CHANGELOG.md
CITATION.cff
LICENSE
MANIFEST.in
README.md
THIRD_PARTY_NOTICES.txt
pyproject.toml
docs/add-elem-info.md
docs/all.md
docs/architecture.md
docs/backends.md
docs/bond-summary.md
docs/cif.md
docs/cli-conventions.md
docs/concepts.md
docs/define-layer.md
docs/device-hpc.md
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/irc.md
docs/json-output.md
docs/mcp_server.md
docs/mlmm-calc.md
docs/mm-parm.md
docs/oniom-export.md
docs/oniom-gaussian.md
docs/oniom-import.md
docs/oniom-orca.md
docs/opt.md
docs/output-layout.md
docs/path-opt.md
docs/path-search.md
docs/python-api.md
docs/quickstart-all.md
docs/quickstart-scan-spec.md
docs/quickstart-tsopt-freq.md
docs/recipes-common-errors.md
docs/reproducibility.md
docs/scan.md
docs/scan2d.md
docs/scan3d.md
docs/sp.md
docs/trj2fig.md
docs/troubleshooting.md
docs/tsopt.md
docs/yaml-reference.md
docs/ja/add-elem-info.md
docs/ja/all.md
docs/ja/architecture.md
docs/ja/backends.md
docs/ja/bond-summary.md
docs/ja/cif.md
docs/ja/cli-conventions.md
docs/ja/concepts.md
docs/ja/define-layer.md
docs/ja/device-hpc.md
docs/ja/dft.md
docs/ja/energy-diagram.md
docs/ja/extract.md
docs/ja/fix-altloc.md
docs/ja/freq.md
docs/ja/getting-started.md
docs/ja/glossary.md
docs/ja/index.md
docs/ja/irc.md
docs/ja/json-output.md
docs/ja/mcp_server.md
docs/ja/mlmm-calc.md
docs/ja/mm-parm.md
docs/ja/oniom-export.md
docs/ja/oniom-gaussian.md
docs/ja/oniom-import.md
docs/ja/oniom-orca.md
docs/ja/opt.md
docs/ja/output-layout.md
docs/ja/path-opt.md
docs/ja/path-search.md
docs/ja/python-api.md
docs/ja/quickstart-all.md
docs/ja/quickstart-scan-spec.md
docs/ja/quickstart-tsopt-freq.md
docs/ja/recipes-common-errors.md
docs/ja/reproducibility.md
docs/ja/scan.md
docs/ja/scan2d.md
docs/ja/scan3d.md
docs/ja/sp.md
docs/ja/trj2fig.md
docs/ja/troubleshooting.md
docs/ja/tsopt.md
docs/ja/yaml-reference.md
docs/reference/yaml.md
docs/reference/commands/add_elem_info.md
docs/reference/commands/all.md
docs/reference/commands/bond_summary.md
docs/reference/commands/define_layer.md
docs/reference/commands/dft.md
docs/reference/commands/energy_diagram.md
docs/reference/commands/extract.md
docs/reference/commands/fix_altloc.md
docs/reference/commands/freq.md
docs/reference/commands/index.md
docs/reference/commands/irc.md
docs/reference/commands/mm_parm.md
docs/reference/commands/oniom_export.md
docs/reference/commands/oniom_import.md
docs/reference/commands/opt.md
docs/reference/commands/path_opt.md
docs/reference/commands/path_search.md
docs/reference/commands/scan.md
docs/reference/commands/scan2d.md
docs/reference/commands/scan3d.md
docs/reference/commands/sp.md
docs/reference/commands/trj2fig.md
docs/reference/commands/tsopt.md
examples/mcp_client_config.json
examples/mlmm_colab.ipynb
examples/beza/1.R.pdb
examples/beza/2.IM.pdb
examples/beza/3.P.pdb
examples/beza/README.md
examples/beza/run.sh
examples/methyltransferase/complex.parm7
examples/methyltransferase/complex.pdb
examples/methyltransferase/complex.rst7
examples/methyltransferase/pocket.pdb
examples/methyltransferase/r_layered.pdb
examples/methyltransferase/run_all.sh
