to PATH. 20 | echo. 21 | echo.If you don't have Sphinx installed, grab it from 22 | echo.https://www.sphinx-doc.org/ 23 | exit /b 1 24 | ) 25 | 26 | if "%1" == "" goto help 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /docs/source/enum.rst: -------------------------------------------------------------------------------- 1 | enum module 2 | ---------------- 3 | 4 | .. automodule:: yarp.enum 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | -------------------------------------------------------------------------------- /docs/source/find_lewis.rst: -------------------------------------------------------------------------------- 1 | find\_lewis module 2 | ------------------ 3 | 4 | .. automodule:: yarp.find_lewis 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | -------------------------------------------------------------------------------- /docs/source/hashes.rst: -------------------------------------------------------------------------------- 1 | hashes module 2 | ---------------- 3 | 4 | .. automodule:: yarp.hashes 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | -------------------------------------------------------------------------------- /docs/source/input_parsers.rst: -------------------------------------------------------------------------------- 1 | input\_parsers module 2 | -------------------------- 3 | 4 | .. automodule:: yarp.input_parsers 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | 9 | -------------------------------------------------------------------------------- /docs/source/installation.rst: -------------------------------------------------------------------------------- 1 | Installation 2 | ============ 3 | 4 | To be completed 5 | 6 | -------------------------------------------------------------------------------- /docs/source/properties.rst: -------------------------------------------------------------------------------- 1 | properties module 2 | ---------------------- 3 | 4 | .. automodule:: yarp.properties 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | 9 | -------------------------------------------------------------------------------- /docs/source/sieve.rst: -------------------------------------------------------------------------------- 1 | sieve module 2 | ---------------- 3 | 4 | .. automodule:: yarp.sieve 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | -------------------------------------------------------------------------------- /docs/source/taffi_functions.rst: -------------------------------------------------------------------------------- 1 | taffi\_functions module 2 | ----------------------- 3 | 4 | .. automodule:: yarp.taffi_functions 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | -------------------------------------------------------------------------------- /docs/source/usage.rst: -------------------------------------------------------------------------------- 1 | Usage 2 | ===== 3 | 4 | To be completed 5 | 6 | Indices and tables 7 | ================== 8 | 9 | * :ref:`genindex` 10 | * :ref:`modindex` 11 | * :ref:`search` 12 | -------------------------------------------------------------------------------- /docs/source/yarpecule.rst: -------------------------------------------------------------------------------- 1 | yarpecule module 2 | ---------------- 3 | 4 | .. automodule:: yarp.yarpecule 5 | :members: 6 | :undoc-members: 7 | :show-inheritance: 8 | -------------------------------------------------------------------------------- /env_linux.yaml: -------------------------------------------------------------------------------- 1 | name: classy-yarp 2 | channels: 3 | - defaults 4 | - conda-forge 5 | dependencies: 6 | - defaults::python=3.9 7 | - defaults::pandas 8 | - defaults::xgboost 9 | - defaults::pip 10 | - conda-forge::xtb 11 | - conda-forge::openbabel 12 | - conda-forge::crest 13 | - conda-forge::ase 14 | - pip: 15 | - pysisyphus 16 | - rdkit 17 | - scikit-learn==1.3.2 18 | -------------------------------------------------------------------------------- /examples/FeCO5.xyz: -------------------------------------------------------------------------------- 1 | 11 2 | 3 | Fe -1.27111 0.18692 0.02307 4 | C -2.41152 -1.48255 -0.09987 5 | C -0.13181 1.85718 0.14575 6 | C 0.36869 -0.95639 0.34817 7 | O 0.50238 2.78757 0.21402 8 | O -3.04691 -2.41210 -0.16837 9 | O 1.28201 -1.59329 0.52888 10 | C -1.79742 0.68523 -1.86826 11 | C -2.38233 0.83018 1.58952 12 | O -2.09008 0.96240 -2.92182 13 | O -3.00086 1.18817 2.46229 14 | -------------------------------------------------------------------------------- /examples/b1.pdf: 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calculator import add 5 | 6 | def truthy(value): 7 | return bool(value) 8 | def falsy(value): 9 | return not bool(value) 10 | 11 | def check_metal(xyz): 12 | 13 | finish = False 14 | FeCO5 = yp.yarpecule(xyz) 15 | # first check adj_mat 16 | nBonds = 20 17 | nE = 58 18 | nDative= 5 19 | if(FeCO5.adj_mat.sum() == nBonds and FeCO5.bond_mats[0].sum() == nE): 20 | # then check bmat 21 | if(FeCO5.adj_mat.sum(axis=1)[0]==nDative): 22 | finish = True 23 | return finish 24 | 25 | def form_bond(a, hashes, nform): 26 | mols = [a] 27 | for i in range(0, nform): 28 | mols = list(set([ y for y in yp.form_bonds(mols,hashes=hashes)])) 29 | hashes.update([ _.hash for _ in mols ]) 30 | print(f"form {i} bond resulted in {len(mols)} new products") 31 | 32 | def break_bond(a, hashes, nbreak): 33 | mols = [a] 34 | mols = list(set([ y for y in yp.break_bonds(mols,n=nbreak)])) 35 | hashes.update([ _.hash for _ in mols ]) 36 | print(f"break {nbreak} bond resulted in {len(mols)} new products") 37 | 38 | def test_file(): 39 | #current_directory = os.getcwd() + '/' 40 | assert os.path.exists('FeCO5.xyz') 41 | assert check_metal("FeCO5.xyz") 42 | print("Organometallics CHECK FINISHED\n") 43 | reactant="C=CC=C.C=C" 44 | a = yp.yarpecule(reactant) 45 | hashes = set([a.hash]) 46 | print(f"reactant: {reactant}") 47 | form_bond(a, hashes, 2) 48 | break_bond(a, hashes, 2) 49 | assert len(hashes) == 29 50 | #print(f"hashes: {len(hashes)}\n") 51 | -------------------------------------------------------------------------------- /meta.yaml: -------------------------------------------------------------------------------- 1 | {% set data = load_setup_py_data() %} 2 | 3 | package: 4 | name: yarp 5 | version: {{ data['version'] }} 6 | 7 | source: 8 | path: . 9 | 10 | build: 11 | number: 0 12 | script: python setup.py install --single-version-externally-managed --record=record.txt 13 | 14 | requirements: 15 | build: 16 | - python >=3.0,{{PY_VER}}* 17 | - setuptools 18 | 19 | run: 20 | - python {{PY_VER}}* 21 | - numpy >=1.8* 22 | - scipy >=1.5* 23 | - matplotlib >=2.0* 24 | 25 | about: 26 | license: BSD 3-Clause 27 | license_file: LICENSE.md 28 | license_family: BSD 29 | summary: data['description'] 30 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/10025_2/10025_2-TS.xyz: -------------------------------------------------------------------------------- 1 | 22 2 | 3 | C 0.14841751950263 0.28949583008538 -1.1364219388631 4 | C 1.87570239517564 0.71347274693701 0.62591127235881 5 | C -0.18389686101912 -1.06603764902239 -1.34911435008146 6 | C 1.55303709058902 0.76896445125636 -0.83395911438995 7 | C -2.84937739764813 0.57357518100977 -0.30848973264534 8 | C 2.23902955875251 -0.57135412019223 1.27671726562597 9 | C -1.64692765250997 -0.30061406010372 -0.11236285037317 10 | N -1.30605301882231 -0.50410986476896 1.21219957926201 11 | N -1.42212142260403 -1.33407298552218 -1.00616892652741 12 | H -0.51962688791047 0.99989771001956 -1.60725556195065 13 | H 1.85660429802563 1.62285590031564 1.21445910801769 14 | H 0.47988825421336 -1.83471311589862 -1.75642974854496 15 | H 1.69485012958404 1.78441348732222 -1.20879380190259 16 | H 2.26197877418808 0.12745726903933 -1.38045570096448 17 | H -2.89538293295655 0.93471989719204 -1.33430151482253 18 | H -2.85362383726448 1.42032520293377 0.37897453756 19 | H -3.73740975518915 -0.03485448623648 -0.11896487521678 20 | H 3.31646281124648 -0.77535309753081 1.19998850931431 21 | H 1.73992184346402 -1.42020490279429 0.79439805559126 22 | H 1.99244601788255 -0.58573905575191 2.34102887314855 23 | H -0.53870331226035 -1.14403791940229 1.34942766205154 24 | H -1.20521561443938 0.33591358111281 1.75961326335227 25 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/10025_2/10025_2-TSOPT.in: -------------------------------------------------------------------------------- 1 | ! wB97X D4 def2-TZVP CPCM(DMSO) defgrid2 OptTS Freq 2 | 3 | %scf 4 | MaxIter 500 5 | end 6 | 7 | %pal 8 | nproc 24 9 | end 10 | 11 | %maxcore 2000 12 | 13 | %geom 14 | Calc_Hess true 15 | Recalc_Hess 1 16 | end 17 | 18 | %base "10025_2-TSOPT" 19 | 20 | *xyz 0 2 21 | C 0.21570760 0.38432434 -1.00298645 22 | C 1.99489260 0.70297556 0.57749622 23 | C -0.08307752 -1.00203671 -1.27387710 24 | C 1.65435620 0.87370960 -0.86881131 25 | C -2.75820424 0.52664622 -0.45639291 26 | C 2.32385839 -0.62688438 1.14539707 27 | C -1.59381494 -0.30253712 0.02183179 28 | N -1.52112617 -0.46307497 1.36238454 29 | N -1.20770908 -1.42035154 -0.76066876 30 | H -0.50524318 1.10645627 -1.35783398 31 | H 1.56509056 1.42827021 1.25628033 32 | H 0.54018777 -1.69168350 -1.84709303 33 | H 1.72155991 1.92585572 -1.15524435 34 | H 2.36095611 0.31788249 -1.50013529 35 | H -2.73627203 0.64794390 -1.53589855 36 | H -2.78484765 1.50459012 0.02461625 37 | H -3.67010242 -0.01515032 -0.20066144 38 | H 2.98558706 -1.19191062 0.48470428 39 | H 1.41111632 -1.22280502 1.26782143 40 | H 2.81045013 -0.54704922 2.12129319 41 | H -0.98735797 -1.23300315 1.71752683 42 | H -1.73600745 0.29783212 1.98025125 43 | * 44 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/10025_2/10025_2-TSOPT.xyz: -------------------------------------------------------------------------------- 1 | 22 2 | Coordinates from ORCA-job 10025_2-TSOPT 3 | C 0.14841751950263 0.28949583008538 -1.13642193886310 4 | C 1.87570239517564 0.71347274693701 0.62591127235881 5 | C -0.18389686101912 -1.06603764902239 -1.34911435008146 6 | C 1.55303709058902 0.76896445125636 -0.83395911438995 7 | C -2.84937739764813 0.57357518100977 -0.30848973264534 8 | C 2.23902955875251 -0.57135412019223 1.27671726562597 9 | C -1.64692765250997 -0.30061406010372 -0.11236285037317 10 | N -1.30605301882231 -0.50410986476896 1.21219957926201 11 | N -1.42212142260403 -1.33407298552218 -1.00616892652741 12 | H -0.51962688791047 0.99989771001956 -1.60725556195065 13 | H 1.85660429802563 1.62285590031564 1.21445910801769 14 | H 0.47988825421336 -1.83471311589862 -1.75642974854496 15 | H 1.69485012958404 1.78441348732222 -1.20879380190259 16 | H 2.26197877418808 0.12745726903933 -1.38045570096448 17 | H -2.89538293295655 0.93471989719204 -1.33430151482253 18 | H -2.85362383726448 1.42032520293377 0.37897453756000 19 | H -3.73740975518915 -0.03485448623648 -0.11896487521678 20 | H 3.31646281124648 -0.77535309753081 1.19998850931431 21 | H 1.73992184346402 -1.42020490279429 0.79439805559126 22 | H 1.99244601788255 -0.58573905575191 2.34102887314855 23 | H -0.53870331226035 -1.14403791940229 1.34942766205154 24 | H -1.20521561443938 0.33591358111281 1.75961326335227 25 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/10025_2/10025_2.xyz: -------------------------------------------------------------------------------- 1 | 22 2 | 3 | C 0.2157076 0.38432434 -1.00298645 4 | C 1.9948926 0.70297556 0.57749622 5 | C -0.08307752 -1.00203671 -1.2738771 6 | C 1.6543562 0.8737096 -0.86881131 7 | C -2.75820424 0.52664622 -0.45639291 8 | C 2.32385839 -0.62688438 1.14539707 9 | C -1.59381494 -0.30253712 0.02183179 10 | N -1.52112617 -0.46307497 1.36238454 11 | N -1.20770908 -1.42035154 -0.76066876 12 | H -0.50524318 1.10645627 -1.35783398 13 | H 1.56509056 1.42827021 1.25628033 14 | H 0.54018777 -1.6916835 -1.84709303 15 | H 1.72155991 1.92585572 -1.15524435 16 | H 2.36095611 0.31788249 -1.50013529 17 | H -2.73627203 0.6479439 -1.53589855 18 | H -2.78484765 1.50459012 0.02461625 19 | H -3.67010242 -0.01515032 -0.20066144 20 | H 2.98558706 -1.19191062 0.48470428 21 | H 1.41111632 -1.22280502 1.26782143 22 | H 2.81045013 -0.54704922 2.12129319 23 | H -0.98735797 -1.23300315 1.71752683 24 | H -1.73600745 0.29783212 1.98025125 25 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/105772_0/105772_0-TSOPT.in: -------------------------------------------------------------------------------- 1 | ! wB97X D4 def2-TZVP CPCM(DMSO) defgrid2 OptTS Freq 2 | 3 | %scf 4 | MaxIter 500 5 | end 6 | 7 | %pal 8 | nproc 24 9 | end 10 | 11 | %maxcore 2000 12 | 13 | %geom 14 | Calc_Hess true 15 | Recalc_Hess 1 16 | end 17 | 18 | %base "105772_0-TSOPT" 19 | 20 | *xyz 0 2 21 | C -0.41630243 0.03291846 -0.85518934 22 | C 0.45346222 -0.58137918 2.11832962 23 | C 0.23169485 -0.39180143 -1.92835555 24 | C 0.28967694 0.89850957 0.16286611 25 | C -1.86150982 -0.26846731 -0.59672250 26 | N 0.00488405 0.55861756 1.54556992 27 | O 1.10797114 -1.42468793 1.55199050 28 | H 4.69278417 -0.48269078 -0.11554457 29 | H 0.15617649 -0.66947690 