MANIFEST.in
README.md
setup.cfg
setup.py
versioneer.py
pysisyphus/Geometry.py
pysisyphus/TableFormatter.py
pysisyphus/TablePrinter.py
pysisyphus/__init__.py
pysisyphus/_version.py
pysisyphus/color.py
pysisyphus/config.py
pysisyphus/constants.py
pysisyphus/elem_data.py
pysisyphus/exceptions.py
pysisyphus/filtertrj.py
pysisyphus/helpers.py
pysisyphus/helpers_pure.py
pysisyphus/init_logging.py
pysisyphus/linalg.py
pysisyphus/pack.py
pysisyphus/peakdetect.py
pysisyphus/plot.py
pysisyphus/run.py
pysisyphus/socket_helper.py
pysisyphus/testing.py
pysisyphus/thermo.py
pysisyphus/trj.py
pysisyphus/xyzloader.py
pysisyphus.egg-info/PKG-INFO
pysisyphus.egg-info/SOURCES.txt
pysisyphus.egg-info/dependency_links.txt
pysisyphus.egg-info/entry_points.txt
pysisyphus.egg-info/requires.txt
pysisyphus.egg-info/top_level.txt
pysisyphus/benchmarks/Benchmark.py
pysisyphus/benchmarks/__init__.py
pysisyphus/benchmarks/data.py
pysisyphus/calculators/AFIR.py
pysisyphus/calculators/AnaPot.py
pysisyphus/calculators/AnaPot2.py
pysisyphus/calculators/AnaPot3.py
pysisyphus/calculators/AnaPot4.py
pysisyphus/calculators/AnaPotBase.py
pysisyphus/calculators/AnaPotCBM.py
pysisyphus/calculators/AtomAtomTransTorque.py
pysisyphus/calculators/Calculator.py
pysisyphus/calculators/CerjanMiller.py
pysisyphus/calculators/Composite.py
pysisyphus/calculators/DFTBp.py
pysisyphus/calculators/Dalton.py
pysisyphus/calculators/Dimer.py
pysisyphus/calculators/ExternalPotential.py
pysisyphus/calculators/FakeASE.py
pysisyphus/calculators/FourWellAnaPot.py
pysisyphus/calculators/FreeEndNEBPot.py
pysisyphus/calculators/Gaussian09.py
pysisyphus/calculators/Gaussian16.py
pysisyphus/calculators/HardSphere.py
pysisyphus/calculators/IDPPCalculator.py
pysisyphus/calculators/IPIServer.py
pysisyphus/calculators/LEPSBase.py
pysisyphus/calculators/LEPSExpr.py
pysisyphus/calculators/LennardJones.py
pysisyphus/calculators/MOPAC.py
pysisyphus/calculators/MullerBrownSympyPot.py
pysisyphus/calculators/MultiCalc.py
pysisyphus/calculators/OBabel.py
pysisyphus/calculators/ONIOMv2.py
pysisyphus/calculators/ORCA.py
pysisyphus/calculators/OpenMM.py
pysisyphus/calculators/OpenMolcas.py
pysisyphus/calculators/OverlapCalculator.py
pysisyphus/calculators/Psi4.py
pysisyphus/calculators/PyPsi4.py
pysisyphus/calculators/PySCF.py
pysisyphus/calculators/PyXTB.py
pysisyphus/calculators/QCEngine.py
pysisyphus/calculators/Rastrigin.py
pysisyphus/calculators/Rosenbrock.py
pysisyphus/calculators/SocketCalc.py
pysisyphus/calculators/TIP3P.py
pysisyphus/calculators/TransTorque.py
pysisyphus/calculators/Turbomole.py
pysisyphus/calculators/WFOWrapper.py
pysisyphus/calculators/WFOWrapper2.py
pysisyphus/calculators/XTB.py
pysisyphus/calculators/__init__.py
