matador
v0.10.2
Installation
Getting Started
Changelog
Tutorials and example notebooks
Command-line usage
Python API
Contributing
matador
Index
Edit on GitHub
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
A
abc2cart() (in module matador.utils.cell_utils)
active_ion (matador.battery.electrode.VoltageProfile attribute)
(matador.battery.VoltageProfile attribute)
add_doi() (matador.db.refine.Refiner method)
(matador.db.Refiner method)
add_noise() (in module matador.utils.cell_utils)
add_raw_data() (matador.db.refine.Refiner method)
(matador.db.Refiner method)
add_root_source() (matador.db.refine.Refiner method)
(matador.db.Refiner method)
add_step() (matador.workflows.Workflow method)
(matador.workflows.workflows.Workflow method)
add_tag() (matador.db.refine.Refiner method)
(matador.db.Refiner method)
angles (matador.crystal.crystal.UnitCell property)
arbitrary2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
are_graphs_the_same() (in module matador.crystal.network)
are_sites_the_same() (in module matador.plugins.voronoi_interface.voronoi_similarity)
args (matador.query.DBQuery attribute)
(matador.query.query.DBQuery attribute)
array_id (matador.compute.queueing.QueueManager property)
ase2dict() (in module matador.utils.ase_utils)
ase_atoms (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
atom_types (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
atomic_scattering_factor() (matador.fingerprints.PXRD method)
(matador.fingerprints.pxrd.PXRD method)
atomic_swaps() (matador.swaps.AtomicSwapper method)
(matador.swaps.swaps.AtomicSwapper method)
AtomicSwapper (class in matador.swaps)
(class in matador.swaps.swaps)
average_voltage (matador.battery.electrode.VoltageProfile attribute)
(matador.battery.VoltageProfile attribute)
B
band_gap (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion property)
band_gap_path_inds (matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion property)
bands2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
bands_as_dos() (matador.orm.spectral.DensityOfStates static method)
(matador.orm.spectral.dos.DensityOfStates static method)
barycentric2cart() (in module matador.utils.hull_utils)
BatchRun (class in matador.compute)
(class in matador.compute.batch)
begin() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
BirchMurnaghanEulerianEOS (class in matador.crystal.elastic)
bond_lengths (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
bonding_stats (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
bulk_modulus (matador.crystal.elastic.EquationOfState property)
bulk_modulus_err (matador.crystal.elastic.EquationOfState property)
BundledErrors
C
cache_files() (matador.workflows.workflows.WorkflowStep method)
(matador.workflows.WorkflowStep method)
calc_dict (matador.query.DBQuery attribute)
(matador.query.query.DBQuery attribute)
calc_doc (matador.workflows.castep.elastic.CastepElasticWorkflow attribute)
(matador.workflows.castep.magres.CastepMagresWorkflow attribute)
(matador.workflows.castep.phonons.CastepPhononWorkflow attribute)
(matador.workflows.castep.spectral.CastepSpectralWorkflow attribute)
(matador.workflows.Workflow attribute)
(matador.workflows.workflows.Workflow attribute)
calc_mp_grid() (in module matador.utils.cell_utils)
calc_mp_spacing() (in module matador.utils.cell_utils)
calc_pairwise_distances_pbc() (in module matador.utils.cell_utils)
calc_pdf() (matador.fingerprints.PDF method)
(matador.fingerprints.pdf.PDF method)
calc_pxrd() (matador.fingerprints.PXRD method)
(matador.fingerprints.pxrd.PXRD method)
calculate() (matador.fingerprints.Fingerprint method)
(matador.fingerprints.fingerprint.Fingerprint method)
(matador.fingerprints.PDF method)
(matador.fingerprints.pdf.PDF method)
(matador.fingerprints.PXRD method)
(matador.fingerprints.pxrd.PXRD method)
calculate_average_voltage() (matador.battery.Electrode class method)
(matador.battery.electrode.Electrode class method)
calculate_energy_density() (matador.battery.Electrode class method)
(matador.battery.electrode.Electrode class method)
calculate_pdf() (matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
calculate_pxrd() (matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
CalculationError
Calculator (class in matador.calculators.calculator)
capacities (matador.battery.electrode.VoltageProfile attribute)
(matador.battery.VoltageProfile attribute)
cart2abc() (in module matador.utils.cell_utils)
cart2abcstar() (in module matador.utils.cell_utils)
cart2frac() (in module matador.utils.cell_utils)
cart2volume() (in module matador.utils.cell_utils)
castep2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
castep_elastic() (in module matador.workflows.castep)
(in module matador.workflows.castep.elastic)
castep_elastic_prerelax() (in module matador.workflows.castep.elastic)
castep_full_magres() (in module matador.workflows.castep)
(in module matador.workflows.castep.magres)
castep_full_phonon() (in module matador.workflows.castep)
(in module matador.workflows.castep.phonons)
castep_full_spectral() (in module matador.workflows.castep)
(in module matador.workflows.castep.spectral)
castep_magres() (in module matador.workflows.castep.magres)
castep_magres_scf() (in module matador.workflows.castep.magres)
castep_phonon_dispersion() (in module matador.workflows.castep.phonons)
castep_phonon_dos() (in module matador.workflows.castep.phonons)
castep_phonon_dynmat() (in module matador.workflows.castep.phonons)
castep_phonon_prerelax() (in module matador.workflows.castep.phonons)
castep_phonon_thermodynamics() (in module matador.workflows.castep.phonons)
castep_prerelax() (in module matador.workflows.castep.common)
castep_rescaled_volume_scf() (in module matador.workflows.castep.elastic)
castep_scf() (in module matador.workflows.castep.common)
castep_setup() (matador.compute.batch.BatchRun method)
(matador.compute.BatchRun method)
castep_spectral_dispersion() (in module matador.workflows.castep.spectral)
castep_spectral_dos() (in module matador.workflows.castep.spectral)
castep_spectral_scf() (in module matador.workflows.castep.spectral)
CastepCalculator (class in matador.calculators)
(class in matador.calculators.castep)
CastepElasticWorkflow (class in matador.workflows.castep.elastic)
CastepMagresWorkflow (class in matador.workflows.castep.magres)
CastepPhononWorkflow (class in matador.workflows.castep.phonons)
CastepSpectralWorkflow (class in matador.workflows.castep.spectral)
cell (matador.crystal.Crystal attribute)
(matador.crystal.crystal.Crystal attribute)
cell2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
cell_volume (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
chempot_cursor (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
chempots (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
cif2dict() (in module matador.scrapers)
(in module matador.scrapers.cif_scraper)
cli
cluster() (in module matador.plugins.voronoi_interface.voronoi_similarity)
collect_unique_sites() (in module matador.plugins.voronoi_interface.voronoi_similarity)
