Modules

• matador package
  • Subpackages
    • matador.battery package
      • Electrode
        • Electrode.kind
        • Electrode.ion
        • Electrode.valence
        • Electrode.valence_data
        • Electrode.calculate_average_voltage()
        • Electrode.calculate_energy_density()
      • VoltageProfile
        • VoltageProfile.starting_stoichiometry
        • VoltageProfile.capacities
        • VoltageProfile.voltage
        • VoltageProfile.average_voltage
        • VoltageProfile.reactions
        • VoltageProfile.active_ion
        • VoltageProfile.voltage_summary()
      • Submodules
      • matador.battery.electrode module
        • Electrode
          • Electrode.kind
          • Electrode.ion
          • Electrode.valence
          • Electrode.valence_data
          • Electrode.calculate_average_voltage()
          • Electrode.calculate_energy_density()
        • VoltageProfile
          • VoltageProfile.starting_stoichiometry
          • VoltageProfile.capacities
          • VoltageProfile.voltage
          • VoltageProfile.average_voltage
          • VoltageProfile.reactions
          • VoltageProfile.active_ion
          • VoltageProfile.voltage_summary()
    • matador.calculators package
      • CastepCalculator
        • CastepCalculator.verify_calculation_parameters()
        • CastepCalculator.verify_simulation_cell()
        • CastepCalculator.do_memcheck()
      • Submodules
      • matador.calculators.ase module
      • matador.calculators.calculator module
        • Calculator
          • Calculator.verify_calculation_parameters()
          • Calculator.verify_simulation_cell()
          • Calculator.do_memcheck()
      • matador.calculators.castep module
        • CastepCalculator
          • CastepCalculator.verify_calculation_parameters()
          • CastepCalculator.verify_simulation_cell()
          • CastepCalculator.do_memcheck()
      • matador.calculators.quantum_espresso module
    • matador.cli package
      • Submodules
      • matador.cli.cli module
      • matador.cli.dispersion module
        • main()
      • matador.cli.run3 module
    • matador.compute package
      • Submodules
      • matador.compute.batch module
      • matador.compute.compute module
      • matador.compute.pbs module
      • matador.compute.queueing module
      • matador.compute.slurm module
    • matador.config package
      • load_custom_settings()
      • set_settings()
      • Submodules
      • matador.config.config module
        • load_custom_settings()
        • set_settings()
      • matador.config.quickstart module
        • quickstart_settings()
      • matador.config.settings module
        • Settings
          • Settings.get()
          • Settings.reset()
    • matador.crystal package
      • Crystal
        • Crystal.elems
        • Crystal.cell
        • Crystal.update()
        • Crystal.print_sites()
        • Crystal.set_positions()
        • Crystal.atom_types
        • Crystal.num_atoms
        • Crystal.num_elements
        • Crystal.positions_frac
        • Crystal.positions_abs
        • Crystal.site_occupancies
        • Crystal.stoichiometry
        • Crystal.num_fu
        • Crystal.concentration
        • Crystal.get_concentration()
        • Crystal.formula
        • Crystal.formula_tex
        • Crystal.formula_unicode
        • Crystal.cell_volume
        • Crystal.lattice_cart
        • Crystal.lattice_abc
        • Crystal.bond_lengths
        • Crystal.voronoi_substructure
        • Crystal.space_group
        • Crystal.space_group_tex
        • Crystal.get_space_group()
        • Crystal.pdf
        • Crystal.calculate_pdf()
        • Crystal.pxrd
        • Crystal.calculate_pxrd()
        • Crystal.coordination_stats
        • Crystal.ase_atoms
        • Crystal.pmg_structure
        • Crystal.from_ase()
        • Crystal.from_pmg()
        • Crystal.coordination_lists
        • Crystal.unique_sites
        • Crystal.network
        • Crystal.network_stats
        • Crystal.bonding_stats
        • Crystal.draw_network()
        • Crystal.supercell()
        • Crystal.standardized()
      • Submodules
      • matador.crystal.crystal module
