Index

A

add_time() (in module goodvibes.utils) all_same() (in module goodvibes.utils) applied_freq_scale_factor (goodvibes.io.QCData attribute)

assign_files_to_labels() (in module goodvibes.selectivity) atom_nums (goodvibes.io.QCData attribute) atom_types (goodvibes.io.QCData attribute)

B

bbe (goodvibes.api.ThermoResult attribute) (goodvibes.ThermoResult attribute) bbe_to_result() (in module goodvibes) (in module goodvibes.api)

bbes (goodvibes.pes_model.ConformerSet attribute) boltzmann_weighted() (goodvibes.pes_model.ConformerSet method) build_pes_result() (in module goodvibes.pes_loader)

C

C() (in module goodvibes.vib_scale_factors) calc_avg_moment_of_inertia() (in module goodvibes.thermo) calc_bbe (class in goodvibes.thermo) calc_damp() (in module goodvibes.thermo) calc_electronic_entropy() (in module goodvibes.thermo) calc_freerot_entropy() (in module goodvibes.thermo) calc_qRRHO_energy() (in module goodvibes.thermo) calc_rotational_energy() (in module goodvibes.thermo) calc_rotational_entropy() (in module goodvibes.thermo) calc_rrho_entropy() (in module goodvibes.thermo) calc_translational_energy() (in module goodvibes.thermo) calc_translational_entropy() (in module goodvibes.thermo) calc_vibrational_energy() (in module goodvibes.thermo) calc_zeropoint_energy() (in module goodvibes.thermo) canonicalize_level() (in module goodvibes.vib_scale_factors) cartesians (goodvibes.io.QCData attribute) charge (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute)

check_files() (in module goodvibes.validation) collect_and_validate_files() (in module goodvibes.validation) compute_batch() (in module goodvibes) (in module goodvibes.api) compute_connectivity() (in module goodvibes.io) compute_media_conc() (in module goodvibes.media) compute_selectivity() (in module goodvibes.selectivity) compute_selectivity_lowest_only() (in module goodvibes.selectivity) compute_selectivity_lowest_only_scan() (in module goodvibes.selectivity) compute_selectivity_scan() (in module goodvibes.selectivity) compute_thermo() (in module goodvibes) (in module goodvibes.api) compute_thermochem() (in module goodvibes.GoodVibes) concentration (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) ConformerSet (class in goodvibes.pes_model) cpu (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute)

D

D() (in module goodvibes.vib_scale_factors) ddG (goodvibes.selectivity.SelectivityResult attribute) decimals (goodvibes.pes_model.PESOptions attribute)

deduplicate() (in module goodvibes.sort) dict_to_qcdata() (in module goodvibes.io) display_name() (in module goodvibes.utils)

E

ee (goodvibes.selectivity.SelectivityResult attribute) element_id() (in module goodvibes.io) empirical_dispersion (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) enthalpy (goodvibes.api.ThermoResult attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

entropy (goodvibes.api.ThermoResult attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) ex_sym() (goodvibes.thermo.calc_bbe method)

F

fatal() (in module goodvibes.utils) file (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) files (goodvibes.pes_model.ConformerSet attribute) files_per_label (goodvibes.selectivity.SelectivityResult attribute) find_spc_file() (in module goodvibes.io) format_extras (goodvibes.pes_loader.PESSpec attribute), [1] fract_modelsys (goodvibes.io.QCData attribute)

freq_scale_factor (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) frequency_wn (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) from_label() (goodvibes.pes_model.Point class method) from_options() (goodvibes.thermo.calc_bbe class method) fund_fac (goodvibes.vib_scale_factors.ScalingData attribute) fund_meth (goodvibes.vib_scale_factors.ScalingData attribute) fund_ref (goodvibes.vib_scale_factors.ScalingData attribute)