examples/methyltransferase/run_stepwise.sh
examples/toy_system/ml_region_p.pdb
examples/toy_system/ml_region_r.pdb
examples/toy_system/opt_ase.py
examples/toy_system/p_complex.pdb
examples/toy_system/p_complex.rst7
examples/toy_system/p_toy.parm7
examples/toy_system/p_toy.pdb
examples/toy_system/r_complex.pdb
examples/toy_system/r_toy.pdb
examples/toy_system/run.sh
examples/toy_system/test_core.py
hessian_ff/__init__.py
hessian_ff/active_space.py
hessian_ff/analytical_hessian.py
hessian_ff/constants.py
hessian_ff/forcefield.py
hessian_ff/loaders.py
hessian_ff/prmtop_parmed.py
hessian_ff/system.py
hessian_ff/workflows.py
hessian_ff/native/Makefile
hessian_ff/native/__init__.py
hessian_ff/native/analytical_hessian.py
hessian_ff/native/analytical_hessian_ext.cpp
hessian_ff/native/bonded.py
hessian_ff/native/bonded_ext.cpp
hessian_ff/native/loader.py
hessian_ff/native/nonbonded.py
hessian_ff/native/nonbonded_ext.cpp
hessian_ff/terms/__init__.py
hessian_ff/terms/angle.py
hessian_ff/terms/bond.py
hessian_ff/terms/cmap.py
hessian_ff/terms/dihedral.py
hessian_ff/terms/nonbonded.py
hessian_ff/tests/__init__.py
hessian_ff/tests/conftest.py
hessian_ff/tests/test_active_space.py
hessian_ff/tests/test_coords_input.py
hessian_ff/tests/test_energy_force.py
hessian_ff/tests/test_hessian.py
hessian_ff/tests/test_input_boundaries.py
hessian_ff/tests/test_native_loader.py
hessian_ff/tests/test_runtime_cache.py
hessian_ff/tests/test_smoke.py
hessian_ff/tests/test_validation.py
mlmm/__init__.py
mlmm/__main__.py
mlmm/_version.py
mlmm/py.typed
mlmm/backends/__init__.py
mlmm/backends/_determinism.py
mlmm/backends/custom.py
mlmm/backends/methods.py
mlmm/backends/mlmm_calc.py
mlmm/backends/xtb_embedcharge_correction.py
mlmm/cli/__init__.py
mlmm/cli/app.py
mlmm/cli/bool_compat.py
mlmm/cli/common_options.py
mlmm/cli/decorators.py
mlmm/cli/default_group.py
mlmm/cli/help_pages.py
mlmm/cli/preflight.py
mlmm/core/__init__.py
mlmm/core/calc_eval.py
mlmm/core/defaults.py
mlmm/core/logging.py
mlmm/core/output.py
mlmm/core/pes_composition.py
mlmm/core/residue_data.py
mlmm/core/result_commit.py
mlmm/core/utils.py
mlmm/domain/__init__.py
mlmm/domain/add_elem_info.py
mlmm/domain/bond_changes.py
mlmm/domain/bond_summary.py
mlmm/io/__init__.py
mlmm/io/altloc.py
mlmm/io/energy_diagram.py
mlmm/io/gaussian_input.py
mlmm/io/hessian_cache.py
mlmm/io/hessian_calc.py
mlmm/io/hessian_file.py
mlmm/io/oniom_identity.py
mlmm/io/path_mode_cache.py
mlmm/io/pdb_fix.py
mlmm/io/pdb_indexing.py
mlmm/io/plotly_image.py
mlmm/io/structure_formats.py
mlmm/io/summary.py
mlmm/io/trj2fig.py
mlmm/io/xyz_trajectory.py
mlmm/mcp/__init__.py
mlmm/mcp/_runner.py
mlmm/mcp/_tools.py
mlmm/mcp/server.py
mlmm/workflows/__init__.py
mlmm/workflows/_all_helpers.py
mlmm/workflows/_microiteration.py
mlmm/workflows/_opt_freq_common.py
mlmm/workflows/_outcomes.py
mlmm/workflows/_run_session.py
mlmm/workflows/align_freeze.py
mlmm/workflows/all.py
mlmm/workflows/charge_prep.py
mlmm/workflows/define_layer.py
mlmm/workflows/dft.py
mlmm/workflows/extract.py
mlmm/workflows/freq.py
mlmm/workflows/irc.py