colour_from_ternary_concentration() (in module matador.utils.viz_utils)
CombinedProjectedPDF (class in matador.fingerprints)
(class in matador.fingerprints.pdf)
compare_docs() (in module matador.plugins.voronoi_interface.voronoi_similarity)
compare_structure_cursor() (in module matador.utils.cursor_utils)
compare_structures() (in module matador.utils.cursor_utils)
ComputationError
compute_dir (matador.workflows.workflows.WorkflowStep attribute)
(matador.workflows.WorkflowStep attribute)
compute_free_energy() (matador.orm.spectral.dos.VibrationalDOS method)
(matador.orm.spectral.VibrationalDOS method)
computer (matador.workflows.castep.elastic.CastepElasticWorkflow attribute)
(matador.workflows.castep.magres.CastepMagresWorkflow attribute)
(matador.workflows.castep.phonons.CastepPhononWorkflow attribute)
(matador.workflows.castep.spectral.CastepSpectralWorkflow attribute)
(matador.workflows.Workflow attribute)
(matador.workflows.workflows.Workflow attribute)
ComputeTask (class in matador.compute)
(class in matador.compute.compute)
concentration (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
construct_phase_diagram() (matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
construct_swap_options() (matador.swaps.AtomicSwapper method)
(matador.swaps.swaps.AtomicSwapper method)
convergence_run_setup() (matador.compute.batch.BatchRun method)
(matador.compute.BatchRun method)
convex_hull (matador.hull.phase_diagram.PhaseDiagram attribute)
(matador.hull.PhaseDiagram attribute)
coordination (matador.crystal.crystal_site.Site property)
coordination_lists (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
coordination_stats (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
coords (matador.crystal.crystal_site.Site property)
coords_cartesian (matador.crystal.crystal_site.Site property)
count_documents() (matador.query.query.EmptyCursor static method)
cp_to_input() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
create_hull() (matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
create_simple_supercell() (in module matador.utils.cell_utils)
create_site_array() (in module matador.plugins.voronoi_interface.voronoi_similarity)
create_supercell_with_minimum_side_length() (in module matador.utils.cell_utils)
CriticalError
Crystal (class in matador.crystal)
(class in matador.crystal.crystal)
CrystalGraph (class in matador.crystal.network)
cursor (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
(matador.query.DBQuery attribute)
(matador.query.query.DBQuery attribute)
cursor_min_limit (matador.query.DBQuery attribute)
,
[1]
(matador.query.query.DBQuery attribute)
,
[1]
D
data_key (matador.hull.hull_temperature.TemperatureDependentHull attribute)
(matador.hull.TemperatureDependentHull attribute)
DatabaseChanges (class in matador.db)
(class in matador.db.changes)
DataContainer (class in matador.orm)
(class in matador.orm.orm)
DBQuery (class in matador.query)
(class in matador.query.query)
debye_freq (matador.orm.spectral.dispersion.VibrationalDispersion property)
(matador.orm.spectral.dos.VibrationalDOS property)
(matador.orm.spectral.VibrationalDispersion property)
(matador.orm.spectral.VibrationalDOS property)
debye_temperature (matador.orm.spectral.dispersion.VibrationalDispersion property)
(matador.orm.spectral.dos.VibrationalDOS property)
(matador.orm.spectral.VibrationalDispersion property)
(matador.orm.spectral.VibrationalDOS property)
default() (matador.utils.print_utils.NumpyEncoder method)
default_key (matador.fingerprints.Fingerprint attribute)
(matador.fingerprints.fingerprint.Fingerprint attribute)
(matador.fingerprints.fingerprint.FingerprintFactory attribute)
(matador.fingerprints.FingerprintFactory attribute)
(matador.fingerprints.pdf.PDFFactory attribute)
(matador.fingerprints.pxrd.PXRDFactory attribute)
DensityOfStates (class in matador.orm.spectral)
(class in matador.orm.spectral.dos)
detect_mpi() (matador.compute.compute.ComputeTask static method)
(matador.compute.ComputeTask static method)
DFTError
diff_hulls() (in module matador.hull)
(in module matador.hull.hull_diff)
Dispersion (class in matador.orm.spectral)
(class in matador.orm.spectral.dispersion)
dispersion_plot() (in module matador.plotting.spectral_plotting)
displacement_between_sites() (matador.crystal.crystal_site.Site method)
display_results() (in module matador.utils.cursor_utils)
distance_between_sites() (matador.crystal.crystal_site.Site method)
do_memcheck() (matador.calculators.calculator.Calculator method)
(matador.calculators.castep.CastepCalculator method)
(matador.calculators.CastepCalculator method)
(matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
doc2arbitrary() (in module matador.export)
(in module matador.export.export)
doc2ase() (in module matador.utils.ase_utils)
doc2cell() (in module matador.export)
(in module matador.export.export)
doc2json() (in module matador.export.export)
doc2param() (in module matador.export)
(in module matador.export.export)
doc2pdb() (in module matador.export)
(in module matador.export.export)
doc2pmg() (in module matador.utils.pmg_utils)
doc2pwscf() (in module matador.export)
(in module matador.export.export)
doc2res() (in module matador.export)
(in module matador.export.export)
doc2spg() (in module matador.utils.cell_utils)
doc2xsf() (in module matador.export)
(in module matador.export.export)
dos_plot() (in module matador.plotting.spectral_plotting)
dr (matador.fingerprints.PDF attribute)
(matador.fingerprints.pdf.PDF attribute)
draw_network() (in module matador.crystal.network)
(matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
dumps() (in module matador.utils.print_utils)
E
E_0 (matador.crystal.elastic.EquationOfState attribute)
eigs (matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.ElectronicDispersion property)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
(matador.orm.spectral.VibrationalDispersion attribute)
eigs_q (matador.orm.spectral.dispersion.VibrationalDispersion property)
(matador.orm.spectral.VibrationalDispersion property)
eigs_s_k (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion property)
Electrode (class in matador.battery)
(class in matador.battery.electrode)
ElectronicDispersion (class in matador.orm.spectral)
(class in matador.orm.spectral.dispersion)
ElectronicDOS (class in matador.orm.spectral)
(class in matador.orm.spectral.dos)
elem_gr (matador.fingerprints.PDF attribute)
(matador.fingerprints.pdf.PDF attribute)
elem_set() (matador.db.refine.Refiner method)
(matador.db.Refiner method)
elements (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
elems (matador.crystal.Crystal attribute)
(matador.crystal.crystal.Crystal attribute)
EmptyCursor (class in matador.query.query)
energy_key (matador.hull.hull_temperature.TemperatureDependentHull attribute)
(matador.hull.TemperatureDependentHull attribute)
EnsembleHull (class in matador.hull)
(class in matador.hull.hull_ensemble)
EquationOfState (class in matador.crystal.elastic)
evaluate() (matador.crystal.elastic.BirchMurnaghanEulerianEOS method)
(matador.crystal.elastic.EquationOfState method)