        • UnitCell
          • UnitCell.lattice_cart
          • UnitCell.lattice_abc
          • UnitCell.lengths
          • UnitCell.recip_lattice_cart
          • UnitCell.angles
          • UnitCell.volume
        • Crystal
          • Crystal.elems
          • Crystal.cell
          • Crystal.update()
          • Crystal.print_sites()
          • Crystal.set_positions()
          • Crystal.atom_types
          • Crystal.num_atoms
          • Crystal.num_elements
          • Crystal.positions_frac
          • Crystal.positions_abs
          • Crystal.site_occupancies
          • Crystal.stoichiometry
          • Crystal.num_fu
          • Crystal.concentration
          • Crystal.get_concentration()
          • Crystal.formula
          • Crystal.formula_tex
          • Crystal.formula_unicode
          • Crystal.cell_volume
          • Crystal.lattice_cart
          • Crystal.lattice_abc
          • Crystal.bond_lengths
          • Crystal.voronoi_substructure
          • Crystal.space_group
          • Crystal.space_group_tex
          • Crystal.get_space_group()
          • Crystal.pdf
          • Crystal.calculate_pdf()
          • Crystal.pxrd
          • Crystal.calculate_pxrd()
          • Crystal.coordination_stats
          • Crystal.ase_atoms
          • Crystal.pmg_structure
          • Crystal.from_ase()
          • Crystal.from_pmg()
          • Crystal.coordination_lists
          • Crystal.unique_sites
          • Crystal.network
          • Crystal.network_stats
          • Crystal.bonding_stats
          • Crystal.draw_network()
          • Crystal.supercell()
          • Crystal.standardized()
      • matador.crystal.crystal_site module
        • Site
          • Site.get()
          • Site.set_position()
          • Site.coords
          • Site.coords_cartesian
          • Site.species
          • Site.lattice
          • Site.occupancy
          • Site.coordination
          • Site.displacement_between_sites()
          • Site.distance_between_sites()
      • matador.crystal.elastic module
      • matador.crystal.network module
        • CrystalGraph
          • CrystalGraph.get_strongly_connected_component_subgraphs()
          • CrystalGraph.get_communities()
          • CrystalGraph.remove_directionality()
          • CrystalGraph.set_unique_subgraphs()
          • CrystalGraph.get_bonds_per_atom()
        • node_match()
        • get_unique_subgraphs()
        • are_graphs_the_same()
        • draw_network()
    • matador.data package
      • Subpackages
        • matador.data.atomic_scattering package
          • Submodules
          • matador.data.atomic_scattering.atomic_scattering_factors_gsas module
          • matador.data.atomic_scattering.atomic_scattering_factors_raspa module
          • matador.data.atomic_scattering.atomic_scattering_loaders module
        • matador.data.magres package
          • Submodules
          • matador.data.magres.electric_quadrupole_moments module
      • Submodules
      • matador.data.constants module
      • matador.data.periodic_table module
    • matador.db package
      • Submodules
      • matador.db.changes module
      • matador.db.connect module
      • matador.db.importer module
      • matador.db.refine module
    • matador.export package
      • Submodules
      • matador.export.export module
      • matador.export.utils module
    • matador.fingerprints package
      • Submodules
      • matador.fingerprints.fingerprint module
        • njit()
        • Fingerprint
          • Fingerprint.fingerprint
          • Fingerprint.default_key
          • Fingerprint.calculate()
        • FingerprintFactory
          • FingerprintFactory.nprocs
          • FingerprintFactory.fingerprint
          • FingerprintFactory.default_key
      • matador.fingerprints.pdf module
        • njit()
        • PDF
          • PDF.r_space
          • PDF.gr
          • PDF.dr
          • PDF.rmax
          • PDF.label
          • PDF.elem_gr
          • PDF.number_density
          • PDF.kwargs
          • PDF.calc_pdf()
          • PDF.calculate()
          • PDF.get_sim_distance()
          • PDF.pdf()
          • PDF.plot_projected_pdf()
