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
        • MatadorCommandLine
          • MatadorCommandLine.print_report()
          • MatadorCommandLine.stats()
        • main()
      • matador.cli.dispersion module
        • main()
      • matador.cli.run3 module
        • main()
    • matador.compute package
      • ComputeTask
        • ComputeTask.begin()
        • ComputeTask.run_castep()
        • ComputeTask.run_generic()
        • ComputeTask.run_castep_relaxation()
        • ComputeTask.run_castep_singleshot()
        • ComputeTask.validate_calc_doc()
        • ComputeTask.get_seekpath_compliant_input()
        • ComputeTask.run_convergence_tests()
        • ComputeTask.parse_executable()
        • ComputeTask.test_exec()
        • ComputeTask.mpi_library
        • ComputeTask.set_mpi_library()
        • ComputeTask.detect_mpi()
        • ComputeTask.do_memcheck()
        • ComputeTask.run_command()
        • ComputeTask.mv_to_bad()
        • ComputeTask.mv_to_completed()
        • ComputeTask.cp_to_input()
        • ComputeTask.tidy_up()
        • ComputeTask.remove_compute_dir_if_finished()
        • ComputeTask.scf()
        • ComputeTask.relax()
      • ComputeTask.self.final_result
      • BatchRun
        • BatchRun.spawn()
        • BatchRun.perform_new_calculations()
        • BatchRun.generic_setup()
        • BatchRun.castep_setup()
        • BatchRun.convergence_run_setup()
      • reset_job_folder()
      • Submodules
      • matador.compute.batch module
        • BatchRun
          • BatchRun.spawn()
          • BatchRun.perform_new_calculations()
          • BatchRun.generic_setup()
          • BatchRun.castep_setup()
          • BatchRun.convergence_run_setup()
        • BundledErrors
        • reset_job_folder()
        • reset_single_seed()
      • matador.compute.compute module
        • ComputeTask
          • ComputeTask.begin()
          • ComputeTask.run_castep()
          • ComputeTask.run_generic()
          • ComputeTask.run_castep_relaxation()
          • ComputeTask.run_castep_singleshot()
          • ComputeTask.validate_calc_doc()
          • ComputeTask.get_seekpath_compliant_input()
          • ComputeTask.run_convergence_tests()
          • ComputeTask.parse_executable()
          • ComputeTask.test_exec()
          • ComputeTask.mpi_library
          • ComputeTask.set_mpi_library()
          • ComputeTask.detect_mpi()
          • ComputeTask.do_memcheck()
          • ComputeTask.run_command()
          • ComputeTask.mv_to_bad()
          • ComputeTask.mv_to_completed()
          • ComputeTask.cp_to_input()
          • ComputeTask.tidy_up()
          • ComputeTask.remove_compute_dir_if_finished()
          • ComputeTask.scf()
          • ComputeTask.relax()
        • ComputeTask.self.final_result
      • matador.compute.pbs module
        • PBSQueueManager
          • PBSQueueManager.token
          • PBSQueueManager.get_ntasks()
          • PBSQueueManager.get_max_memory()
          • PBSQueueManager.get_array_id()
          • PBSQueueManager.get_walltime()
      • matador.compute.queueing module
        • QueueManager
          • QueueManager.token
          • QueueManager.walltime
          • QueueManager.ntasks
          • QueueManager.max_memory
          • QueueManager.array_id
          • QueueManager.get_walltime()
          • QueueManager.get_max_memory()
          • QueueManager.get_array_id()
        • get_queue_env()
        • get_queue_manager()
      • matador.compute.slurm module
        • SlurmQueueManager
          • SlurmQueueManager.token
          • SlurmQueueManager.get_array_id()
          • SlurmQueueManager.get_ntasks()
          • SlurmQueueManager.get_max_memory()
          • SlurmQueueManager.get_walltime()
        • scancel_all_matching_jobs()
        • submit_slurm_script()
        • get_slurm_header()
        • write_slurm_submission_script()
    • 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
        • get_equation_of_state()
        • EquationOfState
          • EquationOfState.E_0
          • EquationOfState.V_0
          • EquationOfState.popt
          • EquationOfState.p0
          • EquationOfState.rrmsd
          • EquationOfState.fit()
          • EquationOfState.evaluate()
          • EquationOfState.residual()
          • EquationOfState.bulk_modulus
          • EquationOfState.bulk_modulus_err
          • EquationOfState.fit_parameters
        • BirchMurnaghanEulerianEOS
          • BirchMurnaghanEulerianEOS.evaluate()
          • BirchMurnaghanEulerianEOS.get_bulk_modulus()
        • PoirerTarantolaEOS
          • PoirerTarantolaEOS.evaluate()
          • PoirerTarantolaEOS.get_bulk_modulus()
        • TaitEOS
          • TaitEOS.evaluate()
          • TaitEOS.get_bulk_modulus()
        • plot_volume_curve()