(matador.crystal.elastic.PoirerTarantolaEOS method)
(matador.crystal.elastic.TaitEOS method)
examples_index
F
f90_float_parse() (in module matador.scrapers.utils)
fake_chempots() (matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
FakeHull (class in matador.utils.hull_utils)
fermi_energy (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion property)
file_writer_function() (in module matador.export.utils)
filter_cursor() (in module matador.utils.cursor_utils)
filter_cursor_by_chempots() (in module matador.utils.cursor_utils)
(matador.hull.hull.QueryConvexHull static method)
(matador.hull.QueryConvexHull static method)
filter_unique_structures() (in module matador.utils.cursor_utils)
final_elec_energy_tol (matador.workflows.castep.magres.CastepMagresWorkflow attribute)
final_result (matador.compute.compute.ComputeTask.self attribute)
(matador.compute.ComputeTask.self attribute)
find_full_kpt_branch() (matador.orm.spectral.Dispersion method)
(matador.orm.spectral.dispersion.Dispersion method)
find_kpoint_branches() (matador.orm.spectral.Dispersion method)
(matador.orm.spectral.dispersion.Dispersion method)
find_site_index() (in module matador.plugins.voronoi_interface.voronoi_similarity)
fine_dr (matador.fingerprints.pdf.PDFOverlap attribute)
(matador.fingerprints.PDFOverlap attribute)
Fingerprint (class in matador.fingerprints)
(class in matador.fingerprints.fingerprint)
fingerprint (matador.fingerprints.Fingerprint attribute)
(matador.fingerprints.fingerprint.Fingerprint attribute)
(matador.fingerprints.fingerprint.FingerprintFactory attribute)
(matador.fingerprints.FingerprintFactory attribute)
(matador.fingerprints.pdf.PDFFactory attribute)
(matador.fingerprints.pxrd.PXRDFactory attribute)
FingerprintFactory (class in matador.fingerprints)
(class in matador.fingerprints.fingerprint)
fit() (matador.crystal.elastic.EquationOfState method)
(matador.magres.MagresReferencer method)
(matador.magres.referencer.MagresReferencer method)
fit_gradient (matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
fit_intercept (matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
fit_model (matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
fit_orthographic_camera() (in module matador.utils.viz_utils)
fit_parameters (matador.crystal.elastic.EquationOfState property)
fit_results (matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
fit_rsquared (matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
formation_key (matador.hull.phase_diagram.PhaseDiagram attribute)
(matador.hull.PhaseDiagram attribute)
formula (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
formula_tex (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
formula_to_colour() (in module matador.utils.viz_utils)
formula_unicode (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
frac2cart() (in module matador.utils.cell_utils)
freq_unit (matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.VibrationalDispersion attribute)
fresnel_plot() (in module matador.utils.viz_utils)
fresnel_view() (in module matador.utils.viz_utils)
from_ase() (matador.crystal.Crystal class method)
(matador.crystal.crystal.Crystal class method)
from_pmg() (matador.crystal.Crystal class method)
(matador.crystal.crystal.Crystal class method)
func_kwargs (matador.workflows.workflows.WorkflowStep attribute)
(matador.workflows.WorkflowStep attribute)
function (matador.workflows.workflows.WorkflowStep attribute)
(matador.workflows.WorkflowStep attribute)
fuzzy_collname_match() (in module matador.db.connect)
G
gaussian_width (matador.orm.spectral.dos.ElectronicDOS attribute)
(matador.orm.spectral.dos.VibrationalDOS attribute)
(matador.orm.spectral.ElectronicDOS attribute)
(matador.orm.spectral.VibrationalDOS attribute)
generate_hash() (in module matador.export.utils)
generate_relevant_path() (in module matador.export.utils)
generate_stability_statistics() (matador.hull.EnsembleHull method)
(matador.hull.hull_ensemble.EnsembleHull method)
generic_setup() (matador.compute.batch.BatchRun method)
(matador.compute.BatchRun method)
get() (matador.config.settings.Settings method)
(matador.crystal.crystal_site.Site method)
(matador.orm.DataContainer method)
(matador.orm.orm.DataContainer method)
get_array_from_cursor() (in module matador.utils.cursor_utils)
get_array_id() (matador.compute.pbs.PBSQueueManager method)
(matador.compute.queueing.QueueManager method)
(matador.compute.slurm.SlurmQueueManager method)
get_atomic_number() (in module matador.utils.chem_utils)
get_atomic_symbol() (in module matador.utils.chem_utils)
get_atoms_per_fu() (in module matador.utils.chem_utils)
get_band_reordering() (matador.orm.spectral.Dispersion static method)
(matador.orm.spectral.dispersion.Dispersion static method)
get_best_mp_offset_for_cell() (in module matador.utils.cell_utils)
get_binary_grav_capacities() (in module matador.utils.chem_utils)
get_binary_volumetric_capacity() (in module matador.utils.chem_utils)
get_bonds_per_atom() (matador.crystal.network.CrystalGraph method)
get_bulk_modulus() (matador.crystal.elastic.BirchMurnaghanEulerianEOS method)
(matador.crystal.elastic.PoirerTarantolaEOS method)
(matador.crystal.elastic.TaitEOS method)
get_chemsys() (in module matador.utils.pmg_utils)
get_communities() (matador.crystal.network.CrystalGraph method)
get_compatible_spacegroups() (in module matador.utils.cell_utils)
get_concentration() (in module matador.utils.chem_utils)
(matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
get_element_colours() (in module matador.utils.viz_utils)
get_element_radii() (in module matador.utils.viz_utils)
get_equation_of_state() (in module matador.crystal.elastic)
get_flines_extension_agnostic() (in module matador.scrapers.utils)
get_formation_energy() (in module matador.utils.chem_utils)
get_formula_from_stoich() (in module matador.utils.chem_utils)
get_generic_grav_capacity() (in module matador.utils.chem_utils)
get_guess_doc_provenance() (in module matador.utils.cursor_utils)
get_hull_distances() (matador.hull.hull.QueryConvexHull method)
(matador.hull.phase_diagram.PhaseDiagram method)
(matador.hull.PhaseDiagram method)
(matador.hull.QueryConvexHull method)
get_image_atoms_near_cell_boundaries() (in module matador.utils.viz_utils)
get_iupac_ordered_elements() (in module matador.utils.chem_utils)
get_linear_cmap() (in module matador.plotting)
(in module matador.plotting.plotting)
get_max_coordination_of_elem() (in module matador.plugins.voronoi_interface.voronoi_similarity)
get_max_memory() (matador.compute.pbs.PBSQueueManager method)
(matador.compute.queueing.QueueManager method)
(matador.compute.slurm.SlurmQueueManager method)
get_molar_mass() (in module matador.utils.chem_utils)
get_ntasks() (matador.compute.pbs.PBSQueueManager method)
(matador.compute.slurm.SlurmQueueManager method)
get_num_intercalated() (in module matador.utils.chem_utils)
get_number_of_chempots() (in module matador.utils.chem_utils)
get_padded_composition() (in module matador.utils.chem_utils)
get_periodic_table() (in module matador.utils.chem_utils)
get_plot() (matador.plotting.plotting.XYvsZPlot method)