          • PDF.plot()
        • PDFFactory
          • PDFFactory.nprocs
          • PDFFactory.default_key
          • PDFFactory.fingerprint
        • PDFOverlap
          • PDFOverlap.pdf_a
          • PDFOverlap.pdf_b
          • PDFOverlap.fine_dr
          • PDFOverlap.similarity_distance
          • PDFOverlap.overlap_int
          • PDFOverlap.pdf_overlap()
          • PDFOverlap.projected_pdf_overlap()
          • PDFOverlap.plot_diff()
          • PDFOverlap.plot_projected_diff()
        • CombinedProjectedPDF
          • CombinedProjectedPDF.plot_projected_pdf()
      • matador.fingerprints.pxrd module
      • matador.fingerprints.similarity module
    • matador.hull package
      • Submodules
      • matador.hull.hull module
      • matador.hull.hull_diff module
      • matador.hull.hull_ensemble module
      • matador.hull.hull_temperature module
      • matador.hull.phase_diagram module
    • matador.magres package
      • MagresReferencer
        • MagresReferencer.fit_model
        • MagresReferencer.fit_results
        • MagresReferencer.fit_intercept
        • MagresReferencer.fit_gradient
        • MagresReferencer.fit_rsquared
        • MagresReferencer.structures_exp
        • MagresReferencer.shifts_exp
        • MagresReferencer.species
        • MagresReferencer.structures
        • MagresReferencer.warn_tolerance
        • MagresReferencer.fit_model
        • MagresReferencer.fit_results
        • MagresReferencer.fit_intercept
        • MagresReferencer.fit_gradient
        • MagresReferencer.fit_rsquared
        • MagresReferencer.structures_exp
        • MagresReferencer.shifts_exp
        • MagresReferencer.species
        • MagresReferencer.structures
        • MagresReferencer.warn_tolerance
        • MagresReferencer.match_exp_structure_shifts()
        • MagresReferencer.set_shifts_from_fit()
        • MagresReferencer.fit()
        • MagresReferencer.predict()
        • MagresReferencer.print_fit_summary()
        • MagresReferencer.plot_fit()
        • MagresReferencer.plot_fit_and_predictions()
      • Submodules
      • matador.magres.referencer module
        • MagresReferencer
          • MagresReferencer.fit_model
          • MagresReferencer.fit_results
          • MagresReferencer.fit_intercept
          • MagresReferencer.fit_gradient
          • MagresReferencer.fit_rsquared
          • MagresReferencer.structures_exp
          • MagresReferencer.shifts_exp
          • MagresReferencer.species
          • MagresReferencer.structures
          • MagresReferencer.warn_tolerance
          • MagresReferencer.fit_model
          • MagresReferencer.fit_results
          • MagresReferencer.fit_intercept
          • MagresReferencer.fit_gradient
          • MagresReferencer.fit_rsquared
          • MagresReferencer.structures_exp
          • MagresReferencer.shifts_exp
          • MagresReferencer.species
          • MagresReferencer.structures
          • MagresReferencer.warn_tolerance
          • MagresReferencer.match_exp_structure_shifts()
          • MagresReferencer.set_shifts_from_fit()
          • MagresReferencer.fit()
          • MagresReferencer.predict()
          • MagresReferencer.print_fit_summary()
          • MagresReferencer.plot_fit()
          • MagresReferencer.plot_fit_and_predictions()
    • matador.orm package
      • DataContainer
        • DataContainer.required_keys
        • DataContainer.root_source
        • DataContainer.provenance
        • DataContainer.source
        • DataContainer.pop()
        • DataContainer.get()
      • Subpackages
        • matador.orm.spectral package
          • VibrationalDOS
          • ElectronicDOS
          • DensityOfStates
          • VibrationalDispersion
          • ElectronicDispersion
          • Dispersion
          • Spectral
          • Submodules
          • matador.orm.spectral.dispersion module
          • matador.orm.spectral.dos module
          • matador.orm.spectral.spectral module
      • Submodules
      • matador.orm.magres module
        • MagneticResonance
      • matador.orm.orm module
        • DataContainer
          • DataContainer.required_keys