G

gaussian_jobtype() (in module goodvibes.io) gconf (goodvibes.pes_model.PESOptions attribute) gconf_corrected() (goodvibes.pes_model.ConformerSet method) get_boltz() (in module goodvibes.selectivity) get_console_dat() (in module goodvibes.utils) get_console_stdout() (in module goodvibes.utils) get_free_space() (in module goodvibes.thermo) get_pes (class in goodvibes.pes) get_selectivity() (in module goodvibes.selectivity) gibbs (goodvibes.pes_model.ThermoVector attribute) gibbs_free_energy (goodvibes.api.ThermoResult attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) goodvibes module goodvibes.api module goodvibes.ase_helper module goodvibes.constants module goodvibes.GoodVibes module goodvibes.io module goodvibes.media module

goodvibes.output module goodvibes.pes module goodvibes.pes_legacy module goodvibes.pes_loader module goodvibes.pes_model module goodvibes.pes_yaml module goodvibes.selectivity module goodvibes.sort module goodvibes.thermo module goodvibes.utils module goodvibes.validation module goodvibes.vib_scale_factors module graph_reaction_profile() (in module goodvibes.pes)

H

h_freq_cutoff (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) harm_fac (goodvibes.vib_scale_factors.ScalingData attribute) harm_meth (goodvibes.vib_scale_factors.ScalingData attribute)

harm_ref (goodvibes.vib_scale_factors.ScalingData attribute) has_oniom (goodvibes.io.QCData attribute) has_thermo (goodvibes.api.ThermoResult property) (goodvibes.ThermoResult property)

I

im_freq (goodvibes.thermo.calc_bbe attribute) im_frequency_wn (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.ThermoResult attribute) inertia (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute)

invert (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) inverted_freqs (goodvibes.api.ThermoResult attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) is_legacy_format() (in module goodvibes.pes_loader) is_single (goodvibes.pes_model.ConformerSet property)

J

jitter() (in module goodvibes.pes) job_type (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

K

kabsch_rmsd() (in module goodvibes.sort)

key (goodvibes.selectivity.SelectivityResult attribute)

L

label (goodvibes.pes_model.Point attribute) labels (goodvibes.selectivity.SelectivityResult attribute) level_basis (goodvibes.vib_scale_factors.ScalingData attribute) level_of_theory (goodvibes.api.ThermoResult attribute) (goodvibes.ThermoResult attribute) level_of_theory() (in module goodvibes.io) linear_mol (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.ThermoResult attribute)

linear_warning (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) load_cache() (in module goodvibes.io) load_label_yaml() (in module goodvibes.selectivity) load_pes() (in module goodvibes.pes_loader) lookup_solvent() (in module goodvibes.media) lowest_conformer() (goodvibes.pes_model.ConformerSet method) lowest_only (goodvibes.pes_model.PESOptions attribute)

M

main() (in module goodvibes.GoodVibes) mm_freq_scale_factor (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) module goodvibes goodvibes.api goodvibes.ase_helper goodvibes.constants goodvibes.GoodVibes goodvibes.io goodvibes.media goodvibes.output goodvibes.pes goodvibes.pes_legacy goodvibes.pes_loader goodvibes.pes_model goodvibes.pes_yaml goodvibes.selectivity goodvibes.sort goodvibes.thermo goodvibes.utils goodvibes.validation goodvibes.vib_scale_factors

molecular_mass (goodvibes.io.QCData attribute) mult (goodvibes.thermo.calc_bbe attribute) multiplicity (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

N

name (goodvibes.api.ThermoResult attribute) (goodvibes.pes_model.ConformerSet attribute) (goodvibes.pes_model.Pathway attribute) (goodvibes.ThermoResult attribute)

natural_key() (in module goodvibes.utils) nprocs (goodvibes.io.QCData attribute)

O

options (goodvibes.pes_loader.PESSpec attribute), [1] (goodvibes.pes_model.PESResult attribute)

P

parse_arguments() (in module goodvibes.GoodVibes) parse_ase_thermo() (in module goodvibes.io) parse_data() (in module goodvibes.io) parse_gaussian_thermo() (in module goodvibes.io) parse_label_args() (in module goodvibes.selectivity) parse_legacy() (in module goodvibes.pes_legacy) parse_nwchem_thermo() (in module goodvibes.io) parse_orca_thermo() (in module goodvibes.io) parse_point_label() (in module goodvibes.pes_model) parse_qcdata() (in module goodvibes.io) parse_qchem_thermo() (in module goodvibes.io) parse_xtb_thermo() (in module goodvibes.io) parse_yaml() (in module goodvibes.pes_yaml) Pathway (class in goodvibes.pes_model) pathways (goodvibes.pes_loader.PESSpec attribute), [1] (goodvibes.pes_model.PESResult attribute) PESOptions (class in goodvibes.pes_model) PESResult (class in goodvibes.pes_model) PESSpec (class in goodvibes.pes_loader)

