Index

Symbols

--adsorbate-tag ccu-adsorb command line option --atoms ccu-pop-bader-sum command line option --atoms-file ccu-thermo-gibbs command line option --bader-file ccu-pop-bader-sum command line option --cache ccu-fed command line option --centers ccu-adsorb command line option --data ccu-fed command line option --destination ccu-structure-permute command line option --dg-file ccu-thermo-gibbs command line option --energy-file ccu-thermo-gibbs command line option --finder ccu-adsorb command line option --freq-file ccu-thermo-gibbs command line option --harmonic ccu-thermo-gibbs command line option --ideal-gas ccu-thermo-gibbs command line option --interactive ccu-thermo-chempot command line option --linear ccu-thermo-gibbs command line option --list ccu-adsorb command line option ccu-thermo-chempot command line option --log-file ccu command line option ccu-thermo-gibbs command line option --log-level ccu command line option --no-smart-mode ccu-pop-bader-sum command line option --no-symmetry ccu-adsorb command line option --non-linear ccu-thermo-gibbs command line option --occupant ccu-structure-permute command line option --pressure ccu-thermo-chempot command line option ccu-thermo-gibbs command line option --quiet ccu command line option --separation ccu-adsorb command line option --smart-mode ccu-pop-bader-sum command line option --solution-phase ccu-thermo-gibbs command line option --sort-file ccu-pop-bader-sum command line option

--source ccu-structure-permute command line option --spin ccu-thermo-gibbs command line option --style ccu-fed command line option --symmetry ccu-adsorb command line option ccu-thermo-gibbs command line option --tag ccu-adsorb command line option --temperature ccu-thermo-chempot command line option ccu-thermo-gibbs command line option --transition-state ccu-thermo-gibbs command line option --verbose ccu command line option ccu-thermo-gibbs command line option --version ccu command line option --vib-file ccu-thermo-gibbs command line option -c ccu-adsorb command line option -d ccu-structure-permute command line option -f ccu-adsorb command line option -i ccu-thermo-chempot command line option -l ccu-adsorb command line option ccu-thermo-chempot command line option -o ccu-structure-permute command line option -p ccu-thermo-chempot command line option ccu-thermo-gibbs command line option -q ccu command line option -S ccu-thermo-gibbs command line option -s ccu-adsorb command line option ccu-structure-permute command line option ccu-thermo-gibbs command line option -T ccu-thermo-gibbs command line option -t ccu-adsorb command line option ccu-thermo-chempot command line option ccu-thermo-gibbs command line option -V ccu command line option -v ccu command line option ccu-thermo-gibbs command line option -Y ccu-adsorb command line option ccu-thermo-gibbs command line option