          • DataContainer.root_source
          • DataContainer.provenance
          • DataContainer.source
          • DataContainer.pop()
          • DataContainer.get()
    • matador.plotting package
      • Submodules
      • matador.plotting.battery_plotting module
        • plot_voltage_curve()
        • plot_volume_curve()
      • matador.plotting.convergence_plotting module
        • plot_cutoff_kpt_grid()
      • matador.plotting.hull_plotting module
        • plot_2d_hull()
        • plot_ternary_hull()
        • plot_ensemble_hull()
        • plot_temperature_hull()
      • matador.plotting.ir_plotting module
        • plot_ir_spectrum()
      • matador.plotting.magres_plotting module
      • matador.plotting.misc_plotting module
      • matador.plotting.pdf_plotting module
        • plot_pdf()
        • plot_projected_pdf()
        • plot_diff_overlap()
        • plot_projected_diff_overlap()
      • matador.plotting.plotting module
        • set_style()
        • plotting_function()
        • get_linear_cmap()
        • XYvsZPlot
          • XYvsZPlot.y_scale
          • XYvsZPlot.get_plot()
          • XYvsZPlot.plot()
      • matador.plotting.pxrd_plotting module
        • plot_pxrd()
      • matador.plotting.spectral_plotting module
        • plot_spectral()
        • dos_plot()
        • dispersion_plot()
      • matador.plotting.temperature_plotting module
        • plot_free_energy()
    • matador.plugins package
      • Subpackages
        • matador.plugins.qmpy_interface package
          • Submodules
          • matador.plugins.qmpy_interface.spatulate_oqmd module
        • matador.plugins.voronoi_interface package
          • Submodules
          • matador.plugins.voronoi_interface.voronoi_interface module
          • matador.plugins.voronoi_interface.voronoi_similarity module
    • matador.query package
      • Submodules
      • matador.query.query module
    • matador.scrapers package
      • res2dict()
      • cell2dict()
      • param2dict()
      • castep2dict()
      • bands2dict()
      • arbitrary2dict()
      • phonon2dict()
      • phonon_dos2dict()
      • optados2dict()
      • usp2dict()
      • pwout2dict()
      • magres2dict()
      • cif2dict()
      • Submodules
      • matador.scrapers.castep_scrapers module
        • res2dict()
        • cell2dict()
        • param2dict()
        • castep2dict()
        • bands2dict()
        • arbitrary2dict()
        • optados2dict()
        • phonon2dict()
        • phonon_dos2dict()
        • usp2dict()
        • get_seed_metadata()
      • matador.scrapers.cif_scraper module
        • cif2dict()
      • matador.scrapers.magres_scrapers module
        • magres2dict()
      • matador.scrapers.qe_scrapers module
        • pwout2dict()
      • matador.scrapers.utils module
        • get_flines_extension_agnostic()
        • scraper_function()
        • f90_float_parse()
        • DFTError
        • ComputationError
    • matador.swaps package
      • AtomicSwapper
        • AtomicSwapper.parse_swaps()
        • AtomicSwapper.construct_swap_options()
        • AtomicSwapper.atomic_swaps()
      • Submodules
      • matador.swaps.swaps module
        • AtomicSwapper
          • AtomicSwapper.parse_swaps()
          • AtomicSwapper.construct_swap_options()
          • AtomicSwapper.atomic_swaps()
    • matador.utils package
      • Submodules
      • matador.utils.ase_utils module
        • ase2dict()
        • doc2ase()
      • matador.utils.castep_help_utils module
        • scrape_castep_params()
        • update_castep_param_list()
      • matador.utils.castep_params module
      • matador.utils.cell_utils module
        • abc2cart()
        • cart2abcstar()
        • cart2volume()
        • cart2abc()
        • frac2cart()
        • wrap_frac_coords()
        • switch_coords()
        • cart2frac()
        • real2recip()
        • calc_mp_grid()
        • shift_to_include_gamma()
        • shift_to_exclude_gamma()
        • get_best_mp_offset_for_cell()
        • calc_mp_spacing()
        • get_seekpath_kpoint_path()
        • doc2spg()
        • get_space_group_label_latex()
        • standardize_doc_cell()
