Index

Symbols

--atoms ccu-bader-sum command line option --atoms-file ccu-thermo-gibbs command line option --bader-file ccu-bader-sum command line option --cache ccu-fancyplots command line option --data ccu-fancyplots 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 --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-adsorption-place-adsorbate 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 --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-adsorption-place-adsorbate command line option --smart-mode ccu-bader-sum command line option --solution-phase ccu-thermo-gibbs command line option --sort-file ccu-bader-sum command line option --source ccu-structure-permute command line option --special-centres ccu-adsorption-place-adsorbate command line option --spin ccu-thermo-gibbs command line option

--style ccu-fancyplots command line option --symmetric ccu-adsorption-place-adsorbate command line option --symmetry ccu-thermo-gibbs 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 --vertical ccu-adsorption-place-adsorbate command line option --vib-file ccu-thermo-gibbs command line option -c ccu-adsorption-place-adsorbate command line option -d ccu-structure-permute command line option -i ccu-thermo-chempot command line option -l ccu-adsorption-place-adsorbate 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-adsorption-place-adsorbate command line option ccu-structure-permute command line option ccu-thermo-gibbs command line option -T ccu-thermo-gibbs command line option -t ccu-thermo-chempot command line option ccu-thermo-gibbs command line option -V ccu command line option ccu-adsorption-place-adsorbate command line option -v ccu command line option ccu-thermo-gibbs command line option -Y ccu-adsorption-place-adsorbate command line option ccu-thermo-gibbs command line option

A

add_annotations() (in module ccu.fancyplots.gui.plotting) add_subcommands() (in module ccu.cli.main) adjacent_linkers (ccu.adsorption.sitefinder.MOFSiteFinder property) ADSORBATE ccu-adsorption-place-adsorbate command line option adsorbate (ccu.adsorption.adsorbatecomplex.AdsorbateComplexFactory property) adsorbate_orientations() (ccu.adsorption.adsorbatecomplex.AdsorbateComplexFactory method) AdsorbateComplex (class in ccu.adsorption.adsorbatecomplex) AdsorbateComplexFactory (class in ccu.adsorption.adsorbatecomplex)

AdsorbateOrientation (class in ccu.adsorption.adsorbateorientation) AdsorbateOrientationFactory (class in ccu.adsorption.adsorbateorientation) AdsorptionSite (class in ccu.adsorption.sitefinder) alerting_validator() (ccu.fancyplots.gui.frames.FancyFormatFrame method) 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.hubbard.vasp) as_matrix() (ccu.structure.symmetry.Rotation method)

B

boxsize (ccu.fancyplots.data.FormattingParameters attribute)

bracket_ts_step() (in module ccu.fancyplots.gui.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_separation() (in module ccu.structure.geometry) ccu module ccu command line option --log-file --log-level --quiet --verbose --version -q -V -v ccu-adsorption-place-adsorbate command line option --list --separation --special-centres --symmetric --vertical -c -l -s -V -Y ADSORBATE DESTINATION STRUCTURE ccu-bader-sum command line option --atoms --bader-file --smart-mode --sort-file INDICES ccu-fancyplots command line option --cache --data --style 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.adsorption module ccu.adsorption.adsorbatecomplex module ccu.adsorption.adsorbateorientation module ccu.adsorption.adsorbates module ccu.adsorption.cli module ccu.adsorption.sitefinder module

ccu.cli module ccu.cli.main module ccu.cli.utils module ccu.fancyplots module ccu.fancyplots.cli module ccu.fancyplots.data 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.plotting module ccu.fancyplots.gui.root module ccu.fancyplots.gui.tooltip module ccu.fancyplots.gui.utils module ccu.fancyplots.styles module ccu.fancyplots.validation module ccu.hubbard module ccu.hubbard.vasp module ccu.relaxation module ccu.structure module ccu.structure.axisfinder module ccu.structure.cli 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.chempot module ccu.thermo.cli module ccu.thermo.gibbs module ccu.thermo.vibration module check_similarity() (ccu.structure.comparator.Comparator static method) check_symmetry() (ccu.structure.symmetry.RotationSymmetry method) (ccu.structure.symmetry.Symmetry method) ChemPotCalculator (class in ccu.thermo.chempot) ChemPotDatabase (class in ccu.thermo.chempot) ChemPotDataPoint (class in ccu.thermo.chempot) color (ccu.fancyplots.data.Annotation attribute) colors (ccu.fancyplots.data.FormattingParameters attribute) Comparator (class in ccu.structure.comparator) configure_logging() (in module ccu.cli.utils) cosort_fingerprints() (ccu.structure.comparator.Comparator static method) cosort_histograms() (ccu.structure.comparator.Comparator static method) create_alignments() (ccu.adsorption.sitefinder.MOFSite method) create_artists() (ccu.fancyplots.gui.plotting.SymHandler method) create_axes() (in module ccu.fancyplots.gui.plotting) create_between_linker_site() (ccu.adsorption.sitefinder.MOFSiteFinder method) create_edit_menu() (in module ccu.fancyplots.gui.menu) create_intermediate_alignments() (ccu.adsorption.sitefinder.MOFSite method) create_linker_sites() (ccu.adsorption.sitefinder.MOFSiteFinder method) create_metal_site() (ccu.adsorption.sitefinder.MOFSiteFinder method) create_orientations() (ccu.adsorption.adsorbateorientation.AdsorbateOrientationFactory method) create_save_button() (ccu.fancyplots.gui.annotation.AnnotationSection method) create_ts_curve() (in module ccu.fancyplots.gui.plotting)