_

_abc_impl (ccu.adsorption.orientation.CenterFactory attribute) (ccu.adsorption.orientation.OctahedralFactory attribute) (ccu.adsorption.orientation.OrientationFactory attribute) (ccu.adsorption.orientation.Transformer attribute) (ccu.adsorption.sites.HubSpokeFinder attribute) (ccu.adsorption.sites.SiteFinder attribute) (ccu.adsorption.sites.Triangulator attribute) (ccu.fancyplots._gui.annotation.AnnotationSection attribute) (ccu.fancyplots._gui.footer.FooterSection attribute) (ccu.fancyplots._gui.formatting.FormattingSection attribute) (ccu.fancyplots._gui.frames.UpdatableFrame attribute) (ccu.fancyplots._gui.mechanism.MechanismSection attribute) (ccu.fancyplots.validation.Serializer attribute) (ccu.fancyplots.validation.Validator attribute) (ccu.structure.fingerprint.Fingerprint attribute) (ccu.structure.symmetry.Inversion attribute) (ccu.structure.symmetry.Reflection attribute) (ccu.structure.symmetry.Rotation attribute) (ccu.structure.symmetry.Transformation attribute) (ccu.structure.symmetry.Translation attribute) _alert_imaginary_frequencies() (in module ccu.thermo.gibbs) _asdict() (ccu.adsorption.orientation.AdsorptionCenter method) (ccu.adsorption.sites.AdsorptionSite method) (ccu.adsorption.sites.SiteAlignment method) (ccu.fancyplots.data.Annotation method) (ccu.structure.geometry.MolecularOrientation method) (ccu.thermo._ThermodynamicState method) (ccu.thermo.chempot.ChemPotDataPoint method) _AtomsType (class in ccu.pop.bader) _bind_keys() (ccu.fancyplots._gui.fed.FreeEnergyDiagram method) (ccu.fancyplots._gui.tooltip.Tooltip method) _build_cache() (ccu.fancyplots._gui.root.FancyPlotsGUI method) _co2rr_adsorbates() (in module ccu.adsorption.adsorbates) _configure_for_hubbard() (in module ccu.workflows.hubbard_u) _configure_key_bindings() (ccu.fancyplots._gui.energy.EnergyWindow method) _configure_windows() (ccu.fancyplots._gui.root.FancyPlotsGUI method) _construct_lines_to_print() (in module ccu.thermo.chempot) _convert_occupancies_to_occupants() (in module ccu.structure.defects) _convert_symbols() (in module ccu.structure.defects) _create_free_energy_widgets() (ccu.fancyplots._gui.energy.EnergyWindow method) _create_legend_widgets() (ccu.fancyplots._gui.energy.EnergyWindow method) _create_sections() (ccu.fancyplots._gui.root.FancyPlotsGUI method) _create_spinbox_frame() (ccu.fancyplots._gui.annotation.AnnotationSection method) _field_defaults (ccu.adsorption.orientation.AdsorptionCenter attribute) (ccu.adsorption.sites.AdsorptionSite attribute) (ccu.adsorption.sites.SiteAlignment attribute) (ccu.fancyplots.data.Annotation attribute) (ccu.structure.geometry.MolecularOrientation attribute) (ccu.thermo._ThermodynamicState attribute) (ccu.thermo.chempot.ChemPotDataPoint attribute) _fields (ccu.adsorption.orientation.AdsorptionCenter attribute) (ccu.adsorption.sites.AdsorptionSite attribute) (ccu.adsorption.sites.SiteAlignment attribute) (ccu.fancyplots.data.Annotation attribute) (ccu.structure.geometry.MolecularOrientation attribute) (ccu.thermo._ThermodynamicState attribute) (ccu.thermo.chempot.ChemPotDataPoint attribute) _filter_for_uniqueness() (in module ccu.structure.defects) _get_structure_with_name() (in module ccu.adsorption.complexes) _get_tag_indices() (in module ccu.pop.bader)