get_queue_env() (in module matador.compute.queueing)
get_queue_manager() (in module matador.compute.queueing)
get_ratios_from_stoichiometry() (in module matador.utils.chem_utils)
get_root_source() (in module matador.utils.chem_utils)
get_seed_metadata() (in module matador.scrapers.castep_scrapers)
get_seekpath_compliant_input() (matador.compute.compute.ComputeTask static method)
(matador.compute.ComputeTask static method)
get_seekpath_kpoint_path() (in module matador.utils.cell_utils)
get_sim_distance() (matador.fingerprints.PDF method)
(matador.fingerprints.pdf.PDF method)
get_slurm_header() (in module matador.compute.slurm)
get_space_group() (matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
get_space_group_label_latex() (in module matador.utils.cell_utils)
get_spacegroup_spg() (in module matador.utils.cell_utils)
get_stoich() (in module matador.utils.chem_utils)
get_stoich_from_formula() (in module matador.utils.chem_utils)
get_strongly_connected_component_subgraphs() (matador.crystal.network.CrystalGraph method)
get_subscripted_formula() (in module matador.utils.chem_utils)
get_subscripted_formula_tex() (in module matador.utils.chem_utils)
get_uniq_cursor() (in module matador.fingerprints)
(in module matador.fingerprints.similarity)
get_unique_sites() (in module matador.plugins.voronoi_interface.voronoi_similarity)
get_unique_subgraphs() (in module matador.crystal.network)
get_voronoi_points() (in module matador.plugins.voronoi_interface.voronoi_interface)
get_voronoi_substructure() (in module matador.plugins.voronoi_interface.voronoi_interface)
get_walltime() (matador.compute.pbs.PBSQueueManager method)
(matador.compute.queueing.QueueManager method)
(matador.compute.slurm.SlurmQueueManager method)
gr (matador.fingerprints.PDF attribute)
(matador.fingerprints.pdf.PDF attribute)
H
hkls (matador.fingerprints.pxrd.PXRD.self attribute)
(matador.fingerprints.PXRD.self attribute)
hull_cursor (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
hull_dist (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
HullDiff (class in matador.hull)
(class in matador.hull.hull_diff)
I
index_cursors_by_structure() (in module matador.utils.cursor_utils)
input_exts (matador.workflows.workflows.WorkflowStep attribute)
(matador.workflows.WorkflowStep attribute)
InputError
ion (matador.battery.Electrode attribute)
(matador.battery.electrode.Electrode attribute)
is_point_in_triangle() (in module matador.utils.hull_utils)
K
kind (matador.battery.Electrode attribute)
(matador.battery.electrode.Electrode attribute)
kpoint_branch_start (matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
kpoint_branches (matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
kpoint_path (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
(matador.orm.spectral.VibrationalDispersion attribute)
kpoint_path_cartesian (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
(matador.orm.spectral.VibrationalDispersion attribute)
kpoint_path_spacing (matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
kpoint_weights (matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
kwargs (matador.fingerprints.PDF attribute)
(matador.fingerprints.pdf.PDF attribute)
L
label (matador.fingerprints.PDF attribute)
(matador.fingerprints.pdf.PDF attribute)
(matador.workflows.Workflow attribute)
(matador.workflows.workflows.Workflow attribute)
lattice (matador.crystal.crystal_site.Site property)
lattice_abc (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
(matador.crystal.crystal.UnitCell property)
lattice_cart (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
(matador.crystal.crystal.UnitCell property)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
lengths (matador.crystal.crystal.UnitCell property)
linearise_path() (matador.orm.spectral.Dispersion method)
(matador.orm.spectral.dispersion.Dispersion method)
load_custom_settings() (in module matador.config)
(in module matador.config.config)
load_scattering_file() (in module matador.data.atomic_scattering.atomic_scattering_loaders)
loading_bar() (in module matador.utils.cursor_utils)
M
MagneticResonance (class in matador.orm.magres)
magres2dict() (in module matador.scrapers)
(in module matador.scrapers.magres_scrapers)
magres_reference_shifts() (in module matador.utils.chem_utils)
MagresReferencer (class in matador.magres)
(class in matador.magres.referencer)
main() (in module matador.cli.cli)
(in module matador.cli.dispersion)
(in module matador.cli.run3)
make_connection_to_collection() (in module matador.db)
(in module matador.db.connect)
matador
module
matador.battery
module
matador.battery.electrode
module
matador.calculators
module
matador.calculators.calculator
module
matador.calculators.castep
module
matador.cli
module
matador.cli.cli
module
matador.cli.dispersion
module
matador.cli.run3
module
matador.compute
module
matador.compute.batch
module
matador.compute.compute
module
matador.compute.pbs
module
matador.compute.queueing
module
matador.compute.slurm
module
matador.config
module
matador.config.config
module
matador.config.quickstart
module
matador.config.settings
module
matador.crystal
module
matador.crystal.crystal
module
matador.crystal.crystal_site
module
matador.crystal.elastic
module
matador.crystal.network
module
matador.data
module
matador.data.atomic_scattering
module
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.constants
module
matador.data.magres
module
matador.data.magres.electric_quadrupole_moments
module
matador.data.periodic_table
module
matador.db
module
matador.db.changes
module
matador.db.connect
module
matador.db.importer
module
matador.db.refine
module
matador.export
module
matador.export.export
module
matador.export.utils
module
matador.fingerprints
module
matador.fingerprints.fingerprint
module
matador.fingerprints.pdf
module
matador.fingerprints.pxrd
module
matador.fingerprints.similarity
module
matador.hull
module
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
module
matador.magres.referencer
module
matador.orm
module
matador.orm.magres
module
matador.orm.orm
module
matador.orm.spectral
module
matador.orm.spectral.dispersion
module
matador.orm.spectral.dos
module
matador.orm.spectral.spectral
module
matador.plotting
module
matador.plotting.battery_plotting
module
matador.plotting.convergence_plotting
module
matador.plotting.hull_plotting
module
matador.plotting.ir_plotting
module
matador.plotting.magres_plotting
module
matador.plotting.misc_plotting
module
matador.plotting.pdf_plotting
module
matador.plotting.plotting
module
matador.plotting.pxrd_plotting
module
matador.plotting.spectral_plotting
module
matador.plotting.temperature_plotting
module
matador.plugins
module
matador.plugins.qmpy_interface
module
matador.plugins.voronoi_interface
module
matador.plugins.voronoi_interface.voronoi_interface
module
matador.plugins.voronoi_interface.voronoi_similarity
module
matador.query
module
matador.query.query
module
matador.scrapers
module
matador.scrapers.castep_scrapers
module
matador.scrapers.cif_scraper
module
