├── .coveragerc ├── .envrc ├── .flake8 ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ ├── build_and_publish.yml │ ├── codeql.yml │ └── pythonapp.yml ├── .gitignore ├── .lgtm.yml ├── Citation.cff ├── LICENSE ├── MANIFEST.in ├── README.md ├── architecture.md ├── codecov.yml ├── doc-requirements.txt ├── docs ├── Makefile ├── _static │ ├── microcycle_layers.svg │ ├── oniom.svg │ └── oniom_links.svg ├── api │ ├── modules.rst │ ├── pysisyphus.benchmarks.rst │ ├── pysisyphus.calculators.rst │ ├── pysisyphus.cos.rst │ ├── pysisyphus.db.rst │ ├── pysisyphus.diabatization.rst │ ├── pysisyphus.drivers.rst │ ├── pysisyphus.dynamics.rst │ ├── pysisyphus.franckcondon.rst │ ├── pysisyphus.hindered_rotor.rst │ ├── pysisyphus.intcoords.rst │ ├── pysisyphus.interpolate.rst │ ├── pysisyphus.io.rst │ ├── pysisyphus.irc.rst │ ├── pysisyphus.line_searches.rst │ ├── pysisyphus.marcus_dim.rst │ ├── pysisyphus.modefollow.rst │ ├── pysisyphus.numerov.rst │ ├── pysisyphus.numint.rst │ ├── pysisyphus.optimizers.rst │ ├── pysisyphus.partfuncs.rst │ ├── pysisyphus.plotters.rst │ ├── pysisyphus.rst │ ├── pysisyphus.stocastic.rst │ ├── pysisyphus.tests.rst │ ├── pysisyphus.tsoptimizers.rst │ ├── pysisyphus.wavefunction.ints.rst │ ├── pysisyphus.wavefunction.ints_numba.rst │ ├── pysisyphus.wavefunction.rst │ └── pysisyphus.wrapper.rst ├── calculators.rst ├── chainofstates.rst ├── conf.py ├── coordinate_systems.rst ├── diabatization.rst ├── es_optimization.rst ├── images │ ├── afir │ │ ├── afir.png │ │ ├── afir_molecules.png │ │ └── afir_molecules.svg │ ├── cytosin │ │ ├── cytosin_ae.png │ │ ├── cytosin_ovlps_0.png │ │ └── cytosin_ovlps_1.png │ ├── diabatization │ │ ├── dithiophene_sds.png │ │ ├── omp3.png │ │ ├── omp3_adiabatic_da.png │ │ ├── omp3_diabatic_da.png │ │ └── omp3_er_couplings.png │ ├── diels_alder │ │ ├── diels_alder.png │ │ ├── diels_alder.svg │ │ ├── diels_alder_finished_irc.png │ │ ├── diels_alder_first_pre_opt.png │ │ ├── diels_alder_last_pre_opt.png │ │ ├── diels_alder_neb_cosforces.png │ │ ├── diels_alder_neb_cycles_splined.png │ │ ├── diels_alder_neb_last_cycle.png │ │ └── diels_alder_tsopt.png │ └── pericyclic_reactants.png ├── index.rst ├── installation.rst ├── irc.rst ├── make.bat ├── marcusdim.rst ├── microiterations.rst ├── min_optimization.rst ├── nix.rst ├── overview.rst ├── plotting.rst ├── pysistrj.rst ├── scans.rst ├── tsoptimization.rst └── worked_example.rst ├── examples ├── calc │ ├── 01_psi4_to_set_1 │ │ └── 01_psi4_to_set_1.yaml │ ├── 02_psi4_to_set_2 │ │ └── 02_psi4_to_set_2.yaml │ ├── 03_psi4_pcm_custom_basis │ │ └── 03_psi4_custom_basis.yaml │ └── 04_pyscf_methane_perf │ │ └── 04_pyscf_methane_perf.yaml ├── complex │ ├── 01_alanine_dipeptide_iso_gs_rsprfo │ │ ├── 01_alanine_dipeptide_iso_gs_rsprfo.yaml │ │ ├── first_preopt.xyz │ │ └── last_preopt.xyz │ ├── 02_alanine_dipeptide_iso_xtb │ │ ├── 02_alanine_dipeptide_iso_xtb.yaml │ │ ├── ala_end.xyz │ │ ├── ala_start.xyz │ │ └── test_plots.sh │ ├── 03_xtb_neb_optimization │ │ ├── 03_xtb_neb_optimization.yaml │ │ ├── 09_htransfer_product.xyz │ │ └── 10_po_diss_product_xtbopt.xyz │ ├── 04_biaryl_pm7_gs_tsopt_irc │ │ ├── 04_biaryl_bare_pm7_gs_tsopt_irc.yaml │ │ ├── split.image_000.xyz │ │ └── split.image_056.xyz │ ├── 05_orca_diels_alder_gs_tsopt │ │ ├── 05_orca_diels_alder_gs_tsopt.yaml │ │ └── diels_alder.trj │ ├── 06_diels_alder_xtb_preopt_neb_tsopt_irc │ │ ├── 06_diels_alder_xtb_preopt_neb_tsopt_irc.yaml │ │ ├── diels_alder.trj │ │ └── make_plots.sh │ ├── 07_diels_alder_xtb_bfgs_preopt_neb_tsopt_irc │ │ ├── 07_diels_alder_xtb_bfgs_preopt_neb_tsopt_irc.yaml │ │ └── diels_alder.trj │ ├── 08_trispericyclic │ │ ├── 08_trispericyclic.yaml │ │ ├── min_xtbopt.xyz │ │ └── prod_xtbopt.xyz │ ├── 09_hcn_iso_constrained_atom │ │ └── 09_hcn_iso_constrained_atom.yaml │ ├── 10_hcn_deuterium_tsopt_irc │ │ └── 10_hcn_deuterium_tsopt_irc.yaml │ ├── 11_turbomole_gs_tsopt │ │ ├── 11_turbomole_gs_tsopt.yaml │ │ └── control_path │ │ │ ├── auxbasis │ │ │ ├── basis │ │ │ ├── control │ │ │ ├── coord │ │ │ └── mos │ ├── 12_qcengine_turbomole_gs_tsopt │ │ └── 12_qcengine_turbomole_gs_tsopt.yaml │ └── 13_orca_parallel_neb │ │ └── 13_orca_parallel_neb.yaml ├── irc │ ├── 01_hcn_pm6_irc │ │ ├── 01_hcn_pm6_irc.yaml │ │ └── ts_opt.xyz │ ├── 02_hf_abstraction_xtb_irc │ │ ├── 02_hf_abstraction_xtb_irc.yaml │ │ └── hfabstraction_ts_opt_xtb.xyz │ ├── 03_hcn_pyscf_imk │ │ └── 03_hcn_pyscf_imk.yaml │ └── 04_hcn_orca_eulerpc │ │ └── 04_hcn_orca_eulerpc.yaml ├── md │ └── 01_cyclobutene_gfn0_xtb_mtd │ │ └── 01_cyclobutene_gfn0_xtb_mtd.yaml ├── mdp │ └── 01_trispericyclic │ │ ├── 01_trispericyclic.yaml │ │ └── ts_opt.input.xyz ├── opt │ ├── 01_turbomole_cytosin_s1_opt │ │ ├── 01_turbomole_cytosin_s1_opt.yaml │ │ └── control_path_pbe0_def2svp_s1 │ │ │ ├── basis │ │ │ ├── control │ │ │ ├── coord │ │ │ ├── energy │ │ │ └── mos │ ├── 02_xtb_cytosin_opt │ │ ├── 02_xtb_cytosin_opt.yaml │ │ └── cytosin.xyz │ ├── 03_xtb_gfn_gbsa_opt │ │ ├── 03_xtb_gfn_gbsa_opt.yaml │ │ └── cytosin.xyz │ ├── 04_orca_numfreq_blocks │ │ └── 04_orca_numfreq_blocks.yaml │ ├── 05_orca_opt_hessian_init_xtb1 │ │ ├── 05_orca_opt_hessian_init_xtb1.yaml │ │ └── h2o2_hf_321g_opt.xyz │ ├── 06_orca_cytosin_s1_opt │ │ └── 06_orca_cytosin_s1_opt.yaml │ ├── 07_openmolcas_trans_butadiene_s1_opt │ │ ├── 07_openmolcas_trans_butadiene_s1_opt.yaml │ │ ├── butadien_vdzp.RasOrb │ │ └── trans_butadien.xyz │ ├── 08_qcengine_gamess_hcn_opt │ │ └── 08_qcengine_gamess_hcn_opt.yaml │ ├── 09_psi4_omp25_define_prims │ │ └── 09_psi4_omp25_define_prims.yaml │ ├── 10_h2o_xtb_ipi_server │ │ ├── 10_h2o_xtb_ipi_server.yaml │ │ ├── client.py │ │ └── h2o.xyz │ ├── 11_xtb_constrain_prims │ │ └── 11_xtb_constrain_prims.yaml │ ├── 12_methane_xtb_micro_opt │ │ ├── 