GoodVibes User Documentation

Getting Started:

• • Features
  • Installation
  • Quick Start
  • Supported Programs
  • Documentation
  • Examples
  • CLI Reference
  • Dependencies
  • Contributing
  • Citing GoodVibes
  • References
  • License

Programmatic API:

• Programmatic API
  • Quick start
  • Common options
  • Batch and parallel processing
  • Pandas DataFrame export
  • Skipping a re-parse
  • What’s new in v4.x at a glance

Cookbook:

• Cookbook
  • 1. One file → one structured result
  • 2. Batch a directory with parallel parsing → DataFrame
  • 3. N-way selectivity (replaces --ee)
  • 4. PES with the new YAML format
  • 5. PES + JSON for downstream analysis
  • 6. Parse once, re-analyze many times
  • See also

Migration:

• Migrating from v4.x to v5.0
  • TL;DR
  • The high-level path: compute_thermo
  • The medium path: from_options
  • ThermoOptions field reference
  • Frequency-scaling defaults
  • Level-of-theory metadata
  • CLI changes in v5.0
  • JSON output schema is now stable (v1.0)
  • Parquet export
  • What’s NOT changing in v5.0
  • When to actually migrate

Module reference:

• Module reference
  • Public API (v4.2)
    • ThermoResult
    • bbe_to_result()
    • compute_batch()
    • compute_thermo()
    • to_dataframe()
    • to_parquet()
  • CLI orchestrator
    • compute_thermochem()
    • main()
    • parse_arguments()
    • resolve_scaling_factor()
    • validate_and_configure()
    • warn_orca_prescaled()
  • Thermochemistry engine
    • ThermoOptions
    • calc_avg_moment_of_inertia()
    • calc_bbe
    • calc_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 QCData
    • QCData
    • compute_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_nwchem_thermo()
    • parse_orca_thermo()
    • parse_qcdata()
    • parse_qchem_thermo()
    • parse_xtb_thermo()
    • qcdata_to_dict()
    • read_initial()
    • save_cache()
    • sp_cpu()
    • write_xyz()
  • ASE (extended XYZ) bridge
    • write_thermo_extxyz()
  • Output rendering (Rich tables, JSON)
    • print_cpu_time()
    • print_pes_results()
    • print_pes_tables()
    • print_results()
    • print_selectivity_results()
    • print_temperature_interval()
    • write_json_results()
  • Selectivity (v4.1 redesign)
    • SelectivityResult
    • assign_files_to_labels()
    • compute_selectivity()
    • compute_selectivity_lowest_only()
    • compute_selectivity_lowest_only_scan()
    • compute_selectivity_scan()
    • get_boltz()
    • get_selectivity()
    • load_label_yaml()
    • parse_label_args()
  • PES — data model (v4.2)
    • ConformerSet
    • PESOptions
    • PESResult
    • Pathway
    • Point
    • ThermoVector
    • parse_point_label()
  • PES — loader and dispatcher (v4.2)
    • PESSpec
    • build_pes_result()
    • is_legacy_format()
    • load_pes()
    • resolve_pattern()
  • PES — legacy line-based parser (deprecated)
    • parse_legacy()
  • PES — true-YAML parser (v4.2)
    • parse_yaml()
  • PES — back-compat surface and reaction-profile plot
    • get_pes
    • graph_reaction_profile()
    • jitter()
  • Sorting and duplicate detection
    • deduplicate()
    • kabsch_rmsd()
    • sort_thermo()
  • File validation
    • check_files()
    • collect_and_validate_files()
    • print_check_fails()
  • Solvent database
    • compute_media_conc()
    • lookup_solvent()
  • Frequency scaling factors (Truhlar v5)
    • D()
    • C()
    • R()
    • ScalingData
    • canonicalize_level()
  • Constants
  • Utilities
    • add_time()
    • all_same()
    • display_name()
    • fatal()
    • get_console_dat()
    • get_console_stdout()
    • natural_key()
    • setup_logging()
  • Top-level package
    • ThermoOptions
    • ThermoResult
    • bbe_to_result()
    • compute_batch()
    • compute_thermo()
    • to_dataframe()
    • to_parquet()

Indices and tables

• Index

• Module Index

• Search Page