GoodVibes User Documentation
Getting Started:
Programmatic API:
Cookbook:
- Cookbook
- 0. A table of numbers → a publication figure
- 1. One file → one structured result
- 2. Batch a directory with parallel parsing → DataFrame
- 3. N-way selectivity (replaces
--ee) - 3b. Selectivity sweeps, populations and temperature scans
- 4. PES with the new YAML format
- 4b. MLIP / ASE workflows without output files
- 4c. Reaction-profile documents and the file-free
goodvibes-profile - 4d. Rates, the energy span and an SI table
- 5. PES + JSON for downstream analysis
- 6. Parse once, re-analyze many times
- See also
Reaction-profile format:
Migration:
Module reference:
- Module reference
- Public API (v4.2)
- CLI orchestrator
- Thermochemistry engine
MissingSinglePointErrorSCALE_FACTOR_SOURCESScaleFactorWarningThermoOptionscalc_avg_moment_of_inertia()calc_bbecalc_damp()calc_electronic_entropy()calc_freerot_entropy()calc_qRRHO_energy()calc_rotational_energy()calc_rotational_entropy()calc_rrho_entropy()calc_translational_energy()calc_translational_entropy()calc_vibrational_energy()calc_zeropoint_energy()get_free_space()
- Native parsers and
QCDataHessianDataQCDatacompute_connectivity()dict_to_qcdata()element_id()find_spc_file()gaussian_jobtype()level_of_theory()load_cache()parse_ase_thermo()parse_data()parse_gaussian_thermo()parse_hessian()parse_nwchem_thermo()parse_orca_thermo()parse_qcdata()parse_qchem_thermo()parse_xtb_thermo()qcdata_to_dict()read_initial()read_xyz_frames()resolve_output_file()save_cache()sp_cpu()write_xyz()
- ASE (extended XYZ) bridge
- Output rendering (Rich tables, JSON)
- Selectivity (v4.1 redesign)
SelectivityResultSelectivityWarningassign_files_to_labels()compute_selectivity()compute_selectivity_lowest_only()compute_selectivity_lowest_only_scan()compute_selectivity_scan()describe_selectivity()get_boltz()get_selectivity()load_label_yaml()parse_label_args()selectivity_from_energies()selectivity_rows()selectivity_to_dict()
- PES — data model (v4.2)
- PES — loader and dispatcher (v4.2)
- PES — legacy line-based parser (deprecated)
- PES — true-YAML parser (v4.2)
- PES — back-compat surface and reaction-profile plot
- Plots (matplotlib,
goodvibes[plot]) - Structured-output schema
- Sorting and duplicate detection
- File validation
- Solvent database
- Frequency scaling factors (Truhlar v5)
- Constants
- Utilities
- Top-level package
ComputedEntryConformerSetEdgeEnergySpanMissingSinglePointErrorPESOptionsPESResultPathwayPointProfileProfileAxesProfileErrorProfileWarningQCDataSelectivityResultSelectivityWarningSeriesThermoOptionsThermoResultThermoVectorbbe_to_result()build_pes_result()calc_bbecompute_batch()compute_selectivity()compute_selectivity_batch()compute_thermo()energy_span()eyring_rate()load_pes()load_profile()merge_point_order()plot_pes()plot_profile()rate_ratio()read_xyz_frames()resolve_quantity()selectivity_from_energies()si_rows()step_table()summarize_selectivity()to_dataframe()to_parquet()validate_document()write_si()