matador.scrapers.magres_scrapers
module
matador.scrapers.qe_scrapers
module
matador.scrapers.utils
module
matador.swaps
module
matador.swaps.swaps
module
matador.utils
module
matador.utils.ase_utils
module
matador.utils.castep_help_utils
module
matador.utils.castep_params
module
matador.utils.cell_utils
module
matador.utils.chem_utils
module
matador.utils.cursor_utils
module
matador.utils.db_utils
module
matador.utils.errors
module
matador.utils.hull_utils
module
matador.utils.optimade_utils
module
matador.utils.pmg_utils
module
matador.utils.print_utils
module
matador.utils.viz_utils
module
matador.workflows
module
matador.workflows.castep
module
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
matador.workflows.workflows
module
MatadorCommandLine (class in matador.cli.cli)
match_exp_structure_shifts() (matador.magres.MagresReferencer method)
(matador.magres.referencer.MagresReferencer method)
max_memory (matador.compute.queueing.QueueManager property)
MaxMemoryEstimateExceeded
module
matador
matador.battery
matador.battery.electrode
matador.calculators
matador.calculators.calculator
matador.calculators.castep
matador.cli
matador.cli.cli
matador.cli.dispersion
matador.cli.run3
matador.compute
matador.compute.batch
matador.compute.compute
matador.compute.pbs
matador.compute.queueing
matador.compute.slurm
matador.config
matador.config.config
matador.config.quickstart
matador.config.settings
matador.crystal
matador.crystal.crystal
matador.crystal.crystal_site
matador.crystal.elastic
matador.crystal.network
matador.data
matador.data.atomic_scattering
matador.data.atomic_scattering.atomic_scattering_factors_gsas
matador.data.atomic_scattering.atomic_scattering_factors_raspa
matador.data.atomic_scattering.atomic_scattering_loaders
matador.data.constants
matador.data.magres
matador.data.magres.electric_quadrupole_moments
matador.data.periodic_table
matador.db
matador.db.changes
matador.db.connect
matador.db.importer
matador.db.refine
matador.export
matador.export.export
matador.export.utils
matador.fingerprints
matador.fingerprints.fingerprint
matador.fingerprints.pdf
matador.fingerprints.pxrd
matador.fingerprints.similarity
matador.hull
matador.hull.hull
matador.hull.hull_diff
matador.hull.hull_ensemble
matador.hull.hull_temperature
matador.hull.phase_diagram
matador.magres
matador.magres.referencer
matador.orm
matador.orm.magres
matador.orm.orm
matador.orm.spectral
matador.orm.spectral.dispersion
matador.orm.spectral.dos
matador.orm.spectral.spectral
matador.plotting
matador.plotting.battery_plotting
matador.plotting.convergence_plotting
matador.plotting.hull_plotting
matador.plotting.ir_plotting
matador.plotting.magres_plotting
matador.plotting.misc_plotting
matador.plotting.pdf_plotting
matador.plotting.plotting
matador.plotting.pxrd_plotting
matador.plotting.spectral_plotting
matador.plotting.temperature_plotting
matador.plugins
matador.plugins.qmpy_interface
matador.plugins.voronoi_interface
matador.plugins.voronoi_interface.voronoi_interface
matador.plugins.voronoi_interface.voronoi_similarity
matador.query
matador.query.query
matador.scrapers
matador.scrapers.castep_scrapers
matador.scrapers.cif_scraper
matador.scrapers.magres_scrapers
matador.scrapers.qe_scrapers
matador.scrapers.utils
matador.swaps
matador.swaps.swaps
matador.utils
matador.utils.ase_utils
matador.utils.castep_help_utils
matador.utils.castep_params
matador.utils.cell_utils
matador.utils.chem_utils
matador.utils.cursor_utils
matador.utils.db_utils
matador.utils.errors
matador.utils.hull_utils
matador.utils.optimade_utils
matador.utils.pmg_utils
matador.utils.print_utils
matador.utils.viz_utils
matador.workflows
matador.workflows.castep
matador.workflows.castep.common
matador.workflows.castep.elastic
matador.workflows.castep.magres
matador.workflows.castep.phonons
matador.workflows.castep.spectral
matador.workflows.workflows
mongo
mp2dict() (in module matador.utils.pmg_utils)
mpi_library (matador.compute.compute.ComputeTask property)
(matador.compute.ComputeTask property)
mv_to_bad() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
mv_to_completed() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
N
name (matador.workflows.workflows.WorkflowStep attribute)
(matador.workflows.WorkflowStep attribute)
nb_viz() (in module matador.utils.viz_utils)
network (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
network_stats (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
new_from_trimmed_path() (matador.orm.spectral.dispersion.ElectronicDispersion method)
(matador.orm.spectral.ElectronicDispersion method)
node_match() (in module matador.crystal.network)
NodeCollisionError
nprocs (matador.fingerprints.fingerprint.FingerprintFactory attribute)
(matador.fingerprints.FingerprintFactory attribute)
(matador.fingerprints.pdf.PDFFactory attribute)
ntasks (matador.compute.queueing.QueueManager property)
num_atoms (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
(matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.dispersion.VibrationalDispersion property)
(matador.orm.spectral.VibrationalDispersion attribute)
(matador.orm.spectral.VibrationalDispersion property)
num_bands (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.VibrationalDispersion property)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
(matador.orm.spectral.VibrationalDispersion property)
num_electrons (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion property)
num_elements (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
(matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
num_fu (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
num_kpoints (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
(matador.orm.spectral.VibrationalDispersion attribute)
num_modes (matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.dispersion.VibrationalDispersion property)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
(matador.orm.spectral.VibrationalDispersion attribute)
(matador.orm.spectral.VibrationalDispersion property)
num_projectors (matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
num_qpoints (matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
num_spins (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion property)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
number_density (matador.fingerprints.PDF attribute)
(matador.fingerprints.pdf.PDF attribute)
NumpyEncoder (class in matador.utils.print_utils)
O
occupancy (matador.crystal.crystal_site.Site property)
optados2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
optados_dos_broadening() (in module matador.workflows.castep.spectral)
optados_pdispersion() (in module matador.workflows.castep.spectral)
optados_pdos() (in module matador.workflows.castep.spectral)
optimade2dict() (in module matador.utils.optimade_utils)
optimade2dict_from_url() (in module matador.utils.optimade_utils)
output_exts (matador.workflows.workflows.WorkflowStep attribute)
(matador.workflows.WorkflowStep attribute)
overlap_int (matador.fingerprints.pdf.PDFOverlap attribute)
(matador.fingerprints.PDFOverlap attribute)