_initialize_windows() (ccu.fancyplots._gui.root.FancyPlotsGUI method) _is_protocol (ccu.adsorption.orientation.CenterFactory attribute) (ccu.adsorption.orientation.OctahedralFactory attribute) (ccu.adsorption.orientation.OrientationFactory attribute) (ccu.adsorption.orientation.Transformer attribute) (ccu.adsorption.sites.HubSpokeFinder attribute) (ccu.adsorption.sites.SiteFinder attribute) (ccu.adsorption.sites.Triangulator attribute) (ccu.fancyplots._gui.annotation.AnnotationSection attribute) (ccu.fancyplots._gui.footer.FooterSection attribute) (ccu.fancyplots._gui.formatting.FormattingSection attribute) (ccu.fancyplots._gui.frames.UpdatableFrame attribute) (ccu.fancyplots._gui.mechanism.MechanismSection attribute) (ccu.fancyplots.validation.Serializer attribute) (ccu.fancyplots.validation.Validator attribute) (ccu.structure.symmetry.Inversion attribute) (ccu.structure.symmetry.Reflection attribute) (ccu.structure.symmetry.Rotation attribute) (ccu.structure.symmetry.Transformation attribute) (ccu.structure.symmetry.Translation attribute) _make() (ccu.adsorption.orientation.AdsorptionCenter class method) (ccu.adsorption.sites.AdsorptionSite class method) (ccu.adsorption.sites.SiteAlignment class method) (ccu.fancyplots.data.Annotation class method) (ccu.structure.geometry.MolecularOrientation class method) (ccu.thermo._ThermodynamicState class method) (ccu.thermo.chempot.ChemPotDataPoint class method) _make_dropdown() (ccu.fancyplots._gui.energy.EnergyWindow method) _missing_displacements() (ccu.structure.comparator.Comparator static method) _name_energy_file() (in module ccu.thermo._cli) _normalize_frequencies() (in module ccu.thermo.gibbs) _nrr_adsorbates() (in module ccu.adsorption.adsorbates) _organize() (ccu.fancyplots._gui.annotation.AnnotationSection method) (ccu.fancyplots._gui.energy.EnergyWindow method) (ccu.fancyplots._gui.fed.FreeEnergyDiagram method) (ccu.fancyplots._gui.footer.FooterSection method) (ccu.fancyplots._gui.formatting.FormattingSection method) (ccu.fancyplots._gui.mechanism.MechanismSection method) (ccu.fancyplots._gui.palette.PaletteWindow method) (ccu.fancyplots._gui.root.FancyPlotsGUI method) _organize_free_energy_widgets() (ccu.fancyplots._gui.energy.EnergyWindow method) _orr_adsorbates() (in module ccu.adsorption.adsorbates) _perform_calc() (in module ccu.workflows.vcdd) _process_prompted_values() (in module ccu.thermo._cli) _quit_all() (ccu.fancyplots._gui.root.FancyPlotsGUI method) _quit_window() (ccu.fancyplots._gui.root.FancyPlotsGUI method) _replace() (ccu.adsorption.orientation.AdsorptionCenter method) (ccu.adsorption.sites.AdsorptionSite method) (ccu.adsorption.sites.SiteAlignment method) (ccu.fancyplots.data.Annotation method) (ccu.structure.geometry.MolecularOrientation method) (ccu.thermo._ThermodynamicState method) (ccu.thermo.chempot.ChemPotDataPoint method) _response_calculation() (in module ccu.workflows.hubbard_u) _select_all() (ccu.fancyplots._gui.root.FancyPlotsGUI method) _summarize_chempot() (in module ccu.thermo._cli) _ThermodynamicState (class in ccu.thermo) _update_graph() (ccu.fancyplots._gui.root.FancyPlotsGUI method) _validate_occupancies() (in module ccu.structure.defects) _verify_hubbard_parameters() (in module ccu.workflows.hubbard_u) _write_completion_script() (in module ccu._cli._init)

A

add_annotations() (in module ccu.fancyplots.plotting) add_subcommands() (in module ccu._cli._main) ADSORBATE ccu-adsorb command line option AdsorbateComplexFactory (class in ccu.adsorption.complexes) AdsorptionCenter (class in ccu.adsorption.orientation) AdsorptionSite (class in ccu.adsorption.sites) alerting_validator() (ccu.fancyplots._gui.frames.FancyFormatFrame method) align() (in module ccu.structure.geometry) alignments (ccu.adsorption.sites.AdsorptionSite attribute)

ALL_ADSORBATES (in module ccu.adsorption.adsorbates) annotation (ccu.fancyplots._gui.root.Sections attribute) Annotation (class in ccu.fancyplots.data) annotations (ccu.fancyplots.data.FancyCache attribute) AnnotationSection (class in ccu.fancyplots._gui.annotation) archive_results() (in module ccu.workflows.hubbard_u) as_matrix() (ccu.structure.symmetry.Rotation method) atomic_centerer() (in module ccu.adsorption.orientation) auto_annotate() (ccu.fancyplots._gui.annotation.AnnotationSection method) (in module ccu.fancyplots._gui.annotation)

B

boxsize (ccu.fancyplots.data.FormattingParameters attribute)

bracket_ts_step() (in module ccu.fancyplots.plotting)

C

C_VECTOR ccu-structure-resize-cell command line option cache (ccu.fancyplots._gui.root.FancyPlotsGUI property) calculate() (ccu.thermo.chempot.ChemPotCalculator method) (in module ccu.thermo.chempot) calculate_chemical_potential() (in module ccu.thermo.chempot) calculate_cumulative_displacement() (ccu.structure.comparator.Comparator static method) calculate_free_energy() (in module ccu.thermo.gibbs) calculate_norm() (in module ccu.structure.geometry) calculate_separation() (in module ccu.structure.geometry) ccu module ccu command line option --log-file --log-level --quiet --verbose --version -q -V -v ccu-adsorb command line option --adsorbate-tag --centers --finder --list --no-symmetry --separation --symmetry --tag -c -f -l -s -t -Y ADSORBATE DESTINATION STRUCTURE ccu-fed command line option --cache --data --style ccu-pop-bader-sum command line option --atoms --bader-file --no-smart-mode --smart-mode --sort-file INDICES ccu-structure-permute command line option --destination --occupant --source -d -o -s SITES ccu-structure-resize-cell command line option C_VECTOR STRUCTURE ccu-thermo-chempot command line option --interactive --list --pressure --temperature -i -l -p -t MOLECULE ccu-thermo-gibbs command line option --atoms-file --dg-file --energy-file --freq-file --harmonic --ideal-gas --linear --log-file --non-linear --pressure --solution-phase --spin --symmetry --temperature --transition-state --verbose --vib-file -p -S -s -T -t -v -Y ccu.__about__ module ccu.__main__ module ccu._cli module ccu._cli._init module ccu._cli._main module ccu._cli._utils module ccu.adsorption module ccu.adsorption._cli module ccu.adsorption.adsorbates module ccu.adsorption.complexes module

ccu.adsorption.orientation module ccu.adsorption.sites module ccu.fancyplots module ccu.fancyplots._cli module ccu.fancyplots._gui module ccu.fancyplots._gui.annotation module ccu.fancyplots._gui.energy module ccu.fancyplots._gui.fed module ccu.fancyplots._gui.footer module ccu.fancyplots._gui.formatting module ccu.fancyplots._gui.frames module ccu.fancyplots._gui.instructions module ccu.fancyplots._gui.mechanism module ccu.fancyplots._gui.menu module ccu.fancyplots._gui.palette module ccu.fancyplots._gui.root module ccu.fancyplots._gui.tooltip module ccu.fancyplots._gui.utils module ccu.fancyplots.data module ccu.fancyplots.plotting module ccu.fancyplots.styles module ccu.fancyplots.validation module ccu.pop module ccu.pop._cli module ccu.pop.bader module ccu.settings module ccu.structure module ccu.structure._cli module ccu.structure.axisfinder module ccu.structure.comparator module ccu.structure.defects module ccu.structure.fingerprint module ccu.structure.geometry module ccu.structure.resizecell module ccu.structure.symmetry module ccu.thermo module ccu.thermo._cli module ccu.thermo.chempot module ccu.thermo.gibbs module ccu.workflows module ccu.workflows.calculation module ccu.workflows.hubbard_u module ccu.workflows.infrared module ccu.workflows.vcdd module ccu.workflows.vibration module CCUSettings (class in ccu.settings) CenterFactory (class in ccu.adsorption.orientation) check_similarity() (ccu.structure.comparator.Comparator static method) check_symmetry() (in module ccu.structure.symmetry) ChemPotCalculator (class in ccu.thermo.chempot) ChemPotDatabase (class in ccu.thermo.chempot) ChemPotDataPoint (class in ccu.thermo.chempot) CO2RR_ADSORBATES (in module ccu.adsorption.adsorbates) color (ccu.fancyplots.data.Annotation attribute) colors (ccu.fancyplots.data.FormattingParameters attribute) com_centerer() (in module ccu.adsorption.orientation) Comparator (class in ccu.structure.comparator) configure_logging() (ccu.settings.CCUSettings method) (in module ccu._cli._utils) convert() (ccu.pop.bader._AtomsType method) cosort_fingerprints() (ccu.structure.comparator.Comparator static method) cosort_histograms() (ccu.structure.comparator.Comparator static method) create_artists() (ccu.fancyplots.plotting.SymHandler method) create_auto_annotate_button() (ccu.fancyplots._gui.annotation.AnnotationSection method) create_axes() (in module ccu.fancyplots.plotting) create_edit_menu() (in module ccu.fancyplots._gui.menu) create_legend() (in module ccu.fancyplots.plotting) create_save_button() (ccu.fancyplots._gui.annotation.AnnotationSection method) create_ts_curve() (in module ccu.fancyplots.plotting)

D

DEFAULT_ADSORBATE_TAG (in module ccu.adsorption.complexes) DEFAULT_PARAMETERS (in module ccu.fancyplots.data) default_serializer() (in module ccu.fancyplots.validation) description (ccu.adsorption.orientation.AdsorptionCenter attribute) (ccu.adsorption.sites.AdsorptionSite attribute) (ccu.adsorption.sites.SiteAlignment attribute) (ccu.structure.geometry.MolecularOrientation attribute)

DESTINATION ccu-adsorb command line option diagram_data (ccu.fancyplots.data.FancyCache attribute) direction (ccu.adsorption.sites.SiteAlignment attribute) directions (ccu.structure.geometry.MolecularOrientation attribute) dpi (ccu.fancyplots.data.FormattingParameters attribute)

E

emit() (ccu._cli._utils.FancyConsoleHandler method) energy_data (ccu.fancyplots.data.FEDData attribute)

energy_window (ccu.fancyplots._gui.root.Windows attribute) EnergyWindow (class in ccu.fancyplots._gui.energy)

F

FancyCache (class in ccu.fancyplots.data) FancyConsoleHandler (class in ccu._cli._utils) FancyFormatFrame (class in ccu.fancyplots._gui.frames) FancyPlotsGUI (class in ccu.fancyplots._gui.root) FEDData (class in ccu.fancyplots.data) find_farthest_atoms() (in module ccu.structure.axisfinder) find_primary_axis() (in module ccu.structure.axisfinder) find_secondary_axis() (in module ccu.structure.axisfinder) find_tertiary_axis() (in module ccu.structure.axisfinder) Fingerprint (class in ccu.structure.fingerprint) font (ccu.fancyplots.data.FormattingParameters attribute)

fontsize (ccu.fancyplots.data.Annotation attribute) (ccu.fancyplots.data.FormattingParameters attribute) footer (ccu.fancyplots._gui.root.Sections attribute) FooterSection (class in ccu.fancyplots._gui.footer) format_primary_axes() (in module ccu.fancyplots.plotting) format_secondary_axes() (in module ccu.fancyplots.plotting) formatting (ccu.fancyplots._gui.root.Sections attribute) FormattingParameters (class in ccu.fancyplots.data) FormattingSection (class in ccu.fancyplots._gui.formatting) FreeEnergyDiagram (class in ccu.fancyplots._gui.fed) from_structure() (ccu.structure.fingerprint.Fingerprint class method)

G

generate_complexes() (in module ccu.adsorption.complexes) generate_figure() (ccu.fancyplots._gui.fed.FreeEnergyDiagram method) (in module ccu.fancyplots.plotting) get() (ccu.thermo.chempot.ChemPotDatabase method) get_adsorbate() (in module ccu.adsorption.adsorbates)

get_axes() (in module ccu.structure.axisfinder) get_complexes() (ccu.adsorption.complexes.AdsorbateComplexFactory method) get_hubbard_u() (in module ccu.workflows.hubbard_u) get_ionic_charges() (in module ccu.workflows.hubbard_u) graph_window (ccu.fancyplots._gui.root.Windows attribute)

H

HER_ADSORBATES (in module ccu.adsorption.adsorbates) hide() (ccu.fancyplots._gui.tooltip.Tooltip method)

highlight_and_warn() (in module ccu.fancyplots.validation) HUB_TAG (in module ccu.adsorption.sites) HubSpokeFinder (class in ccu.adsorption.sites)

