Index

A

add_time() (in module goodvibes.utils) all_same() (in module goodvibes.utils) annotate_barrier() (goodvibes.plot.ProfileAxes method) (goodvibes.ProfileAxes method) applied_freq_scale_factor (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.schema.ThermoBlock attribute) apply_cli_pes_options() (in module goodvibes.output) assign_files_to_labels() (in module goodvibes.selectivity) atom_nums (goodvibes.io.QCData attribute) (goodvibes.QCData attribute)

atom_types (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) ax (goodvibes.plot.ProfileAxes property) (goodvibes.ProfileAxes property) axes (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) axes_for() (goodvibes.plot.ProfileAxes method) (goodvibes.ProfileAxes method) axes_width (goodvibes.plot.StylePreset attribute)

B

bar_width (goodvibes.plot.StylePreset attribute) barriers (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) base_temperature (goodvibes.ComputedEntry property) (goodvibes.ConformerSet property) (goodvibes.pes_model.ComputedEntry property) (goodvibes.pes_model.ConformerSet property) bbe (goodvibes.api.ThermoResult attribute) (goodvibes.ThermoResult attribute) bbe() (goodvibes.ComputedEntry method) (goodvibes.pes_model.ComputedEntry method)

bbe_to_result() (in module goodvibes) (in module goodvibes.api) bbes (goodvibes.ConformerSet attribute) (goodvibes.pes_model.ConformerSet attribute) boltzmann_factor (goodvibes.schema.ResultEntry attribute) boltzmann_weighted() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method) build_pes_result() (in module goodvibes) (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) (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) canonical_solvent() (in module goodvibes.media) canonical_units() (in module goodvibes.constants) canonicalize_level() (in module goodvibes.vib_scale_factors) cartesians (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) charge (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) check_files() (in module goodvibes.validation) close() (goodvibes.plot.ProfileAxes method) (goodvibes.ProfileAxes method) collect_and_validate_files() (in module goodvibes.validation) colors (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute)

computable (goodvibes.Pathway property) (goodvibes.pes_model.Pathway property) 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) (in module goodvibes.selectivity) compute_selectivity_batch() (in module goodvibes) 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) ComputedEntry (class in goodvibes) (class in goodvibes.pes_model) concentration (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) ConformerSet (class in goodvibes) (class in goodvibes.pes_model) connector_width (goodvibes.plot.StylePreset attribute) control (goodvibes.EnergySpan attribute) copy() (goodvibes.Profile method) cpu (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) curtin_hammett (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute)

D

D() (in module goodvibes.vib_scale_factors) ddG (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) decimals (goodvibes.pes_model.PESOptions attribute) (goodvibes.PESOptions attribute) declared (goodvibes.pes_model.Series attribute) (goodvibes.Series attribute) declared_from() (goodvibes.pes_model.Series class method) (goodvibes.Series class method) dedup() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method) deduplicate() (in module goodvibes.sort)

default_method() (goodvibes.Profile method) default_series() (goodvibes.pes_model.PESResult method) (goodvibes.PESResult method) describe_selectivity() (in module goodvibes.selectivity) dict_to_qcdata() (in module goodvibes.io) diff() (goodvibes.Profile method) display (goodvibes.pes_model.Point attribute) (goodvibes.Point attribute) display_label (goodvibes.pes_model.Point property) (goodvibes.Point property) display_name() (in module goodvibes.utils) dst (goodvibes.Edge attribute) (goodvibes.pes_model.Edge attribute) dump() (goodvibes.Profile method)