mlmm/workflows/mm_parm.py
mlmm/workflows/oniom_export.py
mlmm/workflows/oniom_import.py
mlmm/workflows/opt.py
mlmm/workflows/path_opt.py
mlmm/workflows/path_search.py
mlmm/workflows/restraints.py
mlmm/workflows/scan.py
mlmm/workflows/scan2d.py
mlmm/workflows/scan3d.py
mlmm/workflows/scan_common.py
mlmm/workflows/sp.py
mlmm/workflows/tsopt.py
mlmm_toolkit.egg-info/PKG-INFO
mlmm_toolkit.egg-info/SOURCES.txt
mlmm_toolkit.egg-info/dependency_links.txt
mlmm_toolkit.egg-info/entry_points.txt
mlmm_toolkit.egg-info/requires.txt
mlmm_toolkit.egg-info/top_level.txt
pysisyphus/Geometry.py
pysisyphus/LICENSE
pysisyphus/TablePrinter.py
pysisyphus/__init__.py
pysisyphus/_array.py
pysisyphus/config.py
pysisyphus/constants.py
pysisyphus/elem_data.py
pysisyphus/helpers.py
pysisyphus/helpers_pure.py
pysisyphus/linalg.py
pysisyphus/normal_modes.py
pysisyphus/tr_projection.py
pysisyphus/xyzloader.py
pysisyphus/calculators/Calculator.py
pysisyphus/calculators/Dimer.py
pysisyphus/calculators/__init__.py
pysisyphus/cos/ChainOfStates.py
pysisyphus/cos/GrowingChainOfStates.py
pysisyphus/cos/GrowingString.py
pysisyphus/cos/__init__.py
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/helpers.py
pysisyphus/intcoords/logging_conf.py
pysisyphus/intcoords/setup.py
pysisyphus/intcoords/setup_fast.py
pysisyphus/intcoords/update.py
pysisyphus/intcoords/valid.py
pysisyphus/io/__init__.py
pysisyphus/io/cjson.py
pysisyphus/io/crd.py
pysisyphus/io/hdf5.py
pysisyphus/io/hessian.py
pysisyphus/io/mol2.py
pysisyphus/io/pdb.py
pysisyphus/io/qcschema.py
pysisyphus/io/xyz.py
pysisyphus/io/zmat.py
pysisyphus/irc/DWI.py
pysisyphus/irc/EulerPC.py
pysisyphus/irc/IRC.py
pysisyphus/irc/Instanton.py
pysisyphus/irc/__init__.py
pysisyphus/modefollow/NormalMode.py
pysisyphus/modefollow/__init__.py
pysisyphus/modefollow/lanczos.py
pysisyphus/optimizers/BacktrackingOptimizer.py
pysisyphus/optimizers/HessianOptimizer.py
pysisyphus/optimizers/LBFGS.py
pysisyphus/optimizers/Optimizer.py
pysisyphus/optimizers/RFOptimizer.py
pysisyphus/optimizers/StringOptimizer.py
pysisyphus/optimizers/__init__.py
pysisyphus/optimizers/checkpoint.py
pysisyphus/optimizers/closures.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/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
skills/README.md
skills/colab-local-gpu-runtime/SKILL.md
skills/colab-local-gpu-runtime/agents/openai.yaml
skills/colab-local-gpu-runtime/references/colab-connection.md
skills/colab-local-gpu-runtime/scripts/setup.ps1
skills/colab-local-gpu-runtime/scripts/start.ps1
skills/colab-local-gpu-runtime/scripts/status.ps1
skills/colab-local-gpu-runtime/scripts/stop.ps1
skills/mlmm-architecture/SKILL.md
skills/mlmm-cli/SKILL.md
skills/mlmm-cli/add-elem-info.md
skills/mlmm-cli/all-endpoint-mep.md
skills/mlmm-cli/all-scan-list.md
skills/mlmm-cli/all-ts-only.md
skills/mlmm-cli/all.md
skills/mlmm-cli/bond-summary.md
skills/mlmm-cli/define-layer.md
skills/mlmm-cli/dft.md
skills/mlmm-cli/energy-diagram.md
skills/mlmm-cli/extract.md
skills/mlmm-cli/fix-altloc.md
skills/mlmm-cli/freq.md
skills/mlmm-cli/irc.md
skills/mlmm-cli/mm-parm.md