I

INDICES ccu-pop-bader-sum command line option initialize_frames() (ccu.fancyplots._gui.formatting.FormattingSection method) initialize_styles() (in module ccu.fancyplots.styles)

instructions_window (ccu.fancyplots._gui.root.Windows attribute) InstructionsWindow (class in ccu.fancyplots._gui.instructions) interpolate() (in module ccu.fancyplots.plotting) Inversion (class in ccu.structure.symmetry)

L

label_text (ccu.fancyplots._gui.frames.FancyFormatFrame property) launch_energy_window() (ccu.fancyplots._gui.mechanism.MechanismSection method) legend_labels (ccu.fancyplots.data.FEDData attribute) legend_loc (ccu.fancyplots.data.FormattingParameters attribute) linewidth (ccu.fancyplots.data.FormattingParameters attribute)

load_parameter_data() (in module ccu.thermo.chempot) load_zpe_data() (in module ccu.thermo.chempot) LOG_FILE (ccu.settings.CCUSettings attribute) LOG_LEVEL (ccu.settings.CCUSettings attribute) lower (ccu.thermo.chempot.ChemPotDataPoint attribute)

M

markeredgewidth (ccu.fancyplots.data.FormattingParameters attribute) markersize (ccu.fancyplots.data.FormattingParameters attribute) matplotlib_palette (ccu.fancyplots._gui.root.Windows attribute) max_temperature (ccu.thermo.chempot.ChemPotCalculator property) mechanism (ccu.fancyplots._gui.mechanism.MechanismSection property) (ccu.fancyplots._gui.mechanism.StepPanel property) (ccu.fancyplots._gui.root.Sections attribute) (ccu.fancyplots.data.FEDData attribute) MechanismSection (class in ccu.fancyplots._gui.mechanism) model_config (ccu.settings.CCUSettings attribute) module ccu ccu.__about__ ccu.__main__ ccu._cli ccu._cli._init ccu._cli._main ccu._cli._utils ccu.adsorption ccu.adsorption._cli ccu.adsorption.adsorbates ccu.adsorption.complexes ccu.adsorption.orientation ccu.adsorption.sites ccu.fancyplots ccu.fancyplots._cli ccu.fancyplots._gui ccu.fancyplots._gui.annotation ccu.fancyplots._gui.energy ccu.fancyplots._gui.fed ccu.fancyplots._gui.footer ccu.fancyplots._gui.formatting ccu.fancyplots._gui.frames ccu.fancyplots._gui.instructions ccu.fancyplots._gui.mechanism ccu.fancyplots._gui.menu ccu.fancyplots._gui.palette ccu.fancyplots._gui.root ccu.fancyplots._gui.tooltip ccu.fancyplots._gui.utils ccu.fancyplots.data ccu.fancyplots.plotting ccu.fancyplots.styles ccu.fancyplots.validation ccu.pop ccu.pop._cli ccu.pop.bader ccu.settings ccu.structure ccu.structure._cli ccu.structure.axisfinder ccu.structure.comparator ccu.structure.defects ccu.structure.fingerprint ccu.structure.geometry ccu.structure.resizecell ccu.structure.symmetry ccu.thermo ccu.thermo._cli ccu.thermo.chempot ccu.thermo.gibbs ccu.workflows ccu.workflows.calculation ccu.workflows.hubbard_u ccu.workflows.infrared ccu.workflows.vcdd ccu.workflows.vibration

MolecularOrientation (class in ccu.structure.geometry) MOLECULE ccu-thermo-chempot command line option molecule (ccu.thermo.chempot.ChemPotDataPoint attribute) mouse_coordinates() (ccu.fancyplots._gui.fed.FreeEnergyDiagram method)

N

name (ccu.pop.bader._AtomsType attribute) no_validation_validator() (in module ccu.fancyplots.validation) norm (ccu.adsorption.sites.AdsorptionSite attribute)

npaths (ccu.fancyplots._gui.mechanism.MechanismSection property) (ccu.fancyplots._gui.mechanism.PathPanel property) NRR_ADSORBATES (in module ccu.adsorption.adsorbates)