E

Edge (class in goodvibes) (class in goodvibes.pes_model) edge_kind() (goodvibes.Pathway method) (goodvibes.pes_model.Pathway method) EDGE_KINDS (in module goodvibes.pes_model) edges (goodvibes.Pathway attribute) (goodvibes.pes_model.Pathway attribute) ee (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) ee_signed (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) element_id() (in module goodvibes.io) element_ids (goodvibes.plot.ProfileAxes property) (goodvibes.ProfileAxes property) embed_svg_metadata() (in module goodvibes.plot) empirical_dispersion (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) energy_span() (goodvibes.Profile method) (in module goodvibes) EnergySpan (class in goodvibes) ensemble_energies (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) ensemble_free_energy() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method)

enthalpy (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) (goodvibes.ThermoVector attribute) entries (goodvibes.ConformerSet attribute) (goodvibes.pes_model.ConformerSet attribute) entropy (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) (goodvibes.ThermoVector attribute) evaluate() (goodvibes.pes_model.Series method) (goodvibes.Profile method) (goodvibes.Series method) evaluate_selectivity() (goodvibes.Profile method) evaluate_uncertainty() (goodvibes.pes_model.Series method) (goodvibes.Series method) ex_sym() (goodvibes.calc_bbe method) (goodvibes.thermo.calc_bbe method) extensions (goodvibes.pes_model.Series attribute) (goodvibes.Series attribute) eyring_rate() (in module goodvibes)

F

fatal() (in module goodvibes.utils) figsize (goodvibes.plot.StylePreset attribute) figure (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) file (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.ComputedEntry attribute) (goodvibes.io.QCData attribute) (goodvibes.pes_model.ComputedEntry attribute) (goodvibes.QCData attribute) (goodvibes.schema.ResultEntry attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) files (goodvibes.ConformerSet attribute) (goodvibes.pes_model.ConformerSet attribute) files_per_label (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) find_spc_file() (in module goodvibes.io) font_size (goodvibes.plot.StylePreset attribute) format_extras (goodvibes.pes_loader.PESSpec attribute), [1] freq_scale_factor (goodvibes.api.ThermoResult attribute) (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) (goodvibes.ThermoResult attribute) frequency_wn (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

from_atoms() (goodvibes.io.QCData class method) (goodvibes.QCData class method) from_bbe() (goodvibes.ComputedEntry class method) (goodvibes.pes_model.ComputedEntry class method) from_dict() (goodvibes.Profile class method) from_figure() (goodvibes.Profile class method) from_label() (goodvibes.pes_model.Point class method) (goodvibes.Point class method) from_options() (goodvibes.calc_bbe class method) (goodvibes.thermo.calc_bbe class method) from_pes_result() (goodvibes.Profile class method) from_result() (goodvibes.ComputedEntry class method) (goodvibes.pes_model.ComputedEntry class method) from_results() (goodvibes.ConformerSet class method) (goodvibes.pes_model.ConformerSet class method) from_spec() (goodvibes.Profile class method) from_table() (goodvibes.Profile class method) from_vibrations() (goodvibes.io.QCData class method) (goodvibes.QCData 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) (goodvibes.PESOptions attribute) gconf_corrected() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method) generated_at (goodvibes.schema.Payload attribute) get() (goodvibes.pes_model.ThermoVector method) (goodvibes.ThermoVector 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) get_series() (goodvibes.Profile method) gibbs (goodvibes.pes_model.ThermoVector attribute) (goodvibes.ThermoVector attribute) gibbs_free_energy (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.schema.ThermoBlock 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.plot module goodvibes.schema module goodvibes.selectivity module goodvibes.sort module goodvibes.thermo module goodvibes.utils module goodvibes.validation module goodvibes.vib_scale_factors module goodvibes_version (goodvibes.schema.Payload attribute) 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) hartree_factor() (in module goodvibes.constants)

has_oniom (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) has_thermo (goodvibes.api.ThermoResult property) (goodvibes.ThermoResult property) hessian (goodvibes.io.HessianData attribute) HessianData (class in goodvibes.io)

I

id (goodvibes.pes_model.Point property) (goodvibes.pes_model.Series attribute) (goodvibes.Point property) (goodvibes.Series attribute) im_freq (goodvibes.calc_bbe attribute) (goodvibes.thermo.calc_bbe attribute) im_frequency_wn (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.schema.ThermoBlock 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.calc_bbe attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) is_legacy_format() (in module goodvibes.pes_loader) is_single (goodvibes.ConformerSet property) (goodvibes.pes_model.ConformerSet property) is_ts (goodvibes.pes_model.Point property) (goodvibes.Point property)

J

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

K

kabsch_rmsd() (in module goodvibes.sort) key (goodvibes.schema.SelectivityBlock attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute)

kind (goodvibes.Edge attribute) (goodvibes.pes_model.Edge attribute)

L

label (goodvibes.pes_model.Point attribute) (goodvibes.pes_model.Series attribute) (goodvibes.Point attribute) (goodvibes.schema.PESPoint attribute) (goodvibes.Series attribute) label_size (goodvibes.plot.ProfileAxes attribute) (goodvibes.plot.StylePreset attribute) (goodvibes.ProfileAxes attribute) labels (goodvibes.Pathway property) (goodvibes.pes_model.Pathway property) (goodvibes.schema.SelectivityBlock attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) layout (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) level() (goodvibes.plot.ProfileAxes method) (goodvibes.ProfileAxes method) level_basis (goodvibes.vib_scale_factors.ScalingData attribute) level_of_theory (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.ThermoResult attribute) level_of_theory() (in module goodvibes.io) levels (goodvibes.pes_model.Series attribute) (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) (goodvibes.Series attribute)

levels() (goodvibes.Pathway method) (goodvibes.pes_model.Pathway method) (goodvibes.pes_model.PESResult method) (goodvibes.PESResult method) (goodvibes.Profile method) linear_mol (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.ThermoResult attribute) linear_warning (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) linestyles (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) load_cache() (in module goodvibes.io) load_label_yaml() (in module goodvibes.selectivity) load_pes() (in module goodvibes) (in module goodvibes.pes_loader) load_profile() (in module goodvibes) lookup_solvent() (in module goodvibes.media) lowest_conformer() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method) lowest_index() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method) lowest_only (goodvibes.pes_model.PESOptions attribute) (goodvibes.PESOptions attribute)

M

main() (in module goodvibes.GoodVibes) major (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) marker_size (goodvibes.plot.StylePreset attribute) masses (goodvibes.io.HessianData attribute) media_conc (goodvibes.schema.ResultEntry attribute) merge_point_order() (in module goodvibes) (in module goodvibes.pes_model) merged_order() (goodvibes.pes_model.PESResult method) (goodvibes.PESResult method) (goodvibes.Profile method) method (goodvibes.pes_model.Series attribute) (goodvibes.Series attribute) method_thermo() (goodvibes.Profile method) MissingSinglePointError, [1] 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.plot goodvibes.schema goodvibes.selectivity goodvibes.sort goodvibes.thermo goodvibes.utils goodvibes.validation goodvibes.vib_scale_factors

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

N

n_imag (goodvibes.api.ThermoResult attribute) (goodvibes.ThermoResult attribute) name (goodvibes.api.ThermoResult attribute) (goodvibes.ConformerSet attribute) (goodvibes.Pathway attribute) (goodvibes.pes_model.ConformerSet attribute) (goodvibes.pes_model.Pathway attribute) (goodvibes.plot.StylePreset attribute) (goodvibes.schema.PESPathway attribute) (goodvibes.schema.ResultEntry attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) (goodvibes.ThermoResult attribute)

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

O

options (goodvibes.api.ThermoResult attribute) (goodvibes.ComputedEntry attribute) (goodvibes.pes_loader.PESSpec attribute), [1] (goodvibes.pes_model.ComputedEntry attribute) (goodvibes.pes_model.PESResult attribute) (goodvibes.PESResult attribute) (goodvibes.schema.Payload attribute) (goodvibes.ThermoResult attribute)

order (goodvibes.pes_model.PESResult attribute) (goodvibes.PESResult attribute) (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute)

P

panel_height (goodvibes.plot.StylePreset attribute) 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_hessian() (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_temperature_interval() (in module goodvibes.utils) parse_xtb_thermo() (in module goodvibes.io) parse_yaml() (in module goodvibes.pes_yaml) parse_yaml_data() (in module goodvibes.pes_yaml) Pathway (class in goodvibes) (class in goodvibes.pes_model) pathway() (goodvibes.pes_model.PESResult method) (goodvibes.PESResult method) pathways (goodvibes.pes_loader.PESSpec attribute), [1] (goodvibes.pes_model.PESResult attribute) (goodvibes.PESResult attribute) (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) (goodvibes.schema.PESBlock attribute) Payload (class in goodvibes.schema) per_atom_masses (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) pes (goodvibes.schema.Payload attribute) pes_options() (goodvibes.Profile method) pes_result (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) pes_tables() (in module goodvibes.output) PESBlock (class in goodvibes.schema) PESOptions (class in goodvibes) (class in goodvibes.pes_model) PESPathway (class in goodvibes.schema) PESPoint (class in goodvibes.schema) PESResult (class in goodvibes) (class in goodvibes.pes_model) PESSpec (class in goodvibes.pes_loader) plot() (goodvibes.Profile method) plot_boltzmann_histogram() (in module goodvibes.plot) plot_pes() (in module goodvibes) (in module goodvibes.plot) plot_profile() (in module goodvibes) (in module goodvibes.plot)

plot_selectivity_strip() (in module goodvibes.plot) plot_temperature_scan() (in module goodvibes.plot) Point (class in goodvibes) (class in goodvibes.pes_model) point() (goodvibes.Pathway method) (goodvibes.pes_model.Pathway method) point_group (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) POINT_ROLES (in module goodvibes.pes_model) points (goodvibes.Pathway attribute) (goodvibes.pes_model.Pathway attribute) (goodvibes.schema.PESPathway attribute) populations (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) populations() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method) preferred (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) preset (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes 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_profile_selectivity() (in module goodvibes.output) print_results() (in module goodvibes.output) print_selectivity_results() (in module goodvibes.output) print_temperature_interval() (in module goodvibes.output) Profile (class in goodvibes) profile (goodvibes.schema.Payload attribute) ProfileAxes (class in goodvibes) (class in goodvibes.plot) ProfileError ProfileWarning program (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.io.HessianData attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute)

Q

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

qh_entropy (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) (goodvibes.ThermoVector attribute) qh_gibbs (goodvibes.pes_model.ThermoVector attribute) (goodvibes.ThermoVector attribute) qh_gibbs_free_energy (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) QS (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) quantity (goodvibes.pes_model.Series attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) (goodvibes.Series attribute)

R

R() (in module goodvibes.vib_scale_factors) rate_ratio() (in module goodvibes) ratio (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) raw_boltzmann (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) rc (goodvibes.plot.ProfileAxes attribute) (goodvibes.plot.StylePreset property) (goodvibes.ProfileAxes attribute) reaction_energy (goodvibes.EnergySpan attribute) read_initial() (in module goodvibes.io) read_svg_metadata() (in module goodvibes.plot) read_xyz_frames() (in module goodvibes) (in module goodvibes.io) recomputable (goodvibes.ConformerSet property) (goodvibes.pes_model.ConformerSet property) (goodvibes.pes_model.PESResult property) (goodvibes.PESResult property) reference (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute)

relative (goodvibes.schema.PESPoint attribute) relative() (goodvibes.Pathway method) (goodvibes.pes_model.Pathway method) resolve_output_file() (in module goodvibes.io) resolve_pattern() (in module goodvibes.pes_loader) resolve_preset() (in module goodvibes.plot) resolve_quantity() (in module goodvibes) resolve_scaling_factor() (in module goodvibes.GoodVibes) ResultEntry (class in goodvibes.schema) results (goodvibes.schema.Payload attribute) (goodvibes.schema.SelectivityBlock attribute) roconst (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) role (goodvibes.pes_model.Point attribute) (goodvibes.Point attribute) rollup() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method) rollup_kw (goodvibes.pes_model.PESOptions property) (goodvibes.PESOptions property) rotemp (goodvibes.io.QCData attribute) (goodvibes.QCData attribute)