Point (class in goodvibes.pes_model) point_group (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) points (goodvibes.pes_model.Pathway attribute) populations (goodvibes.selectivity.SelectivityResult attribute) preferred (goodvibes.selectivity.SelectivityResult attribute) print_check_fails() (in module goodvibes.validation) print_cpu_time() (in module goodvibes.output) print_pes_results() (in module goodvibes.output) print_pes_tables() (in module goodvibes.output) print_results() (in module goodvibes.output) print_selectivity_results() (in module goodvibes.output) print_temperature_interval() (in module goodvibes.output) program (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

Q

QCData (class in goodvibes.io) qcdata (goodvibes.api.ThermoResult attribute) (goodvibes.ThermoResult attribute) qcdata_to_dict() (in module goodvibes.io) QH (goodvibes.pes_model.PESOptions attribute) (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) qh_enthalpy (goodvibes.api.ThermoResult attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

qh_entropy (goodvibes.api.ThermoResult attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) qh_gibbs (goodvibes.pes_model.ThermoVector attribute) qh_gibbs_free_energy (goodvibes.api.ThermoResult attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) QS (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute)

R

R() (in module goodvibes.vib_scale_factors) raw_boltzmann (goodvibes.selectivity.SelectivityResult attribute) read_initial() (in module goodvibes.io) relative() (goodvibes.pes_model.Pathway method)

resolve_pattern() (in module goodvibes.pes_loader) resolve_scaling_factor() (in module goodvibes.GoodVibes) roconst (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) rotemp (goodvibes.io.QCData attribute)

S

s_freq_cutoff (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) save_cache() (in module goodvibes.io) ScalingData (class in goodvibes.vib_scale_factors) scf_energy (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) SelectivityResult (class in goodvibes.selectivity) setup_logging() (in module goodvibes.utils) solv (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) solvation_model (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sort_thermo() (in module goodvibes.sort) sp_charge (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_cpu() (in module goodvibes.io) sp_empirical_dispersion (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_energy (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

sp_file (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_multiplicity (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_program (goodvibes.thermo.calc_bbe attribute) sp_solvation_model (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_suffix (goodvibes.io.QCData attribute) sp_version_program (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) spc (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) spc_used (goodvibes.pes_model.PESOptions attribute) species (goodvibes.pes_loader.PESSpec attribute), [1] (goodvibes.pes_model.Point attribute) sym_correction() (goodvibes.thermo.calc_bbe method) symm (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) symmno (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.ThermoResult attribute)

T

temperature (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) temperatures (goodvibes.pes_model.PESResult attribute) thermo() (goodvibes.pes_model.Point method) ThermoOptions (class in goodvibes) (class in goodvibes.thermo)

ThermoResult (class in goodvibes) (class in goodvibes.api) ThermoVector (class in goodvibes.pes_model) to_dataframe() (in module goodvibes) (in module goodvibes.api) to_parquet() (in module goodvibes) (in module goodvibes.api) to_user_units() (goodvibes.pes_model.PESOptions method)

U

units (goodvibes.pes_model.PESOptions attribute)

V

validate_and_configure() (in module goodvibes.GoodVibes)

version_program (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute)

W

warn_orca_prescaled() (in module goodvibes.GoodVibes) write_json_results() (in module goodvibes.output)

write_thermo_extxyz() (in module goodvibes.ase_helper) write_xyz() (in module goodvibes.io)

X

xyz (goodvibes.thermo.calc_bbe attribute)

Z

zero (goodvibes.pes_loader.PESSpec attribute), [1] (goodvibes.pes_model.Pathway attribute) zero() (goodvibes.pes_model.ThermoVector class method) zero_point_corr (goodvibes.io.QCData attribute) (goodvibes.thermo.calc_bbe attribute) zpe (goodvibes.api.ThermoResult attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

zpe_fac (goodvibes.vib_scale_factors.ScalingData attribute) zpe_meth (goodvibes.vib_scale_factors.ScalingData attribute) zpe_ref (goodvibes.vib_scale_factors.ScalingData attribute) zpe_scale_factor (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute)