.gitignore
CHANGELOG.md
CITATION.cff
CONTRIBUTING.md
LICENSE
MANIFEST.in
README.md
THIRD_PARTY_NOTICES.txt
pyproject.toml
.github/workflows/docs.yml
.github/workflows/docs_quality.yml
.github/workflows/release.yml
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docs/Makefile
docs/add_elem_info.md
docs/all.md
docs/cli_conventions.md
docs/concepts.md
docs/conf.py
docs/dft.md
docs/energy_diagram.md
docs/extract.md
docs/fix_altloc.md
docs/freq.md
docs/getting_started.md
docs/glossary.md
docs/index.md
docs/installation.md
docs/irc.md
docs/make.bat
docs/opt.md
docs/path_opt.md
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docs/quickstart_all.md
docs/quickstart_scan.md
docs/quickstart_tsopt_freq.md
docs/recipes_common_errors.md
docs/requirements_docs.txt
docs/scan.md
docs/scan2d.md
docs/scan3d.md
docs/trj2fig.md
docs/troubleshooting.md
docs/tsopt.md
docs/uma_pysis.md
docs/yaml_reference.md
docs/_static/.gitkeep
docs/_static/custom.css
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docs/ja/add_elem_info.md
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pdb2reaction/__init__.py
pdb2reaction/__main__.py
pdb2reaction/_version.py
pdb2reaction/add_elem_info.py
pdb2reaction/advanced_help.py
pdb2reaction/align_freeze_atoms.py
pdb2reaction/all.py
pdb2reaction/bond_changes.py
pdb2reaction/bool_compat.py
pdb2reaction/cli.py
pdb2reaction/cli_utils.py
pdb2reaction/default_group.py
pdb2reaction/defaults.py
pdb2reaction/dft.py
pdb2reaction/energy_diagram.py
pdb2reaction/extract.py
pdb2reaction/fix_altloc.py
pdb2reaction/freq.py
pdb2reaction/harmonic_constraints.py
pdb2reaction/hessian_cache.py
pdb2reaction/irc.py
pdb2reaction/opt.py
pdb2reaction/path_opt.py
pdb2reaction/path_search.py
pdb2reaction/py.typed
pdb2reaction/scan.py
pdb2reaction/scan2d.py
pdb2reaction/scan3d.py
pdb2reaction/scan_common.py
pdb2reaction/summary_log.py
pdb2reaction/trj2fig.py
pdb2reaction/tsopt.py
pdb2reaction/uma_pysis.py
pdb2reaction/utils.py
pdb2reaction.egg-info/PKG-INFO
pdb2reaction.egg-info/SOURCES.txt
pdb2reaction.egg-info/dependency_links.txt
pdb2reaction.egg-info/entry_points.txt
pdb2reaction.egg-info/requires.txt
pdb2reaction.egg-info/top_level.txt
pdb2reaction/backends/__init__.py
pdb2reaction/backends/aimnet2.py
pdb2reaction/backends/base.py
pdb2reaction/backends/mace.py
pdb2reaction/backends/orb.py
pdb2reaction/backends/solvent.py
pdb2reaction/backends/uma.py
pdb2reaction/backends/xtb_alpb_correction.py
pysisyphus/Geometry.py
pysisyphus/LICENSE
pysisyphus/TableFormatter.py
pysisyphus/TablePrinter.py
pysisyphus/__init__.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/yaml_mods.py
pysisyphus/calculators/AFIR.py
pysisyphus/calculators/AnaPot.py
pysisyphus/calculators/AnaPot2.py
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pysisyphus/calculators/AnaPot4.py
pysisyphus/calculators/AnaPotBase.py
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pysisyphus/calculators/CFOUR.py
pysisyphus/calculators/Calculator.py
pysisyphus/calculators/CerjanMiller.py
pysisyphus/calculators/Composite.py
pysisyphus/calculators/ConicalIntersection.py
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pysisyphus/calculators/DFTD3.py
pysisyphus/calculators/DFTD4.py
pysisyphus/calculators/Dalton.py
pysisyphus/calculators/Dimer.py
pysisyphus/calculators/Dummy.py
pysisyphus/calculators/EGO.py
pysisyphus/calculators/EnergyMin.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
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pysisyphus/calculators/IPIClient.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
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pysisyphus/calculators/NFK.py
pysisyphus/calculators/OBabel.py
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pysisyphus/calculators/ORCA.py
pysisyphus/calculators/ORCA5.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/Remote.py
pysisyphus/calculators/Rosenbrock.py
pysisyphus/calculators/SocketCalc.py
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pysisyphus/calculators/cosmo_data.py
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pysisyphus/cos/AdaptiveNEB.py
pysisyphus/cos/ChainOfStates.py
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pysisyphus/dynamics/rattle.py
pysisyphus/dynamics/thermostats.py
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pysisyphus/intcoords/Bend.py
pysisyphus/intcoords/Bend2.py
pysisyphus/intcoords/BondedFragment.py
pysisyphus/intcoords/Cartesian.py
pysisyphus/intcoords/CartesianCoords.py
pysisyphus/intcoords/Coords.py
pysisyphus/intcoords/DLC.py
pysisyphus/intcoords/DistanceFunction.py
pysisyphus/intcoords/DummyImproper.py
pysisyphus/intcoords/DummyTorsion.py
pysisyphus/intcoords/LinearBend.py
pysisyphus/intcoords/LinearDisplacement.py
pysisyphus/intcoords/OutOfPlane.py
pysisyphus/intcoords/PrimTypes.py
pysisyphus/intcoords/Primitive.py
pysisyphus/intcoords/RedundantCoords.py
pysisyphus/intcoords/RobustTorsion.py
pysisyphus/intcoords/Rotation.py
pysisyphus/intcoords/Stretch.py
pysisyphus/intcoords/Torsion.py
pysisyphus/intcoords/Torsion2.py
pysisyphus/intcoords/Translation.py
pysisyphus/intcoords/__init__.py
pysisyphus/intcoords/augment_bonds.py
pysisyphus/intcoords/derivatives.py
pysisyphus/intcoords/eval.py
pysisyphus/intcoords/exceptions.py
pysisyphus/intcoords/findiffs.py
pysisyphus/intcoords/generate_derivatives.py
pysisyphus/intcoords/helpers.py
pysisyphus/intcoords/logging_conf.py
pysisyphus/intcoords/mp_derivatives.py
pysisyphus/intcoords/setup.py
pysisyphus/intcoords/setup_fast.py
pysisyphus/intcoords/update.py
pysisyphus/intcoords/valid.py
pysisyphus/interpolate/Geodesic.py
pysisyphus/interpolate/IDPP.py
pysisyphus/interpolate/Interpolator.py
pysisyphus/interpolate/LST.py
pysisyphus/interpolate/Redund.py
pysisyphus/interpolate/__init__.py
pysisyphus/interpolate/helpers.py
pysisyphus/io/__init__.py
pysisyphus/io/aomix.py
pysisyphus/io/cjson.py
pysisyphus/io/crd.py
pysisyphus/io/cube.py
pysisyphus/io/fchk.py
pysisyphus/io/hdf5.py
pysisyphus/io/hessian.py
pysisyphus/io/mol2.py
pysisyphus/io/molden.py
pysisyphus/io/orca.py
pysisyphus/io/pdb.py
pysisyphus/io/psf.py
pysisyphus/io/pubchem.py
pysisyphus/io/qcschema.py
pysisyphus/io/sdf.py
pysisyphus/io/xyz.py
pysisyphus/io/zmat.py
pysisyphus/irc/DWI.py
pysisyphus/irc/DampedVelocityVerlet.py
pysisyphus/irc/Euler.py
pysisyphus/irc/EulerPC.py
pysisyphus/irc/GonzalezSchlegel.py
pysisyphus/irc/IMKMod.py
pysisyphus/irc/IRC.py
pysisyphus/irc/IRCDummy.py
pysisyphus/irc/Instanton.py
pysisyphus/irc/LQA.py
pysisyphus/irc/ModeKill.py
pysisyphus/irc/ParamPlot.py
pysisyphus/irc/RK4.py
pysisyphus/irc/__init__.py
pysisyphus/irc/initial_displ.py
pysisyphus/line_searches/Backtracking.py
pysisyphus/line_searches/HagerZhang.py
pysisyphus/line_searches/LineSearch.py
pysisyphus/line_searches/StrongWolfe.py
pysisyphus/line_searches/__init__.py
pysisyphus/line_searches/interpol.py
pysisyphus/modefollow/NormalMode.py
pysisyphus/modefollow/__init__.py
pysisyphus/modefollow/davidson.py
pysisyphus/modefollow/lanczos.py
pysisyphus/optimizers/BFGS.py
pysisyphus/optimizers/BacktrackingOptimizer.py