S

s_conf() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method) s_freq_cutoff (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) save() (goodvibes.plot.ProfileAxes method) (goodvibes.ProfileAxes method) save_cache() (in module goodvibes.io) scale_factor_source (goodvibes.api.ThermoResult attribute) (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) (goodvibes.ThermoResult attribute) SCALE_FACTOR_SOURCES (in module goodvibes.thermo) ScaleFactorWarning ScalingData (class in goodvibes.vib_scale_factors) scf_energy (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.QCData attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) (goodvibes.ThermoVector attribute) SCHEMA_MIN_COMPATIBLE (in module goodvibes.schema) schema_version (goodvibes.schema.Payload attribute) SCHEMA_VERSION (in module goodvibes.schema) selectivity (goodvibes.Profile attribute) (goodvibes.schema.Payload attribute) selectivity_from_energies() (in module goodvibes) (in module goodvibes.selectivity) selectivity_lowest (goodvibes.schema.Payload attribute) selectivity_rows() (in module goodvibes.selectivity) selectivity_to_dict() (in module goodvibes.selectivity) SelectivityBlock (class in goodvibes.schema) SelectivityResult (class in goodvibes) (class in goodvibes.schema) (class in goodvibes.selectivity) SelectivityWarning, [1] Series (class in goodvibes) (class in goodvibes.pes_model) series (goodvibes.pes_model.PESResult attribute) (goodvibes.PESResult attribute) (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) setup_logging() (in module goodvibes.utils) si_rows() (in module goodvibes) solv (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) solvation_model (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sort_thermo() (in module goodvibes.sort) source (goodvibes.io.HessianData attribute) (goodvibes.pes_model.PESResult attribute) (goodvibes.PESResult attribute) source_methods() (goodvibes.Profile method) sp_charge (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_cpu() (in module goodvibes.io) sp_empirical_dispersion (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute)

sp_energy (goodvibes.api.ThermoResult attribute) (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.pes_model.ThermoVector attribute) (goodvibes.QCData attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.thermo.calc_bbe attribute) (goodvibes.ThermoResult attribute) (goodvibes.ThermoVector attribute) sp_file (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_level_of_theory (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) sp_multiplicity (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_program (goodvibes.calc_bbe attribute) (goodvibes.thermo.calc_bbe attribute) sp_solvation_model (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) sp_suffix (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) sp_version_program (goodvibes.calc_bbe attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.thermo.calc_bbe attribute) span (goodvibes.EnergySpan attribute) spc (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) spc_applied (goodvibes.api.ThermoResult attribute) (goodvibes.ThermoResult attribute) spc_used (goodvibes.pes_model.PESOptions attribute) (goodvibes.PESOptions attribute) species (goodvibes.pes_loader.PESSpec attribute), [1] (goodvibes.pes_model.Point attribute) (goodvibes.Point attribute) (goodvibes.schema.PESPoint attribute) src (goodvibes.Edge attribute) (goodvibes.pes_model.Edge attribute) standard_state (goodvibes.pes_model.Series attribute) (goodvibes.Series attribute) step_table() (goodvibes.Profile method) (in module goodvibes) strict_spc (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) style (goodvibes.pes_model.Series attribute) (goodvibes.Series attribute) STYLE_PRESETS (in module goodvibes.plot) StylePreset (class in goodvibes.plot) summarize_selectivity() (in module goodvibes) SVG_METADATA_ID (in module goodvibes.plot) sym_correction() (goodvibes.calc_bbe method) (goodvibes.thermo.calc_bbe method) symm (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) symmetry_source (goodvibes.api.ThermoResult attribute) (goodvibes.ThermoResult attribute) symmno (goodvibes.api.ThermoResult attribute) (goodvibes.io.QCData attribute) (goodvibes.QCData attribute) (goodvibes.schema.ThermoBlock attribute) (goodvibes.ThermoResult attribute)