12_methane_xtb_micro_opt.yaml │ │ └── client.py │ ├── 13_h2_xtb_restraint │ │ └── 13_h2_xtb_restraint.yaml │ ├── 14_tric_xtb_solvated │ │ └── 14_tric_xtb_solvated.yaml │ ├── 15_orca_cytosin_s1_prnto_opt │ │ └── 15_orca_cytosin_s1_prnto_opt.yaml │ ├── 16_orca_sn2_dist_func │ │ └── 16_orca_sn2_dist_func.yaml │ ├── 17_orca_conical_intersection │ │ └── 17_orca_conical_intersection.yaml │ ├── 18_orca_1methylcytosin_iterative_opt │ │ └── 18_orca_1methylcytosin_iterative_opt.yaml │ ├── 19_xtb_1methylcytosin_iterative_opt │ │ └── 19_xtb_1methylcytosin_iterative_opt.yaml │ ├── 21_xtb_layeropt │ │ └── 21_xtb_layeropt.yaml │ ├── 22_ipi_layeropt │ │ └── 22_ipi_layeropt.yaml │ ├── 23_orca_afir │ │ └── 23_orca_afir.yaml │ ├── 24_xtb_three_frag_afir │ │ └── 24_xtb_three_frag_afir.yaml │ ├── 25_uracil_dimer_rmsd_restraint │ │ └── 25_uracil_dimer_rmsd_restraint.yaml │ ├── 26_turbomole_simple_input │ │ └── 26_turbomole_simple_input.yaml │ └── 28_ascii_art │ │ └── 28_ascii_art.yaml └── tsopt │ ├── 01_biaryl_xtb_tsopt_recalc │ ├── 01_biaryl_xtb_tsopt_recalc.yaml │ └── input.got.geom_000.xyz │ ├── 02_hcn_tsopt_dimer │ ├── 01_hcn.xyz │ └── 02_hcn_tsopt_dimer.yaml │ ├── 03_orca_ala_dipep_initial_hessian_xtb │ ├── 03_orca_ala_dipep_initial_hessian_xtb.yaml │ └── ts_guess_from_xtb.xyz │ ├── 04_diels_alder_xtb_tsopt_davidson │ └── 04_diels_alder_xtb_tsopt_davidson.yaml │ ├── 05_orca_baker_ts_tetrazine │ └── 05_orca_baker_ts_tetrazine.yaml │ └── 06_orca_baker_ts_trans_butadiene │ └── 06_baker_ts_trans_butadiene_tsopt.yaml ├── flake.lock ├── flake.nix ├── flake8.ini ├── nix ├── default.nix ├── overlay.nix ├── pkgs.nix ├── pysisyphus.nix └── shell.nix ├── pyproject.toml ├── pyrightconfig.json ├── pysisyphus ├── Geometry.py ├── MOCoeffs.py ├── TablePrinter.py ├── __init__.py ├── basis_library │ ├── def2-universal-jfit.json │ ├── minao.json │ └── parse_minao.py ├── benchmarks │ ├── Benchmark.py │ ├── __init__.py │ └── data.py ├── calculators │ ├── AFIR.py │ ├── AnaPot.py │ ├── AnaPot2.py │ ├── AnaPot3.py │ ├── AnaPot4.py │ ├── AnaPotBase.py │ ├── AnaPotCBM.py │ ├── AtomAtomTransTorque.py │ ├── CFOUR.py │ ├── Calculator.py │ ├── CerjanMiller.py │ ├── Composite.py │ ├── ConicalIntersection.py │ ├── DFTBp.py │ ├── DFTD3.py │ ├── DFTD4.py │ ├── Dalton.py │ ├── Dimer.py │ ├── Dummy.py │ ├── EGO.py │ ├── EnergyMin.py │ ├── ExternalPotential.py │ ├── FakeASE.py │ ├── FourWellAnaPot.py │ ├── FreeEndNEBPot.py │ ├── Gaussian09.py │ ├── Gaussian16.py │ ├── HardSphere.py │ ├── IDPPCalculator.py │ ├── IPIClient.py │ ├── IPIServer.py │ ├── LEPSBase.py │ ├── LEPSExpr.py │ ├── LennardJones.py │ ├── MOPAC.py │ ├── MullerBrownSympyPot.py │ ├── MultiCalc.py │ ├── NFK.py │ ├── OBabel.py │ ├── ONIOMv2.py │ ├── ORCA.py │ ├── ORCA5.py │ ├── OpenMM.py │ ├── OpenMolcas.py │ ├── OverlapCalculator.py │ ├── Pots1d.py │ ├── Psi4.py │ ├── PyPsi4.py │ ├── PySCF.py │ ├── QCEngine.py │ ├── Rastrigin.py │ ├── Remote.py │ ├── RobinDayClass2.py │ ├── Rosenbrock.py │ ├── SerpentinePot.py │ ├── SocketCalc.py │ ├── TBLite.py │ ├── TIP3P.py │ ├── TransTorque.py │ ├── Turbomole.py │ ├── VRIPot.py │ ├── WFOWrapper.py │ ├── WFOWrapper2.py │ ├── XTB.py │ ├── __init__.py │ ├── cosmo_data.py │ ├── parser.py │ └── pyscf_lazy.py ├── color.py ├── config.py ├── constants.py ├── cos │ ├── AdaptiveNEB.py │ ├── ChainOfStates.py │ ├── FreeEndNEB.py │ ├── FreezingString.py │ ├── GrowingChainOfStates.py │ ├── GrowingNT.py │ ├── GrowingString.py │ ├── NEB.py │ ├── SimpleZTS.py │ ├── __init__.py │ ├── distributed.py │ ├── multi_state.py │ └── stiffness.py ├── db │ ├── __init__.py │ ├── generate_db.py │ ├── guess │ │ ├── 14dioxane.xyz │ │ ├── acetone.xyz │ │ ├── acetonitrile.xyz │ │ ├── chloroform.xyz │ │ ├── dichloromethane.xyz │ │ ├── tetrahydrofuran.xyz │ │ └── water.xyz │ ├── helpers.py │ ├── level.py │ ├── levels │ │ ├── b973c_orca │ │ │ ├── 14dioxane.xyz │ │ │ ├── acetone.xyz │ │ │ ├── acetonitrile.xyz │ │ │ ├── chloroform.xyz │ │ │ ├── dichloromethane.xyz │ │ │ ├── tetrahydrofuran.xyz │ │ │ └── water.xyz │ │ ├── gfn0_xtb │ │ │ ├── 14dioxane.xyz │ │ │ ├── acetone.xyz │ │ │ ├── acetonitrile.xyz │ │ │ ├── chloroform.xyz │ │ │ ├── dichloromethane.xyz │ │ │ ├── tetrahydrofuran.xyz │ │ │ └── water.xyz │ │ ├── gfn1_xtb │ │ │ ├── 14dioxane.xyz │ │ │ ├── acetone.xyz │ │ │ ├── acetonitrile.xyz │ │ │ ├── chloroform.xyz │ │ │ ├── dichloromethane.xyz │ │ │ ├── tetrahydrofuran.xyz │ │ │ └── water.xyz │ │ └── gfn2_xtb │ │ │ ├── 14dioxane.xyz │ │ │ ├── acetone.xyz │ │ │ ├── acetonitrile.xyz │ │ │ ├── chloroform.xyz │ │ │ ├── dichloromethane.xyz │ │ │ ├── tetrahydrofuran.xyz │ │ │ └── water.xyz │ └── molecules.py ├── diabatization │ ├── __init__.py │ ├── chimerabatch.py │ ├── coulomb.py │ ├── coulomb_eta.py │ ├── driver.py │ ├── driver_yaml.py │ ├── helpers.py │ ├── multipole.py │ ├── plot.py │ └── results.py ├── drivers │ ├── __init__.py │ ├── afir.py │ ├── barriers.py │ ├── birkholz.py │ ├── boltzmann.py │ ├── calculations.py │ ├── cluster.py │ ├── local_force_constants.py │ ├── merge.py │ ├── merge_mol2.py │ ├── opt.py │ ├── perf.py │ ├── pka.py │ ├── precon_pos_rot.py │ ├── rates.py │ ├── replace.py │ ├── scan.py │ ├── spectrum.py │ ├── spectrum_ctnum.py │ └── thermo.py ├── dynamics │ ├── Gaussian.py │ ├── __init__.py │ ├── colvars.py │ ├── driver.py │ ├── helpers.py │ ├── lincs.py │ ├── mdp.py │ ├── rattle.py │ ├── thermostats.py │ └── wigner.py ├── elem_data.py ├── exceptions.py ├── executors.py ├── filtertrj.py ├── finite_diffs.py ├── franckcondon │ ├── __init__.py │ ├── duschinsky.py │ ├── helpers.py │ ├── imdho.py │ └── lq2.py ├── geom_library │ ├── 01_h2o.xyz │ ├── 01_h2o_hdiss.xyz │ ├── 01_opt_aus_04_b3lyp_scan_min.xyz │ ├── 01_run6fbpb_photoprod_guess.xyz │ ├── 08_allene.xyz │ ├── 09_htransfer_product.xyz │ ├── 10_po_diss_product_xtbopt.xyz │ ├── SulfateInSolution.xyz │ ├── acet_tm.xyz │ ├── acetaldehyd.xyz │ ├── acetaldehyd_oniom.xyz │ ├── acetaldehyd_oniom_opt.xyz │ ├── affine3_input.xyz │ ├── affine3_output.xyz │ ├── afir3test.xyz │ ├── ala_dipeptide_cycle_021_gs_opt_xtb.trj │ ├── ala_dipeptide_iso_b3lyp_631gd_10_images.trj │ ├── ala_dipeptide_iso_b3lyp_631gd_start_end.trj │ ├── alkyl17_sto3g_opt.xyz │ ├── ar14cluster.xyz │ ├── azb_mp2.crd │ ├── azet_bad.xyz │ ├── azetidine_guess.xyz │ ├── azetidine_hf_321g_opt.xyz │ ├── azetidine_not_opt.xyz │ ├── azetidine_xtbopt.xyz │ ├── azobenzene_fragmentation.xyz │ ├── azobenzene_fragmentation_2.xyz │ ├── baker │ │ ├── 00_water.xyz │ │ ├── 01_ammonia.xyz │ │ ├── 02_ethane.xyz │ │ ├── 03_acetylene.xyz │ │ ├── 04_allene.xyz │ │ ├── 05_hydroxysulphane.xyz │ │ ├── 06_benzene.xyz │ │ ├── 07_methylamine.xyz │ │ ├── 08_ethanol.xyz │ │ ├── 09_acetone.xyz │ │ ├── 10_disilylether.xyz │ │ ├── 11_135trisilacyclohexane.xyz │ │ ├── 12_benzaldehyde.xyz │ │ ├── 13_13difluorobenzene.xyz │ │ ├── 14_135trifluorobenzene.xyz │ │ ├── 15_neopentane.xyz │ │ ├── 16_furan.xyz │ │ ├── 17_naphthalene.xyz │ │ ├── 18_15difluoronaphthalene.xyz │ │ ├── 19_2hydroxybicyclopentane.xyz │ │ ├── 20_achtar10.xyz │ │ ├── 21_acanil01.xyz │ │ ├── 22_benzidine.xyz │ │ ├── 23_pterin.xyz │ │ ├── 24_difuropyrazine.xyz │ │ ├── 25_mesityloxide.xyz │ │ ├── 26_histidine.xyz │ │ ├── 27_dimethylpentane.xyz │ │ ├── 28_caffeine.xyz │ │ └── 29_menthone.xyz │ ├── baker_ts │ │ ├── 01_hcn.xyz │ │ ├── 01_hcn.zmat │ │ ├── 01_hcn_downhill.xyz │ │ ├── 02_hcch.xyz │ │ ├── 02_hcch.zmat │ │ ├── 02_hcch_downhill.xyz │ │ ├── 03_h2co.xyz │ │ ├── 03_h2co.zmat │ │ ├── 03_h2co_downhill.xyz │ │ ├── 04_ch3o.xyz │ │ ├── 04_ch3o.zmat │ │ ├── 04_ch3o_downhill.xyz │ │ ├── 05_cyclopropyl.xyz │ │ ├── 05_cyclopropyl.zmat │ │ ├── 05_cyclopropyl_downhill.xyz │ │ ├── 06_bicyclobutane.xyz │ │ ├── 06_bicyclobutane.zmat │ │ ├── 06_bicyclobutane_downhill.xyz │ │ ├── 07_bicyclobutane.xyz │ │ ├── 07_bicyclobutane.zmat │ │ ├── 07_bicyclobutane_downhill.xyz │ │ ├── 08_formyloxyethyl.xyz │ │ ├── 08_formyloxyethyl.zmat │ │ ├── 08_formyloxyethyl_downhill.xyz │ │ ├── 09_parentdielsalder.zmat │ │ ├── 09_parentdieslalder.xyz │ │ ├── 09_parentdieslalder_downhill.xyz │ │ ├── 10_tetrazine.xyz │ │ ├── 10_tetrazine.zmat │ │ ├── 10_tetrazine_downhill.xyz │ │ ├── 11_trans_butadiene.xyz │ │ ├── 11_trans_butadiene.zmat │ │ ├── 11_trans_butadiene_downhill.xyz │ │ ├── 12_ethane_h2_abstraction.xyz │ │ ├── 12_ethane_h2_abstraction.zmat │ │ ├── 12_ethane_h2_abstraction_downhill.xyz │ │ ├── 13_hf_abstraction.xyz │ │ ├── 13_hf_abstraction.zmat │ │ ├── 13_hf_abstraction_downhill.xyz │ │ ├── 14_vinyl_alcohol.xyz │ │ ├── 14_vinyl_alcohol.zmat │ │ ├── 14_vinyl_alcohol_downhill.xyz │ │ ├── 15_hocl.xyz │ │ ├── 15_hocl.zmat │ │ ├── 15_hocl_downhill.xyz │ │ ├── 16_h2po4_anion.xyz │ │ ├── 16_h2po4_anion.zmat │ │ ├── 16_h2po4_anion_downhill.xyz │ │ ├── 17_claisen.xyz │ │ ├── 17_claisen.zmat │ │ ├── 17_claisen_downhill.xyz │ │ ├── 18_silyene_insertion.xyz │ │ ├── 18_silyene_insertion_downhill.xyz │ │ ├── 18_silylene_insertion.zmat │ │ ├── 19_hnccs.xyz │ │ ├── 19_hnccs.zmat │ │ ├── 19_hnccs_downhill.xyz │ │ ├── 20_hconh3_cation.xyz │ │ ├── 20_hconh3_cation.zmat │ │ ├── 20_hconh3_cation_downhill.xyz │ │ ├── 21_acrolein_rot.xyz │ │ ├── 21_acrolein_rot.zmat │ │ ├── 21_acrolein_rot_downhill.xyz │ │ ├── 22_hconhoh.xyz │ │ ├── 22_hconhoh.zmat │ │ ├── 22_hconhoh_downhill.xyz │ │ ├── 23_hcn_h2.xyz │ │ ├── 23_hcn_h2.zmat │ │ ├── 23_hcn_h2_downhill.xyz │ │ ├── 24_h2cnh.xyz │ │ ├── 24_h2cnh.zmat │ │ ├── 24_h2cnh_downhill.xyz │ │ ├── 25_hcnh2.xyz │ │ ├── 25_hcnh2.zmat │ │ └── 25_hcnh2_downhill.xyz │ ├── bare_solvated.xyz │ ├── benzene.xyz │ ├── benzene_and_chlorine.xyz │ ├── benzene_and_no.xyz │ ├── benzene_bp86sto3g_opt.xyz │ ├── benzene_pm6_opt.xyz │ ├── benzene_shaken.xyz │ ├── benzene_xtb_opt.xyz │ ├── biaryl_bare_pm6_splined_hei.xyz │ ├── birkholz │ │ ├── artemisin.xyz │ │ ├── aspartame.xyz │ │ ├── avobenzone.xyz │ │ ├── azadirachtin.xyz │ │ ├── bisphenol_a.xyz │ │ ├── cetirizine.xyz │ │ ├── codeine.xyz │ │ ├── diisobutyl_phthalate.xyz │ │ ├── easc.xyz │ │ ├── estradiol.xyz │ │ ├── inosine.xyz │ │ ├── maltose.xyz │ │ ├── mg_porphin.xyz │ │ ├── ochratoxin_a.xyz │ │ ├── penicillin_v.xyz │ │ ├── raffinose.xyz │ │ ├── sphingomyelin.xyz │ │ ├── tamoxifen.xyz │ │ ├── vitamin_c.xyz │ │ └── zn_edta.xyz │ ├── birkholz_rx │ │ ├── 00_c2no2.trj │ │ ├── 01_c5ht.trj │ │ ├── 02_hcn.trj │ │ ├── 02_hcn_original.trj │ │ ├── 03_cope.trj │ │ ├── 04_cpht.trj │ │ ├── 05_cycbut.trj │ │ ├── 06_dacp2.trj │ │ ├── 07_dacp_eth.trj │ │ ├── 08_dfcp.trj │ │ ├── 09_ene.trj │ │ ├── 10_grignard.trj │ │ ├── 11_h2co.trj │ │ ├── 12_hf_eth.trj │ │ ├── 13_hydro.trj │ │ ├── 14_meoh.trj │ │ ├── 15_oxirane.trj │ │ ├── 16_oxycope.trj │ │ ├── 17_silane.trj │ │ ├── 18_sn2.trj │ │ └── 19_sulfolene.trj │ ├── bonded_frag_test.xyz │ ├── butadiene_hf_sto3g.xyz │ ├── c4_lb_test.xyz │ ├── c4_lb_test_02.xyz │ ├── c6.xyz │ ├── ch2s_bp86def2sv_opt.xyz │ ├── ch4_12.xyz │ ├── ciscis_24hexadiene_xtbopt.xyz │ ├── claisen_forward.xyz │ ├── claisen_scfafir_paper_ref_opt.xyz │ ├── co2.xyz │ ├── co2_bent.xyz │ ├── co2_linear.xyz │ ├── co2_short.xyz │ ├── codein.xyz │ ├── coord │ ├── cytosin.xyz │ ├── diels_alder_extrapol.trj │ ├── diels_alder_interpolated.trj │ ├── dieniminium_cation_s1_opt.xyz │ ├── dihedral_gen_test.cjson │ ├── dipeptide_fin.xyz │ ├── dipeptide_init.xyz │ ├── dynamics │ │ └── 10_water.xyz │ ├── ethan.xyz │ ├── ethene.xyz │ ├── ethene_b3lyp_631gd.xyz │ ├── ethene_hf321g_opt.xyz │ ├── ethene_rot.xyz │ ├── ethene_rot_b3lyp_631gd.xyz │ ├── ethene_rot_xtb.xyz │ ├── ethene_xtb.xyz │ ├── fe_opt.xyz │ ├── fe_opt_cart.xyz │ ├── fluorethylene.xyz │ ├── frozen_atom_internal_setup.xyz │ ├── gjfs │ │ ├── azet │ │ │ ├── 02_azetidine_not_opt_sym.gjf │ │ │ ├── 03_azetidine_not_opt.gjf │ │ │ ├── 04_azetidine_dft.gjf │ │ │ └── azetidine_not_opt.gjf │ │ ├── azetidine_not_opt.gjf │ │ ├── benzene_and_chlorine.gjf │ │ ├── benzene_and_no.gjf │ │ ├── butadiene │ │ │ ├── 01_buta_trans.gjf │ │ │ ├── 02_buta_twist.gjf │ │ │ ├── 03_buta_cis_no_opt.gjf │ │ │ └── butadiene_hf_sto3g.gjf │ │ ├── butadiene_hf_sto3g.gjf │ │ ├── c6.gjf │ │ ├── ch2s │ │ │ ├── ch2s_bp86def2sv_opt.gjf │ │ │ └── ch2s_bp86def2sv_opt.xyz │ │ ├── co2 │ │ │ └── co2_linear.gjf │ │ ├── co2_linear.gjf │ │ ├── dmso │ │ │ ├── dmso.gjf │ │ │ ├── dmso.xyz │ │ │ ├── dmso_stretch.gjf │ │ │ └── dmso_stretch.xyz │ │ ├── hydrogen_bond.gjf │ │ ├── ma_proton_transfer │ │ │ ├── ma_end.gjf │ │ │ ├── ma_end.xyz │ │ │ ├── ma_irc.gjf │ │ │ ├── ma_start.gjf │ │ │ ├── ma_start.xyz │ │ │ └── ma_ts.gjf │ │ ├── methane │ │ │ ├── methane.gjf │ │ │ ├── methane.xyz │ │ │ ├── methane_stretch.gjf │ │ │ └── methane_stretch.xyz │ │ ├── selenoacroleine │ │ │ ├── interpolated │ │ │ │ ├── selenoacrolein.xyz │ │ │ │ └── selenoacrolein_twisted.xyz │ │ │ ├── selenoacrolein.gjf │ │ │ └── selenoacrolein_twisted.gjf │ │ ├── sf6.gjf │ │ └── sf6 │ │ │ └── sf6.gjf │ ├── h2.xyz │ ├── h2o.xyz │ ├── h2o2_def2svp_hf_opt.xyz │ ├── h2o2_guess.xyz │ ├── h2o2_guess_bad.xyz │ ├── h2o2_h2o_fragments.xyz │ ├── h2o2_hf_321g_opt.xyz │ ├── h2o2_rot2.xyz │ ├── h2o_30_sphere.xyz │ ├── h2o_30_sphere_translated_2_2_2.xyz │ ├── h2o_bp86_def2svp_opt.xyz │ ├── h2o_guess.xyz │ ├── h2o_hf_sto3g_orca_opt.xyz │ ├── h2o_inv_educt.xyz │ ├── h2o_inv_middle.xyz │ ├── h2o_inv_product.xyz │ ├── h2o_pt.xyz │ ├── h2o_shaken.xyz │ ├── hcfclbr_xtbopt.xyz │ ├── hcn.xyz │ ├── hcn_bent.pdb │ ├── hcn_bent.xyz │ ├── hcn_downhill_model_hessian.xyz │ ├── hcn_iso_hf_sto3g_ts_opt.xyz │ ├── hcn_iso_pm6_near_ts.xyz │ ├── hcn_iso_ts.xyz │ ├── hcn_iso_ts_opt_xtb.xyz │ ├── hcn_sto3g_freq_ref.xyz │ ├── hcn_ts_hf_321g.xyz │ ├── hf_hf_sto3g_opt.xyz │ ├── hfabstraction_hf321g_displ_forward.xyz │ ├── hfabstraction_ts.xyz │ ├── hfabstraction_ts_opt_xtb.xyz │ ├── hydrogen_bond.xyz │ ├── hydrogen_bond_fragments_test.xyz │ ├── hydrogen_bond_test.xyz │ ├── interfrag_hydrogen_bond.xyz │ ├── menthone.xyz │ ├── methane.xyz │ ├── methane_bp86_def2svp_opt.xyz │ ├── na_cube_54_bonds.xyz │ ├── nhc.xyz │ ├── ohch3f_anion_cs.xyz │ ├── oniom3alkyl.pdb │ ├── oniom_13_coupling_example.xyz │ ├── oniom_ee_model_system.xyz │ ├── oxygen_extrpol.trj │ ├── ozone.xyz │ ├── pdbs │ │ ├── 00_zn_h2o_im3_2plus_mp2_631gd_opt.pdb │ │ ├── 1bl8.pdb │ │ └── 1gcn.pdb │ ├── redox │ │ ├── ferrocen_pm6.xyz │ │ ├── nitrobenzene.xyz │ │ └── nitrobenzene_anion.xyz │ ├── replacements │ │ ├── benzene.xyz │ │ ├── ethanol.xyz │ │ ├── hbr.xyz │ │ ├── hcl.xyz │ │ ├── hf.xyz │ │ ├── methanol.xyz │ │ └── water.xyz │ ├── runo_nto_track.xyz │ ├── s22 │ │ ├── 00_adenine_thymine_wc.xyz │ │ ├── 01_adenine_thymine_stack.xyz │ │ ├── 02_ammonia_dimer.xyz │ │ ├── 03_water_dimer.xyz │ │ ├── 04_methane_dimer.xyz │ │ ├── 05_ethene_dimer.xyz │ │ ├── 06_ethene_ethine.xyz │ │ ├── 07_formic_acid_dimer.xyz │ │ ├── 08_formamide_dimer.xyz │ │ ├── 09_benzene_water.xyz │ │ ├── 10_benzene_ammonia.xyz │ │ ├── 11_benzene_methane.xyz │ │ ├── 12_benzene_dimer_c2v.xyz │ │ ├── 13_benzene_dimer_c2h.xyz │ │ ├── 14_indole_benzene_t-shape.xyz │ │ ├── 15_indole_benzene_stack.xyz │ │ ├── 16_pyrazine_dimer.xyz │ │ ├── 17_2-pyridoxine_2-aminopyridine.xyz │ │ ├── 18_phenol_dimer.xyz │ │ ├── 19_uracil_dimer_stack.xyz │ │ ├── 20_uracil_dimer_hb.xyz │ │ └── 21_benzene_hcn.xyz │ ├── sf6.xyz │ ├── single_atom_fragments.xyz │ ├── so3hcl_diss_ts_opt.xyz │ ├── split.image_021.xyz │ ├── subst_effect │ │ ├── ch3_b3lypG_631g.xyz │ │ ├── ch4_model.xyz │ │ ├── toluene_b3lypG_631g.xyz │ │ └── toluene_minus_H_b3lypG_631g.xyz │ ├── test_bond_mode.trj │ ├── test_full_run_split.geom_008.xyz │ ├── test_full_run_split.geom_034.xyz │ ├── test_reject.trj │ ├── test_union_rx_001.trj │ ├── test_union_ts_001.xyz │ ├── thr75_from_1bl8.xyz │ ├── tip3p_h2o.xyz │ ├── tip3p_water.xyz │ ├── toluene_and_cl2.xyz │ ├── trans34dimethylcyclobutene.xyz │ ├── trans_butadien.xyz │ ├── tsbfgs_init.xyz │ ├── uracil_dimer.xyz │ ├── water_dimer_oniomopt_test.pdb │ ├── water_dimer_uff.xyz │ ├── xtb_rx │ │ ├── 00_c2no2.trj │ │ ├── 01_c5ht.trj │ │ ├── 02_hcn.trj │ │ ├── 03_cope.trj │ │ ├── 04_cpht.trj │ │ ├── 05_cycbut.trj │ │ ├── 06_dacp2.trj │ │ ├── 07_dacp_eth.trj │ │ ├── 08_ene.trj │ │ ├── 09_grignard.trj │ │ ├── 10_h2co.trj │ │ ├── 11_hf_eth.trj │ │ ├── 12_hydro.trj │ │ ├── 13_meoh.trj │ │ ├── 14_oxirane.trj │ │ ├── 15_oxycope.trj │ │ ├── 16_silane.trj │ │ ├── 17_sulfolene.trj │ │ ├── 18_mobh35_14.trj │ │ └── 19_mobh35_30.trj │ ├── xtb_rx_00_c2no2_endpoints.trj │ ├── xtbopt.anfang.xyz │ ├── xtbopt.ende2.xyz │ ├── zimmerman │ │ ├── case_000.trj │ │ ├── case_001.trj │ │ ├── case_002.trj │ │ ├── case_003.trj │ │ ├── case_004.trj │ │ ├── case_005.trj │ │ ├── case_006.trj │ │ ├── case_007.trj │ │ ├── case_008.trj │ │ ├── case_009.trj │ │ ├── case_010.trj │ │ ├── case_011.trj │ │ ├── case_012.trj │ │ ├── case_013.trj │ │ ├── case_014.trj │ │ ├── case_015.trj │ │ ├── case_016.trj │ │ ├── case_017.trj │ │ ├── case_018.trj │ │ ├── case_019.trj │ │ ├── case_020.trj │ │ ├── case_021.trj │ │ ├── case_022.trj │ │ ├── case_023.trj │ │ ├── case_024.trj │ │ ├── case_025.trj │ │ ├── case_026.trj │ │ ├── case_027.trj │ │ ├── case_028.trj │ │ ├── case_029.trj │ │ ├── case_030.trj │ │ ├── case_031.trj │ │ ├── case_032.trj │ │ ├── case_033.trj │ │ ├── case_034.trj │ │ ├── case_035.trj │ │ ├── case_036.trj │ │ ├── case_037.trj │ │ ├── case_038.trj │ │ ├── case_039.trj │ │ ├── case_040.trj │ │ ├── case_041.trj │ │ ├── case_042.trj │ │ ├── case_043.trj │ │ ├── case_044.trj │ │ ├── case_045.trj │ │ ├── case_046.trj │ │ ├── case_047.trj │ │ ├── case_048.trj │ │ ├── case_049.trj │ │ ├── case_050.trj │ │ ├── case_051.trj │ │ ├── case_052.trj │ │ ├── case_053.trj │ │ ├── case_054.trj │ │ ├── case_055.trj │ │ ├── case_056.trj │ │ ├── case_057.trj │ │ ├── case_058.trj │ │ ├── case_059.trj │ │ ├── case_060.trj │ │ ├── case_061.trj │ │ ├── case_062.trj │ │ ├── case_063.trj │ │ ├── case_064.trj │ │ ├── case_065.trj │ │ ├── case_066.trj │ │ ├── case_067.trj │ │ ├── case_068.trj │ │ ├── case_069.trj │ │ ├── case_070.trj │ │ ├── case_071.trj │ │ ├── case_072.trj │ │ ├── case_073.trj │ │ ├── case_074.trj │ │ ├── case_075.trj │ │ ├── case_076.trj │ │ ├── case_077.trj │ │ ├── case_078.trj │ │ ├── case_079.trj │ │ ├── case_080.trj │ │ ├── case_081.trj │ │ ├── case_082.trj │ │ ├── case_083.trj │ │ ├── case_084.trj │ │ ├── case_085.trj │ │ ├── case_086.trj │ │ ├── case_087.trj │ │ ├── case_088.trj │ │ ├── case_089.trj │ │ ├── case_090.trj │ │ ├── case_091.trj │ │ ├── case_092.trj │ │ ├── case_093.trj │ │ ├── case_094.trj │ │ ├── case_095.trj │ │ ├── case_096.trj │ │ ├── case_097.trj │ │ ├── case_098.trj │ │ ├── case_099.trj │ │ ├── case_100.trj │ │ ├── case_101.trj │ │ ├── case_102.trj │ │ ├── case_103.trj │ │ └── case_104.trj │ └── zimmerman_xtb │ │ ├── 00_zm_xtb.trj │ │ ├── 01_zm_xtb.trj │ │ ├── 02_zm_xtb.trj │ │ ├── 03_zm_xtb.trj │ │ ├── 04_zm_xtb.trj │ │ ├── 05_zm_xtb.trj │ │ ├── 06_zm_xtb.trj │ │ ├── 07_zm_xtb.trj │ │ ├── 08_zm_xtb.trj │ │ ├── 09_zm_xtb.trj │ │ ├── 10_zm_xtb.trj │ │ ├── 11_zm_xtb.trj │ │ ├── 12_zm_xtb.trj │ │ ├── 13_zm_xtb.trj │ │ ├── 14_zm_xtb.trj │ │ ├── 15_zm_xtb.trj │ │ ├── 16_zm_xtb.trj │ │ ├── 17_zm_xtb.trj │ │ ├── 18_zm_xtb.trj │ │ ├── 19_zm_xtb.trj │ │ ├── 20_zm_xtb.trj │ │ ├── 21_zm_xtb.trj │ │ ├── 22_zm_xtb.trj │ │ ├── 23_zm_xtb.trj │ │ ├── 24_zm_xtb.trj │ │ ├── 25_zm_xtb.trj │ │ ├── 26_zm_xtb.trj │ │ ├── 27_zm_xtb.trj │ │ ├── 28_zm_xtb.trj │ │ ├── 29_zm_xtb.trj │ │ ├── 30_zm_xtb.trj │ │ ├── 31_zm_xtb.trj │ │ ├── 32_zm_xtb.trj │ │ ├── 33_zm_xtb.trj │ │ ├── 34_zm_xtb.trj │ │ ├── 35_zm_xtb.trj │ │ ├── 36_zm_xtb.trj │ │ ├── 37_zm_xtb.trj │ │ ├── 38_zm_xtb.trj │ │ ├── 39_zm_xtb.trj │ │ ├── 40_zm_xtb.trj │ │ ├── 41_zm_xtb.trj │ │ ├── 42_zm_xtb.trj │ │ ├── 43_zm_xtb.trj │ │ ├── 44_zm_xtb.trj │ │ ├── 45_zm_xtb.trj │ │ ├── 46_zm_xtb.trj │ │ ├── 47_zm_xtb.trj │ │ ├── 48_zm_xtb.trj │ │ ├── 49_zm_xtb.trj │ │ ├── 50_zm_xtb.trj │ │ ├── 51_zm_xtb.trj │ │ ├── 52_zm_xtb.trj │ │ ├── 53_zm_xtb.trj │ │ ├── 54_zm_xtb.trj │ │ ├── 55_zm_xtb.trj │ │ ├── 56_zm_xtb.trj │ │ ├── 57_zm_xtb.trj │ │ ├── 58_zm_xtb.trj │ │ ├── 59_zm_xtb.trj │ │ ├── 60_zm_xtb.trj │ │ ├── 61_zm_xtb.trj │ │ ├── 62_zm_xtb.trj │ │ ├── 63_zm_xtb.trj │ │ └── 64_zm_xtb.trj ├── helpers.py ├── helpers_pure.py ├── hessian_proj.py ├── hindered_rotor │ ├── RotorInfo.py │ ├── TorsionGPRResult.py │ ├── __init__.py │ ├── fragment.py │ ├── inertmom.py │ ├── opt.py │ ├── torsion_driver.py │ ├── torsion_gpr.py │ └── types.py ├── init_logging.py ├── intcoords │ ├── Bend.py │ ├── Bend2.py │ ├── BondedFragment.py │ ├── Cartesian.py │ ├── CartesianCoords.py │ ├── Coords.py │ ├── DLC.py │ ├── DistanceFunction.py │ ├── DummyImproper.py │ ├── DummyTorsion.py │ ├── LinearBend.py │ ├── LinearDisplacement.py │ ├── OutOfPlane.py │ ├── PrimTypes.py │ ├── Primitive.py │ ├── RedundantCoords.py │ ├── RobustTorsion.py │ ├── Rotation.py │ ├── Stretch.py │ ├── Torsion.py │ ├── Torsion2.py │ ├── Translation.py │ ├── __init__.py │ ├── augment_bonds.py │ ├── derivatives.py │ ├── eval.py │ ├── exceptions.py │ ├── findiffs.py │ ├── generate_derivatives.py │ ├── helpers.py │ ├── logging_conf.py │ ├── mp_derivatives.py │ ├── setup.py │ ├── setup_fast.py │ ├── update.py │ └── valid.py ├── interpolate │ ├── Geodesic.py │ ├── IDPP.py │ ├── Interpolator.py │ ├── LST.py │ ├── Redund.py │ ├── __init__.py │ └── helpers.py ├── io │ ├── __init__.py │ ├── aomix.py │ ├── bson.py │ ├── cjson.py │ ├── coord.py │ ├── crd.py │ ├── cube.py │ ├── fchk.py │ ├── hdf5.py │ ├── hessian.py │ ├── mol2.py │ ├── molcas.py │ ├── molden.py │ ├── orca.py │ ├── pdb.py │ ├── psf.py │ ├── pubchem.py │ ├── qcschema.py │ ├── sdf.py │ ├── trexio.py │ ├── xyz.py │ ├── zip.py │ └── zmat.py ├── irc │ ├── DWI.py │ ├── DampedVelocityVerlet.py │ ├── Euler.py │ ├── EulerPC.py │ ├── GonzalezSchlegel.py │ ├── IMKMod.py │ ├── IRC.py │ ├── IRCDummy.py │ ├── Instanton.py │ ├── LQA.py │ ├── ModeKill.py │ ├── ParamPlot.py │ ├── RK4.py │ ├── __init__.py │ └── initial_displ.py ├── linalg.py ├── linalg_affine3.py ├── line_searches │ ├── Backtracking.py │ ├── HagerZhang.py │ ├── LineSearch.py │ ├── StrongWolfe.py │ ├── __init__.py │ └── interpol.py ├── marcus_dim │ ├── __init__.py │ ├── config.py │ ├── fit.py │ ├── param.py │ ├── run.py │ ├── scan.py │ └── types.py ├── modefollow │ ├── NormalMode.py │ ├── __init__.py │ ├── davidson.py │ └── lanczos.py ├── numerov │ ├── __init__.py │ └── driver.py ├── numint │ ├── __init__.py │ ├── angint.py │ ├── atomint.py │ ├── lebedev_grids_4pi.npz │ ├── molint.py │ └── radint.py ├── optimizers │ ├── BFGS.py │ ├── BacktrackingOptimizer.py │ ├── ConjugateGradient.py │ ├── CubicNewton.py │ ├── FIRE.py │ ├── HessianOptimizer.py │ ├── LBFGS.py │ ├── LayerOpt.py │ ├── NCOptimizer.py │ ├── Optimizer.py │ ├── PreconLBFGS.py │ ├── PreconSteepestDescent.py │ ├── QuickMin.py │ ├── RFOptimizer.py │ ├── RSA.py │ ├── StabilizedQNMethod.py │ ├── SteepestDescent.py │ ├── StringOptimizer.py │ ├── __init__.py │ ├── closures.py │ ├── cls_map.py │ ├── exceptions.py │ ├── gdiis.py │ ├── guess_hessians.py │ ├── hessian_updates.py │ ├── poly_fit.py │ ├── precon.py │ └── restrict_step.py ├── pack.py ├── partfuncs │ ├── __init__.py │ ├── driver.py │ └── partfuncs.py ├── peakdetect.py ├── plot.py ├── plot_ascii.py ├── plot_helpers.py ├── plotters │ ├── AnimPlot.py │ └── __init__.py ├── run.py ├── socket_helper.py ├── stocastic │ ├── FragmentKick.py │ ├── Kick.py │ ├── Pipeline.py │ ├── __init__.py │ └── align.py ├── testing.py ├── tests │ ├── __init__.py │ ├── h2o_input.RasOrb │ └── test_calculators.py ├── thermo.py ├── timing.py ├── trj.py ├── tsoptimizers │ ├── RSIRFOptimizer.py │ ├── RSPRFOptimizer.py │ ├── TRIM.py │ ├── TSHessianOptimizer.py │ └── __init__.py ├── typing.py ├── wavefunction │ ├── Basis.py │ ├── DIIS.py │ ├── __init__.py │ ├── backend_numba.py │ ├── backend_numba_multipole.py │ ├── backend_python.py │ ├── bond_order.py │ ├── cart2sph.py │ ├── density_numba.py │ ├── dma.py │ ├── excited_states.py │ ├── gdma_int.py │ ├── gen_ints.py │ ├── helpers.py │ ├── ints │ │ ├── __init__.py │ │ ├── boys.py │ │ ├── boys_table_N_64_xasym_27.1_step_0.01.npy │ │ ├── cart_gto3d.py │ │ ├── coulomb3d.py │ │ ├── diag_quadrupole3d.py │ │ ├── dipole3d.py │ │ ├── int2c2e3d.py │ │ ├── int3c2e3d_sph.py │ │ ├── kinetic3d.py │ │ ├── multipole3d_sph.py │ │ ├── ovlp3d.py │ │ └── quadrupole3d.py │ ├── ints_numba │ │ ├── __init__.py │ │ ├── diag_quadrupole3d.py │ │ ├── dipole3d.py │ │ ├── kinetic3d.py │ │ ├── multipole3d_sph.py │ │ ├── ovlp3d.py │ │ └── quadrupole3d.py │ ├── localization.py │ ├── multipole.py │ ├── normalization.py │ ├── pop_analysis.py │ ├── shells.py │ ├── shells_molcas.py │ ├── shells_pyscf.py │ ├── shells_trexio.py │ ├── so_coupling.py │ ├── solid_harmonics.py │ └── wavefunction.py ├── wf_library │ ├── 00_h.json │ ├── 01_ch4_freq.fchk │ ├── 01_ch4_tzvp.json │ ├── 01_he.json │ ├── 02_ne.json │ ├── 03_c.json │ ├── 03_ch3f_freq.fchk │ ├── 04_h2.json │ ├── 05_acn_freq.fchk │ ├── 06_acn_non_statpt.fchk │ ├── g16_ch4_qzvpp.fchk │ ├── iao_ref.json │ ├── iao_ref_uhf.json │ ├── indole_bp86_def2svp.bson │ ├── orca_benzene_quad.json │ ├── orca_ch4_def2svp.json │ ├── orca_ch4_qzvpp.json │ ├── orca_ch4_qzvpp.molden.input │ ├── orca_ch4_sto3g.json │ ├── orca_ch4_sto3g_rhf.densities │ ├── orca_ch4_sto3g_rhf.json │ ├── orca_ch4_sto3g_rhf_cis.densities │ ├── orca_ch4_sto3g_rhf_cis.json │ ├── orca_ch4_sto3g_triplet.json │ ├── orca_ch4_sto3g_uhf.densities │ ├── orca_ch4_sto3g_uhf.json │ ├── orca_ch4_sto3g_uhf_cis.densities │ ├── orca_ch4_sto3g_uhf_cis.json │ ├── orca_ch4_triplet.molden.input │ ├── orca_ch4_tzvpp.json │ ├── orca_dipmom.json │ ├── orca_dipmom_uhf.json │ ├── orca_h2o_def2svp.json │ ├── orca_h2o_sto3g.json │ ├── orca_hcho_def2svp.json │ ├── orca_lih_ccpvdz.molden.input │ ├── orca_n2o4_sto3g.json │ ├── orca_yttrium_ecp.molden.input │ └── turbomole_ch4_def2svp_aomix.in ├── wrapper │ ├── __init__.py │ ├── crest.py │ ├── exceptions.py │ ├── jmol.py │ ├── mwfn.py │ └── packmol.py ├── xyzloader.py └── yaml_mods.py ├── readthedocs.yml ├── resources ├── derivs │ ├── edmiston_ruedenberg.ipynb │ └── numerov_coefficients.ipynb ├── logo.svg ├── logo_200dpi.png ├── logo_new_cut.png ├── logo_new_cut.xcf ├── logo_new_cut_small.png ├── logo_new_cut_small.xcf └── logo_small.png ├── scripts ├── aciddrain.py ├── atomhess.py ├── batchnt.py ├── batchnt_multi.py ├── couplings.py ├── crest_gnts.py ├── fbdia.py ├── frag.py ├── gen_m2m.py ├── modes3d.py ├── molcas_scan.py ├── orca2cdd.py ├── orca2pysis.py ├── orca_ctnums.py ├── orca_overlaps.py ├── pysis_validate_md.py ├── pysissoc.py ├── rotvecs.py └── tddispl.py ├── setup.cfg ├── test-requirements.txt └── tests ├── conftest.py ├── pytest.ini ├── test_adaptive_neb └── test_adaptive_neb.py ├── test_affine3 └── test_affine3.py ├── test_afir ├── test_afir.py └── test_sc_afir.py ├── test_baker └── test_baker.py ├── test_baker_ts └── test_baker_ts.py ├── test_baker_ts_dimer ├── Ns ├── Ns_start └── test_baker_ts_dimer.py ├── test_barriers ├── inp_backward_end_frag000_final_hessian.h5 ├── inp_backward_end_frag001_final_hessian.h5 ├── inp_forward_end_frag000_final_hessian.h5 ├── inp_hess_init_irc.h5 ├── inp_ts_final_hessian.h5 └── test_barriers.py ├── test_benchmarks └── test_benchmarks.py ├── test_birkholz └── test_birkholz.py ├── test_birkholz_interpolation └── test_birkholz_interpolation.py ├── test_birkholz_rx └── test_birkholz_rx.py ├── test_boltzmann └── test_boltzmann.py ├── test_bond_order └── test_bond_order.py ├── test_calculator └── test_calculator.py ├── test_calculator_restart ├── benzene_control_path │ ├── basis │ ├── control │ ├── coord │ └── mos ├── benzene_control_path_uhf │ ├── alpha │ ├── basis │ ├── beta │ ├── control │ └── coord └── test_calculator_restart.py ├── test_cfour ├── FCMFINAL ├── ch2oo_ts_bohr.xyz └── test_cfour.py ├── test_check_for_end_sign └── test_check_for_end_sign.py ├── test_check_mem └── test_check_mem.py ├── test_cjson ├── test.cjson └── test_cjson.py ├── test_composite ├── 00_ch4.xyz └── test_composite.py ├── test_conic_intersect ├── ethene_b3lyp_def2svp_ci01_opt.xyz ├── ethene_init.xyz └── test_conic_intersect.py ├── test_constraints └── test_constraints.py ├── test_coord_sys └── test_coord_sys.py ├── test_cos ├── multi_state_inp.npz ├── test_cos.py └── test_multi_state.py ├── test_cos_dimer └── test_cos_dimer.py ├── test_cube └── test_cube.py ├── test_cubic_newton └── test_cubic_newton.py ├── test_cytosin_opt ├── control_path_hf_sto3g_gs │ ├── basis │ ├── control │ ├── coord │ ├── energy │ └── mos ├── control_path_pbe0_def2svp_s1 │ ├── basis │ ├── control │ ├── coord │ ├── energy │ └── mos └── test_cytosin_opt.py ├── test_daltonproject └── test_daltonproject.py ├── test_damped_bfgs ├── neb_input.trj └── test_damped_bfgs.py ├── test_dask └── test_dask.py ├── test_davidson ├── hessian_precon └── test_davidson.py ├── test_dftbp ├── slakos │ └── mio-ext │ │ ├── H-H.skf │ │ ├── H-O.skf │ │ ├── LICENSE │ │ ├── O-H.skf │ │ └── O-O.skf └── test_dftbp.py ├── test_diabatization ├── 00_bena2_cat │ ├── 00_bena2_dcat.bson │ ├── 00_bena2_dcat.cis │ ├── 00_bena2_dcat.inp │ ├── 00_bena2_dcat.log │ └── 00_bena2_dcat.xyz ├── guanine_indole_dia.yaml └── test_diabatization.py ├── test_diels_alder_neb └── test_diels_alder.py ├── test_dimer └── test_dimer.py ├── test_dispersion └── test_dispersion.py ├── test_dma ├── data │ ├── 00_h2.fchk │ ├── 00_h2_ref.npy │ ├── 05_h_porb.fchk │ ├── 05_h_porb_ref.npy │ ├── 06_ethene_from_orca_geom.fchk │ ├── 06_ethene_from_orca_geom_ref.npy │ ├── 07_oh_minus.fchk │ ├── 07_oh_minus_ref.npy │ ├── 09_o_atom_def2_tzvp.fchk │ ├── 09_o_atom_ref.npy │ ├── 13_h2o_sto3g.fchk │ ├── 13_h2o_sto3g_ref.npy │ ├── 15_o_double_cation.fchk │ ├── 15_o_double_cation_ref.npy │ ├── 16_methane_def2svp.fchk │ ├── 16_methane_def2svp_ref.npy │ ├── 17_h2_prims.fchk │ ├── 17_h2_prims_ref.npy │ ├── 18_h2_small.fchk │ ├── 18_h2_small_ref.npy │ ├── 23_he.fchk │ ├── 23_he_ref.npy │ ├── 24_oh_minus_tzvp.fchk │ ├── 24_oh_minus_tzvp_ref.npy │ ├── 24_oh_minus_tzvp_ref_shift.npy │ └── 24_oh_minus_tzvp_switch40_ref.npy └── test_dma.py ├── test_dump └── test_dump.py ├── test_dynamics └── test_dynamics.py ├── test_ego ├── butene.xyz ├── gbutene.xyz ├── pyranose.xyz ├── tbutene.xyz └── test_ego.py ├── test_endopt ├── all_coords └── test_endopt.py ├── test_endopt_barriers ├── hcn_backward_end_opt.xyz ├── hcn_forward_end_opt.xyz ├── hcn_ts_opt.xyz ├── test_endopt_barriers.py └── test_quick_downhill.xyz ├── test_energymin └── test_energymin.py ├── test_es_capabilities ├── control_path_h2o_mult_1 │ ├── basis │ ├── control │ ├── coord │ ├── energy │ └── mos ├── control_path_h2o_mult_3 │ ├── alpha │ ├── basis │ ├── beta │ ├── control │ ├── coord │ └── mos ├── control_path_hf │ ├── basis │ ├── ciss_a │ ├── control │ ├── coord │ ├── energy │ └── mos ├── control_path_mult_1 │ ├── basis │ ├── control │ ├── coord │ ├── energy │ └── mos ├── control_path_mult_3 │ ├── alpha │ ├── basis │ ├── beta │ ├── control │ ├── coord │ ├── energy │ └── unrs_a └── test_es_capabilities.py ├── test_es_tracking └── test_es_tracking.py ├── test_exc_densities ├── data │ ├── 00_h2o_restricted.bson │ ├── 00_h2o_restricted.cis │ ├── 01_h2o_unrestricted.bson │ ├── 01_h2o_unrestricted.cis │ ├── 02_h2o_dotrans_restricted.bson │ ├── 02_h2o_dotrans_restricted.cis │ ├── 02_trans_moms_ref │ ├── 03_h2o_dotrans_unrestricted.bson │ ├── 03_h2o_dotrans_unrestricted.cis │ └── 03_trans_moms_ref └── test_exc_densities.py ├── test_external_potential ├── test_external_potential.py └── test_get_optimal_bias.py ├── test_fake_ase └── test_fake_ase.py ├── test_finite_diffs ├── test_finite_diffs.py └── test_periodic_fd.py ├── test_franckcondon ├── coco4_anion.h5 ├── coco4_neutral.h5 ├── naphthalene_gradient ├── naphthalene_hessian.h5 ├── test_duschinsky.py ├── test_imdho.py └── test_lq2.py ├── test_freeend_neb └── test_freeend_neb.py ├── test_freeze_atoms └── test_freeze_atoms.py ├── test_full_run └── test_full_run.py ├── test_gaussian └── test_gaussian.py ├── test_generate_derivatives └── test_generate_derivatives.py ├── test_geom_section └── test_geom_section.py ├── test_geometry ├── benzene_inertia_tensor_ref ├── benzene_trans_rot_vecs_ref └── test_geometry.py ├── test_growingnt └── test_growingnt.py ├── test_growingstring └── test_growingstring.py ├── test_guess_hessians └── test_guess_hessians.py ├── test_helpers ├── test_full_expand.py ├── test_helpers.py └── test_helpers_pure.py ├── test_hessian └── test_hessian.py ├── test_hessian_updates ├── test_hessian_updates.py └── tsbfgs_init_hess.h5 ├── test_hindered_rotor ├── ethane_xtbopt.xyz ├── h2o2_b3lyp_tzvp_opt.xyz ├── h2o2_g16_b3_tz_relaxed_scan.dat ├── meoh_mp2_631gd_opt.xyz ├── test_gpr_torsion.py └── test_inertmom.py ├── test_imag_modes_from_geom ├── calculated_final_cart_hessian └── test_imag_modes_from_geom.py ├── test_instanton └── test_instanton.py ├── test_intcoord_setup_fast └── test_intcoord_setup_fast.py ├── test_intcoords ├── test_dihedral.py ├── test_intcoords.py └── test_setup.py ├── test_intcoords_v2 ├── 02_test.xyz ├── c4.xyz └── test_intcoords_v2.py ├── test_integrals ├── 00_ch4.json ├── 01_ch4_sto3g.json ├── 02_ch4_tzvpp.json ├── 04_qzvpp.json ├── methane_def2svp_aomix.in └── test_integrals.py ├── test_interpolate ├── test_extrapolate.py └── test_interpolate.py ├── test_ipi └── test_ipi.py ├── test_irc ├── hf_abstr_control_path │ ├── basis │ ├── control │ ├── coord │ ├── energy │ ├── mos │ └── statistics ├── test_initial_displ.py ├── test_irc.py └── test_run_irc.py ├── test_lanczos └── test_lanczos.py ├── test_layeropt └── test_layeropt.py ├── test_lbfgs └── test_lbfgs.py ├── test_lennardjones └── test_lennardjones.py ├── test_linalg └── test_linalg.py ├── test_line_searches └── test_line_searches.py ├── test_local_force_constants ├── bf3_ccsd_t_ccpvdz.h5 └── test_local_force_constants.py ├── test_localization ├── ch4_checkpoint.h5 └── test_localization.py ├── test_marcusdim ├── pdnb_xtb_final_hessian.h5 ├── pdnb_xtb_marcus_dim_fit.npz ├── test_marcus_dim.py ├── test_marcus_dim_fit_replay.py └── test_param_marcus.py ├── test_mdp └── test_mdp.py ├── test_merge ├── cis_linker_guess.xyz ├── fk4x_cis_merged.xyz └── fk4x_cn_fix_no_box.pdb ├── test_merge_mol2 ├── alexa-488_amid.mol2 ├── alexa_merged.mol2 ├── dy-490_amid.mol2 ├── dy_linker.mol2 ├── dy_linker_phallo.mol2 ├── linker.mol2 ├── phallo.mol2 ├── phalloidin-F_linker.mol2 ├── rhodamin_amid.mol2 ├── rhodamin_merged.mol2 └── test_merge.py ├── test_modekill ├── ethane_shaked.xyz ├── shaked.geom_000.xyz └── test_modekill.py ├── test_mol2 └── test_mol2.py ├── test_molden ├── geometries.molden ├── ref.xyz └── test_molden.py ├── test_mopac └── test_mopac.py ├── test_numerov ├── 03_h2_scan_qz.dat ├── h2o2_pot.dat ├── relaxed_scan_cut.dat └── test_numerov.py ├── test_numint ├── test_atomint.py ├── test_molint.py └── test_radint.py ├── test_obabel └── test_obabel.py ├── test_oniom ├── test_oniom.py └── test_subst_effect.py ├── test_openmolcas ├── butadien_vdzp.RasOrb ├── butadien_vdzp.rasscf.h5 ├── cms_pdft.rasscf.h5 ├── cms_pdft_opt.yaml └── test_openmolcas.py ├── test_opt └── test_opt.py ├── test_opt_coord_types ├── test_geoms.trj └── test_opt_coord_types.py ├── test_orca ├── fail_term.orca.out ├── normal_term.orca.out ├── orca_tddft_triplets.out ├── ref_cis │ ├── rhf_000.000.orca.cis │ ├── rhf_tda_000.000.orca.cis │ ├── rhf_tda_triplets_000.000.orca.cis │ ├── rhf_triplets_000.000.orca.cis │ ├── uhf_000.000.orca.cis │ └── uhf_tda_000.000.orca.cis ├── restricted.gbw ├── test_orca.py └── unrestricted.gbw ├── test_orca_stable └── test_orca_stable.py ├── test_overlap_calculator ├── benzene │ ├── calculator_000.000.orca.cis │ ├── calculator_000.000.orca.inp │ ├── calculator_000.000.orca.json │ ├── calculator_000.000.orca.out │ ├── calculator_000.001.orca.cis │ ├── calculator_000.001.orca.inp │ ├── calculator_000.001.orca.json │ └── calculator_000.001.orca.out ├── control_path │ ├── basis │ ├── control │ ├── coord │ └── mos ├── cytosin_orca_overlap_data.h5 ├── cytosin_trip_orca_overlap_data.h5 ├── test_calculators.py ├── test_canonical.py ├── test_overlap_calculator.py └── test_top.py ├── test_partfuncs ├── test_anharm_partfuncs.py └── ts_final_hessian_xtb.h5 ├── test_pdb ├── five_chloroforms_ref.pdb ├── five_chloroforms_xtbopt.xyz ├── h2o_ref.pdb └── test_pdb.py ├── test_perf └── test_perf.py ├── test_pka ├── formic_base_opt_hessian.h5 ├── formic_opt_hessian.h5 └── test_pka.py ├── test_plot └── test_plot.py ├── test_point_charges ├── methane_control_path │ ├── basis │ ├── control │ ├── coord │ ├── energy │ ├── hessapprox │ ├── mos │ └── wherefrom └── test_point_charges.py ├── test_precon └── test_precon.py ├── test_precon_pos_rot ├── figure2_mod.trj └── test_precon_pos_rot.py ├── test_preopt ├── ref_first_preopt.xyz ├── ref_last_preopt.xyz └── test_preopt.py ├── test_psf ├── step1_pdbreader.psf └── test_psf.py ├── test_psi4 └── test_psi4.py ├── test_pubchem ├── 4311764.sdf ├── test_pubchem.py └── test_sdf.py ├── test_pyscf └── test_pyscf.py ├── test_qcengine ├── h2o_bp86_def2svp_control │ ├── auxbasis │ ├── basis │ ├── control │ ├── coord │ └── mos └── test_qcengine.py ├── test_qcschema └── test_qcschema.py ├── test_quartic_fit └── test_quartic_fit.py ├── test_rastrigin └── test_rastrigin.py ├── test_rates ├── ethyl_propionate │ ├── 00_h_final_hessian.h5 │ ├── 01_ep_final_hessian.h5 │ ├── 02_ts3_final_hessian.h5 │ └── 03_ts2_final_hessian.h5 ├── peroxyl_r1_h5s │ ├── product.h5 │ ├── reactant.h5 │ └── ts.h5 ├── test_ethyl_propionate.py └── test_rates.py ├── test_rattle ├── output_10.xyz ├── output_2.xyz └── test_rattle.py ├── test_replacements └── test_replacements.py ├── test_rmsd └── test_rmsd.py ├── test_run ├── test_run.py └── ts_inp_run_constrained_endopt.xyz ├── test_run_tsopt_from_cos ├── input.cycle_019.trj └── test_run_tsopt_from_cos.py ├── test_s22_set └── test_s22_set.py ├── test_save_hessian ├── inp_hess_calc_cyc_0.h5 ├── inp_hess_init_irc.h5 └── test_save_hessian.py ├── test_scan └── test_scan.py ├── test_so_coupling ├── data │ ├── 00_h2co_cart.fchk │ ├── 00_h2co_cart.log │ ├── 00_h2co_cart.npy │ ├── 00_methanal.fchk │ ├── 00_methanal.log │ ├── 00_methanal.npy │ ├── 01_h2co_sph.fchk │ ├── 01_h2co_sph.log │ └── 01_h2co_sph.npy └── test_so_coupling.py ├── test_socketcalc ├── test_socketcalc_client.py └── test_socketcalc_server.py ├── test_spectrum_ctnum ├── baseline_images │ └── test_spectrum_ctnum │ │ └── spectrum_ctnum.png ├── data │ ├── combined.xyz │ ├── omegas.npy │ └── states └── test_spectrum_ctnum.py ├── test_stocastic └── test_stocastic.py ├── test_tblite └── test_tblite.py ├── test_thermo ├── h2o_hessian.h5 ├── hcn_orca_b973c_hessian.h5 ├── irc_000.024.orca.h5 ├── irc_000.063.orca.h5 ├── irc_000.084.orca.h5 └── test_thermo.py ├── test_timing └── test_timing.py ├── test_tric └── test_tric.py ├── test_tsopt ├── inp_hessian_ref.h5 ├── test_augment_coordinates.py └── test_tsopt.py ├── test_turbomole ├── control_path_big_hess │ ├── auxbasis │ ├── basis │ ├── control │ ├── coord │ ├── dipgrad │ ├── energy │ ├── hessian │ ├── mos │ ├── nprhessian │ ├── turbomole.out │ ├── vib_normal_modes │ └── vibspectrum ├── control_path_dft_es1 │ ├── auxbasis │ ├── basis │ ├── control │ ├── coord │ ├── energy │ ├── mos │ └── wherefrom ├── control_path_dft_es1_unrs │ ├── alpha │ ├── auxbasis │ ├── basis │ ├── beta │ ├── control │ ├── coord │ ├── energy │ ├── moments │ └── mos ├── control_path_dft_gs │ ├── auxbasis │ ├── basis │ ├── control │ ├── coord │ ├── energy │ ├── mos │ └── wherefrom ├── control_path_ricc2 │ ├── auxbasis │ ├── basis │ ├── control │ ├── coord │ ├── energy │ ├── mos │ └── wherefrom ├── make_dens │ ├── rtd │ │ ├── dipl_a │ │ ├── sing_a │ │ ├── turbomole.out │ │ └── wavefunction.molden │ ├── rtda │ │ ├── ciss_a │ │ ├── dipl_a │ │ ├── turbomole.out │ │ └── wavefunction.molden │ ├── utd │ │ ├── dipl_a │ │ ├── turbomole.out │ │ ├── unrs_a │ │ └── wavefunction.molden │ └── utda │ │ ├── dipl_a │ │ ├── turbomole.out │ │ ├── ucis_a │ │ └── wavefunction.molden ├── test_turbomole.py └── test_turbomole_density.py ├── test_wavefunction ├── bases │ ├── 631G_CH.json │ └── ccpvdz_CH.json ├── h2o2 │ ├── overlap_data.h5 │ └── rhf_000.000.orca.json ├── h2o2_anion │ ├── 00_h2o2_anion.cis │ ├── 00_h2o2_anion.json │ └── 00_h2o2_anion.log ├── pyrrole │ ├── 00_pyrrole_rhf.cis │ ├── 00_pyrrole_rhf.json │ ├── 01_pyrrole_uhf.cis │ ├── 01_pyrrole_uhf.json │ └── pyrrole_guess.xyz ├── test_basis.py ├── 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