pysisyphus/calculators/parser.py
pysisyphus/cos/AdaptiveNEB.py
pysisyphus/cos/ChainOfStates.py
pysisyphus/cos/FreeEndNEB.py
pysisyphus/cos/FreezingString.py
pysisyphus/cos/GrowingChainOfStates.py
pysisyphus/cos/GrowingNT.py
pysisyphus/cos/GrowingString.py
pysisyphus/cos/NEB.py
pysisyphus/cos/SimpleZTS.py
pysisyphus/cos/__init__.py
pysisyphus/db/__init__.py
pysisyphus/db/generate_db.py
pysisyphus/db/helpers.py
pysisyphus/db/level.py
pysisyphus/db/molecules.py
pysisyphus/db/guess/14dioxane.xyz
pysisyphus/db/guess/acetone.xyz
pysisyphus/db/guess/acetonitrile.xyz
pysisyphus/db/guess/chloroform.xyz
pysisyphus/db/guess/dichloromethane.xyz
pysisyphus/db/guess/tetrahydrofuran.xyz
pysisyphus/db/guess/water.xyz
pysisyphus/db/levels/b973c_orca/14dioxane.xyz
pysisyphus/db/levels/b973c_orca/acetone.xyz
pysisyphus/db/levels/b973c_orca/acetonitrile.xyz
pysisyphus/db/levels/b973c_orca/chloroform.xyz
pysisyphus/db/levels/b973c_orca/dichloromethane.xyz
pysisyphus/db/levels/b973c_orca/tetrahydrofuran.xyz
pysisyphus/db/levels/b973c_orca/water.xyz
pysisyphus/db/levels/gfn0_xtb/14dioxane.xyz
pysisyphus/db/levels/gfn0_xtb/acetone.xyz
pysisyphus/db/levels/gfn0_xtb/acetonitrile.xyz
pysisyphus/db/levels/gfn0_xtb/chloroform.xyz
pysisyphus/db/levels/gfn0_xtb/dichloromethane.xyz
pysisyphus/db/levels/gfn0_xtb/tetrahydrofuran.xyz
pysisyphus/db/levels/gfn0_xtb/water.xyz
pysisyphus/db/levels/gfn1_xtb/14dioxane.xyz
pysisyphus/db/levels/gfn1_xtb/acetone.xyz
pysisyphus/db/levels/gfn1_xtb/acetonitrile.xyz
pysisyphus/db/levels/gfn1_xtb/chloroform.xyz
pysisyphus/db/levels/gfn1_xtb/dichloromethane.xyz
pysisyphus/db/levels/gfn1_xtb/tetrahydrofuran.xyz
pysisyphus/db/levels/gfn1_xtb/water.xyz
pysisyphus/db/levels/gfn2_xtb/14dioxane.xyz
pysisyphus/db/levels/gfn2_xtb/acetone.xyz
pysisyphus/db/levels/gfn2_xtb/acetonitrile.xyz
pysisyphus/db/levels/gfn2_xtb/chloroform.xyz
pysisyphus/db/levels/gfn2_xtb/dichloromethane.xyz
pysisyphus/db/levels/gfn2_xtb/tetrahydrofuran.xyz
pysisyphus/db/levels/gfn2_xtb/water.xyz
pysisyphus/drivers/__init__.py
pysisyphus/drivers/barriers.py
pysisyphus/drivers/birkholz.py
pysisyphus/drivers/merge.py
pysisyphus/drivers/opt.py
pysisyphus/drivers/precon_pos_rot.py
pysisyphus/drivers/scan.py
pysisyphus/drivers/thermo.py
pysisyphus/dynamics/Gaussian.py
pysisyphus/dynamics/__init__.py
pysisyphus/dynamics/colvars.py
pysisyphus/dynamics/driver.py
pysisyphus/dynamics/helpers.py
pysisyphus/dynamics/lincs.py
pysisyphus/dynamics/mdp.py
pysisyphus/dynamics/rattle.py
pysisyphus/dynamics/thermostats.py
pysisyphus/geom_library/01_h2o.xyz
pysisyphus/geom_library/01_h2o_hdiss.xyz
pysisyphus/geom_library/01_opt_aus_04_b3lyp_scan_min.xyz
pysisyphus/geom_library/01_run6fbpb_photoprod_guess.xyz
pysisyphus/geom_library/08_allene.xyz
pysisyphus/geom_library/09_htransfer_product.xyz
pysisyphus/geom_library/10_po_diss_product_xtbopt.xyz
pysisyphus/geom_library/SulfateInSolution.xyz
pysisyphus/geom_library/acet_tm.xyz
pysisyphus/geom_library/acetaldehyd.xyz
pysisyphus/geom_library/acetaldehyd_oniom.xyz
pysisyphus/geom_library/acetaldehyd_oniom_opt.xyz
pysisyphus/geom_library/afir3test.xyz
pysisyphus/geom_library/ala_dipeptide_cycle_021_gs_opt_xtb.trj
pysisyphus/geom_library/ala_dipeptide_iso_b3lyp_631gd_10_images.trj
pysisyphus/geom_library/ala_dipeptide_iso_b3lyp_631gd_start_end.trj
pysisyphus/geom_library/alkyl17_sto3g_opt.xyz
pysisyphus/geom_library/ar14cluster.xyz
pysisyphus/geom_library/azet_bad.xyz
pysisyphus/geom_library/azetidine_guess.xyz
pysisyphus/geom_library/azetidine_hf_321g_opt.xyz
pysisyphus/geom_library/azetidine_not_opt.xyz
pysisyphus/geom_library/azetidine_xtbopt.xyz
pysisyphus/geom_library/bare_solvated.xyz
pysisyphus/geom_library/benzene.xyz
pysisyphus/geom_library/benzene_and_chlorine.xyz
pysisyphus/geom_library/benzene_and_no.xyz
pysisyphus/geom_library/benzene_bp86sto3g_opt.xyz
pysisyphus/geom_library/benzene_pm6_opt.xyz
pysisyphus/geom_library/benzene_shaken.xyz
pysisyphus/geom_library/biaryl_bare_pm6_splined_hei.xyz
pysisyphus/geom_library/butadiene_hf_sto3g.xyz
pysisyphus/geom_library/c4_lb_test.xyz
pysisyphus/geom_library/c4_lb_test_02.xyz
pysisyphus/geom_library/c6.xyz
pysisyphus/geom_library/ch2s_bp86def2sv_opt.xyz
pysisyphus/geom_library/ciscis_24hexadiene_xtbopt.xyz
pysisyphus/geom_library/claisen_forward.xyz
pysisyphus/geom_library/co2.xyz
pysisyphus/geom_library/co2_bent.xyz
pysisyphus/geom_library/co2_linear.xyz
pysisyphus/geom_library/co2_short.xyz
pysisyphus/geom_library/codein.xyz
pysisyphus/geom_library/cytosin.xyz
pysisyphus/geom_library/diels_alder_interpolated.trj
pysisyphus/geom_library/dieniminium_cation_s1_opt.xyz
pysisyphus/geom_library/dipeptide_fin.xyz
pysisyphus/geom_library/dipeptide_init.xyz
pysisyphus/geom_library/ethan.xyz
pysisyphus/geom_library/fe_opt.xyz
pysisyphus/geom_library/fe_opt_cart.xyz
pysisyphus/geom_library/fluorethylene.xyz
pysisyphus/geom_library/h2.xyz
pysisyphus/geom_library/h2o.xyz
pysisyphus/geom_library/h2o2_guess.xyz
pysisyphus/geom_library/h2o2_guess_bad.xyz
pysisyphus/geom_library/h2o2_h2o_fragments.xyz
pysisyphus/geom_library/h2o2_hf_321g_opt.xyz
pysisyphus/geom_library/h2o2_rot2.xyz
pysisyphus/geom_library/h2o_30_sphere.xyz
pysisyphus/geom_library/h2o_30_sphere_translated_2_2_2.xyz
pysisyphus/geom_library/h2o_bp86_def2svp_opt.xyz
pysisyphus/geom_library/h2o_inv_educt.xyz
pysisyphus/geom_library/h2o_inv_middle.xyz
pysisyphus/geom_library/h2o_inv_product.xyz
pysisyphus/geom_library/h2o_pt.xyz
pysisyphus/geom_library/h2o_shaken.xyz
pysisyphus/geom_library/hcfclbr_xtbopt.xyz
pysisyphus/geom_library/hcn.xyz
pysisyphus/geom_library/hcn_bent.pdb
pysisyphus/geom_library/hcn_bent.xyz
pysisyphus/geom_library/hcn_downhill_model_hessian.xyz
pysisyphus/geom_library/hcn_iso_hf_sto3g_ts_opt.xyz
pysisyphus/geom_library/hcn_iso_pm6_near_ts.xyz
pysisyphus/geom_library/hcn_iso_ts.xyz
pysisyphus/geom_library/hcn_iso_ts_opt_xtb.xyz
pysisyphus/geom_library/hcn_sto3g_freq_ref.xyz
pysisyphus/geom_library/hcn_ts_hf_321g.xyz
pysisyphus/geom_library/hfabstraction_hf321g_displ_forward.xyz
pysisyphus/geom_library/hfabstraction_ts.xyz
pysisyphus/geom_library/hfabstraction_ts_opt_xtb.xyz
pysisyphus/geom_library/hydrogen_bond.xyz
pysisyphus/geom_library/hydrogen_bond_fragments_test.xyz
pysisyphus/geom_library/interfrag_hydrogen_bond.xyz
pysisyphus/geom_library/menthone.xyz
pysisyphus/geom_library/methane.xyz
pysisyphus/geom_library/methane_bp86_def2svp_opt.xyz
pysisyphus/geom_library/nhc.xyz
pysisyphus/geom_library/ohch3f_anion_cs.xyz
pysisyphus/geom_library/oniom3alkyl.pdb
pysisyphus/geom_library/oniom_13_coupling_example.xyz
pysisyphus/geom_library/oniom_ee_model_system.xyz
pysisyphus/geom_library/ozone.xyz
pysisyphus/geom_library/runo_nto_track.xyz
pysisyphus/geom_library/sf6.xyz
pysisyphus/geom_library/single_atom_fragments.xyz
pysisyphus/geom_library/so3hcl_diss_ts_opt.xyz
pysisyphus/geom_library/split.image_021.xyz
pysisyphus/geom_library/test_full_run_split.geom_008.xyz
pysisyphus/geom_library/test_full_run_split.geom_034.xyz
pysisyphus/geom_library/test_reject.trj
pysisyphus/geom_library/test_union_rx_001.trj
pysisyphus/geom_library/test_union_ts_001.xyz
pysisyphus/geom_library/thr75_from_1bl8.xyz
pysisyphus/geom_library/tip3p_h2o.xyz
pysisyphus/geom_library/tip3p_water.xyz
pysisyphus/geom_library/toluene_and_cl2.xyz
pysisyphus/geom_library/trans34dimethylcyclobutene.xyz
pysisyphus/geom_library/water_dimer_oniomopt_test.pdb
pysisyphus/geom_library/xtbopt.anfang.xyz
pysisyphus/geom_library/xtbopt.ende2.xyz
pysisyphus/geom_library/baker/00_water.xyz
pysisyphus/geom_library/baker/01_ammonia.xyz
pysisyphus/geom_library/baker/02_ethane.xyz
pysisyphus/geom_library/baker/03_acetylene.xyz
pysisyphus/geom_library/baker/04_allene.xyz
pysisyphus/geom_library/baker/05_hydroxysulphane.xyz
pysisyphus/geom_library/baker/06_benzene.xyz
pysisyphus/geom_library/baker/07_methylamine.xyz
pysisyphus/geom_library/baker/08_ethanol.xyz
pysisyphus/geom_library/baker/09_acetone.xyz
pysisyphus/geom_library/baker/10_disilylether.xyz
pysisyphus/geom_library/baker/11_135trisilacyclohexane.xyz
pysisyphus/geom_library/baker/12_benzaldehyde.xyz
pysisyphus/geom_library/baker/13_13difluorobenzene.xyz