T

tdi (goodvibes.EnergySpan attribute) tdts (goodvibes.EnergySpan attribute) tdts_after_tdi (goodvibes.EnergySpan attribute) temperature (goodvibes.api.ThermoResult attribute) (goodvibes.EnergySpan attribute) (goodvibes.pes_model.PESResult property) (goodvibes.pes_model.Series attribute) (goodvibes.PESResult property) (goodvibes.schema.PESPathway attribute) (goodvibes.schema.SelectivityResult attribute) (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) (goodvibes.Series attribute) (goodvibes.thermo.ThermoOptions attribute) (goodvibes.ThermoOptions attribute) (goodvibes.ThermoResult attribute) temperatures (goodvibes.pes_model.PESResult attribute) (goodvibes.PESResult attribute) thermo (goodvibes.schema.ResultEntry attribute) thermo() (goodvibes.ComputedEntry method) (goodvibes.pes_model.ComputedEntry method) (goodvibes.pes_model.Point method) (goodvibes.Point method)

ThermoBlock (class in goodvibes.schema) ThermoOptions (class in goodvibes) (class in goodvibes.thermo) ThermoResult (class in goodvibes) (class in goodvibes.api) ThermoVector (class in goodvibes) (class in goodvibes.pes_model) to_dataframe() (goodvibes.Profile method) (in module goodvibes) (in module goodvibes.api) to_dict() (goodvibes.Profile method) to_document() (goodvibes.plot.ProfileAxes method) (goodvibes.ProfileAxes method) to_json() (goodvibes.Profile method) to_parquet() (in module goodvibes) (in module goodvibes.api) to_pes_result() (goodvibes.Profile method) to_rows() (goodvibes.Profile method) to_user_units() (goodvibes.pes_model.PESOptions method) (goodvibes.PESOptions method) to_yaml() (goodvibes.Profile method) tof (goodvibes.EnergySpan attribute) tof_span (goodvibes.EnergySpan attribute)

U

uncertainty (goodvibes.pes_model.Series attribute) (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) (goodvibes.Series attribute) units (goodvibes.EnergySpan attribute) (goodvibes.pes_model.PESOptions attribute) (goodvibes.pes_model.Series attribute) (goodvibes.PESOptions attribute) (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute) (goodvibes.schema.PESPathway attribute) (goodvibes.Series attribute)

V

validate() (goodvibes.Profile method) (in module goodvibes.schema) validate_and_configure() (in module goodvibes.GoodVibes) validate_document() (in module goodvibes) vectors() (goodvibes.ConformerSet method) (goodvibes.pes_model.ConformerSet method)

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

W

warn_orca_prescaled() (in module goodvibes.GoodVibes) warnings (goodvibes.selectivity.SelectivityResult attribute) (goodvibes.SelectivityResult attribute) weight_by (goodvibes.ConformerSet attribute) (goodvibes.pes_model.ConformerSet attribute) with_edges() (goodvibes.Pathway method) (goodvibes.pes_model.Pathway method)

with_single_point() (goodvibes.io.QCData method) (goodvibes.QCData method) write_json_results() (in module goodvibes.output) write_mikimo() (goodvibes.Profile method) write_si() (in module goodvibes) write_table() (goodvibes.Profile method) write_thermo_extxyz() (in module goodvibes.ase_helper) write_xyz() (in module goodvibes.io)

X

x (goodvibes.plot.ProfileAxes attribute) (goodvibes.ProfileAxes attribute)

xyz (goodvibes.calc_bbe attribute) (goodvibes.thermo.calc_bbe attribute)

Z

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