pysisyphus/optimizers/ConjugateGradient.py
pysisyphus/optimizers/CubicNewton.py
pysisyphus/optimizers/FIRE.py
pysisyphus/optimizers/HessianOptimizer.py
pysisyphus/optimizers/LBFGS.py
pysisyphus/optimizers/LayerOpt.py
pysisyphus/optimizers/MicroOptimizer.py
pysisyphus/optimizers/NCOptimizer.py
pysisyphus/optimizers/Optimizer.py
pysisyphus/optimizers/PreconLBFGS.py
pysisyphus/optimizers/PreconSteepestDescent.py
pysisyphus/optimizers/QuickMin.py
pysisyphus/optimizers/RFOptimizer.py
pysisyphus/optimizers/RSA.py
pysisyphus/optimizers/StabilizedQNMethod.py
pysisyphus/optimizers/SteepestDescent.py
pysisyphus/optimizers/StringOptimizer.py
pysisyphus/optimizers/__init__.py
pysisyphus/optimizers/closures.py
pysisyphus/optimizers/cls_map.py
pysisyphus/optimizers/exceptions.py
pysisyphus/optimizers/gdiis.py
pysisyphus/optimizers/guess_hessians.py
pysisyphus/optimizers/hessian_updates.py
pysisyphus/optimizers/poly_fit.py
pysisyphus/optimizers/precon.py
pysisyphus/optimizers/restrict_step.py
pysisyphus/stocastic/FragmentKick.py
pysisyphus/stocastic/Kick.py
pysisyphus/stocastic/Pipeline.py
pysisyphus/stocastic/__init__.py
pysisyphus/stocastic/align.py
pysisyphus/tsoptimizers/RSIRFOptimizer.py
pysisyphus/tsoptimizers/RSPRFOptimizer.py
pysisyphus/tsoptimizers/TRIM.py
pysisyphus/tsoptimizers/TSHessianOptimizer.py
pysisyphus/tsoptimizers/__init__.py
pysisyphus/wavefunction/Basis.py
pysisyphus/wavefunction/DIIS.py
pysisyphus/wavefunction/__init__.py
pysisyphus/wavefunction/build_ext.py
pysisyphus/wavefunction/cart2sph.py
pysisyphus/wavefunction/diabatization.py
pysisyphus/wavefunction/excited_states.py
pysisyphus/wavefunction/gen_ints.py
pysisyphus/wavefunction/helpers.py
pysisyphus/wavefunction/localization.py
pysisyphus/wavefunction/multipole.py
pysisyphus/wavefunction/normalization.py
pysisyphus/wavefunction/pop_analysis.py
pysisyphus/wavefunction/shells.py
pysisyphus/wavefunction/wavefunction.py
pysisyphus/wavefunction/ints/__init__.py
pysisyphus/wavefunction/ints/boys.py
pysisyphus/wavefunction/ints/boys_table_N_64_xasym_27.1_step_0.01.npy
pysisyphus/wavefunction/ints/cart_gto3d.py
pysisyphus/wavefunction/ints/coulomb3d.py
pysisyphus/wavefunction/ints/diag_quadrupole3d.py
pysisyphus/wavefunction/ints/dipole3d.py
pysisyphus/wavefunction/ints/int2c2e3d.py
pysisyphus/wavefunction/ints/int3c2e3d_sph.py
pysisyphus/wavefunction/ints/kinetic3d.py
pysisyphus/wavefunction/ints/ovlp3d.py
pysisyphus/wavefunction/ints/quadrupole3d.py
pysisyphus/wavefunction/ints/self_ovlp3d.py
pysisyphus/wrapper/__init__.py
pysisyphus/wrapper/exceptions.py
pysisyphus/wrapper/jmol.py
pysisyphus/wrapper/mwfn.py
pysisyphus/wrapper/packmol.py
scripts/check_all_scan_contract.py
scripts/check_intro_template.py
scripts/check_markdown_links.py
scripts/generate_reference.py
scripts/run_docs_quality.py
scripts/smoke_core_cli_commands.py
scripts/smoke_docs_commands.py
scripts/smoke_dump_trajectories.py
tests/README.md
tests/conftest.py
tests/test_align_math.py
tests/test_all_multiplicity_option.py
tests/test_bond_changes.py
tests/test_bool_compat_cli.py
tests/test_cli_smoke_low_coverage.py
tests/test_cli_utils.py
tests/test_default_group.py
tests/test_defaults.py
tests/test_extract.py
tests/test_summary_log.py
tests/test_utils.py
tests/test_utils_extended.py
tests/smoke/h2.gjf
tests/smoke/input.yaml
tests/smoke/p.gjf
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thermoanalysis/LICENSE
thermoanalysis/QCData.py
thermoanalysis/__init__.py
thermoanalysis/config.py
thermoanalysis/constants.py
thermoanalysis/thermo.py