3.17948809 30 | H 1.28595887 -0.18101148 -2.06389843 31 | H -0.26291677 -0.97248278 -2.69813480 32 | H -0.03159649 1.93471391 0.02589792 33 | H 1.36796000 0.85494824 -0.00975990 34 | H -1.96615662 -0.91638929 0.27693346 35 | H -2.31695993 -0.77001483 -1.44973228 36 | H -2.42736146 0.64487290 -0.38866920 37 | H -0.49790651 1.20844588 2.12109126 38 | * 39 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/105772_0/105772_0-TSOPT.xyz: -------------------------------------------------------------------------------- 1 | 17 2 | Coordinates from ORCA-job 105772_0-TSOPT 3 | C -0.41630242535718 0.03291845776711 -0.85518933916018 4 | C 0.45346221579508 -0.58137917618038 2.11832961987630 5 | C 0.23169485455909 -0.39180142552924 -1.92835554802735 6 | C 0.28967694295473 0.89850957409094 0.16286610608020 7 | C -1.86150981602200 -0.26846730897021 -0.59672250394354 8 | N 0.00488404775173 0.55861755689091 1.54556991820460 9 | O 1.10797113603021 -1.42468792564862 1.55199050300065 10 | H 4.69278417455649 -0.48269077945189 -0.11554457023671 11 | H 0.15617649118332 -0.66947690176198 3.17948808548172 12 | H 1.28595887391204 -0.18101147674156 -2.06389843255302 13 | H -0.26291676892496 -0.97248278245473 -2.69813479925413 14 | H -0.03159648667880 1.93471391087300 0.02589792131207 15 | H 1.36796000038931 0.85494823587739 -0.00975989686175 16 | H -1.96615661674891 -0.91638929230762 0.27693346029044 17 | H -2.31695993104549 -0.77001483068445 -1.44973228045413 18 | H -2.42736146063763 0.64487289514058 -0.38866920339814 19 | H -0.49790651171702 1.20844587909075 2.12109125964297 20 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/105772_0/105772_0.xyz: -------------------------------------------------------------------------------- 1 | 17 2 | 3 | C -0.41764402 -0.00505847 -0.83216249 4 | C 0.21682055 -0.79847268 2.00238696 5 | C 0.27618036 -0.57367766 -1.81402706 6 | C 0.29070363 0.95073413 0.09056017 7 | C -1.89346927 -0.20670272 -0.62733855 8 | N 0.33992749 0.48741779 1.53895253 9 | O -0.15088503 -1.82679806 1.36463173 10 | H 4.49867615 0.40128125 0.20873347 11 | H 0.4911548 -0.80034449 3.10206255 12 | H 1.33333244 -0.36588198 -1.93288249 13 | H -0.17773992 -1.26730599 -2.51188158 14 | H -0.21744483 1.97749366 0.06864464 15 | H 1.35353824 1.10160923 -0.28908936 16 | H -2.08697663 -0.65299069 0.34786918 17 | H -2.30777294 -0.86641938 -1.39039794 18 | H -2.4318406 0.7416795 -0.670357 19 | H 0.6932983 1.17806117 2.22045554 20 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/586_0/586_0-TSOPT.in: -------------------------------------------------------------------------------- 1 | ! wB97X D4 def2-TZVP CPCM(DMSO) defgrid2 OptTS Freq 2 | 3 | %scf 4 | MaxIter 500 5 | end 6 | 7 | %pal 8 | nproc 24 9 | end 10 | 11 | %maxcore 2000 12 | 13 | %geom 14 | Calc_Hess true 15 | Recalc_Hess 1 16 | end 17 | 18 | %base "586_0-TSOPT" 19 | 20 | *xyz 0 2 21 | C 0.29052396 -0.99802254 0.54641318 22 | C -0.05107471 1.54906552 -0.24445350 23 | C -0.68191974 -0.38549663 1.46699601 24 | C 0.74689737 -0.89842338 -1.67407037 25 | C -1.08093470 0.92704236 0.63892759 26 | N -0.14764373 -1.46754442 -0.64862561 27 | C 1.55421992 -0.41846422 0.43631099 28 | C 1.64860527 0.02280265 -0.88708601 29 | H -0.36470276 1.98009865 -1.18238175 30 | H 0.75198510 2.07349236 0.23502813 31 | H -0.21836811 -0.10717265 2.40933787 32 | H -1.57092004 -0.99103582 1.64299179 33 | H 0.19888752 -0.36912139 -2.45005453 34 | H 1.33856053 -1.67950172 -2.15301701 35 | H -1.94185227 0.64794742 0.02719800 36 | H -1.42976407 1.66610013 1.36935337 37 | H -1.13563038 -1.53886805 -0.81048509 38 | H 2.09313083 -0.01289828 1.27761694 39 | * 40 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/586_0/586_0.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | 3 | C 0.29052396 -0.99802254 0.54641318 4 | C -0.05107471 1.54906552 -0.2444535 5 | C -0.68191974 -0.38549663 1.46699601 6 | C 0.74689737 -0.89842338 -1.67407037 7 | C -1.0809347 0.92704236 0.63892759 8 | N -0.14764373 -1.46754442 -0.64862561 9 | C 1.55421992 -0.41846422 0.43631099 10 | C 1.64860527 0.02280265 -0.88708601 11 | H -0.36470276 1.98009865 -1.18238175 12 | H 0.7519851 2.07349236 0.23502813 13 | H -0.21836811 -0.10717265 2.40933787 14 | H -1.57092004 -0.99103582 1.64299179 15 | H 0.19888752 -0.36912139 -2.45005453 16 | H 1.33856053 -1.67950172 -2.15301701 17 | H -1.94185227 0.64794742 0.027198 18 | H -1.42976407 1.66610013 1.36935337 19 | H -1.13563038 -1.53886805 -0.81048509 20 | H 2.09313083 -0.01289828 1.27761694 21 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/70099_1/70099_1-TSOPT.in: -------------------------------------------------------------------------------- 1 | ! wB97X D4 def2-TZVP CPCM(DMSO) defgrid2 OptTS Freq 2 | 3 | %scf 4 | MaxIter 500 5 | end 6 | 7 | %pal 8 | nproc 24 9 | end 10 | 11 | %maxcore 2000 12 | 13 | %geom 14 | Calc_Hess true 15 | Recalc_Hess 1 16 | end 17 | 18 | %base "70099_1-TSOPT" 19 | 20 | *xyz 0 2 21 | C 0.58788894 0.67623236 -1.24134147 22 | N -0.68935335 1.16036633 -0.76933616 23 | N 0.40507991 -2.31040883 -0.24438249 24 | C -1.26035432 0.44347757 0.14625213 25 | N 0.19815811 2.02651273 1.58056069 26 | N -1.81010280 -0.21889884 0.93911276 27 | H 0.17326952 1.67758108 2.55685029 28 | H -0.70897028 2.52233973 1.54039580 29 | H 0.88521460 1.26969241 -2.09975139 30 | H 0.54206862 -0.39068242 -1.48706614 31 | H 1.33859493 0.77300072 -0.45096990 32 | H -0.28842920 -2.98929707 -0.64496354 33 | H -0.11777667 -1.61893773 0.40186950 34 | H 0.98824871 -2.89219743 0.36970209 35 | * 36 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/70099_1/70099_1-TSOPT.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | Coordinates from ORCA-job 70099_1-TSOPT 3 | C 0.58788894000000 0.67623236000000 -1.24134147000000 4 | N -0.68935335000000 1.16036633000000 -0.76933616000000 5 | N 0.40507991000000 -2.31040883000000 -0.24438249000000 6 | C -1.26035432000000 0.44347757000000 0.14625213000000 7 | N 0.19815811000000 2.02651273000000 1.58056069000000 8 | N -1.81010280000000 -0.21889884000000 0.93911276000000 9 | H 0.17326952000000 1.67758108000000 2.55685029000000 10 | H -0.70897028000000 2.52233973000000 1.54039580000000 11 | H 0.88521460000000 1.26969241000000 -2.09975139000000 12 | H 0.54206862000000 -0.39068242000000 -1.48706614000000 13 | H 1.33859493000000 0.77300072000000 -0.45096990000000 14 | H -0.28842920000000 -2.98929707000000 -0.64496354000000 15 | H -0.11777667000000 -1.61893773000000 0.40186950000000 16 | H 0.98824871000000 -2.89219743000000 0.36970209000000 17 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/70099_1/70099_1.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | 3 | C 0.58788894 0.67623236 -1.24134147 4 | N -0.68935335 1.16036633 -0.76933616 5 | N 0.40507991 -2.31040883 -0.24438249 6 | C -1.26035432 0.44347757 0.14625213 7 | N 0.19815811 2.02651273 1.58056069 8 | N -1.8101028 -0.21889884 0.93911276 9 | H 0.17326952 1.67758108 2.55685029 10 | H -0.70897028 2.52233973 1.5403958 11 | H 0.8852146 1.26969241 -2.09975139 12 | H 0.54206862 -0.39068242 -1.48706614 13 | H 1.33859493 0.77300072 -0.4509699 14 | H -0.2884292 -2.98929707 -0.64496354 15 | H -0.11777667 -1.61893773 0.4018695 16 | H 0.98824871 -2.89219743 0.36970209 17 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/SINGLE_RXN.p: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/pyTEST_Example/Class-Refinement-Example/SINGLE_RXN.p -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/job_test.submit: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # 3 | #SBATCH --job-name=classy-yarp 4 | #SBATCH --output=runyarp.1.out 5 | #SBATCH --error=runyarp.1.err 6 | #SBATCH -A standby 7 | #SBATCH --nodes=1 8 | #SBATCH --mem 5GB 9 | #SBATCH -n 1 10 | #SBATCH --time 4:00:00 11 | 12 | # activate a correct anaconda environment 13 | module load anaconda/2022.10-py39 14 | #source activate /scratch/negishi/li1724/100624_copy_yarp/ 15 | conda activate copy-classy-yarp 16 | module load intel-mkl 17 | module load openmpi 18 | 19 | # Load environment for Gaussian 20 | #python /home/li1724/Classy-YARP-Codes_100724-Github/main_dft.py parameters.yaml 21 | #python main_dft.py parameters.yaml 22 | #dir=/home/li1724/Classy-YARP-Codes_012525/GitClone/ 23 | dir=/scratch/negishi/li1724/013125-yarp/yarp/pyTEST_Example/ 24 | python $dir/class_refinement.py parameters.yaml 25 | 26 | wait 27 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/reaction_xyz/10025_2.xyz: -------------------------------------------------------------------------------- 1 | 22 2 | 3 | C 0.2157076 0.38432434 -1.00298645 4 | C 1.9948926 0.70297556 0.57749622 5 | C -0.08307752 -1.00203671 -1.2738771 6 | C 1.6543562 0.8737096 -0.86881131 7 | C -2.75820424 0.52664622 -0.45639291 8 | C 2.32385839 -0.62688438 1.14539707 9 | C -1.59381494 -0.30253712 0.02183179 10 | N -1.52112617 -0.46307497 1.36238454 11 | N -1.20770908 -1.42035154 -0.76066876 12 | H -0.50524318 1.10645627 -1.35783398 13 | H 1.56509056 1.42827021 1.25628033 14 | H 0.54018777 -1.6916835 -1.84709303 15 | H 1.72155991 1.92585572 -1.15524435 16 | H 2.36095611 0.31788249 -1.50013529 17 | H -2.73627203 0.6479439 -1.53589855 18 | H -2.78484765 1.50459012 0.02461625 19 | H -3.67010242 -0.01515032 -0.20066144 20 | H 2.98558706 -1.19191062 0.48470428 21 | H 1.41111632 -1.22280502 1.26782143 22 | H 2.81045013 -0.54704922 2.12129319 23 | H -0.98735797 -1.23300315 1.71752683 24 | H -1.73600745 0.29783212 1.98025125 25 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/reaction_xyz/105772_0.xyz: -------------------------------------------------------------------------------- 1 | 17 2 | 3 | C -0.41764402 -0.00505847 -0.83216249 4 | C 0.21682055 -0.79847268 2.00238696 5 | C 0.27618036 -0.57367766 -1.81402706 6 | C 0.29070363 0.95073413 0.09056017 7 | C -1.89346927 -0.20670272 -0.62733855 8 | N 0.33992749 0.48741779 1.53895253 9 | O -0.15088503 -1.82679806 1.36463173 10 | H 4.49867615 0.40128125 0.20873347 11 | H 0.4911548 -0.80034449 3.10206255 12 | H 1.33333244 -0.36588198 -1.93288249 13 | H -0.17773992 -1.26730599 -2.51188158 14 | H -0.21744483 1.97749366 0.06864464 15 | H 1.35353824 1.10160923 -0.28908936 16 | H -2.08697663 -0.65299069 0.34786918 17 | H -2.30777294 -0.86641938 -1.39039794 18 | H -2.4318406 0.7416795 -0.670357 19 | H 0.6932983 1.17806117 2.22045554 20 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/reaction_xyz/112_0.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | 3 | C -0.70912305 1.10169732 0.28474079 4 | C -0.94446854 -0.26203785 0.6448362 5 | C 1.18900172 -0.93938936 -0.61351573 6 | C 0.58638689 0.80868733 -0.28029935 7 | C 1.73553381 0.08650756 0.3232392 8 | C -1.7666506 0.16231495 -0.44665607 9 | O 0.30162432 -1.75644785 -0.27590497 10 | H -0.98788335 -0.85705213 1.53653529 11 | H -1.0298609 2.02337076 0.7581149 12 | H 1.60153882 -0.93514788 -1.62595536 13 | H 2.71345032 0.47217647 0.07618687 14 | H 1.60894557 -0.13624654 1.37926296 15 | H -1.47732721 -0.14858298 -1.44282645 16 | H -2.82116778 0.3801502 -0.31775829 17 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/reaction_xyz/586_0.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | 3 | C 0.29052396 -0.99802254 0.54641318 4 | C -0.05107471 1.54906552 -0.2444535 5 | C -0.68191974 -0.38549663 1.46699601 6 | C 0.74689737 -0.89842338 -1.67407037 7 | C -1.0809347 0.92704236 0.63892759 8 | N -0.14764373 -1.46754442 -0.64862561 9 | C 1.55421992 -0.41846422 0.43631099 10 | C 1.64860527 0.02280265 -0.88708601 11 | H -0.36470276 1.98009865 -1.18238175 12 | H 0.7519851 2.07349236 0.23502813 13 | H -0.21836811 -0.10717265 2.40933787 14 | H -1.57092004 -0.99103582 1.64299179 15 | H 0.19888752 -0.36912139 -2.45005453 16 | H 1.33856053 -1.67950172 -2.15301701 17 | H -1.94185227 0.64794742 0.027198 18 | H -1.42976407 1.66610013 1.36935337 19 | H -1.13563038 -1.53886805 -0.81048509 20 | H 2.09313083 -0.01289828 1.27761694 21 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/reaction_xyz/70099_1.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | 3 | C 0.58788894 0.67623236 -1.24134147 4 | N -0.68935335 1.16036633 -0.76933616 5 | N 0.40507991 -2.31040883 -0.24438249 6 | C -1.26035432 0.44347757 0.14625213 7 | N 0.19815811 2.02651273 1.58056069 8 | N -1.8101028 -0.21889884 0.93911276 9 | H 0.17326952 1.67758108 2.55685029 10 | H -0.70897028 2.52233973 1.5403958 11 | H 0.8852146 1.26969241 -2.09975139 12 | H 0.54206862 -0.39068242 -1.48706614 13 | H 1.33859493 0.77300072 -0.4509699 14 | H -0.2884292 -2.98929707 -0.64496354 15 | H -0.11777667 -1.61893773 0.4018695 16 | H 0.98824871 -2.89219743 0.36970209 17 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/reaction_xyz/70635_0.xyz: -------------------------------------------------------------------------------- 1 | 17 2 | 3 | C -0.14573867 -1.17989547 0.3005922 4 | C -1.57115471 -0.89920282 0.03940172 5 | C 0.12273075 0.96532005 -1.66965048 6 | C 0.46834396 0.80347442 -0.23458194 7 | C -0.94770119 1.17105312 -0.61519764 8 | C 1.61101109 0.96932779 0.48633103 9 | N 0.10796818 -1.72793071 1.54583999 10 | N -1.98723264 0.21363629 -0.4312309 11 | H 0.52145634 -1.54436618 -0.46916651 12 | H -1.26774776 2.18123066 -0.40502875 13 | H -2.32471854 -1.63844815 0.31616125 14 | H 0.01362093 0.08053565 -2.28475762 15 | H 0.49789256 1.83611301 -2.19117518 16 | H 2.55594404 1.17034385 -0.00327427 17 | H 1.6384835 0.77444441 1.54715448 18 | H 1.07739228 -1.8957536 1.75676886 19 | H -0.37055012 -1.27988232 2.31181376 20 | -------------------------------------------------------------------------------- /pyTEST_Example/Class-Refinement-Example/reaction_xyz/75482_0.xyz: -------------------------------------------------------------------------------- 1 | 21 2 | 3 | C -0.16143291 1.76597638 0.20478333 4 | C -1.01979408 -0.51974182 0.05260809 5 | C -0.5046309 -1.85889532 0.51608324 6 | C 1.16605355 -0.58834668 -0.17927021 7 | C 1.59207482 0.25963728 0.9643991 8 | C -1.42025969 -0.56309541 -1.38347501 9 | N 1.09827012 1.65578873 0.78887012 10 | O -0.18846612 2.16808271 -1.09271271 11 | O 0.87836669 -1.91271666 0.13864604 12 | H -0.95894217 2.22615119 0.78316958 13 | H -1.78852263 -0.12275555 0.71260865 14 | H 1.7614852 -0.47895233 -1.08167017 15 | H -1.03302761 -2.68366484 0.02863848 16 | H -0.5828867 -1.99921059 1.59746405 17 | H 2.67877818 0.29257728 1.0704528 18 | H 1.19793067 -0.1672819 1.89511471 19 | H -1.58188471 0.42443607 -1.80414669 20 | H -2.34995059 -1.13809315 -1.48415832 21 | H -0.65887348 -1.07064014 -1.9761899 22 | H 1.15949605 2.161121 1.66214078 23 | H 0.71621633 2.14962376 -1.41335595 24 | -------------------------------------------------------------------------------- /pyTEST_Example/ML.py: -------------------------------------------------------------------------------- 1 | from typing import Dict, List 2 | import torch 3 | import torch.nn as nn 4 | from torch import Tensor 5 | 6 | 7 | elem_to_num = {'H':1, 'C':6, 'N':7, 'O':8} 8 | 9 | class EnsembledModel(nn.Module): 10 | def __init__(self, models: List, x=['coord', 'numbers', 'charge'], out=['energy'], detach=False): 11 | super().__init__() 12 | self.models = nn.ModuleList(models) 13 | self.x = x 14 | self.out = out 15 | self.detach = detach 16 | 17 | def forward(self, data: Dict[str, Tensor]) -> Dict[str, Tensor]: 18 | res : List[Dict[str, Tensor]] = [] 19 | for model in self.models: 20 | _in = dict() 21 | for k in data: 22 | if k in self.x: 23 | _in[k] = data[k] 24 | _out = model(_in) 25 | _r = dict() 26 | for k in _out: 27 | if k in self.out: 28 | _r[k] = _out[k] 29 | if self.detach: 30 | _r[k] = _r[k].detach() 31 | res.append(_r) 32 | 33 | for k in res[0]: 34 | v = [] 35 | for x in res: 36 | v.append(x[k]) 37 | vv = torch.stack(v, dim=0) 38 | data[k] = vv.mean(dim=0) 39 | data[k + '_std'] = vv.std(dim=0) 40 | return data 41 | -------------------------------------------------------------------------------- /pyTEST_Example/RESULT/YARPrun.log: -------------------------------------------------------------------------------- 1 | running PYSIS job HGCIXCUEYOPUTN on PID 1467610 2 | PYSIS job HGCIXCUEYOPUTN is finished. 3 | running PYSIS job KAKZBPTYRLMSJV-VGGSQFUCUMXWEO on PID 1467610 4 | PYSIS job KAKZBPTYRLMSJV-VGGSQFUCUMXWEO is finished. 5 | running CREST job HGCIXCUEYOPUTN on PID 1467610 6 | -------------------------------------------------------------------------------- /pyTEST_Example/bin/DFT_models/Delta2_model_1.jpt: 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detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 300 # opt steps first node 23 | FINAL_OPT 300 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 12 # including endpoints 27 | TS_FINAL_OPT 150 # Final TS opt 28 | TS_CONV_TOL 0.0001 # TS ene conv 29 | TS_GRAD_MAX_TOL 0.005 # TS grad conv 30 | --------------------------------------------------------- 31 | -------------------------------------------------------------------------------- /pyTEST_Example/bin/poor_model.sav: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/pyTEST_Example/bin/poor_model.sav -------------------------------------------------------------------------------- /pyTEST_Example/bin/rich_model.sav: 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18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 2.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 0 # opt steps first node 23 | FINAL_OPT 150 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 30 # including endpoints 27 | --------------------------------------------------------- 28 | -------------------------------------------------------------------------------- /pyTEST_Example/constants.py: -------------------------------------------------------------------------------- 1 | class Constants: 2 | 3 | n_a = 6.022140857E23 # molecules mol-1 4 | 5 | ha_to_kcalmol = ha2kcalmol = 627.509 # Hartree^-1 kcal mol^-1 6 | ha_to_kJmol = ha2kJmol = 2625.50 # Hartree^-1 kJ mol^-1 7 | 8 | ha_to_J = ha_to_kJmol * 1000 / n_a # Hartree^-1 J 9 | J_to_ha = 1.0 / ha_to_J # J Hartree^-1 10 | 11 | eV_to_ha = eV2ha = 0.0367493 # Hartree eV^-1 12 | ha_to_eV = ha2eV = 1.0 / eV_to_ha # eV Hartree^-1 13 | 14 | kcal_to_kJ = kcal2kJ = 4.184 # kJ kcal^-1 15 | 16 | rad_to_deg = 57.29577951308232087679815 # deg rad^-1 17 | 18 | a0_to_ang = a02ang = 0.529177 # Å bohr^-1 19 | ang_to_a0 = ang2a0 = 1.0 / a0_to_ang # bohr Å^-1 20 | ang_to_nm = 0.1 # nm ang^-1 21 | ang_to_pm = 100 # pm ang^-1 22 | ang_to_m = 1E-10 # m ang^-1 23 | a0_to_m = a0_to_ang * ang_to_m # Å m^-1 24 | 25 | per_cm_to_hz = c_in_cm = 299792458 * 100 # cm s^-1 26 | 27 | amu_to_kg = 1.66053906660E-27 # kg amu^-1 28 | amu_to_me = 1822.888486209 # m_e amu^-1 29 | 30 | atm_to_pa = 101325 # Pa atm^-1 31 | dm_to_m = 0.1 # m dm^-1 32 | -------------------------------------------------------------------------------- /pyTEST_Example/read_yarp_reaction.py: -------------------------------------------------------------------------------- 1 | import pickle 2 | import os, sys 3 | 4 | data=pickle.load(open(sys.argv[1], 'rb')) 5 | for i in data: 6 | print(i.product_inchi) 7 | print(i.reactant_dft_opt) 8 | print(i.TS_dft) 9 | -------------------------------------------------------------------------------- /pyTEST_Example/readme.md: -------------------------------------------------------------------------------- 1 | # pytest folder for different applications/calculators 2 | ## Currently, it supports: 3 | * base (`./`) 4 | * Zimmerman Grow-String Method (**GSM**) calculator (`GSM/`) 5 | ## How to extend 6 | * Create your own folder here, for example `XTB`, that is for testing using `XTB` as the geometry optimization calculator 7 | * copy `template.yaml` to the newly created folder 8 | * modify `template.yaml` in the new folder, add the keyword related to your intended test 9 | * for example, add `XTB_Calculator: XTB` to use XTB as the calculator 10 | * In `test_rxn.py`, add your new folder to the `CASES` in `test_file()` function 11 | * for example, if you want the base, the GSM, and your `XTB` get tested, you should have `CASES = ["", "GSM", "XTB"]` 12 | * run `pytest -s` 13 | ## Issues 14 | * GSM test requires Intel OneMKL library, need to install it (tested on Negishi@Purdue) 15 | -------------------------------------------------------------------------------- /pyTEST_Example/scripts/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /pyTEST_Example/scripts/ograd: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # The path to ORCA should be added to .bashrc or exported in command line 3 | 4 | if [ -z $2 ] 5 | then 6 | echo " need two arguments! " 7 | exit 8 | fi 9 | 10 | #echo " in ograd: $1 $2 " 11 | 12 | ofile=$SLURM_LOCAL_SCRATCH/orcain$1.in 13 | ofileout=scratch/orcain$1.out 14 | molfile=scratch/structure$1 15 | ncpu=$2 16 | 17 | #echo " ofile: $ofile ofileout: $ofileout molfile: $molfile ncpu: $ncpu" 18 | 19 | ########## DFT settings: ################# 20 | #echo '! DFT B3LYP ENGRAD 6-31G*' > $ofile 21 | echo '! B97-3c ENGRAD' > $ofile 22 | echo '! nomoprint' >> $ofile 23 | echo '%scf' >> $ofile 24 | echo ' maxiter 200' >> $ofile 25 | echo 'end' >> $ofile 26 | # charge and spin multiplicity 27 | echo '* xyz 0 1' >> $ofile 28 | cat $molfile >> $ofile 29 | echo '*' >> $ofile 30 | 31 | #echo "running: orca $ofile > $ofileout" 32 | orca $ofile > $ofileout 33 | -------------------------------------------------------------------------------- /pyTEST_Example/scripts/ograd_xtb: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | if [ -z $2 ] 4 | then 5 | echo " need two arguments! " 6 | exit 7 | fi 8 | 9 | ofile=orcain$1.in 10 | ofileout=orcain$1.out 11 | molfile=structure$1 12 | ncpu=$2 13 | 14 | basename="${ofile%.*}" 15 | 16 | ########## XTB settings: ################# 17 | cd scratch 18 | wc -l < $molfile > $ofile.xyz 19 | echo "Dummy for XTB/TM calculation" >> $ofile.xyz 20 | cat $molfile >> $ofile.xyz 21 | 22 | 23 | -------------------------------------------------------------------------------- /pyTEST_Example/scripts/qend: -------------------------------------------------------------------------------- 1 | $end 2 | -------------------------------------------------------------------------------- /pyTEST_Example/scripts/qstart: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE FORCE 3 | METHOD B3LYP 4 | SCF_MAX_CYCLES 150 5 | BASIS 6-31G* 6 | WAVEFUNCTION_ANALYSIS FALSE 7 | GEOM_OPT_MAX_CYCLES 300 8 | xc_grid 1 9 | scf_convergence 6 10 | SYM_IGNORE TRUE 11 | SYMMETRY FALSE 12 | molden_format true 13 | $end 14 | 15 | $molecule 16 | 0 1 17 | -------------------------------------------------------------------------------- /pyTEST_Example/template.yaml: -------------------------------------------------------------------------------- 1 | verbose: False 2 | # Note that a bimolecular reaction is recommended to use .xyz or .mol file 3 | # Enumetation part 4 | #input: {current_path}/reaction_xyz/DA.xyz # (1) The input folder with .xyz or .mol file (2) a text file with multiple smiles 5 | input: reaction_xyz # (1) The input folder with .xyz or .mol file (2) a text file with multiple smiles 6 | scratch: {current_path}/RESULT/ # The output folder with reaction geometry for constructing reaction network. 7 | reaction_data: DA.p 8 | n_break: 1 # Indicate the number of breaking bonds 9 | form_all: False # Forming all possible bonds (matters for lone paired electrons (oxygen, sulfur, and other similar atoms)) (default: 0) 10 | lewis_criteria: 5.0 # the criteria to find the products 11 | ff: uff # force field for driving the reaction coordinate 12 | lot: gfn2 13 | crest_quick: False 14 | method: crest 15 | enumeration: False # if you only have reactant, you will need to do enumeration. Ohterwise, you need to provide reaction geometry. 16 | n_conf: 5 17 | nconf_dft: 5 18 | strategy: 2 19 | nprocs: 1 20 | c_nprocs: 1 21 | mem: 1 # in GB 22 | #xtb: {conda_path}/xtb 23 | xtb: xtb 24 | crest: {conda_path}/crest 25 | opt_level: vtight 26 | crest_quick: False 27 | opt: False 28 | pysis_wt: 3600 29 | select: network 30 | charge: 0 31 | multiplicity: 1 32 | skip_low_IRC: False 33 | skip_low_TS: False 34 | constrained_TS: True 35 | model_path: {model_path} 36 | gsm_inp: {gsm_file_path} 37 | 38 | package: ORCA #Gaussian or ORCA 39 | dft_nprocs: 4 40 | dft_lot: UHF 6-31G 41 | dft_wt: 4 42 | ppn: 8 43 | partition: standby 44 | dft_njobs: 1 45 | hess_recalc: 3 46 | dft_irc: True 47 | backward_DE: False 48 | dielectric: 95.3 49 | solvation: CPCM/read 50 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = ["setuptools>=61.0"] 3 | build-backend = "setuptools.build_meta" 4 | 5 | [project] 6 | name = "yarp" 7 | version = "0.0.1" 8 | authors = [ 9 | { name="Savoie Research Group", email="brettsavoie@gmail.com" }, 10 | ] 11 | description = "An object-oriented (i.e., classy) refactoring of the YARP framework." 12 | readme = "README.md" 13 | requires-python = ">=3.8" 14 | classifiers = [ 15 | "Programming Language :: Python :: 3", 16 | "License :: OSI Approved :: BSD License", 17 | "Operating System :: OS Independent", 18 | ] 19 | 20 | [project.urls] 21 | "Homepage" = "https://github.com/Savoie-Research-Group/yarp" 22 | "Bug Tracker" = "https://github.com/Savoie-Research-Group/yarp/issues" 23 | -------------------------------------------------------------------------------- /pytest_requirements.txt: -------------------------------------------------------------------------------- 1 | pytest>=6.0 -------------------------------------------------------------------------------- /reaction/.job_dft.submit.swp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/.job_dft.submit.swp -------------------------------------------------------------------------------- /reaction/.opt.xtboptok: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/.opt.xtboptok -------------------------------------------------------------------------------- /reaction/.xtboptok: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/.xtboptok -------------------------------------------------------------------------------- /reaction/DA.p: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/DA.p -------------------------------------------------------------------------------- /reaction/DA/IRC-record.txt: -------------------------------------------------------------------------------- 1 | reaction R P type barrier 2 | KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0 C=CC=C.C=C C1CCC=CC1 intended 6.747132 3 | -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-TS.