skills/mlmm-cli/oniom-export.md
skills/mlmm-cli/oniom-import.md
skills/mlmm-cli/opt.md
skills/mlmm-cli/path-opt.md
skills/mlmm-cli/path-search.md
skills/mlmm-cli/scan.md
skills/mlmm-cli/scan2d.md
skills/mlmm-cli/scan3d.md
skills/mlmm-cli/sp.md
skills/mlmm-cli/trj2fig.md
skills/mlmm-cli/tsopt.md
skills/mlmm-env-detect/SKILL.md
skills/mlmm-hpc/SKILL.md
skills/mlmm-hpc/dynamic-dispatch.md
skills/mlmm-install-backends/SKILL.md
skills/mlmm-install-backends/aimnet2.md
skills/mlmm-install-backends/ambertools.md
skills/mlmm-install-backends/core.md
skills/mlmm-install-backends/dft.md
skills/mlmm-install-backends/env-cuda.md
skills/mlmm-install-backends/mace.md
skills/mlmm-install-backends/orb.md
skills/mlmm-install-backends/uma.md
skills/mlmm-install-backends/xtb.md
skills/mlmm-mcp/SKILL.md
skills/mlmm-overview/SKILL.md
skills/mlmm-structure-io/SKILL.md
skills/mlmm-structure-io/charge-multiplicity.md
skills/mlmm-structure-io/cif.md
skills/mlmm-structure-io/gjf.md
skills/mlmm-structure-io/parm7.md
skills/mlmm-structure-io/pdb.md
skills/mlmm-structure-io/xyz.md
skills/mlmm-ts-strategy/SKILL.md
skills/mlmm-workflows-output/SKILL.md
tests/README.md
tests/conftest.py
tests/test_active_map_invalidation.py
tests/test_add_elem_info_output.py
tests/test_advanced_help_dedup.py
tests/test_align_log.py
tests/test_all_calculator_template.py
tests/test_all_dry_run_semantics.py
tests/test_all_helpers.py
tests/test_all_layer_honor.py
tests/test_all_ml_region_subset.py
tests/test_all_multiplicity_option.py
tests/test_all_path_tangent.py
tests/test_all_postprocessing_contract.py
tests/test_all_run_ownership.py
tests/test_all_scan_contract_checker.py
tests/test_all_summary_provenance.py
tests/test_array_shim_equivalence.py
tests/test_backend_model_load_announcement.py
tests/test_beza_example_contract.py
tests/test_bond_changes.py
tests/test_bool_compat_cli.py
tests/test_bundled_pysis_policy.py
tests/test_bundled_pysisyphus_regressions.py
tests/test_calc_eval.py
tests/test_charge_prep_exact_model.py
tests/test_cli_feature_regressions.py
tests/test_cli_help.py
tests/test_cli_utils.py
tests/test_colab_notebook.py
tests/test_confirmed_runtime_boundaries.py
tests/test_custom_calc_file.py
tests/test_cycle_limit_defaults.py
tests/test_default_group.py
tests/test_defaults.py
tests/test_dependency_metadata.py
tests/test_determinism.py
tests/test_dft_model_parm7_lj_tables.py
tests/test_dft_output_boundary.py
tests/test_dft_result_payload.py
tests/test_dimer_constraints.py
tests/test_dmf_result_contract.py
tests/test_docs_command_contract.py
tests/test_docs_command_smoke.py
tests/test_docs_deploy_workflow.py
tests/test_docs_link_contract.py
tests/test_dry_run_footer_contract.py
tests/test_dynamic_dispatch_skill.py
tests/test_e2e_minimal.py
tests/test_embedcharge_contract.py
tests/test_energy_plateau_stall.py
tests/test_error_envelope.py
tests/test_error_handling.py
tests/test_example_scripts_contract.py
tests/test_extract.py
tests/test_freeze_noncart_geometry.py
tests/test_freq_active_dof.py
tests/test_frequency_zero_cutoff.py
tests/test_gaussian_input.py