P
p0 (matador.crystal.elastic.EquationOfState attribute)
param2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
parse_element_string() (in module matador.utils.chem_utils)
parse_executable() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
parse_swaps() (matador.swaps.AtomicSwapper method)
(matador.swaps.swaps.AtomicSwapper method)
pattern (matador.fingerprints.pxrd.PXRD.self attribute)
(matador.fingerprints.PXRD.self attribute)
PBSQueueManager (class in matador.compute.pbs)
PDF (class in matador.fingerprints)
(class in matador.fingerprints.pdf)
pdf (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
pdf() (matador.fingerprints.PDF method)
(matador.fingerprints.pdf.PDF method)
pdf_a (matador.fingerprints.pdf.PDFOverlap attribute)
(matador.fingerprints.PDFOverlap attribute)
pdf_b (matador.fingerprints.pdf.PDFOverlap attribute)
(matador.fingerprints.PDFOverlap attribute)
pdf_overlap() (matador.fingerprints.pdf.PDFOverlap method)
(matador.fingerprints.PDFOverlap method)
PDFFactory (class in matador.fingerprints.pdf)
PDFOverlap (class in matador.fingerprints)
(class in matador.fingerprints.pdf)
peak_intensities (matador.fingerprints.pxrd.PXRD.self attribute)
(matador.fingerprints.PXRD.self attribute)
peak_positions (matador.fingerprints.pxrd.PXRD.self attribute)
(matador.fingerprints.PXRD.self attribute)
perform_hull_query() (matador.query.DBQuery method)
(matador.query.query.DBQuery method)
perform_id_query() (matador.query.DBQuery method)
(matador.query.query.DBQuery method)
perform_new_calculations() (matador.compute.batch.BatchRun method)
(matador.compute.BatchRun method)
perform_query() (matador.query.DBQuery method)
(matador.query.query.DBQuery method)
phase_diagrams (matador.hull.EnsembleHull attribute)
(matador.hull.hull_ensemble.EnsembleHull attribute)
PhaseDiagram (class in matador.hull)
(class in matador.hull.phase_diagram)
phonon2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
phonon_dos2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
plot() (matador.fingerprints.PDF method)
(matador.fingerprints.pdf.PDF method)
(matador.fingerprints.PXRD method)
(matador.fingerprints.pxrd.PXRD method)
(matador.plotting.plotting.XYvsZPlot method)
plot_2d_hull() (in module matador.plotting)
(in module matador.plotting.hull_plotting)
plot_class_hull() (in module matador.plugins.voronoi_interface.voronoi_similarity)
plot_cutoff_kpt_grid() (in module matador.plotting)
(in module matador.plotting.convergence_plotting)
plot_diff() (matador.fingerprints.pdf.PDFOverlap method)
(matador.fingerprints.PDFOverlap method)
(matador.hull.hull_diff.HullDiff method)
(matador.hull.HullDiff method)
plot_diff_overlap() (in module matador.plotting)
(in module matador.plotting.pdf_plotting)
plot_dispersion() (matador.orm.spectral.Dispersion method)
(matador.orm.spectral.dispersion.Dispersion method)
plot_dos() (matador.orm.spectral.DensityOfStates method)
(matador.orm.spectral.dos.DensityOfStates method)
plot_ensemble_hull() (in module matador.plotting)
(in module matador.plotting.hull_plotting)
plot_fit() (matador.magres.MagresReferencer method)
(matador.magres.referencer.MagresReferencer method)
plot_fit_and_predictions() (matador.magres.MagresReferencer method)
(matador.magres.referencer.MagresReferencer method)
plot_free_energy() (in module matador.plotting)
(in module matador.plotting.temperature_plotting)
(matador.orm.spectral.dos.VibrationalDOS method)
(matador.orm.spectral.VibrationalDOS method)
plot_hull() (matador.hull.EnsembleHull method)
(matador.hull.hull.QueryConvexHull method)
(matador.hull.hull_ensemble.EnsembleHull method)
(matador.hull.hull_temperature.TemperatureDependentHull method)
(matador.hull.QueryConvexHull method)
(matador.hull.TemperatureDependentHull method)
plot_ir_spectrum() (in module matador.plotting)
(in module matador.plotting.ir_plotting)
plot_magres() (in module matador.plotting)
(in module matador.plotting.magres_plotting)
plot_pdf() (in module matador.plotting)
(in module matador.plotting.pdf_plotting)
plot_projected_diff() (matador.fingerprints.pdf.PDFOverlap method)
(matador.fingerprints.PDFOverlap method)
plot_projected_diff_overlap() (in module matador.plotting)
(in module matador.plotting.pdf_plotting)
plot_projected_pdf() (in module matador.plotting)
(in module matador.plotting.pdf_plotting)
(matador.fingerprints.CombinedProjectedPDF method)
(matador.fingerprints.PDF method)
(matador.fingerprints.pdf.CombinedProjectedPDF method)
(matador.fingerprints.pdf.PDF method)
plot_pxrd() (in module matador.plotting)
(in module matador.plotting.pxrd_plotting)
plot_relative_diffs() (in module matador.plotting.misc_plotting)
plot_spectral() (in module matador.plotting)
(in module matador.plotting.spectral_plotting)
plot_temperature_hull() (in module matador.plotting)
(in module matador.plotting.hull_plotting)
plot_ternary_hull() (in module matador.plotting)
(in module matador.plotting.hull_plotting)
plot_voltage_curve() (in module matador.plotting)
(in module matador.plotting.battery_plotting)
(matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
plot_volume_curve() (in module matador.crystal.elastic)
(in module matador.plotting)
(in module matador.plotting.battery_plotting)
(matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
plotting_function() (in module matador.plotting.plotting)
pmg2dict() (in module matador.utils.pmg_utils)
pmg_structure (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
PoirerTarantolaEOS (class in matador.crystal.elastic)
pop() (matador.orm.DataContainer method)
(matador.orm.orm.DataContainer method)
popt (matador.crystal.elastic.EquationOfState attribute)
positions_abs (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
positions_frac (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
postprocess() (matador.workflows.castep.elastic.CastepElasticWorkflow method)
(matador.workflows.Workflow method)
(matador.workflows.workflows.Workflow method)
predict() (matador.magres.MagresReferencer method)
(matador.magres.referencer.MagresReferencer method)
preprocess() (matador.workflows.castep.elastic.CastepElasticWorkflow method)
(matador.workflows.castep.magres.CastepMagresWorkflow method)
(matador.workflows.castep.phonons.CastepPhononWorkflow method)
(matador.workflows.castep.spectral.CastepSpectralWorkflow method)
(matador.workflows.Workflow method)
(matador.workflows.workflows.Workflow method)
print_change_summary() (matador.db.changes.DatabaseChanges static method)
(matador.db.DatabaseChanges static method)
print_diff() (matador.hull.hull_diff.HullDiff method)
(matador.hull.HullDiff method)
print_failure() (in module matador.utils.print_utils)
print_fit_summary() (matador.magres.MagresReferencer method)
(matador.magres.referencer.MagresReferencer method)
print_notify() (in module matador.utils.print_utils)
print_report() (matador.cli.cli.MatadorCommandLine method)
print_sites() (matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
print_success() (in module matador.utils.print_utils)
print_volume_summary() (matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