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.67199385 -1.41250426 -0.45775643 4 | C -0.67844841 -1.41704821 -0.43359965 5 | H 1.24202345 -1.94448516 0.28416925 6 | H 1.20549881 -1.11379641 -1.34296004 7 | H -1.21798998 -1.95273065 0.32819611 8 | H -1.24527648 -1.12203295 -1.29911178 9 | C -1.4262144 0.51575739 0.59882636 10 | C -0.7150537 1.41084028 -0.12684168 11 | C 0.70063747 1.41555082 -0.15213155 12 | C 1.44319403 0.5252878 0.54755511 13 | H -1.0210666 0.06090405 1.48364739 14 | H -2.49798165 0.45943155 0.49778496 15 | H -1.22333683 2.01144376 -0.8697054 16 | H 1.17805823 2.01943593 -0.9126023 17 | H 2.5110205 0.47608328 0.40829555 18 | H 1.07294168 0.0678628 1.44623411 19 | -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-TSguess.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.67444474 -1.44683252 -0.4366869 4 | C -0.67871561 -1.4528278 -0.40677496 5 | H 1.2416026 -1.9808878 0.30755125 6 | H 1.20310907 -1.20359987 -1.34141967 7 | H -1.20718658 -1.98905651 0.36391223 8 | H -1.24931331 -1.21649328 -1.28742498 9 | C -1.43362303 0.51892728 0.55613047 10 | C -0.71296477 1.45552957 -0.10871931 11 | C 0.70005144 1.4599185 -0.13157073 12 | C 1.44753183 0.52641628 0.50760026 13 | H -1.05482705 0.05051048 1.44475718 14 | H -2.5030038 0.48117105 0.4249184 15 | H -1.21357549 2.11953443 -0.80193155 16 | H 1.17386512 2.12815756 -0.83936084 17 | H 2.51245348 0.49648946 0.34264293 18 | H 1.10015134 0.05304319 1.40637622 19 | -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0_input.yaml: -------------------------------------------------------------------------------- 1 | geom: 2 | type: cart 3 | fn: /Users/hsu205/github/classy-yarp/reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-TS.xyz 4 | calc: 5 | type: xtb 6 | pal: 1 7 | mem: 4000 8 | charge: 0 9 | mult: 1 10 | irc: 11 | type: eulerpc 12 | forward: True 13 | backward: True 14 | downhill: False 15 | hessian_init: /Users/hsu205/github/classy-yarp/reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/ts_final_hessian.h5 16 | endopt: 17 | fragments: False 18 | do_hess: False 19 | thresh: gau 20 | max_cycles: 300 21 | -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/P.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.68356 -1.21092 0.33495 4 | C -0.68275 -1.21124 -0.33465 5 | H 0.53247 -1.17506 1.43709 6 | H 1.25479 -2.13225 0.09131 7 | H -1.25364 -2.13282 -0.09096 8 | H -0.53174 -1.17541 -1.43673 9 | C -1.48157 0.0185 0.13102 10 | C -0.66912 1.29191 0.07219 11 | C 0.66868 1.29213 -0.07233 12 | C 1.48174 0.01916 -0.13082 13 | H -1.83175 -0.10476 1.17827 14 | H -2.37237 0.10444 -0.52696 15 | H -1.18945 2.24103 0.15658 16 | H 1.18859 2.24149 -0.157 17 | H 1.83203 -0.10409 -1.17807 18 | H 2.37247 0.10562 0.52712 19 | -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/R.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.68478788 -1.19829153 0.33548591 4 | C -0.68434499 -1.19850016 -0.33551471 5 | H 0.55237783 -1.1595414 1.41891648 6 | H 1.2282426 -2.11418583 0.0944476 7 | H -1.22751452 -2.11457515 -0.09455138 8 | H -0.5518888 -1.15960344 -1.41892582 9 | C -1.48359863 0.01901871 0.12144677 10 | C -0.65908393 1.2679597 0.05490035 11 | C 0.65860974 1.26819603 -0.05484021 12 | C 1.48359391 0.01955451 -0.12143446 13 | H -1.82365878 -0.12520748 1.15302992 14 | H -2.37804459 0.13778777 -0.49590626 15 | H -1.20501894 2.20009547 0.11189836 16 | H 1.20413269 2.20058612 -0.11246546 17 | H 1.82390717 -0.12455017 -1.15296758 18 | H 2.37789453 0.13874134 0.49600395 19 | -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/RUN.yaml: -------------------------------------------------------------------------------- 1 | assert: null 2 | barrier: null 3 | calc: 4 | charge: 0 5 | mem: 4000 6 | mult: 1 7 | pal: 1 8 | type: xtb 9 | cos: null 10 | endopt: 11 | T: 298.15 12 | do_hess: false 13 | dump: true 14 | fragments: false 15 | geom: 16 | coord_kwargs: {} 17 | type: redund 18 | max_cycles: 300 19 | overachieve_factor: 5 20 | p: 101325 21 | thresh: gau 22 | type: rfo 23 | geom: 24 | coord_kwargs: {} 25 | fn: /Users/hsu205/github/classy-yarp/reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0-TS.xyz 26 | type: cart 27 | glob: null 28 | interpol: null 29 | irc: 30 | backward: true 31 | downhill: false 32 | forward: true 33 | hessian_init: /Users/hsu205/github/classy-yarp/reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/ts_final_hessian.h5 34 | rms_grad_thresh: 0.001 35 | type: eulerpc 36 | md: null 37 | mdp: null 38 | opt: null 39 | perf: null 40 | precontr: null 41 | preopt: null 42 | scan: null 43 | shake: null 44 | stocastic: null 45 | tsopt: null 46 | version: 0.7.6.post2 47 | -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/backward_end_initial.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.65574027 -1.60805815 -0.55501584 4 | C -0.66438051 -1.61248771 -0.53139296 5 | H 1.24279343 -2.04903227 0.23301515 6 | H 1.20806968 -1.20418225 -1.38605014 7 | H -1.21989266 -2.05729145 0.27708622 8 | H -1.24878632 -1.21242393 -1.34208413 9 | C -1.48560820 0.68945678 0.69202286 10 | C -0.73045198 1.42390036 -0.12286411 11 | C 0.71607850 1.42871306 -0.14870586 12 | C 1.50472639 0.69940774 0.63860421 13 | H -1.06858675 0.10725890 1.49335573 14 | H -2.55983978 0.69401587 0.61852290 15 | H -1.21057699 2.02610849 -0.88397005 16 | H 1.16469537 2.03400704 -0.92640691 17 | H 2.57559337 0.71110284 0.52678329 18 | H 1.12047358 0.11455122 1.45425653 -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/backward_end_opt.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -17.82301231 , 3 | C 0.65770239 -2.01132709 -0.60916328 4 | C -0.65555417 -1.95393688 -0.67921619 5 | H 1.16544209 -2.50719166 0.20202687 6 | H 1.28929782 -1.56420130 -1.35854927 7 | H -1.28745558 -2.39888976 0.07181037 8 | H -1.16263375 -1.45808281 -1.48994260 9 | C -1.49392541 0.90394532 0.78927402 10 | C -0.75071193 1.61328710 -0.05311337 11 | C 0.70139087 1.62718782 -0.11567253 12 | C 1.52697901 0.93257666 0.65959597 13 | H -1.06315640 0.25284566 1.52958639 14 | H -2.56920393 0.95088822 0.76683193 15 | H -1.24385509 2.25078488 -0.77677468 16 | H 1.11844303 2.27355053 -0.87823312 17 | H 2.59535100 0.99884753 0.54534030 18 | H 1.17193747 0.27476234 1.43335609 -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/backward_first.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.66430502 -1.45091077 -0.47733164 4 | C -0.67120820 -1.45540280 -0.45343989 5 | H 1.24379178 -1.94674554 0.28317315 6 | H 1.20733168 -1.11401565 -1.34373945 7 | H -1.21977839 -1.95500753 0.32726028 8 | H -1.24713230 -1.12226272 -1.29982465 9 | C -1.44023954 0.55208131 0.61734085 10 | C -0.72086466 1.41084225 -0.12537376 11 | C 0.70649650 1.41559132 -0.15087195 12 | C 1.45763015 0.56170889 0.56556332 13 | H -1.02439507 0.05582796 1.47539029 14 | H -2.51140375 0.49462439 0.51670806 15 | H -1.22070703 2.00744909 -0.87742247 16 | H 1.17517834 2.01542161 -0.92022327 17 | H 2.52487543 0.51136510 0.42673025 18 | H 1.07600608 0.06280938 1.43786444 -------------------------------------------------------------------------------- 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1.49335573 14 | H -2.55983978 0.69401587 0.61852290 15 | H -1.21057699 2.02610849 -0.88397005 16 | H 1.16469537 2.03400704 -0.92640691 17 | H 2.57559337 0.71110284 0.52678329 18 | H 1.12047358 0.11455122 1.45425653 -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/finished_first.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.76883355 -1.07044598 -0.27238483 4 | C -0.77091063 -1.07559290 -0.24484541 5 | H 1.16412960 -1.94774357 0.24197577 6 | H 1.12133607 -1.10865548 -1.30481816 7 | H -1.14168592 -1.95543022 0.28325472 8 | H -1.15984092 -1.11632950 -1.26401698 9 | C -1.32623695 0.19026590 0.43536864 10 | C -0.66988153 1.39363058 -0.16382775 11 | C 0.65429225 1.39804418 -0.18748346 12 | C 1.33963915 0.19915353 0.38774084 13 | H -1.09234173 0.14236767 1.50537381 14 | H -2.41055856 0.22619440 0.33088834 15 | H -1.27411495 2.17746702 -0.58892663 16 | H 1.23771815 2.18583984 -0.63380076 17 | H 2.41927499 0.24230609 0.24461731 18 | H 1.14441911 0.14980486 1.46540719 -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/finished_irc_data.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/finished_irc_data.h5 -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/finished_last.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.65574027 -1.60805815 -0.55501584 4 | C -0.66438051 -1.61248771 -0.53139296 5 | H 1.24279343 -2.04903227 0.23301515 6 | H 1.20806968 -1.20418225 -1.38605014 7 | H -1.21989266 -2.05729145 0.27708622 8 | H -1.24878632 -1.21242393 -1.34208413 9 | C -1.48560820 0.68945678 0.69202286 10 | C -0.73045198 1.42390036 -0.12286411 11 | C 0.71607850 1.42871306 -0.14870586 12 | C 1.50472639 0.69940774 0.63860421 13 | H -1.06858675 0.10725890 1.49335573 14 | H -2.55983978 0.69401587 0.61852290 15 | H -1.21057699 2.02610849 -0.88397005 16 | H 1.16469537 2.03400704 -0.92640691 17 | H 2.57559337 0.71110284 0.52678329 18 | H 1.12047358 0.11455122 1.45425653 -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/forward_end_initial.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C 0.76883355 -1.07044598 -0.27238483 4 | C -0.77091063 -1.07559290 -0.24484541 5 | H 1.16412960 -1.94774357 0.24197577 6 | H 1.12133607 -1.10865548 -1.30481816 7 | H -1.14168592 -1.95543022 0.28325472 8 | H -1.15984092 -1.11632950 -1.26401698 9 | C -1.32623695 0.19026590 0.43536864 10 | C -0.66988153 1.39363058 -0.16382775 11 | C 0.65429225 1.39804418 -0.18748346 12 | C 1.33963915 0.19915353 0.38774084 13 | H -1.09234173 0.14236767 1.50537381 14 | H -2.41055856 0.22619440 0.33088834 15 | H -1.27411495 2.17746702 -0.58892663 16 | H 1.23771815 2.18583984 -0.63380076 17 | H 2.41927499 0.24230609 0.24461731 18 | H 1.14441911 0.14980486 1.46540719 -------------------------------------------------------------------------------- /reaction/DA/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO_0_0/forward_end_opt.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -17.92483682 , 3 | C 0.76847552 -1.07809472 -0.25627765 4 | C -0.76993204 -1.08323823 -0.22876691 5 | H 1.16103406 -1.94451956 0.27851372 6 | H 1.11112000 -1.15119141 -1.28988276 7 | H -1.13731825 -1.95218194 0.31964920 8 | H -1.14881482 -1.15878991 -1.24946632 9 | C -1.35731482 0.18871284 0.40440410 10 | C -0.66923113 1.39598040 -0.14762122 11 | C 0.65420694 1.40039641 -0.17126040 12 | C 1.36960291 0.19780747 0.35568643 13 | H -1.19587612 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2.51102050 0.47608328 0.40829555 18 | H 1.07294168 0.06786280 1.44623411 -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/.CHRG: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/.UHF: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/HGCIXCUEYOPUTN.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.99565911 1.11365923 0.1813245 4 | C -1.27606981 2.60235503 0.00621402 5 | H -1.87015336 0.60701239 0.59652452 6 | H -0.78124129 0.67212641 -0.79519026 7 | H -1.41874 3.05865194 0.98976411 8 | H -2.19153547 2.75281318 -0.5721487 9 | C -0.09768571 3.27066793 -0.69802487 10 | C 1.20712103 2.85883263 -0.08807867 11 | C 1.34217747 1.81494158 0.71224009 12 | C 0.20657606 0.91889618 1.10162547 13 | H -0.19651844 4.35903197 -0.65048292 14 | H -0.09394222 2.99564591 -1.75944204 15 | H 2.06428798 3.46565933 -0.34755614 16 | H 2.30699363 1.56935898 1.13582647 17 | H 0.53724804 -0.12289726 1.07602732 18 | H -0.07794548 1.13896956 2.13677414 19 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/coord: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.293432977449 -2.264778022774 -0.633922156065 c 3 | -1.293854883711 -2.264479476310 0.634064934687 c 4 | 2.319984866130 -3.995685525111 -0.178227912515 h 5 | 1.043292534906 -2.191669350833 -2.681272653326 h 6 | -1.043717565641 -2.191071651681 2.681452448467 h 7 | -2.320673913879 -3.995345993326 0.178598898033 h 8 | -2.803581553939 0.036691365574 -0.229545125390 c 9 | 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2.67917636506157 h 7 | -2.32816355553430 -3.99108489164830 0.17497114494512 h 8 | -2.80358096796058 0.04176406472431 -0.22900269133128 c 9 | -1.24055494797795 2.39844938012659 -0.10403502342424 c 10 | 1.24948209747503 2.39380842370174 0.10314975906347 c 11 | 2.80353820246957 0.03111793870503 0.22991931781369 c 12 | -4.49274889999852 0.26949054683444 0.93810149865600 h 13 | -3.44821794514283 -0.22901198341497 -2.17769179605724 h 14 | -2.26857161003517 4.16207665517186 -0.21254320148121 h 15 | 2.28400261323545 4.15354327988768 0.21174362977547 h 16 | 4.49482647027747 0.25248354271482 -0.93561964880352 h 17 | 3.44474090234100 -0.24231276294914 2.17955271276427 h 18 | $end 19 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/cre_members: -------------------------------------------------------------------------------- 1 | 2 2 | 2 1 2 3 | 2 3 4 4 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/cregen_0.