        • get_spacegroup_spg()
        • get_compatible_spacegroups()
        • add_noise()
        • calc_pairwise_distances_pbc()
        • create_simple_supercell()
        • create_supercell_with_minimum_side_length()
      • matador.utils.chem_utils module
        • get_iupac_ordered_elements()
        • get_periodic_table()
        • get_molar_mass()
        • get_atomic_number()
        • get_atomic_symbol()
        • get_concentration()
        • get_subscripted_formula()
        • get_subscripted_formula_tex()
        • get_num_intercalated()
        • get_binary_grav_capacities()
        • get_generic_grav_capacity()
        • get_binary_volumetric_capacity()
        • get_atoms_per_fu()
        • get_formation_energy()
        • get_number_of_chempots()
        • get_stoich()
        • get_padded_composition()
        • get_ratios_from_stoichiometry()
        • get_stoich_from_formula()
        • parse_element_string()
        • get_root_source()
        • get_formula_from_stoich()
        • magres_reference_shifts()
      • matador.utils.cursor_utils module
      • matador.utils.db_utils module
      • matador.utils.errors module
        • CalculationError
        • MaxMemoryEstimateExceeded
        • CriticalError
        • InputError
        • WalltimeError
        • NodeCollisionError
      • matador.utils.hull_utils module
        • vertices2plane()
        • vertices2line()
        • is_point_in_triangle()
        • barycentric2cart()
        • FakeHull
      • matador.utils.optimade_utils module
        • optimade2dict_from_url()
        • optimade2dict()
      • matador.utils.pmg_utils module
        • get_chemsys()
        • doc2pmg()
        • pmg2dict()
        • mp2dict()
      • matador.utils.print_utils module
        • print_warning()
        • print_failure()
        • print_success()
        • print_notify()
        • dumps()
        • NumpyEncoder
          • NumpyEncoder.default()
      • matador.utils.viz_utils module
        • viz()
        • get_element_colours()
        • get_element_radii()
        • nb_viz()
        • fresnel_view()
        • rerender_scenes_to_axes()
        • fit_orthographic_camera()
        • get_image_atoms_near_cell_boundaries()
        • fresnel_plot()
        • formula_to_colour()
        • colour_from_ternary_concentration()
    • matador.workflows package
      • Workflow
        • Workflow.computer
        • Workflow.calc_doc
        • Workflow.seed
        • Workflow.label
        • Workflow.success
        • Workflow.steps
        • Workflow.preprocess()
        • Workflow.postprocess()
        • Workflow.add_step()
        • Workflow.run_steps()
      • WorkflowStep
        • WorkflowStep.function
        • WorkflowStep.name
        • WorkflowStep.compute_dir
        • WorkflowStep.func_kwargs
        • WorkflowStep.input_exts
        • WorkflowStep.output_exts
        • WorkflowStep.success
        • WorkflowStep.cache_files()
        • WorkflowStep.run_step()
      • Subpackages
        • matador.workflows.castep package
          • castep_full_phonon()
          • castep_full_spectral()
          • castep_elastic()
          • castep_full_magres()
          • Submodules
          • matador.workflows.castep.common module
          • matador.workflows.castep.elastic module
          • matador.workflows.castep.magres module
          • matador.workflows.castep.phonons module
          • matador.workflows.castep.spectral module
      • Submodules
      • matador.workflows.workflows module
        • Workflow
          • Workflow.computer
          • Workflow.calc_doc
          • Workflow.seed
          • Workflow.label
          • Workflow.success
          • Workflow.steps
          • Workflow.preprocess()
          • Workflow.postprocess()
          • Workflow.add_step()
          • Workflow.run_steps()
        • WorkflowStep
          • WorkflowStep.function
          • WorkflowStep.name
          • WorkflowStep.compute_dir
          • WorkflowStep.func_kwargs
          • WorkflowStep.input_exts
          • WorkflowStep.output_exts
          • WorkflowStep.success
          • WorkflowStep.cache_files()
          • WorkflowStep.run_step()