print_warning() (in module matador.utils.print_utils)
projected_pdf_overlap() (matador.fingerprints.pdf.PDFOverlap method)
(matador.fingerprints.PDFOverlap method)
projector_weights (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
projectors (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
provenance (matador.orm.DataContainer property)
(matador.orm.orm.DataContainer property)
pwout2dict() (in module matador.scrapers)
(in module matador.scrapers.qe_scrapers)
PXRD (class in matador.fingerprints)
(class in matador.fingerprints.pxrd)
pxrd (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
PXRDFactory (class in matador.fingerprints.pxrd)
Q
query2files() (in module matador.export)
(in module matador.export.export)
query_composition() (matador.query.DBQuery method)
(matador.query.query.DBQuery method)
query_dict (matador.query.DBQuery attribute)
(matador.query.query.DBQuery attribute)
query_quality() (matador.query.DBQuery method)
(matador.query.query.DBQuery method)
query_stoichiometry() (matador.query.DBQuery method)
(matador.query.query.DBQuery method)
query_tags() (matador.query.DBQuery method)
(matador.query.query.DBQuery method)
QueryConvexHull (class in matador.hull)
(class in matador.hull.hull)
QueueManager (class in matador.compute.queueing)
quickstart_settings() (in module matador.config.quickstart)
R
r_space (matador.fingerprints.PDF attribute)
(matador.fingerprints.pdf.PDF attribute)
reactions (matador.battery.electrode.VoltageProfile attribute)
(matador.battery.VoltageProfile attribute)
real2recip() (in module matador.utils.cell_utils)
recip_lattice_cart (matador.crystal.crystal.UnitCell property)
recursive_get() (in module matador.utils.cursor_utils)
recursive_set() (in module matador.utils.cursor_utils)
Refiner (class in matador.db)
(class in matador.db.refine)
relax() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
remove_compute_dir_if_finished() (matador.compute.compute.ComputeTask static method)
(matador.compute.ComputeTask static method)
remove_directionality() (matador.crystal.network.CrystalGraph method)
reorder_bands() (matador.orm.spectral.Dispersion method)
(matador.orm.spectral.dispersion.Dispersion method)
repo (matador.query.DBQuery attribute)
(matador.query.query.DBQuery attribute)
required_keys (matador.orm.DataContainer attribute)
(matador.orm.orm.DataContainer attribute)
(matador.orm.spectral.DensityOfStates attribute)
(matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.dos.DensityOfStates attribute)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.VibrationalDispersion attribute)
rerender_scenes_to_axes() (in module matador.utils.viz_utils)
res2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
reset() (matador.config.settings.Settings method)
reset_job_folder() (in module matador.compute)
(in module matador.compute.batch)
reset_single_seed() (in module matador.compute.batch)
residual() (matador.crystal.elastic.EquationOfState method)
rmax (matador.fingerprints.PDF attribute)
(matador.fingerprints.pdf.PDF attribute)
root_source (matador.orm.DataContainer property)
(matador.orm.orm.DataContainer property)
rrmsd (matador.crystal.elastic.EquationOfState attribute)
run3
run3_elastic
run3_geom
run3_phonon
run3_qe
run3_spectral
run_castep() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
run_castep_relaxation() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
run_castep_singleshot() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
run_command() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
run_convergence_tests() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
run_generic() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
run_step() (matador.workflows.workflows.WorkflowStep method)
(matador.workflows.WorkflowStep method)
run_steps() (matador.workflows.Workflow method)
(matador.workflows.workflows.Workflow method)
S
sample_dos (matador.orm.spectral.DensityOfStates property)
(matador.orm.spectral.dos.DensityOfStates property)
sample_energies (matador.orm.spectral.DensityOfStates property)
(matador.orm.spectral.dos.DensityOfStates property)
save_pattern() (matador.fingerprints.PXRD method)
(matador.fingerprints.pxrd.PXRD method)
save_peaks() (matador.fingerprints.PXRD method)
(matador.fingerprints.pxrd.PXRD method)
savefig (matador.hull.hull.QueryConvexHull property)
(matador.hull.QueryConvexHull property)
savefig_ext (matador.hull.hull.QueryConvexHull property)
(matador.hull.QueryConvexHull property)
scancel_all_matching_jobs() (in module matador.compute.slurm)
scf() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
scrape_castep_params() (in module matador.utils.castep_help_utils)
scraper_function() (in module matador.scrapers.utils)
seed (matador.workflows.castep.elastic.CastepElasticWorkflow attribute)
(matador.workflows.castep.magres.CastepMagresWorkflow attribute)
(matador.workflows.castep.phonons.CastepPhononWorkflow attribute)
(matador.workflows.castep.spectral.CastepSpectralWorkflow attribute)
(matador.workflows.Workflow attribute)
(matador.workflows.workflows.Workflow attribute)
set_branches_and_spacing() (matador.orm.spectral.Dispersion method)
(matador.orm.spectral.dispersion.Dispersion method)
set_chempots() (matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
set_cursor_from_array() (in module matador.utils.cursor_utils)
set_gap_data() (matador.orm.spectral.dispersion.ElectronicDispersion method)
(matador.orm.spectral.ElectronicDispersion method)
set_mpi_library() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
set_position() (matador.crystal.crystal_site.Site method)
set_positions() (matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
set_settings() (in module matador.config)
(in module matador.config.config)
set_shifts_from_fit() (matador.magres.MagresReferencer method)
(matador.magres.referencer.MagresReferencer method)
set_site_array() (in module matador.plugins.voronoi_interface.voronoi_similarity)
set_style() (in module matador.plotting)
(in module matador.plotting.plotting)
set_substruc_dict() (in module matador.plugins.voronoi_interface.voronoi_similarity)
set_unique_subgraphs() (matador.crystal.network.CrystalGraph method)
Settings (class in matador.config.settings)
shift_to_exclude_gamma() (in module matador.utils.cell_utils)
shift_to_include_gamma() (in module matador.utils.cell_utils)
shifts_exp (matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
similarity_distance (matador.fingerprints.pdf.PDFOverlap attribute)
(matador.fingerprints.PDFOverlap attribute)
Site (class in matador.crystal.crystal_site)
site_occupancies (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
SlurmQueueManager (class in matador.compute.slurm)
softest_mode_freq (matador.orm.spectral.dispersion.VibrationalDispersion property)
(matador.orm.spectral.VibrationalDispersion property)
source (matador.orm.DataContainer property)
(matador.orm.orm.DataContainer property)
(matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.VibrationalDispersion attribute)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.VibrationalDispersion attribute)