      • 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
      • Spatula
      • DatabaseChanges
        • DatabaseChanges.view_changeset()
        • DatabaseChanges.print_change_summary()
      • Refiner
        • Refiner.update_docs()
        • Refiner.symmetry()
        • Refiner.elem_set()
        • Refiner.add_tag()
        • Refiner.add_doi()
        • Refiner.add_root_source()
        • Refiner.tidy_pspots()
        • Refiner.add_raw_data()
      • make_connection_to_collection()
      • Submodules
      • matador.db.changes module
        • DatabaseChanges
          • DatabaseChanges.view_changeset()
          • DatabaseChanges.print_change_summary()
      • matador.db.connect module
        • make_connection_to_collection()
        • fuzzy_collname_match()
      • matador.db.importer module
        • Spatula
      • matador.db.refine module
        • Refiner
          • Refiner.update_docs()
          • Refiner.symmetry()
          • Refiner.elem_set()
          • Refiner.add_tag()
          • Refiner.add_doi()
          • Refiner.add_root_source()
          • Refiner.tidy_pspots()
          • Refiner.add_raw_data()
    • matador.export package
      • doc2param()
      • doc2cell()
      • doc2pdb()
      • doc2pwscf()
      • doc2res()
      • doc2xsf()
      • query2files()
      • doc2arbitrary()
      • Submodules
      • matador.export.export module
        • query2files()
        • doc2param()
        • doc2cell()
        • doc2pdb()
        • doc2json()
        • doc2pwscf()
        • doc2res()
        • doc2xsf()
        • doc2arbitrary()
      • matador.export.utils module
        • file_writer_function()
        • generate_hash()
        • generate_relevant_path()
    • matador.fingerprints package
      • get_uniq_cursor()
      • Fingerprint
        • Fingerprint.fingerprint
        • Fingerprint.default_key
        • Fingerprint.calculate()
      • FingerprintFactory
        • FingerprintFactory.nprocs
        • FingerprintFactory.fingerprint
        • FingerprintFactory.default_key
      • 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()
      • 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()
      • PXRD
        • PXRD.calc_pxrd()
        • PXRD.calculate()
        • PXRD.atomic_scattering_factor()
        • PXRD.plot()
        • PXRD.save_pattern()
        • PXRD.save_peaks()
      • PXRD.self.peak_positions
      • PXRD.self.hkls
      • PXRD.self.peak_intensities
      • PXRD.self.pattern
      • PXRD.self.two_thetas
      • Submodules
      • matador.fingerprints.fingerprint module
        • Fingerprint
          • Fingerprint.fingerprint
          • Fingerprint.default_key
          • Fingerprint.calculate()
        • FingerprintFactory
          • FingerprintFactory.nprocs
          • FingerprintFactory.fingerprint
          • FingerprintFactory.default_key
      • matador.fingerprints.pdf module
        • 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
        • PXRD
          • PXRD.calc_pxrd()
          • PXRD.calculate()
          • PXRD.atomic_scattering_factor()
          • PXRD.plot()
          • PXRD.save_pattern()
          • PXRD.save_peaks()
        • PXRD.self.peak_positions
        • PXRD.self.hkls
        • PXRD.self.peak_intensities
        • PXRD.self.pattern
        • PXRD.self.two_thetas
        • PXRDFactory
          • PXRDFactory.fingerprint
          • PXRDFactory.default_key
      • matador.fingerprints.similarity module
        • get_uniq_cursor()
    • matador.hull package
      • QueryConvexHull
        • QueryConvexHull.cursor
        • QueryConvexHull.hull_cursor
        • QueryConvexHull.chempot_cursor
        • QueryConvexHull.chempots
        • QueryConvexHull.structures
        • QueryConvexHull.hull_dist
        • QueryConvexHull.species
        • QueryConvexHull.num_elements
        • QueryConvexHull.elements
        • QueryConvexHull.voltage_data
        • QueryConvexHull.volume_data
        • QueryConvexHull.create_hull()
        • QueryConvexHull.savefig
        • QueryConvexHull.savefig_ext
        • QueryConvexHull.plot_hull()
        • QueryConvexHull.plot_voltage_curve()
        • QueryConvexHull.plot_volume_curve()
        • QueryConvexHull.fake_chempots()
        • QueryConvexHull.construct_phase_diagram()
        • QueryConvexHull.set_chempots()
        • QueryConvexHull.filter_cursor_by_chempots()
        • QueryConvexHull.voltage_curve()
        • QueryConvexHull.volume_curve()
        • QueryConvexHull.print_volume_summary()
        • QueryConvexHull.get_hull_distances()
      • PhaseDiagram
        • PhaseDiagram.structures
        • PhaseDiagram.convex_hull
        • PhaseDiagram.formation_key
        • PhaseDiagram.get_hull_distances()
      • EnsembleHull
        • EnsembleHull.phase_diagrams