pysisyphus/geom_library/baker/14_135trifluorobenzene.xyz
pysisyphus/geom_library/baker/15_neopentane.xyz
pysisyphus/geom_library/baker/16_furan.xyz
pysisyphus/geom_library/baker/17_naphthalene.xyz
pysisyphus/geom_library/baker/18_15difluoronaphthalene.xyz
pysisyphus/geom_library/baker/19_2hydroxybicyclopentane.xyz
pysisyphus/geom_library/baker/20_achtar10.xyz
pysisyphus/geom_library/baker/21_acanil01.xyz
pysisyphus/geom_library/baker/22_benzidine.xyz
pysisyphus/geom_library/baker/23_pterin.xyz
pysisyphus/geom_library/baker/24_difuropyrazine.xyz
pysisyphus/geom_library/baker/25_mesityloxide.xyz
pysisyphus/geom_library/baker/26_histidine.xyz
pysisyphus/geom_library/baker/27_dimethylpentane.xyz
pysisyphus/geom_library/baker/28_caffeine.xyz
pysisyphus/geom_library/baker/29_menthone.xyz
pysisyphus/geom_library/baker_ts/01_hcn.xyz
pysisyphus/geom_library/baker_ts/01_hcn_downhill.xyz
pysisyphus/geom_library/baker_ts/02_hcch.xyz
pysisyphus/geom_library/baker_ts/02_hcch_downhill.xyz
pysisyphus/geom_library/baker_ts/03_h2co.xyz
pysisyphus/geom_library/baker_ts/03_h2co_downhill.xyz
pysisyphus/geom_library/baker_ts/04_ch3o.xyz
pysisyphus/geom_library/baker_ts/04_ch3o_downhill.xyz
pysisyphus/geom_library/baker_ts/05_cyclopropyl.xyz
pysisyphus/geom_library/baker_ts/05_cyclopropyl_downhill.xyz
pysisyphus/geom_library/baker_ts/06_bicyclobutane.xyz
pysisyphus/geom_library/baker_ts/06_bicyclobutane_downhill.xyz
pysisyphus/geom_library/baker_ts/07_bicyclobutane.xyz
pysisyphus/geom_library/baker_ts/07_bicyclobutane_downhill.xyz
pysisyphus/geom_library/baker_ts/08_formyloxyethyl.xyz
pysisyphus/geom_library/baker_ts/08_formyloxyethyl_downhill.xyz
pysisyphus/geom_library/baker_ts/09_parentdieslalder.xyz
pysisyphus/geom_library/baker_ts/09_parentdieslalder_downhill.xyz
pysisyphus/geom_library/baker_ts/10_tetrazine.xyz
pysisyphus/geom_library/baker_ts/10_tetrazine_downhill.xyz
pysisyphus/geom_library/baker_ts/11_trans_butadiene.xyz
pysisyphus/geom_library/baker_ts/11_trans_butadiene_downhill.xyz
pysisyphus/geom_library/baker_ts/12_ethane_h2_abstraction.xyz
pysisyphus/geom_library/baker_ts/12_ethane_h2_abstraction_downhill.xyz
pysisyphus/geom_library/baker_ts/13_hf_abstraction.xyz
pysisyphus/geom_library/baker_ts/13_hf_abstraction_downhill.xyz
pysisyphus/geom_library/baker_ts/14_vinyl_alcohol.xyz
pysisyphus/geom_library/baker_ts/14_vinyl_alcohol_downhill.xyz
pysisyphus/geom_library/baker_ts/15_hocl.xyz
pysisyphus/geom_library/baker_ts/15_hocl_downhill.xyz
pysisyphus/geom_library/baker_ts/16_h2po4_anion.xyz
pysisyphus/geom_library/baker_ts/16_h2po4_anion_downhill.xyz
pysisyphus/geom_library/baker_ts/17_claisen.xyz
pysisyphus/geom_library/baker_ts/17_claisen_downhill.xyz