space_group (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
space_group_tex (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
Spatula (class in matador.db)
(class in matador.db.importer)
spawn() (matador.compute.batch.BatchRun method)
(matador.compute.BatchRun method)
species (matador.crystal.crystal_site.Site property)
(matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
(matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
Spectral (class in matador.orm.spectral)
(class in matador.orm.spectral.spectral)
spin_band_gap (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion property)
spin_band_gap_path_inds (matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion property)
spin_fermi_energy (matador.orm.spectral.dispersion.ElectronicDispersion attribute)
(matador.orm.spectral.dispersion.ElectronicDispersion property)
(matador.orm.spectral.ElectronicDispersion attribute)
(matador.orm.spectral.ElectronicDispersion property)
(matador.orm.spectral.Spectral property)
(matador.orm.spectral.spectral.Spectral property)
standardize_doc_cell() (in module matador.utils.cell_utils)
standardized() (matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
starting_stoichiometry (matador.battery.electrode.VoltageProfile attribute)
(matador.battery.VoltageProfile attribute)
stats() (matador.cli.cli.MatadorCommandLine method)
steps (matador.workflows.Workflow attribute)
(matador.workflows.workflows.Workflow attribute)
stoichiometry (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
structures (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.phase_diagram.PhaseDiagram attribute)
(matador.hull.PhaseDiagram attribute)
(matador.hull.QueryConvexHull attribute)
(matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
structures_exp (matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
submit_slurm_script() (in module matador.compute.slurm)
success (matador.workflows.castep.elastic.CastepElasticWorkflow attribute)
(matador.workflows.castep.magres.CastepMagresWorkflow attribute)
(matador.workflows.castep.phonons.CastepPhononWorkflow attribute)
(matador.workflows.castep.spectral.CastepSpectralWorkflow attribute)
(matador.workflows.Workflow attribute)
(matador.workflows.workflows.Workflow attribute)
(matador.workflows.workflows.WorkflowStep attribute)
(matador.workflows.WorkflowStep attribute)
supercell() (matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
switch_coords() (in module matador.utils.cell_utils)
symmetry() (matador.db.refine.Refiner method)
(matador.db.Refiner method)
T
TaitEOS (class in matador.crystal.elastic)
TemperatureDependentHull (class in matador.hull)
(class in matador.hull.hull_temperature)
test_exec() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
tidy_pspots() (matador.db.refine.Refiner method)
(matador.db.Refiner method)
tidy_up() (matador.compute.compute.ComputeTask method)
(matador.compute.ComputeTask method)
token (matador.compute.pbs.PBSQueueManager attribute)
(matador.compute.queueing.QueueManager attribute)
(matador.compute.slurm.SlurmQueueManager attribute)
top (matador.query.DBQuery attribute)
(matador.query.query.DBQuery attribute)
two_thetas (matador.fingerprints.pxrd.PXRD.self attribute)
(matador.fingerprints.PXRD.self attribute)
U
unique_sites (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
UnitCell (class in matador.crystal.crystal)
update() (matador.crystal.Crystal method)
(matador.crystal.crystal.Crystal method)
update_castep_param_list() (in module matador.utils.castep_help_utils)
update_docs() (matador.db.refine.Refiner method)
(matador.db.Refiner method)
usp2dict() (in module matador.scrapers)
(in module matador.scrapers.castep_scrapers)
V
V_0 (matador.crystal.elastic.EquationOfState attribute)
valence (matador.battery.Electrode attribute)
(matador.battery.electrode.Electrode attribute)
valence_data (matador.battery.Electrode attribute)
(matador.battery.electrode.Electrode attribute)
validate_calc_doc() (matador.compute.compute.ComputeTask static method)
(matador.compute.ComputeTask static method)
vdos_function (matador.orm.spectral.dos.VibrationalDOS property)
(matador.orm.spectral.VibrationalDOS property)
verify_calculation_parameters() (matador.calculators.calculator.Calculator static method)
(matador.calculators.castep.CastepCalculator static method)
(matador.calculators.CastepCalculator static method)
verify_simulation_cell() (matador.calculators.calculator.Calculator static method)
(matador.calculators.castep.CastepCalculator static method)
(matador.calculators.CastepCalculator static method)
vertices2line() (in module matador.utils.hull_utils)
vertices2plane() (in module matador.utils.hull_utils)
vibrational_free_energy() (matador.orm.spectral.dos.VibrationalDOS method)
(matador.orm.spectral.VibrationalDOS method)
vibrational_free_energy_from_dos() (matador.orm.spectral.dos.VibrationalDOS method)
(matador.orm.spectral.VibrationalDOS method)
VibrationalDispersion (class in matador.orm.spectral)
(class in matador.orm.spectral.dispersion)
VibrationalDOS (class in matador.orm.spectral)
(class in matador.orm.spectral.dos)
view_changeset() (matador.db.changes.DatabaseChanges static method)
(matador.db.DatabaseChanges static method)
viz() (in module matador.utils.viz_utils)
viz_site() (in module matador.plugins.voronoi_interface.voronoi_similarity)
voltage (matador.battery.electrode.VoltageProfile attribute)
(matador.battery.VoltageProfile attribute)
voltage_curve() (matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
voltage_data (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.hull_temperature.TemperatureDependentHull attribute)
(matador.hull.QueryConvexHull attribute)
voltage_summary() (matador.battery.electrode.VoltageProfile method)
(matador.battery.VoltageProfile method)
VoltageProfile (class in matador.battery)
(class in matador.battery.electrode)
volume (matador.crystal.crystal.UnitCell property)
volume_curve() (matador.hull.hull.QueryConvexHull method)
(matador.hull.QueryConvexHull method)
volume_data (matador.hull.hull.QueryConvexHull attribute)
(matador.hull.QueryConvexHull attribute)
volume_rescale (matador.workflows.castep.elastic.CastepElasticWorkflow attribute)
voronoi_substructure (matador.crystal.Crystal property)
(matador.crystal.crystal.Crystal property)
W
walltime (matador.compute.queueing.QueueManager property)
WalltimeError
warn_tolerance (matador.magres.MagresReferencer attribute)
,
[1]
(matador.magres.referencer.MagresReferencer attribute)
,
[1]
Workflow (class in matador.workflows)
(class in matador.workflows.workflows)
WorkflowStep (class in matador.workflows)
(class in matador.workflows.workflows)
wrap_frac_coords() (in module matador.utils.cell_utils)
write_slurm_submission_script() (in module matador.compute.slurm)
X
XYvsZPlot (class in matador.plotting.plotting)
Y
y_scale (matador.plotting.plotting.XYvsZPlot property)
Z
zpe (matador.orm.spectral.dos.VibrationalDOS property)
(matador.orm.spectral.VibrationalDOS property)
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