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 42 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 42 12 | reference state Etot : -17.931438900000000 13 | number of doubles removed by rot/RMSD : 38 14 | total number unique points considered further : 4 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -17.93144 0.49955 0.99908 1 2 mtd3 17 | 2 0.000 -17.93144 0.49953 mtd11 18 | 3 4.143 -17.92484 0.00046 0.00092 2 2 mtd2 19 | 4 4.148 -17.92483 0.00046 mtd14 20 | T /K : 298.15 21 | E lowest : -17.93144 22 | ensemble average energy (kcal) : 0.004 23 | ensemble entropy (J/mol K, cal/mol K) : 5.824 1.392 24 | ensemble free energy (kcal/mol) : -0.415 25 | population of lowest in % : 99.908 26 | number of unique conformers for further calc 2 27 | list of relative energies saved as "crest.energies" 28 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/cregen_1.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 46 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 46 12 | reference state Etot : -17.931438900000000 13 | number of doubles removed by rot/RMSD : 42 14 | total number unique points considered further : 4 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -17.93144 0.49955 0.99908 1 2 input 17 | 2 0.000 -17.93144 0.49953 mtd1 18 | 3 4.144 -17.92484 0.00046 0.00092 2 2 mtd8 19 | 4 4.147 -17.92483 0.00046 mtd4 20 | T /K : 298.15 21 | E lowest : -17.93144 22 | ensemble average energy (kcal) : 0.004 23 | ensemble entropy (J/mol K, cal/mol K) : 5.824 1.392 24 | ensemble free energy (kcal/mol) : -0.415 25 | population of lowest in % : 99.908 26 | number of unique conformers for further calc 2 27 | list of relative energies saved as "crest.energies" 28 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/crest.energies: -------------------------------------------------------------------------------- 1 | 1 0.000 2 | 2 4.143 3 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/crest_best.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -17.93143890 3 | C 0.6844553190 -1.1984690286 -0.3354571896 4 | C -0.6846785822 -1.1983110446 0.3355327448 5 | H 1.2276832347 -2.1144259180 -0.0943141584 6 | H 0.5520866850 -1.1597815819 -1.4188685160 7 | H -0.5523116016 -1.1594652931 1.4189636595 8 | H -1.2280478631 -2.1142462455 0.0945104755 9 | C -1.4835916049 0.0194162363 -0.1214700605 10 | C -0.6587291082 1.2681054366 -0.0549148533 11 | C 0.6589456922 1.2680077915 0.0549674353 12 | C 1.4836011424 0.0191718153 0.1213500484 13 | H -2.3778748219 0.1385212802 0.4960079976 14 | H -1.8239492907 -0.1247281841 -1.1529465622 15 | H -1.2043384141 2.2004451558 -0.1123584550 16 | H 1.2047369002 2.2002140887 0.1124901349 17 | H 2.3777563828 0.1381628997 -0.4963280082 18 | H 1.8242247273 -0.1249577477 1.1527466058 19 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/gfnff_adjacency: -------------------------------------------------------------------------------- 1 | # indices of neighbouring atoms (max seven) 2 | 2 3 4 10 3 | 1 5 6 7 4 | 1 5 | 1 6 | 2 7 | 2 8 | 2 8 11 12 9 | 7 9 13 10 | 8 10 14 11 | 1 9 15 16 12 | 7 13 | 7 14 | 8 15 | 9 16 | 10 17 | 10 18 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/gfnff_charges: -------------------------------------------------------------------------------- 1 | -0.04920891 2 | -0.04921297 3 | 0.02442185 4 | 0.03058669 5 | 0.03058188 6 | 0.02442383 7 | -0.04703062 8 | -0.04311763 9 | -0.04311976 10 | -0.04702738 11 | 0.02607117 12 | 0.02828606 13 | 0.02999329 14 | 0.02999599 15 | 0.02606952 16 | 0.02828701 17 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/gfnff_topo: 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-1.7594420400 15 | H 2.0642879800 3.4656593300 -0.3475561400 16 | H 2.3069936300 1.5693589800 1.1358264700 17 | H 0.5372480400 -0.1228972600 1.0760273200 18 | H -0.0779454800 1.1389695600 2.1367741400 19 | -------------------------------------------------------------------------------- /reaction/DA/conformer/HGCIXCUEYOPUTN/wbo: -------------------------------------------------------------------------------- 1 | 1 2 1.0089739661018344 2 | 1 3 0.97869921018783057 3 | 1 4 0.97856020777952768 4 | 2 5 0.97856192979666290 5 | 2 6 0.97869730987913295 6 | 2 7 1.0067487354697569 7 | 7 8 1.0239128394649228 8 | 8 9 1.9287010756457805 9 | 1 10 1.0067391022562531 10 | 9 10 1.0238819134926351 11 | 7 11 0.96826183140181699 12 | 7 12 0.95921256778779629 13 | 8 13 0.96803568646708138 14 | 9 14 0.96804328531611961 15 | 10 15 0.96830079145230652 16 | 10 16 0.95921010512575577 17 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/.CHRG: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/.UHF: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.99565911 1.11365923 0.1813245 4 | C -1.27606981 2.60235503 0.00621402 5 | H -1.87015336 0.60701239 0.59652452 6 | H -0.78124129 0.67212641 -0.79519026 7 | H -1.41874 3.05865194 0.98976411 8 | H -2.19153547 2.75281318 -0.5721487 9 | C -0.09768571 3.27066793 -0.69802487 10 | C 1.20712103 2.85883263 -0.08807867 11 | C 1.34217747 1.81494158 0.71224009 12 | C 0.20657606 0.91889618 1.10162547 13 | H -0.19651844 4.35903197 -0.65048292 14 | H -0.09394222 2.99564591 -1.75944204 15 | H 2.06428798 3.46565933 -0.34755614 16 | H 2.30699363 1.56935898 1.13582647 17 | H 0.53724804 -0.12289726 1.07602732 18 | H -0.07794548 1.13896956 2.13677414 19 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/coord: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.295271315324 -2.263698235068 0.634156076737 c 3 | -1.291638197378 -2.265333580283 -0.634626688607 c 4 | 1.044283036274 -2.189892663377 2.681345301006 h 5 | 2.323449245722 -3.993912208359 0.179508612483 h 6 | -2.317067237356 -3.997378133936 -0.180479038158 h 7 | -1.041018918500 -2.190453597345 -2.681924174897 h 8 | -2.803460607888 0.034099772541 0.229932573822 c 9 | -1.247014618882 2.395294393414 0.103506392546 c 10 | 1.243061644410 2.397185818605 -0.103908325539 c 11 | 2.803472397510 0.038580949227 -0.229220113502 c 12 | -3.444723391175 -0.239261367731 2.179689420328 h 13 | -4.494656154537 0.257584243888 -0.935424333993 h 14 | -2.279611310584 4.156407408739 0.212529316547 h 15 | 2.272904264443 4.159820818831 -0.212524289687 h 16 | 3.446811071776 -0.233333179699 -2.178438707476 h 17 | 4.493300581359 0.264816098863 0.937625594116 h 18 | $end 19 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/coord.original: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.28992987729590 -2.26746584231045 -0.63329408207487 c 3 | -1.29832783423424 -2.26284730523319 0.63200754470198 c 4 | 2.31317594012813 -4.00001656081938 -0.17693927163430 h 5 | 1.04148082848777 -2.19472984006670 -2.68058403105090 h 6 | -1.04993135682674 -2.19263122112133 2.67917636506157 h 7 | -2.32816355553430 -3.99108489164830 0.17497114494512 h 8 | -2.80358096796058 0.04176406472431 -0.22900269133128 c 9 | -1.24055494797795 2.39844938012659 -0.10403502342424 c 10 | 1.24948209747503 2.39380842370174 0.10314975906347 c 11 | 2.80353820246957 0.03111793870503 0.22991931781369 c 12 | -4.49274889999852 0.26949054683444 0.93810149865600 h 13 | -3.44821794514283 -0.22901198341497 -2.17769179605724 h 14 | -2.26857161003517 4.16207665517186 -0.21254320148121 h 15 | 2.28400261323545 4.15354327988768 0.21174362977547 h 16 | 4.49482647027747 0.25248354271482 -0.93561964880352 h 17 | 3.44474090234100 -0.24231276294914 2.17955271276427 h 18 | $end 19 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/cre_members: -------------------------------------------------------------------------------- 1 | 2 2 | 2 1 2 3 | 2 3 4 4 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/cregen_0.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 38 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 38 12 | reference state Etot : -17.931438870000001 13 | number of doubles removed by rot/RMSD : 34 14 | total number unique points considered further : 4 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -17.93144 0.49954 0.99908 1 2 mtd3 17 | 2 0.000 -17.93144 0.49954 mtd11 18 | 3 4.143 -17.92484 0.00046 0.00092 2 2 mtd8 19 | 4 4.146 -17.92483 0.00046 mtd10 20 | T /K : 298.15 21 | E lowest : -17.93144 22 | ensemble average energy (kcal) : 0.004 23 | ensemble entropy (J/mol K, cal/mol K) : 5.824 1.392 24 | ensemble free energy (kcal/mol) : -0.415 25 | population of lowest in % : 99.908 26 | number of unique conformers for further calc 2 27 | list of relative energies saved as "crest.energies" 28 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/cregen_1.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 53 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 53 12 | reference state Etot : -17.931438900000000 13 | number of doubles removed by rot/RMSD : 49 14 | total number unique points considered further : 4 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -17.93144 0.49955 0.99908 1 2 mtd2 17 | 2 0.000 -17.93144 0.49953 mtd3 18 | 3 4.143 -17.92484 0.00046 0.00092 2 2 mtd11 19 | 4 4.147 -17.92483 0.00046 mtd1 20 | T /K : 298.15 21 | E lowest : -17.93144 22 | ensemble average energy (kcal) : 0.004 23 | ensemble entropy (J/mol K, cal/mol K) : 5.824 1.392 24 | ensemble free energy (kcal/mol) : -0.415 25 | population of lowest in % : 99.908 26 | number of unique conformers for further calc 2 27 | list of relative energies saved as "crest.energies" 28 | -------------------------------------------------------------------------------- /reaction/DA/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/crest.energies: -------------------------------------------------------------------------------- 1 | 1 0.000 2 | 2 4.143 3 | -------------------------------------------------------------------------------- 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self.models: 20 | _in = dict() 21 | for k in data: 22 | if k in self.x: 23 | _in[k] = data[k] 24 | _out = model(_in) 25 | _r = dict() 26 | for k in _out: 27 | if k in self.out: 28 | _r[k] = _out[k] 29 | if self.detach: 30 | _r[k] = _r[k].detach() 31 | res.append(_r) 32 | 33 | for k in res[0]: 34 | v = [] 35 | for x in res: 36 | v.append(x[k]) 37 | vv = torch.stack(v, dim=0) 38 | data[k] = vv.mean(dim=0) 39 | data[k + '_std'] = vv.std(dim=0) 40 | return data 41 | -------------------------------------------------------------------------------- /reaction/YARPrun.log: -------------------------------------------------------------------------------- 1 | running PYSIS job HGCIXCUEYOPUTN on PID 56884 2 | running PYSIS job HGCIXCUEYOPUTN on PID 57183 3 | running PYSIS job HGCIXCUEYOPUTN on PID 57238 4 | PYSIS job HGCIXCUEYOPUTN is finished. 5 | running PYSIS job KAKZBPTYRLMSJV-VGGSQFUCUMXWEO on PID 57238 6 | PYSIS job KAKZBPTYRLMSJV-VGGSQFUCUMXWEO is finished. 7 | running PYSIS job HGCIXCUEYOPUTN on PID 57325 8 | PYSIS job HGCIXCUEYOPUTN is finished. 9 | running PYSIS job KAKZBPTYRLMSJV-VGGSQFUCUMXWEO on PID 57325 10 | PYSIS job KAKZBPTYRLMSJV-VGGSQFUCUMXWEO is finished. 11 | running CREST job HGCIXCUEYOPUTN on PID 57325 12 | CREST job HGCIXCUEYOPUTN is finished. 13 | running CREST job KAKZBPTYRLMSJV-VGGSQFUCUMXWEO on PID 57325 14 | CREST job KAKZBPTYRLMSJV-VGGSQFUCUMXWEO is finished. 15 | -------------------------------------------------------------------------------- /reaction/bin/DFT_models/Delta2_model_1.jpt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/bin/DFT_models/Delta2_model_1.jpt -------------------------------------------------------------------------------- /reaction/bin/DFT_models/Delta2_model_2.jpt: -------------------------------------------------------------------------------- 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-------------------------------- 10 | SM_TYPE GSM # SSM, FSM or GSM 11 | RESTART 0 # read restart.xyz 12 | MAX_OPT_ITERS 100 # maximum iterations 13 | STEP_OPT_ITERS 100 # for FSM/SSM 14 | CONV_TOL 0.0005 # perp grad 15 | ADD_NODE_TOL 0.1 # for GSM 16 | SCALING 1.0 # for opt steps 17 | SSM_DQMAX 0.8 # add step size 18 | GROWTH_DIRECTION 0 # normal/react/prod: 0/1/2 19 | INT_THRESH 1.0 # intermediate detection 20 | MIN_SPACING 5.0 # node spacing SSM 21 | BOND_FRAGMENTS 1 # make IC's for fragments 22 | INITIAL_OPT 300 # opt steps first node 23 | FINAL_OPT 300 # opt steps last SSM node 24 | PRODUCT_LIMIT 100.0 # kcal/mol 25 | TS_FINAL_TYPE 1 # any/delta bond: 0/1 26 | NNODES 12 # including endpoints 27 | TS_FINAL_OPT 150 # Final TS opt 28 | TS_CONV_TOL 0.0001 # TS ene conv 29 | TS_GRAD_MAX_TOL 0.005 # TS grad conv 30 | --------------------------------------------------------- 31 | -------------------------------------------------------------------------------- /reaction/bin/poor_model.sav: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/bin/poor_model.sav -------------------------------------------------------------------------------- /reaction/bin/rich_model.sav: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/bin/rich_model.sav -------------------------------------------------------------------------------- /reaction/charges: -------------------------------------------------------------------------------- 1 | -0.09801205 2 | -0.03454117 3 | -0.06668850 4 | -0.09616556 5 | 0.04174169 6 | 0.03743094 7 | 0.03337503 8 | 0.04507206 9 | 0.04777225 10 | 0.04682307 11 | 0.04319223 12 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/.CHRG: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/.UHF: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/HGCIXCUEYOPUTN.