O

OctahedralFactory (class in ccu.adsorption.orientation) on_enter() (ccu.fancyplots._gui.tooltip.Tooltip method) on_leave() (ccu.fancyplots._gui.tooltip.Tooltip method) open_image() (in module ccu.fancyplots._gui.utils)

options (ccu.fancyplots._gui.energy.EnergyWindow property) OrientationFactory (class in ccu.adsorption.orientation) ORR_ADSORBATES (in module ccu.adsorption.adsorbates) OUTPUT_ATOMS (ccu.settings.CCUSettings attribute)

P

PaletteWindow (class in ccu.fancyplots._gui.palette) param (ccu.thermo.chempot.ChemPotDataPoint attribute) parameter_data (ccu.thermo.chempot.ChemPotDatabase attribute) PathPanel (class in ccu.fancyplots._gui.mechanism) pathway (ccu.fancyplots._gui.energy.EnergyWindow property) pathway_index (ccu.fancyplots._gui.energy.EnergyWindow property) permute() (in module ccu.structure.defects) place_adsorbate() (ccu.adsorption.complexes.AdsorbateComplexFactory method) plot_energy_data() (in module ccu.fancyplots.plotting)

plot_fed() (in module ccu.fancyplots.plotting) position (ccu.adsorption.orientation.AdsorptionCenter attribute) (ccu.adsorption.sites.AdsorptionSite attribute) pressure (ccu.thermo._ThermodynamicState attribute) print_adsorbates() (in module ccu.adsorption._cli) print_easter_egg() (in module ccu.fancyplots._gui.utils) print_instructions() (in module ccu.thermo.chempot) print_molecules() (in module ccu.thermo._cli) python_value (ccu.fancyplots._gui.frames.FancyFormatFrame property)

Q

quit_window() (ccu.fancyplots._gui.energy.EnergyWindow method)

R

Reflection (class in ccu.structure.symmetry) report_state() (in module ccu.thermo._cli) reset_defaults() (ccu.fancyplots._gui.footer.FooterSection method) (ccu.fancyplots._gui.formatting.FormattingSection method) resize() (ccu.fancyplots._gui.fed.FreeEnergyDiagram method) Rotation (class in ccu.structure.symmetry)

run() (in module ccu.structure.resizecell) run_bader() (in module ccu.workflows.calculation) run_calculation() (in module ccu.workflows.calculation) run_chargemol() (in module ccu.workflows.calculation) run_infrared() (in module ccu.workflows.infrared) run_vcdd() (in module ccu.workflows.vcdd) run_vibration() (in module ccu.workflows.vibration)

S

save() (ccu.fancyplots.data.FancyCache method) save_annotation() (ccu.fancyplots._gui.annotation.AnnotationSection method) save_cache() (ccu.fancyplots._gui.root.FancyPlotsGUI method) save_energy_data() (ccu.fancyplots._gui.energy.EnergyWindow method) save_fed_plot() (in module ccu.fancyplots.plotting) save_figure() (ccu.fancyplots._gui.footer.FooterSection method) save_legend_data() (ccu.fancyplots._gui.energy.EnergyWindow method) savename (ccu.fancyplots.data.FormattingParameters attribute) schedule() (ccu.fancyplots._gui.tooltip.Tooltip method) Sections (class in ccu.fancyplots._gui.root) select_frequencies() (in module ccu.thermo.gibbs) Serializer (class in ccu.fancyplots.validation) SETTINGS (in module ccu) settings_customise_sources() (ccu.settings.CCUSettings class method) show() (ccu.fancyplots._gui.tooltip.Tooltip method) show_edit_menu() (in module ccu.fancyplots._gui.menu) show_graph() (ccu.fancyplots._gui.footer.FooterSection method)