        • EnsembleHull.generate_stability_statistics()
        • EnsembleHull.plot_hull()
      • TemperatureDependentHull
        • TemperatureDependentHull.data_key
        • TemperatureDependentHull.energy_key
        • TemperatureDependentHull.plot_hull()
      • HullDiff
        • HullDiff.print_diff()
        • HullDiff.plot_diff()
      • diff_hulls()
      • Submodules
      • matador.hull.hull module
        • QueryConvexHull
          • QueryConvexHull.cursor
          • QueryConvexHull.hull_cursor
          • QueryConvexHull.chempot_cursor
          • QueryConvexHull.chempots
          • QueryConvexHull.structures
          • QueryConvexHull.hull_dist
          • QueryConvexHull.species
          • QueryConvexHull.num_elements
          • QueryConvexHull.elements
          • QueryConvexHull.voltage_data
          • QueryConvexHull.volume_data
          • QueryConvexHull.create_hull()
          • QueryConvexHull.savefig
          • QueryConvexHull.savefig_ext
          • QueryConvexHull.plot_hull()
          • QueryConvexHull.plot_voltage_curve()
          • QueryConvexHull.plot_volume_curve()
          • QueryConvexHull.fake_chempots()
          • QueryConvexHull.construct_phase_diagram()
          • QueryConvexHull.set_chempots()
          • QueryConvexHull.filter_cursor_by_chempots()
          • QueryConvexHull.voltage_curve()
          • QueryConvexHull.volume_curve()
          • QueryConvexHull.print_volume_summary()
          • QueryConvexHull.get_hull_distances()
      • matador.hull.hull_diff module
        • HullDiff
          • HullDiff.print_diff()
          • HullDiff.plot_diff()
        • diff_hulls()
      • matador.hull.hull_ensemble module
        • EnsembleHull
          • EnsembleHull.phase_diagrams
          • EnsembleHull.generate_stability_statistics()
          • EnsembleHull.plot_hull()
      • matador.hull.hull_temperature module
        • TemperatureDependentHull
          • TemperatureDependentHull.data_key
          • TemperatureDependentHull.energy_key
          • TemperatureDependentHull.plot_hull()
          • TemperatureDependentHull.voltage_data
      • matador.hull.phase_diagram module
        • PhaseDiagram
          • PhaseDiagram.structures
          • PhaseDiagram.convex_hull
          • PhaseDiagram.formation_key
          • PhaseDiagram.get_hull_distances()
    • 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
      • plot_spectral()
      • plot_voltage_curve()
      • plot_volume_curve()
      • plot_2d_hull()
      • plot_ternary_hull()
      • plot_ir_spectrum()
      • get_linear_cmap()
      • plot_free_energy()
      • plot_cutoff_kpt_grid()
      • plot_ensemble_hull()
      • plot_temperature_hull()
      • plot_pdf()
      • plot_projected_pdf()
      • plot_diff_overlap()
      • plot_magres()
      • plot_projected_diff_overlap()
      • plot_pxrd()
      • set_style()
      • 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
        • plot_magres()
      • matador.plotting.misc_plotting module
        • plot_relative_diffs()
      • 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
      • DBQuery
        • DBQuery.cursor
        • DBQuery.args
        • DBQuery.query_dict
        • DBQuery.calc_dict
        • DBQuery.repo
        • DBQuery.top
        • DBQuery.cursor_min_limit
        • DBQuery.cursor_min_limit
        • DBQuery.perform_query()
        • DBQuery.perform_hull_query()
        • DBQuery.perform_id_query()
        • DBQuery.query_stoichiometry()
        • DBQuery.query_composition()
        • DBQuery.query_tags()
        • DBQuery.query_quality()
      • Submodules
      • matador.query.query module
        • DBQuery
          • DBQuery.cursor
          • DBQuery.args
          • DBQuery.query_dict
          • DBQuery.calc_dict
          • DBQuery.repo
          • DBQuery.top
          • DBQuery.cursor_min_limit
          • DBQuery.cursor_min_limit
          • DBQuery.perform_query()
          • DBQuery.perform_hull_query()
          • DBQuery.perform_id_query()
          • DBQuery.query_stoichiometry()
          • DBQuery.query_composition()
          • DBQuery.query_tags()
          • DBQuery.query_quality()
        • EmptyCursor
          • EmptyCursor.count_documents()
    • 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
        • recursive_get()
        • recursive_set()
        • display_results()
        • loading_bar()
        • set_cursor_from_array()
        • get_array_from_cursor()
        • get_guess_doc_provenance()
        • filter_unique_structures()
        • filter_cursor()
        • filter_cursor_by_chempots()
        • index_cursors_by_structure()
        • compare_structures()
        • compare_structure_cursor()
      • 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()