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.99565911 1.11365923 0.1813245 4 | C -1.27606981 2.60235503 0.00621402 5 | H -1.87015336 0.60701239 0.59652452 6 | H -0.78124129 0.67212641 -0.79519026 7 | H -1.41874 3.05865194 0.98976411 8 | H -2.19153547 2.75281318 -0.5721487 9 | C -0.09768571 3.27066793 -0.69802487 10 | C 1.20712103 2.85883263 -0.08807867 11 | C 1.34217747 1.81494158 0.71224009 12 | C 0.20657606 0.91889618 1.10162547 13 | H -0.19651844 4.35903197 -0.65048292 14 | H -0.09394222 2.99564591 -1.75944204 15 | H 2.06428798 3.46565933 -0.34755614 16 | H 2.30699363 1.56935898 1.13582647 17 | H 0.53724804 -0.12289726 1.07602732 18 | H -0.07794548 1.13896956 2.13677414 19 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/coord: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.306774522775 -2.278260696992 -0.619012171460 c 3 | -1.306596805577 -2.278364338823 0.618957775699 c 4 | 2.329679849811 -4.000570922492 -0.108453898227 h 5 | 1.091953834902 -2.253306416833 -2.677359219480 h 6 | -1.091795706414 -2.253678187343 2.677392514183 h 7 | -2.329489774750 -4.000620331078 0.108096698637 h 8 | -2.815593670635 0.040958591456 -0.226390133809 c 9 | -1.248377675375 2.408788321138 -0.102137192743 c 10 | 1.248150103616 2.408912478968 0.102187194136 c 11 | 2.815602253014 0.041193093974 0.226458015222 c 12 | -4.494352482380 0.259557598904 0.963874407226 h 13 | -3.483278041275 -0.224588588897 -2.171522454876 h 14 | -2.290658782276 4.173696905835 -0.203063022776 h 15 | 2.290237740186 4.173858629715 0.202231050896 h 16 | 4.494586054208 0.259868348462 -0.963623214837 h 17 | 3.483609144694 -0.224409411886 2.171670573675 h 18 | $end 19 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/coord.original: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.30174480322639 -2.27625733729388 -0.62072764747063 c 3 | -1.31047045280711 -2.27174023606626 0.61994091934708 c 4 | 2.32192198760914 -4.00082998586061 -0.11232386923517 h 5 | 1.08461350144687 -2.24941810001899 -2.67876673362025 h 6 | -1.09321091441530 -2.24684181575133 2.67799016334704 h 7 | -2.33709375213523 -3.99220205394283 0.11058361861117 h 8 | -2.81568724075857 0.05056651825713 -0.22404394899079 c 9 | -1.24384285521509 2.41582902866063 -0.10061032277397 c 10 | 1.25276232641133 2.41116270581034 0.10077342176246 c 11 | 2.81557637682851 0.03996306600510 0.22449192016838 c 12 | -4.49370130232104 0.27217689815343 0.96649479165191 h 13 | -3.48388274919569 -0.21377487781242 -2.16909548704311 h 14 | -2.28343480180150 4.18230710797824 -0.20019649907288 h 15 | 2.29901535706708 4.17374563233729 0.19961122007415 h 16 | 4.49510033620748 0.25535150778807 -0.96507132289938 h 17 | 3.48166919385274 -0.22740463394089 2.16986200306798 h 18 | $end 19 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/cre_members: -------------------------------------------------------------------------------- 1 | 2 2 | 2 1 2 3 | 2 3 4 4 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/cregen_0.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 71 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 71 12 | reference state Etot : -18.072364400000001 13 | number of doubles removed by rot/RMSD : 66 14 | total number unique points considered further : 5 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -18.07236 0.49655 0.99309 1 2 mtd2 17 | 2 0.000 -18.07236 0.49653 mtd6 18 | 3 3.176 -18.06730 0.00234 0.00691 2 3 mtd6 19 | 4 3.178 -18.06730 0.00234 mtd7 20 | 5 3.205 -18.06726 0.00223 mtd6 21 | T /K : 298.15 22 | E lowest : -18.07236 23 | ensemble average energy (kcal) : 0.022 24 | ensemble entropy (J/mol K, cal/mol K) : 6.130 1.465 25 | ensemble free energy (kcal/mol) : -0.437 26 | population of lowest in % : 99.309 27 | number of unique conformers for further calc 2 28 | list of relative energies saved as "crest.energies" 29 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/cregen_1.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 67 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 67 12 | reference state Etot : -18.072364400000001 13 | number of doubles removed by rot/RMSD : 64 14 | total number unique points considered further : 3 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -18.07236 0.49888 0.99775 1 2 mtd3 17 | 2 0.000 -18.07236 0.49887 mtd6 18 | 3 3.204 -18.06726 0.00225 0.00225 2 1 mtd5 19 | T /K : 298.15 20 | E lowest : -18.07236 21 | ensemble average energy (kcal) : 0.007 22 | ensemble entropy (J/mol K, cal/mol K) : 5.883 1.406 23 | ensemble free energy (kcal/mol) : -0.419 24 | population of lowest in % : 99.775 25 | number of unique conformers for further calc 2 26 | list of relative energies saved as "crest.energies" 27 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/crest.energies: -------------------------------------------------------------------------------- 1 | 1 0.000 2 | 2 3.176 3 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/crest_best.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -18.07236443 3 | C 0.6919351265 -1.2053754673 -0.3276207649 4 | C -0.6909863189 -1.2059139617 0.3275096085 5 | H 1.2335168911 -2.1166714673 -0.0575280988 6 | H 0.5782967042 -1.1920104476 -1.4168842707 7 | H -0.5772603924 -1.1927481064 1.4167675312 8 | H -1.2319273486 -2.1175487907 0.0572798743 9 | C -1.4899608401 0.0211686428 -0.1197889135 10 | C -0.6610280315 1.2745199471 -0.0539703392 11 | C 0.6600892948 1.2750190987 0.0538982855 12 | C 1.4898872812 0.0222423274 0.1199401116 13 | H -2.3784816420 0.1364402814 0.5099273764 14 | H -1.8431132058 -0.1194667181 -1.1491801561 15 | H -1.2128870564 2.2082472299 -0.1071637268 16 | H 1.2112462744 2.2091887182 0.1069508605 17 | H 2.3786522346 0.1380782108 -0.5093383773 18 | H 1.8427141192 -0.1183321171 1.1495504690 19 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/gfnff_adjacency: -------------------------------------------------------------------------------- 1 | # indices of neighbouring atoms (max seven) 2 | 2 3 4 10 3 | 1 5 6 7 4 | 1 5 | 1 6 | 2 7 | 2 8 | 2 8 11 12 9 | 7 9 13 10 | 8 10 14 11 | 1 9 15 16 12 | 7 13 | 7 14 | 8 15 | 9 16 | 10 17 | 10 18 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/gfnff_charges: -------------------------------------------------------------------------------- 1 | -0.04907836 2 | -0.04907896 3 | 0.02443256 4 | 0.03027533 5 | 0.03027173 6 | 0.02443288 7 | -0.04700533 8 | -0.04296360 9 | -0.04296355 10 | -0.04700486 11 | 0.02612283 12 | 0.02828959 13 | 0.02992817 14 | 0.02992841 15 | 0.02612060 16 | 0.02829257 17 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/gfnff_topo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/conformer/HGCIXCUEYOPUTN/gfnff_topo -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/struc.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.9956591100 1.1136592300 0.1813245000 4 | C -1.2760698100 2.6023550300 0.0062140200 5 | H -1.8701533600 0.6070123900 0.5965245200 6 | H -0.7812412900 0.6721264100 -0.7951902600 7 | H -1.4187400000 3.0586519400 0.9897641100 8 | H -2.1915354700 2.7528131800 -0.5721487000 9 | C -0.0976857100 3.2706679300 -0.6980248700 10 | C 1.2071210300 2.8588326300 -0.0880786700 11 | C 1.3421774700 1.8149415800 0.7122400900 12 | C 0.2065760600 0.9188961800 1.1016254700 13 | H -0.1965184400 4.3590319700 -0.6504829200 14 | H -0.0939422200 2.9956459100 -1.7594420400 15 | H 2.0642879800 3.4656593300 -0.3475561400 16 | H 2.3069936300 1.5693589800 1.1358264700 17 | H 0.5372480400 -0.1228972600 1.0760273200 18 | H -0.0779454800 1.1389695600 2.1367741400 19 | -------------------------------------------------------------------------------- /reaction/conformer/HGCIXCUEYOPUTN/wbo: -------------------------------------------------------------------------------- 1 | 1 2 1.0062718519459246 2 | 1 3 0.98045409355399771 3 | 1 4 0.98041561041294223 4 | 2 5 0.98041547602140777 5 | 2 6 0.98045422602137056 6 | 2 7 1.0047284114653141 7 | 7 8 1.0184242305261400 8 | 8 9 1.9328874188122263 9 | 1 10 1.0047273018209408 10 | 9 10 1.0184235462326596 11 | 7 11 0.97063693182071531 12 | 7 12 0.96360994838904535 13 | 8 13 0.97094606086813207 14 | 9 14 0.97094683502640844 15 | 10 15 0.97064851864460111 16 | 10 16 0.96360404208080286 17 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/.CHRG: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/.UHF: -------------------------------------------------------------------------------- 1 | 0 2 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.99565911 1.11365923 0.1813245 4 | C -1.27606981 2.60235503 0.00621402 5 | H -1.87015336 0.60701239 0.59652452 6 | H -0.78124129 0.67212641 -0.79519026 7 | H -1.41874 3.05865194 0.98976411 8 | H -2.19153547 2.75281318 -0.5721487 9 | C -0.09768571 3.27066793 -0.69802487 10 | C 1.20712103 2.85883263 -0.08807867 11 | C 1.34217747 1.81494158 0.71224009 12 | C 0.20657606 0.91889618 1.10162547 13 | H -0.19651844 4.35903197 -0.65048292 14 | H -0.09394222 2.99564591 -1.75944204 15 | H 2.06428798 3.46565933 -0.34755614 16 | H 2.30699363 1.56935898 1.13582647 17 | H 0.53724804 -0.12289726 1.07602732 18 | H -0.07794548 1.13896956 2.13677414 19 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/coord: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.304604621143 -2.278947724624 0.619734195116 c 3 | -1.308337491486 -2.277299193280 -0.619147683519 c 4 | 1.089300019619 -2.252172678206 2.678092459604 h 5 | 2.326216323052 -4.002475835035 0.110735927693 h 6 | -2.332779693141 -3.998886883386 -0.109148293334 h 7 | -1.092791164911 -2.252085844165 -2.677482695307 h 8 | -2.815549248469 0.043160349521 0.226158721371 c 9 | -1.246226695002 2.409874282580 0.102234549534 c 10 | 1.250337717649 2.407829808484 -0.101897717033 c 11 | 2.815534698524 0.038552547402 -0.227049280236 c 12 | -3.483132281232 -0.221964095169 2.171385791597 h 13 | -4.494437799349 0.263098020879 -0.963846778488 h 14 | -2.287180106152 4.175505535140 0.203362271652 h 15 | 2.293910769333 4.172046150093 -0.201956158698 h 16 | 3.480713626470 -0.228091838451 -2.172892725965 h 17 | 4.495847306439 0.255518871880 0.961359507020 h 18 | $end 19 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/coord.original: -------------------------------------------------------------------------------- 1 | $coord 2 | 1.30174480322639 -2.27625733729388 -0.62072764747063 c 3 | -1.31047045280711 -2.27174023606626 0.61994091934708 c 4 | 2.32192198760914 -4.00082998586061 -0.11232386923517 h 5 | 1.08461350144687 -2.24941810001899 -2.67876673362025 h 6 | -1.09321091441530 -2.24684181575133 2.67799016334704 h 7 | -2.33709375213523 -3.99220205394283 0.11058361861117 h 8 | -2.81568724075857 0.05056651825713 -0.22404394899079 c 9 | -1.24384285521509 2.41582902866063 -0.10061032277397 c 10 | 1.25276232641133 2.41116270581034 0.10077342176246 c 11 | 2.81557637682851 0.03996306600510 0.22449192016838 c 12 | -4.49370130232104 0.27217689815343 0.96649479165191 h 13 | -3.48388274919569 -0.21377487781242 -2.16909548704311 h 14 | -2.28343480180150 4.18230710797824 -0.20019649907288 h 15 | 2.29901535706708 4.17374563233729 0.19961122007415 h 16 | 4.49510033620748 0.25535150778807 -0.96507132289938 h 17 | 3.48166919385274 -0.22740463394089 2.16986200306798 h 18 | $end 19 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/cre_members: -------------------------------------------------------------------------------- 1 | 2 2 | 2 1 2 3 | 2 3 4 4 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/cregen_0.