tests/test_generated_reference_contract.py
tests/test_gpu_kernel_parity.py
tests/test_heavy_ts_cycle_budget.py
tests/test_help_grouping.py
tests/test_hessian_basis_reconciliation.py
tests/test_hessian_cache_handoff.py
tests/test_hessian_calc_boundaries.py
tests/test_hessian_file.py
tests/test_hessian_method_contract.py
tests/test_hessian_optimizer_internal_partial.py
tests/test_hessian_writeback.py
tests/test_import_graph_gate.py
tests/test_imports.py
tests/test_inline_xyz.py
tests/test_irc_active_space.py
tests/test_irc_endpoint_hessian_guard.py
tests/test_irc_never_stop.py
tests/test_layer_index_validation.py
tests/test_mace_anicc_factory.py
tests/test_mcp_runner.py
tests/test_mcp_tools.py
tests/test_mep_threshold_flags.py
tests/test_micro_force_equilibrium.py
tests/test_microiteration_contract.py
tests/test_microiteration_cycle_carry.py
tests/test_ml_layer_precedence.py
tests/test_ml_region_outputs.py
tests/test_mlmm_calc_serial_gap.py
tests/test_mlmm_result_constraints.py
tests/test_mm_parm_preflight.py
tests/test_normal_modes_lowering.py
tests/test_oniom_export_regressions.py
tests/test_opt.py
tests/test_opt_flatten_mass_unweight.py
tests/test_optimizer_checkpoint.py
tests/test_optimizer_trial_safeguards.py
tests/test_orb_analytical_hessian_guard.py
tests/test_output_adapter.py
tests/test_path_logging_sections.py
tests/test_path_opt_output_boundary.py
tests/test_path_semantics.py
tests/test_pdb_fix.py
tests/test_pdb_indexing_resolver.py
tests/test_plotly_image_timeout.py
tests/test_prealign_activation_contract.py
tests/test_precision_dispatch.py
tests/test_preflight.py
tests/test_reject_uphill_flag.py
tests/test_release_metadata_contract.py
tests/test_release_workflow.py
tests/test_residue_catalog_parity.py
tests/test_restrained_pes_contract.py
tests/test_result_commit.py
tests/test_rfo_uphill_rejection.py
tests/test_run_session.py
tests/test_scan3d_csv_provenance.py
tests/test_scan_energy_accounting.py
tests/test_scan_oniom_smoke.py
tests/test_scan_precedence.py
tests/test_scan_validation_regressions.py
tests/test_scientific_outcomes.py
tests/test_silent_noop_warnings.py
tests/test_skill_command_checker.py
tests/test_skill_drift_checker.py
tests/test_smoke_cli_contract.py
tests/test_sp_ml_region_contract.py
tests/test_stop_plateau_flag.py
tests/test_structure_formats.py
tests/test_summary_log.py
tests/test_symmetrize.py
tests/test_thermo_policy.py
tests/test_thermo_symmetry_number.py
tests/test_thermochemistry_golden.py
tests/test_toy_system_contract.py
tests/test_tr_projection.py
tests/test_tr_projection_default.py
tests/test_tsopt_microiter_modes.py
tests/test_tsopt_output_boundary.py
tests/test_tsopt_probe_core_lifetime.py
tests/test_tsopt_reference_mode.py
tests/test_tsopt_soft_imaginary_warning.py
tests/test_tsopt_terminal_phva.py
tests/test_utils.py
tests/test_workers_option.py
tests/test_write_result_json.py
tests/test_xtb_embedcharge_parsers.py
tests/test_xyz_trajectory.py
thermoanalysis/LICENSE
thermoanalysis/QCData.py
thermoanalysis/__init__.py
thermoanalysis/config.py
thermoanalysis/constants.py
thermoanalysis/thermo.py