D

DEFAULT_SBU_TAG (ccu.adsorption.sitefinder.MOFSiteFinder attribute) default_serializer() (in module ccu.fancyplots.validation) DESTINATION ccu-adsorption-place-adsorbate command line option

diagram_data (ccu.fancyplots.data.FancyCache 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.gui.plotting) format_secondary_axes() (in module ccu.fancyplots.gui.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.adsorbatecomplex) generate_figure() (ccu.fancyplots.gui.fed.FreeEnergyDiagram method) (in module ccu.fancyplots.gui.plotting) get() (ccu.thermo.chempot.ChemPotDatabase method)

get_adsorbate() (in module ccu.adsorption.adsorbates) get_axes() (in module ccu.structure.axisfinder) get_hubbard_u() (in module ccu.hubbard.vasp) get_ionic_charges() (in module ccu.hubbard.vasp) graph_window (ccu.fancyplots.gui.root.Windows attribute)

H

hide() (ccu.fancyplots.gui.tooltip.Tooltip method)

highlight_and_warn() (in module ccu.fancyplots.validation)

I

INDICES ccu-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.gui.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) 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.data.FEDData attribute) (ccu.fancyplots.gui.mechanism.MechanismSection property) (ccu.fancyplots.gui.mechanism.StepPanel property) (ccu.fancyplots.gui.root.Sections attribute) MechanismSection (class in ccu.fancyplots.gui.mechanism) module ccu ccu.adsorption ccu.adsorption.adsorbatecomplex ccu.adsorption.adsorbateorientation ccu.adsorption.adsorbates ccu.adsorption.cli ccu.adsorption.sitefinder ccu.cli ccu.cli.main ccu.cli.utils ccu.fancyplots ccu.fancyplots.cli ccu.fancyplots.data 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.plotting ccu.fancyplots.gui.root ccu.fancyplots.gui.tooltip ccu.fancyplots.gui.utils ccu.fancyplots.styles ccu.fancyplots.validation ccu.hubbard ccu.hubbard.vasp ccu.relaxation ccu.structure ccu.structure.axisfinder ccu.structure.cli ccu.structure.comparator ccu.structure.defects ccu.structure.fingerprint ccu.structure.geometry ccu.structure.resizecell ccu.structure.symmetry ccu.thermo ccu.thermo.chempot ccu.thermo.cli ccu.thermo.gibbs ccu.thermo.vibration

MOFSite (class in ccu.adsorption.sitefinder) MOFSiteFinder (class in ccu.adsorption.sitefinder) MOLECULE ccu-thermo-chempot command line option molecule (ccu.thermo.chempot.ChemPotDataPoint attribute) mouse_coordinates() (ccu.fancyplots.gui.fed.FreeEnergyDiagram method)

N

next_complex() (ccu.adsorption.adsorbatecomplex.AdsorbateComplexFactory method) no_validation_validator() (in module ccu.fancyplots.validation)

npaths (ccu.fancyplots.gui.mechanism.MechanismSection property) (ccu.fancyplots.gui.mechanism.PathPanel property)

O

on_enter() (ccu.fancyplots.gui.tooltip.Tooltip method) on_leave() (ccu.fancyplots.gui.tooltip.Tooltip method) open_image() (in module ccu.fancyplots.gui.utils)

operation (ccu.structure.symmetry.RotationSymmetry property) (ccu.structure.symmetry.Symmetry property) options (ccu.fancyplots.gui.energy.EnergyWindow property) orient_adsorbate() (ccu.adsorption.adsorbatecomplex.AdsorbateComplexFactory method)

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.adsorbatecomplex.AdsorbateComplexFactory method)

plot_dashed_lines() (in module ccu.fancyplots.gui.plotting) plot_energy_data() (in module ccu.fancyplots.gui.plotting) plot_fed() (in module ccu.fancyplots.gui.plotting) plot_solid_lines() (in module ccu.fancyplots.gui.plotting) 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

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) RotationSymmetry (class in ccu.structure.symmetry) run() (in module ccu.structure.resizecell) run_relaxation() (in module ccu.relaxation) run_vibration() (in module ccu.thermo.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.gui.plotting) save_figure() (ccu.fancyplots.gui.fed.FreeEnergyDiagram method) (ccu.fancyplots.gui.footer.FooterSection method) save_legend_data() (ccu.fancyplots.gui.energy.EnergyWindow method) savename (ccu.fancyplots.data.FormattingParameters attribute) sbu_metal (ccu.adsorption.sitefinder.MOFSiteFinder property) 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) 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)

SiteAlignment (class in ccu.adsorption.sitefinder) SiteFinder (class in ccu.adsorption.sitefinder) SITES ccu-structure-permute command line option sites() (ccu.adsorption.sitefinder.MOFSiteFinder method) (ccu.adsorption.sitefinder.SiteFinder method) 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-adsorption-place-adsorbate command line option ccu-structure-resize-cell command line option structure (ccu.adsorption.adsorbatecomplex.AdsorbateComplexFactory property) style_parameters (ccu.fancyplots.data.FancyCache attribute) surface_norm (ccu.adsorption.sitefinder.MOFSiteFinder property) SymHandler (class in ccu.fancyplots.gui.plotting) Symmetry (class in ccu.structure.symmetry) SymmetryOperation (class in ccu.structure.symmetry)

T

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) transform() (ccu.structure.symmetry.Rotation method) (ccu.structure.symmetry.SymmetryOperation method) 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_annotation() (ccu.fancyplots.gui.annotation.AnnotationSection method) 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

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() (ccu.adsorption.adsorbatecomplex.AdsorbateComplex method)

X

x (ccu.fancyplots.data.Annotation attribute)

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

Y

y (ccu.fancyplots.data.Annotation attribute)

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

Z

zpe_data (ccu.thermo.chempot.ChemPotDatabase attribute)