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 71 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 71 12 | reference state Etot : -18.072364400000001 13 | number of doubles removed by rot/RMSD : 66 14 | total number unique points considered further : 5 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -18.07236 0.49656 0.99311 1 2 mtd5 17 | 2 0.000 -18.07236 0.49655 mtd14 18 | 3 3.176 -18.06730 0.00234 0.00465 2 2 mtd10 19 | 4 3.184 -18.06729 0.00231 mtd1 20 | 5 3.204 -18.06726 0.00224 0.00224 3 1 mtd3 21 | T /K : 298.15 22 | E lowest : -18.07236 23 | ensemble average energy (kcal) : 0.022 24 | ensemble entropy (J/mol K, cal/mol K) : 6.129 1.465 25 | ensemble free energy (kcal/mol) : -0.437 26 | population of lowest in % : 99.311 27 | number of unique conformers for further calc 3 28 | list of relative energies saved as "crest.energies" 29 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/cregen_1.tmp: -------------------------------------------------------------------------------- 1 | input file name : crest_rotamers_2.xyz 2 | output file name : crest_rotamers_3.xyz 3 | number of atoms : 16 4 | number of points on xyz files : 65 5 | RMSD threshold : 0.1250 6 | Bconst threshold : 0.0100 7 | population threshold : 0.0500 8 | conformer energy window /kcal : 6.0000 9 | # fragment in coord : 1 10 | # bonds in reference structure : 16 11 | number of reliable points : 65 12 | reference state Etot : -18.072364400000001 13 | number of doubles removed by rot/RMSD : 61 14 | total number unique points considered further : 4 15 | Erel/kcal Etot weight/tot conformer set degen origin 16 | 1 0.000 -18.07236 0.49766 0.99530 1 2 input 17 | 2 0.000 -18.07236 0.49764 mtd12 18 | 3 3.176 -18.06730 0.00235 0.00470 2 2 mtd3 19 | 4 3.176 -18.06730 0.00235 mtd3 20 | T /K : 298.15 21 | E lowest : -18.07236 22 | ensemble average energy (kcal) : 0.015 23 | ensemble entropy (J/mol K, cal/mol K) : 6.012 1.437 24 | ensemble free energy (kcal/mol) : -0.428 25 | population of lowest in % : 99.530 26 | number of unique conformers for further calc 2 27 | list of relative energies saved as "crest.energies" 28 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/crest.energies: -------------------------------------------------------------------------------- 1 | 1 0.000 2 | 2 3.176 3 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/crest_best.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -18.07236442 3 | C 0.6914931614 -1.2055739989 -0.3276363710 4 | C -0.6914398183 -1.2056607032 0.3274624426 5 | H 1.2328092368 -2.1170825894 -0.0577265808 6 | H 0.5777338469 -1.1920543870 -1.4168795990 7 | H -0.5776818089 -1.1926755671 1.4167084760 8 | H -1.2327633714 -2.1170454400 0.0571336948 9 | C -1.4899856170 0.0217204809 -0.1197472223 10 | C -0.6605580556 1.2747308726 -0.0539256001 11 | C 0.6605817494 1.2747281065 0.0538751734 12 | C 1.4899253571 0.0217036055 0.1200247652 13 | H -2.3785037030 0.1372864893 0.5098863221 14 | H -1.8430839431 -0.1188308216 -1.1491590614 15 | H -1.2120574001 2.2086869600 -0.1071993517 16 | H 1.2120832812 2.2087400976 0.1062781227 17 | H 2.3787128877 0.1371979145 -0.5092340736 18 | H 1.8425510449 -0.1189001968 1.1495582207 19 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/gfnff_adjacency: -------------------------------------------------------------------------------- 1 | # indices of neighbouring atoms (max seven) 2 | 2 3 4 10 3 | 1 5 6 7 4 | 1 5 | 1 6 | 2 7 | 2 8 | 2 8 11 12 9 | 7 9 13 10 | 8 10 14 11 | 1 9 15 16 12 | 7 13 | 7 14 | 8 15 | 9 16 | 10 17 | 10 18 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/gfnff_charges: -------------------------------------------------------------------------------- 1 | -0.04907836 2 | -0.04907896 3 | 0.02443256 4 | 0.03027533 5 | 0.03027173 6 | 0.02443288 7 | -0.04700533 8 | -0.04296360 9 | -0.04296355 10 | -0.04700486 11 | 0.02612283 12 | 0.02828959 13 | 0.02992817 14 | 0.02992841 15 | 0.02612060 16 | 0.02829257 17 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/gfnff_topo: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/gfnff_topo -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/struc.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -0.9956591100 1.1136592300 0.1813245000 4 | C -1.2760698100 2.6023550300 0.0062140200 5 | H -1.8701533600 0.6070123900 0.5965245200 6 | H -0.7812412900 0.6721264100 -0.7951902600 7 | H -1.4187400000 3.0586519400 0.9897641100 8 | H -2.1915354700 2.7528131800 -0.5721487000 9 | C -0.0976857100 3.2706679300 -0.6980248700 10 | C 1.2071210300 2.8588326300 -0.0880786700 11 | C 1.3421774700 1.8149415800 0.7122400900 12 | C 0.2065760600 0.9188961800 1.1016254700 13 | H -0.1965184400 4.3590319700 -0.6504829200 14 | H -0.0939422200 2.9956459100 -1.7594420400 15 | H 2.0642879800 3.4656593300 -0.3475561400 16 | H 2.3069936300 1.5693589800 1.1358264700 17 | H 0.5372480400 -0.1228972600 1.0760273200 18 | H -0.0779454800 1.1389695600 2.1367741400 19 | -------------------------------------------------------------------------------- /reaction/conformer/KAKZBPTYRLMSJV-VGGSQFUCUMXWEO/wbo: -------------------------------------------------------------------------------- 1 | 1 2 1.0062718519459246 2 | 1 3 0.98045409355399771 3 | 1 4 0.98041561041294223 4 | 2 5 0.98041547602140777 5 | 2 6 0.98045422602137056 6 | 2 7 1.0047284114653141 7 | 7 8 1.0184242305261400 8 | 8 9 1.9328874188122263 9 | 1 10 1.0047273018209408 10 | 9 10 1.0184235462326596 11 | 7 11 0.97063693182071531 12 | 7 12 0.96360994838904535 13 | 8 13 0.97094606086813207 14 | 9 14 0.97094683502640844 15 | 10 15 0.97064851864460111 16 | 10 16 0.96360404208080286 17 | -------------------------------------------------------------------------------- /reaction/constants.py: -------------------------------------------------------------------------------- 1 | class Constants: 2 | 3 | n_a = 6.022140857E23 # molecules mol-1 4 | 5 | ha_to_kcalmol = ha2kcalmol = 627.509 # Hartree^-1 kcal mol^-1 6 | ha_to_kJmol = ha2kJmol = 2625.50 # Hartree^-1 kJ mol^-1 7 | 8 | ha_to_J = ha_to_kJmol * 1000 / n_a # Hartree^-1 J 9 | J_to_ha = 1.0 / ha_to_J # J Hartree^-1 10 | 11 | eV_to_ha = eV2ha = 0.0367493 # Hartree eV^-1 12 | ha_to_eV = ha2eV = 1.0 / eV_to_ha # eV Hartree^-1 13 | 14 | kcal_to_kJ = kcal2kJ = 4.184 # kJ kcal^-1 15 | 16 | rad_to_deg = 57.29577951308232087679815 # deg rad^-1 17 | 18 | a0_to_ang = a02ang = 0.529177 # Å bohr^-1 19 | ang_to_a0 = ang2a0 = 1.0 / a0_to_ang # bohr Å^-1 20 | ang_to_nm = 0.1 # nm ang^-1 21 | ang_to_pm = 100 # pm ang^-1 22 | ang_to_m = 1E-10 # m ang^-1 23 | a0_to_m = a0_to_ang * ang_to_m # Å m^-1 24 | 25 | per_cm_to_hz = c_in_cm = 299792458 * 100 # cm s^-1 26 | 27 | amu_to_kg = 1.66053906660E-27 # kg amu^-1 28 | amu_to_me = 1822.888486209 # m_e amu^-1 29 | 30 | atm_to_pa = 101325 # Pa atm^-1 31 | dm_to_m = 0.1 # m dm^-1 32 | -------------------------------------------------------------------------------- /reaction/job_dft.submit: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # 3 | #SBATCH --job-name=classy-yarp 4 | #SBATCH --output=runyarp.1.out 5 | #SBATCH --error=runyarp.1.err 6 | #SBATCH -A standby 7 | #SBATCH --nodes=1 8 | #SBATCH --mem 5GB 9 | #SBATCH -n 1 10 | #SBATCH --time 4:00:00 11 | 12 | # activate a correct anaconda environment 13 | source ~/anaconda3/bin/activate 14 | conda activate /depot/bsavoie/apps/anaconda3/envs/yarp/ 15 | module load intel-mkl 16 | module load openmpi 17 | 18 | python main_dft.py parameters.yaml 19 | 20 | wait 21 | -------------------------------------------------------------------------------- /reaction/job_xtb.submit: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # 3 | #SBATCH --job-name=yarp/lithium 4 | #SBATCH --output=runyarp.1.out 5 | #SBATCH --error=runyarp.1.err 6 | #SBATCH -A bsavoie 7 | #SBATCH --nodes=1 8 | #SBATCH --mem-per-cpu=4500MB 9 | #SBATCH --ntasks-per-node=24 10 | #SBATCH --time 72:00:00 11 | 12 | # activate a correct anaconda environment 13 | source ~/anaconda3/bin/activate 14 | conda activate /depot/bsavoie/apps/anaconda3/envs/yarp/ 15 | module load intel-mkl 16 | module load openmpi 17 | 18 | # Load environment for Gaussian 19 | python main_xtb.py parameters.yaml 20 | 21 | wait 22 | -------------------------------------------------------------------------------- /reaction/parameters.yaml: -------------------------------------------------------------------------------- 1 | # Note that a bimolecular reaction is recommended to use .xyz or .mol file 2 | # Enumetation part 3 | input: /Users/hsu205/github/classy-yarp/reaction/reaction_xyz/DA.xyz # (1) The input folder with .xyz or .mol file (2) a text file with multiple smiles 4 | scratch: /Users/hsu205/github/classy-yarp/reaction/DA # The output folder with reaction geometry for constructing reaction network. 5 | reaction_data: DA.p 6 | n_break: 1 # Indicate the number of breaking bonds 7 | form_all: False # Forming all possible bonds (matters for lone paired electrons (oxygen, sulfur, and other similar atoms)) (default: 0) 8 | lewis_criteria: 5.0 # the criteria to find the products 9 | ff: uff # force field for driving the reaction coordinate 10 | crest: crest 11 | lot: gfn2 12 | crest_quick: False 13 | xtb: xtb 14 | method: crest 15 | enumeration: False # if you only have reactant, you will need to do enumeration. Ohterwise, you need to provide reaction geometry. 16 | n_conf: 5 17 | nconf_dft: 5 18 | strategy: 2 19 | nprocs: 1 20 | c_nprocs: 1 21 | mem: 1 # in GB 22 | crest: crest 23 | opt_level: vtight 24 | crest_quick: False 25 | opt: False 26 | pysis_wt: 3600 27 | select: network 28 | charge: 0 29 | multiplicity: 1 30 | skip_low_IRC: False 31 | skip_low_TS: False 32 | constrained_TS: True 33 | model_path: /Users/hsu205/github/classy-yarp/reaction/bin 34 | gsm_inp: /home/hsu205/classy-yarp/reaction/bin/inpfileq 35 | 36 | package: ORCA #Gaussian or ORCA 37 | dft_nprocs: 4 38 | dft_lot: UHF 6-31G 39 | dft_wt: 4 40 | ppn: 8 41 | partition: standby 42 | dft_njobs: 1 43 | hess_recalc: 3 44 | dft_irc: True 45 | backward_DE: False 46 | dielectric: 95.3 47 | solvation: CPCM/read 48 | -------------------------------------------------------------------------------- /reaction/radicals.p: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/radicals.p -------------------------------------------------------------------------------- /reaction/read_yarp_reaction.py: -------------------------------------------------------------------------------- 1 | import pickle 2 | import os, sys 3 | 4 | data=pickle.load(open(sys.argv[1], 'rb')) 5 | for i in data: 6 | print(i.product_inchi) 7 | print(i.reactant_dft_opt) 8 | print(i.TS_dft) 9 | -------------------------------------------------------------------------------- /reaction/scripts/gscreate: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | file=molecule 4 | 5 | #nl $file > tmp.mole 6 | #nl link > tmp.link 7 | #join tmp.mole tmp.link > tmp.geom2 8 | #awk '{ print $2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10 }' tmp.geom2 > tmp.geom 9 | 10 | #cat qstart tmp.geom qend > qcin 11 | #cat qstart molecule$1 qend > scratch/qcin$1 12 | cat qstart $QCSCRATCH/molecule$1 qend > $QCSCRATCH/qcin$1 13 | 14 | #rm tmp.geom tmp.geom2 tmp.link tmp.mole 15 | -------------------------------------------------------------------------------- /reaction/scripts/ograd: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | # The path to ORCA should be added to .bashrc or exported in command line 3 | 4 | if [ -z $2 ] 5 | then 6 | echo " need two arguments! " 7 | exit 8 | fi 9 | 10 | #echo " in ograd: $1 $2 " 11 | 12 | ofile=$SLURM_LOCAL_SCRATCH/orcain$1.in 13 | ofileout=scratch/orcain$1.out 14 | molfile=scratch/structure$1 15 | ncpu=$2 16 | 17 | #echo " ofile: $ofile ofileout: $ofileout molfile: $molfile ncpu: $ncpu" 18 | 19 | ########## DFT settings: ################# 20 | #echo '! DFT B3LYP ENGRAD 6-31G*' > $ofile 21 | echo '! B97-3c ENGRAD' > $ofile 22 | echo '! nomoprint' >> $ofile 23 | echo '%scf' >> $ofile 24 | echo ' maxiter 200' >> $ofile 25 | echo 'end' >> $ofile 26 | # charge and spin multiplicity 27 | echo '* xyz 0 1' >> $ofile 28 | cat $molfile >> $ofile 29 | echo '*' >> $ofile 30 | 31 | #echo "running: orca $ofile > $ofileout" 32 | orca $ofile > $ofileout 33 | -------------------------------------------------------------------------------- /reaction/scripts/ograd_xtb: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | if [ -z $2 ] 4 | then 5 | echo " need two arguments! " 6 | exit 7 | fi 8 | 9 | ofile=orcain$1.in 10 | ofileout=orcain$1.out 11 | molfile=structure$1 12 | ncpu=$2 13 | 14 | basename="${ofile%.*}" 15 | 16 | ########## XTB settings: ################# 17 | cd scratch 18 | wc -l < $molfile > $ofile.xyz 19 | echo "Dummy for XTB/TM calculation" >> $ofile.xyz 20 | cat $molfile >> $ofile.xyz 21 | 22 | 23 | -------------------------------------------------------------------------------- /reaction/scripts/qend: -------------------------------------------------------------------------------- 1 | $end 2 | -------------------------------------------------------------------------------- /reaction/scripts/qstart: -------------------------------------------------------------------------------- 1 | $rem 2 | JOBTYPE FORCE 3 | METHOD B3LYP 4 | SCF_MAX_CYCLES 150 5 | BASIS 6-31G* 6 | WAVEFUNCTION_ANALYSIS FALSE 7 | GEOM_OPT_MAX_CYCLES 300 8 | xc_grid 1 9 | scf_convergence 6 10 | SYM_IGNORE TRUE 11 | SYMMETRY FALSE 12 | molden_format true 13 | $end 14 | 15 | $molecule 16 | 0 1 17 | -------------------------------------------------------------------------------- /reaction/tst.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | 3 | C -5.7083521536 -0.6266785876 -0.1825544680 4 | C -6.5598120706 -1.8069040709 0.2776430594 5 | C -4.2496550938 -0.7876607361 0.2369602287 6 | H -6.1114085240 0.3034752125 0.2335390979 7 | H -5.7658841660 -0.5398749297 -1.2745994133 8 | C -3.6710738104 -2.1179645354 -0.2376406574 9 | H -4.1761715523 -0.7276396985 1.3298479186 10 | H -3.6556423954 0.0388293452 -0.1690434512 11 | C -4.5225890468 -3.2982007892 0.2224389469 12 | H -2.6486566618 -2.2313008994 0.1399761805 13 | H -3.6093683982 -2.1183382533 -1.3329021774 14 | C -5.9812705103 -3.1371667873 -0.1971066317 15 | H -6.6213370545 -1.8065649423 1.3729157556 16 | H -7.5822880208 -1.6935613566 -0.0998085364 17 | H -6.0547275844 -3.1970548634 -1.2900040790 18 | H -6.5753076490 -3.9636921029 0.2087869904 19 | H -4.4650986645 -3.3850881171 1.3144790976 20 | H -4.1195380663 -4.2283335900 -0.1937079926 21 | -------------------------------------------------------------------------------- /reaction/wrappers/.reaction.py.swp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/reaction/wrappers/.reaction.py.swp -------------------------------------------------------------------------------- /reaction/xtb_run/HGCIXCUEYOPUTN/HGCIXCUEYOPUTN-init.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | 3 | C -1.0130998647 1.2188100173 0.4131533656 4 | C -1.2165513306 2.5155395913 -0.1903843632 5 | H -1.8343383803 0.9722823872 1.1317190614 6 | H -1.2350027141 0.43677503 -0.3693100239 7 | H -1.925936237 3.1208321785 0.4343687424 8 | H -1.8682970459 2.401417917 -1.0996707941 9 | C -0.0706470891 3.31426552 -0.5325170884 10 | C 1.2041191104 2.9167873587 -0.0673717451 11 | C 1.3729637658 1.7429627418 0.6634192445 12 | C 0.27563756 0.90533103 0.9679057377 13 | H -0.2284205994 4.4102378878 -0.3761047893 14 | H 0.0086180232 3.4221533822 -1.6517286587 15 | H 2.0707320972 3.5401940159 -0.2821124798 16 | H 2.3678522185 1.4707353948 1.0123078712 17 | H 0.5543546657 -0.1733362366 0.8792394704 18 | H 0.2029295834 0.8607365858 2.0924832284 19 | -------------------------------------------------------------------------------- /reaction/xtb_run/HGCIXCUEYOPUTN/HGCIXCUEYOPUTN_input.yaml: -------------------------------------------------------------------------------- 1 | geom: 2 | type: cart 3 | fn: /Users/hsu205/github/classy-yarp/reaction/xtb_run/HGCIXCUEYOPUTN/HGCIXCUEYOPUTN-init.xyz 4 | calc: 5 | type: xtb 6 | pal: 1 7 | mem: 4000 8 | charge: 0 9 | mult: 1 10 | opt: 11 | type: rfo 12 | max_cycles: 50 13 | overachieve_factor: 3 14 | hessian_recalc: 1 15 | do_hess: True 16 | -------------------------------------------------------------------------------- /reaction/xtb_run/HGCIXCUEYOPUTN/RUN.yaml: -------------------------------------------------------------------------------- 1 | assert: null 2 | barrier: null 3 | calc: 4 | charge: 0 5 | mem: 4000 6 | mult: 1 7 | pal: 1 8 | type: xtb 9 | cos: null 10 | endopt: null 11 | geom: 12 | coord_kwargs: {} 13 | fn: /Users/hsu205/github/classy-yarp/reaction/xtb_run/HGCIXCUEYOPUTN/HGCIXCUEYOPUTN-init.xyz 14 | type: cart 15 | glob: null 16 | interpol: null 17 | irc: null 18 | md: null 19 | mdp: null 20 | opt: 21 | T: 298.15 22 | do_hess: true 23 | dump: true 24 | hessian_recalc: 1 25 | max_cycles: 50 26 | overachieve_factor: 3 27 | p: 101325 28 | type: rfo 29 | perf: null 30 | precontr: null 31 | preopt: null 32 | scan: null 33 | shake: null 34 | stocastic: null 35 | tsopt: null 36 | version: 0.7.6.post2 37 | -------------------------------------------------------------------------------- /reaction/xtb_run/HGCIXCUEYOPUTN/final_geometry.xyz: -------------------------------------------------------------------------------- 1 | 16 2 | -17.93143469 , 3 | C -0.99565911 1.11365923 0.18132450 4 | C -1.27606981 2.60235503 0.00621402 5 | H -1.87015336 0.60701239 0.59652452 6 | H -0.78124129 0.67212641 -0.79519026 7 | H -1.41874000 3.05865194 0.98976411 8 | H -2.19153547 2.75281318 -0.57214870 9 | C -0.09768571 3.27066793 -0.69802487 10 | C 1.20712103 2.85883263 -0.08807867 11 | C 1.34217747 1.81494158 0.71224009 12 | C 0.20657606 0.91889618 1.10162547 13 | H -0.19651844 4.35903197 -0.65048292 14 | H -0.09394222 2.99564591 -1.75944204 15 | H 2.06428798 3.46565933 -0.34755614 16 | H 2.30699363 1.56935898 1.13582647 17 | H 0.53724804 -0.12289726 1.07602732 18 | H -0.07794548 1.13896956 2.13677414 -------------------------------------------------------------------------------- /reaction/xtb_run/HGCIXCUEYOPUTN/final_hessian.h5: 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-3.1607539050 1.2485991406 -0.1073412723 7 | C -2.0716602679 2.3131086134 -0.1197067520 8 | O -0.8349075554 1.7084398640 -0.0351476891 9 | C 0.3333021778 2.3940654395 -0.0439044155 10 | O 0.3488251014 3.7380410895 -0.1548601767 11 | Li -7.1713576933 -1.0911900792 -0.2603447503 12 | O -6.6185210964 1.7717208490 -0.2965949923 13 | O 1.3869857059 1.7864179295 0.0437449720 14 | Li 1.9507032114 4.6377613481 -0.1816731171 15 | H -2.2142128489 2.9994602321 0.7443054233 16 | H -2.1410878069 2.8952400397 -1.0653584896 17 | H -3.0950908055 0.6619982662 0.8358013339 18 | H -3.0139284647 0.5664708743 -0.9739912749 19 | -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [tool.setuptools_scm] 2 | write_to = "pysisyphus/version.py" 3 | 4 | #[metadata] 5 | #name = pysisyphus 6 | #description = Python suite for exploring potential energy surfaces. 7 | #long_description = file: README.md 8 | #long_description_content_type = text/markdown 9 | #url = https://github.com/eljost/pysisyphus 10 | #maintainer = Johannes Steinmetzer 11 | #maintainer_email = johannes.steinmetzer@uni-jena.de 12 | #license = GNU General Public License v3 (GPLv3) 13 | #platform = unix 14 | #classifiers = 15 | # License :: OSI Approved :: GNU General Public License v3 (GPLv3) 16 | 17 | [options] 18 | packages = find: 19 | include_package_data = True 20 | python_requires = >=3.8 21 | install_requires = 22 | autograd 23 | dask 24 | distributed 25 | h5py 26 | fabric 27 | jinja2 28 | joblib 29 | matplotlib 30 | numpy 31 | natsort 32 | psutil 33 | pyyaml 34 | rmsd 35 | scipy 36 | sympy 37 | scikit-learn 38 | pysisyphus 39 | yaml 40 | 41 | [options.extras_require] 42 | test = pyscf; pytest; pytest-cov; ase; qcengine 43 | doc = sphinx; sphinx-rtd-theme ; sphinx_autodoc_typehints 44 | 45 | -------------------------------------------------------------------------------- /tutorial/.ipynb_checkpoints/joint_opt_tutorial-checkpoint.ipynb: -------------------------------------------------------------------------------- 1 | { 2 | "cells": [], 3 | "metadata": {}, 4 | "nbformat": 4, 5 | "nbformat_minor": 5 6 | } 7 | -------------------------------------------------------------------------------- /tutorial/butylacid.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/tutorial/butylacid.pdf -------------------------------------------------------------------------------- /tutorial/butylacid.xyz: -------------------------------------------------------------------------------- 1 | 17 2 | 3 | C -5.8657845028 0.7023035226 -0.0294527215 4 | C -4.5317046800 1.4371089855 -0.0380101576 5 | H -5.7662607624 -0.3458428744 -0.3285294181 6 | H -6.5694616871 1.1848788248 -0.7154216341 7 | H -6.3107885738 0.7286354338 0.9707176950 8 | C -3.3471074615 0.4718461806 -0.0225534210 9 | H -4.4835980331 2.1069648131 0.8290406177 10 | H -4.4722833683 2.0688384943 -0.9319824989 11 | C -2.0148098920 1.2196099421 -0.0018445778 12 | H -3.3880818215 -0.1711418744 -0.9113589765 13 | H -3.4183634026 -0.1897755295 0.8493326749 14 | C -0.8387633465 0.2715692758 0.0633048889 15 | H -1.9721895783 1.8765840292 0.8737277408 16 | O -0.9103740086 -0.9447174995 0.1060015360 17 | O 0.3462405452 0.9269033313 0.0724670429 18 | H 0.2587198144 1.8977683125 0.0346505118 19 | H -1.9174536606 1.8250434844 -0.9100616023 20 | -------------------------------------------------------------------------------- /tutorial/cyclopentene_H2.xyz: -------------------------------------------------------------------------------- 1 | 15 2 | 3 | C -2.7553264507 2.3624792824 -0.1746648851 4 | C -3.8973382821 1.4162256271 0.1766183373 5 | C -3.3506816194 0.0195251499 -0.0942742603 6 | H -4.8861837329 1.6521816223 -0.2697235441 7 | H -4.0103014179 1.4829632360 1.2850672416 8 | C -1.5660397445 1.5356596604 0.1702174530 9 | H -2.8440858550 3.2996553383 0.4154122564 10 | H -2.7078524955 2.5857685061 -1.2622026444 11 | C -1.9055840623 0.1994167983 0.2160656125 12 | H -3.4332323205 -0.2688791803 -1.1642548400 13 | H -3.8659312540 -0.7216996420 0.5533921466 14 | H -0.5510632594 1.9004258669 0.2546355478 15 | H -1.1861517973 -0.5989067720 0.3403905711 16 | H 2.9379190927 -0.6292233688 0.0554400041 17 | H 3.3594109958 -0.0603512142 0.0536973431 18 | -------------------------------------------------------------------------------- /tutorial/cyclopetene_H2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/tutorial/cyclopetene_H2.pdf -------------------------------------------------------------------------------- /tutorial/enumeration_tutorial.py: -------------------------------------------------------------------------------- 1 | import yarp as yp 2 | import numpy as np 3 | reactant=yp.yarpecule("test.xyz") 4 | 5 | print("running enumeration") 6 | yp.draw_bmats(reactant,"reactant.pdf") 7 | 8 | reactant=yp.yarpecule("test2.xyz") 9 | 10 | print("running enumeration") 11 | yp.draw_bmats(reactant,"reactant2.pdf") 12 | exit() 13 | break_mols=list(yp.break_bonds(reactant, n=2)) 14 | print(f"We have {len(break_mols)} reaction intermediates with breaking 2 bonds.") 15 | import numpy as np 16 | products=yp.form_n_bonds(break_mols, n=2) 17 | print(f"Raw products: {len(products)}") 18 | products=[_ for _ in products if _.bond_mat_scores[0]<=5.0] 19 | # Question: what's the purpose of this line? 20 | print(f"We have {len(products)} products") 21 | yp.draw_yarpecules(products, "cyclopetene_H2.pdf", label_ind=True, mol_labels=[f"score {_.bond_mat_scores[0]}" for _ in products]) 22 | 23 | -------------------------------------------------------------------------------- /tutorial/ethanol.xyz: -------------------------------------------------------------------------------- 1 | 10 2 | 3 | C -14.7487857567 -4.9922190058 2.3068624496 4 | C -13.3922927661 -4.4980917954 1.8235617109 5 | O -15.6975306470 -3.9342284271 2.2650449169 6 | H -14.6751208007 -5.3672604444 3.3331930399 7 | H -15.1020133413 -5.8154572679 1.6768100429 8 | H -16.5380198263 -4.3005355513 2.5903718931 9 | O -12.4401603589 -5.5524036128 1.8787207118 10 | H -13.0440839080 -3.6676584506 2.4469165008 11 | H -13.4636327792 -4.1331384792 0.7934258487 12 | H -11.5954822129 -5.1815994394 1.5696280898 13 | -------------------------------------------------------------------------------- /tutorial/ethanol_form_all.pdf: -------------------------------------------------------------------------------- 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-12.2688970657 -4.7718563387 1.4501242101 18 | H -13.6737012993 -3.7515474646 2.7119609727 19 | H -14.1218085805 -3.7818331250 1.0048571261 20 | H -11.8031717111 -5.3528583776 2.2527638749 21 | H -11.6612453293 -3.8773574369 1.2818012152 22 | H -12.2496606766 -5.3731371192 0.5355816252 23 | -------------------------------------------------------------------------------- /tutorial/reactant.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/tutorial/reactant.pdf -------------------------------------------------------------------------------- /tutorial/reactant2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Savoie-Research-Group/yarp/e6ebc2cc3988f3160f60945f320b4d284494e848/tutorial/reactant2.pdf -------------------------------------------------------------------------------- /yarp/__init__.py: -------------------------------------------------------------------------------- 1 | # yarp/__init__.py 2 | version_info = (5, 0, 0) 3 | version = '.'.join(str(c) for c in version_info) 4 | __version__ = version 5 | __author__ = 'Savoie Research Group' 6 | __email__ = 'brettsavoie@gmail.com' 7 | __description__ = 'This is a class-based refactoring of many of the routines associated with the Yet Another Reaction Program (YARP) methodology.' 8 | from .properties import * 9 | from .hashes import * 10 | from .input_parsers import * 11 | from .taffi_functions import * 12 | from .find_lewis import * 13 | from .sieve import * 14 | from .yarpecule import * 15 | from .enum import * 16 | from .misc import * 17 | yp = __import__('yarp') 18 | -------------------------------------------------------------------------------- /yarp/constants.py: -------------------------------------------------------------------------------- 1 | class Constants: 2 | 3 | n_a = 6.022140857E23 # molecules mol-1 4 | 5 | ha_to_kcalmol = ha2kcalmol = 627.509 # Hartree^-1 kcal mol^-1 6 | ha_to_kJmol = ha2kJmol = 2625.50 # Hartree^-1 kJ mol^-1 7 | 8 | ha_to_J = ha_to_kJmol * 1000 / n_a # Hartree^-1 J 9 | J_to_ha = 1.0 / ha_to_J # J Hartree^-1 10 | 11 | eV_to_ha = eV2ha = 0.0367493 # Hartree eV^-1 12 | ha_to_eV = ha2eV = 1.0 / eV_to_ha # eV Hartree^-1 13 | 14 | kcal_to_kJ = kcal2kJ = 4.184 # kJ kcal^-1 15 | 16 | rad_to_deg = 57.29577951308232087679815 # deg rad^-1 17 | 18 | a0_to_ang = a02ang = 0.529177 # Å bohr^-1 19 | ang_to_a0 = ang2a0 = 1.0 / a0_to_ang # bohr Å^-1 20 | ang_to_nm = 0.1 # nm ang^-1 21 | ang_to_pm = 100 # pm ang^-1 22 | ang_to_m = 1E-10 # m ang^-1 23 | a0_to_m = a0_to_ang * ang_to_m # Å m^-1 24 | 25 | per_cm_to_hz = c_in_cm = 299792458 * 100 # cm s^-1 26 | 27 | amu_to_kg = 1.66053906660E-27 # kg amu^-1 28 | amu_to_me = 1822.888486209 # m_e amu^-1 29 | 30 | atm_to_pa = 101325 # Pa atm^-1 31 | dm_to_m = 0.1 # m dm^-1 32 | 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