pysisyphus/geom_library/baker_ts/18_silyene_insertion.xyz
pysisyphus/geom_library/baker_ts/18_silyene_insertion_downhill.xyz
pysisyphus/geom_library/baker_ts/19_hnccs.xyz
pysisyphus/geom_library/baker_ts/19_hnccs_downhill.xyz
pysisyphus/geom_library/baker_ts/20_hconh3_cation.xyz
pysisyphus/geom_library/baker_ts/20_hconh3_cation_downhill.xyz
pysisyphus/geom_library/baker_ts/21_acrolein_rot.xyz
pysisyphus/geom_library/baker_ts/21_acrolein_rot_downhill.xyz
pysisyphus/geom_library/baker_ts/22_hconhoh.xyz
pysisyphus/geom_library/baker_ts/22_hconhoh_downhill.xyz
pysisyphus/geom_library/baker_ts/23_hcn_h2.xyz
pysisyphus/geom_library/baker_ts/23_hcn_h2_downhill.xyz
pysisyphus/geom_library/baker_ts/24_h2cnh.xyz
pysisyphus/geom_library/baker_ts/24_h2cnh_downhill.xyz
pysisyphus/geom_library/baker_ts/25_hcnh2.xyz
pysisyphus/geom_library/baker_ts/25_hcnh2_downhill.xyz
pysisyphus/geom_library/birkholz/artemisin.xyz
pysisyphus/geom_library/birkholz/aspartame.xyz
pysisyphus/geom_library/birkholz/avobenzone.xyz
pysisyphus/geom_library/birkholz/azadirachtin.xyz
pysisyphus/geom_library/birkholz/bisphenol_a.xyz
pysisyphus/geom_library/birkholz/cetirizine.xyz
pysisyphus/geom_library/birkholz/codeine.xyz
pysisyphus/geom_library/birkholz/diisobutyl_phthalate.xyz
pysisyphus/geom_library/birkholz/easc.xyz
pysisyphus/geom_library/birkholz/estradiol.xyz
pysisyphus/geom_library/birkholz/inosine.xyz
pysisyphus/geom_library/birkholz/maltose.xyz
pysisyphus/geom_library/birkholz/mg_porphin.xyz
pysisyphus/geom_library/birkholz/ochratoxin_a.xyz
pysisyphus/geom_library/birkholz/penicillin_v.xyz
pysisyphus/geom_library/birkholz/raffinose.xyz
pysisyphus/geom_library/birkholz/sphingomyelin.xyz
pysisyphus/geom_library/birkholz/tamoxifen.xyz
pysisyphus/geom_library/birkholz/vitamin_c.xyz
pysisyphus/geom_library/birkholz/zn_edta.xyz
pysisyphus/geom_library/birkholz_rx/00_c2no2.trj
pysisyphus/geom_library/birkholz_rx/01_c5ht.trj
pysisyphus/geom_library/birkholz_rx/02_hcn.trj
pysisyphus/geom_library/birkholz_rx/02_hcn_original.trj
pysisyphus/geom_library/birkholz_rx/03_cope.trj
pysisyphus/geom_library/birkholz_rx/04_cpht.trj
pysisyphus/geom_library/birkholz_rx/05_cycbut.trj
pysisyphus/geom_library/birkholz_rx/06_dacp2.trj
pysisyphus/geom_library/birkholz_rx/07_dacp_eth.trj
pysisyphus/geom_library/birkholz_rx/08_dfcp.trj
pysisyphus/geom_library/birkholz_rx/09_ene.trj
pysisyphus/geom_library/birkholz_rx/10_grignard.trj
pysisyphus/geom_library/birkholz_rx/11_h2co.trj
pysisyphus/geom_library/birkholz_rx/12_hf_eth.trj
pysisyphus/geom_library/birkholz_rx/13_hydro.trj
pysisyphus/geom_library/birkholz_rx/14_meoh.trj
pysisyphus/geom_library/birkholz_rx/15_oxirane.trj
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