show_instructions() (ccu.fancyplots._gui.footer.FooterSection method) show_palette() (ccu.fancyplots._gui.footer.FooterSection method) SITE_TAG (in module ccu.adsorption.sites) SiteAlignment (class in ccu.adsorption.sites) SiteFinder (class in ccu.adsorption.sites) SITES ccu-structure-permute command line option special_centerer() (in module ccu.adsorption.orientation) SPOKE_TAG (in module ccu.adsorption.sites) StepPanel (class in ccu.fancyplots._gui.mechanism) string_to_primitive() (in module ccu.fancyplots.validation) string_to_sequence() (in module ccu.fancyplots.validation) string_to_union() (in module ccu.fancyplots.validation) STRUCTURE ccu-adsorb command line option ccu-structure-resize-cell command line option style_parameters (ccu.fancyplots.data.FancyCache attribute) SymHandler (class in ccu.fancyplots.plotting)

T

temperature (ccu.thermo._ThermodynamicState attribute) TEMPLATE_DIR (ccu.settings.CCUSettings attribute) text (ccu.fancyplots.data.Annotation attribute) tick_dec (ccu.fancyplots.data.FormattingParameters attribute) tick_double (ccu.fancyplots.data.FormattingParameters attribute) tick_loc (ccu.fancyplots.data.FormattingParameters attribute) tick_min (ccu.fancyplots.data.FormattingParameters attribute) tight_layout (ccu.fancyplots._gui.root.Windows attribute) tight_layout_on_press() (ccu.fancyplots._gui.fed.FreeEnergyDiagram method)

tight_layout_on_release() (ccu.fancyplots._gui.fed.FreeEnergyDiagram method) TightFreeEnergyDiagram (class in ccu.fancyplots._gui.fed) title (ccu.fancyplots.data.FormattingParameters attribute) Tooltip (class in ccu.fancyplots._gui.tooltip) Transformation (class in ccu.structure.symmetry) Transformer (class in ccu.adsorption.orientation) Translation (class in ccu.structure.symmetry) Triangulator (class in ccu.adsorption.sites) type_hint_to_validator() (in module ccu.fancyplots.validation)

U

unschedule() (ccu.fancyplots._gui.tooltip.Tooltip method) UpdatableFrame (class in ccu.fancyplots._gui.frames) update_data() (ccu.fancyplots._gui.mechanism.MechanismSection method) (ccu.fancyplots._gui.mechanism.PathPanel method) (ccu.fancyplots._gui.mechanism.StepPanel method) update_frames() (ccu.fancyplots._gui.annotation.AnnotationSection method) (ccu.fancyplots._gui.footer.FooterSection method) (ccu.fancyplots._gui.formatting.FormattingSection method) (ccu.fancyplots._gui.frames.UpdatableFrame method) (ccu.fancyplots._gui.mechanism.MechanismSection method)

update_graph() (ccu.fancyplots._gui.fed.FreeEnergyDiagram method) update_parameters() (ccu.fancyplots._gui.formatting.FormattingSection method) update_widgets() (ccu.fancyplots._gui.energy.EnergyWindow method) upper (ccu.thermo.chempot.ChemPotDataPoint attribute)

V

validate_log_level() (ccu.settings.CCUSettings class method) ValidationError Validator (class in ccu.fancyplots.validation)

validator_from_type() (in module ccu.fancyplots.validation) value (ccu.fancyplots._gui.frames.FancyFormatFrame property) (ccu.thermo.chempot.ChemPotDataPoint attribute) visual (ccu.fancyplots.data.FormattingParameters attribute)

W

Windows (class in ccu.fancyplots._gui.root)

write_complexes() (in module ccu.adsorption.complexes)

X

x (ccu.fancyplots.data.Annotation attribute) xlabel (ccu.fancyplots.data.FormattingParameters attribute)

xlim (ccu.fancyplots.data.FormattingParameters attribute) xscale (ccu.fancyplots.data.FormattingParameters attribute)

Y

y (ccu.fancyplots.data.Annotation attribute) ylabel (ccu.fancyplots.data.FormattingParameters attribute)

ylim (ccu.fancyplots.data.FormattingParameters attribute) yscale (ccu.fancyplots.data.FormattingParameters attribute)

Z

zpe_data (ccu.thermo.chempot.ChemPotDatabase attribute)