Index

_

__add__() (pyextal.roi.BaseROI method) __call__() (pyextal.callBloch.DataCollector method) (pyextal.callBloch.SimParams method) (pyextal.gof.BaseGOF method) (pyextal.gof.Chi2 method) (pyextal.gof.XCorrelation method) __contains__() (pyextal.jaxMultipole.model.Layout method) __getitem__() (pyextal.jaxMultipole.model.Layout method) __len__() (pyextal.acom.library.ReflectionLibrary method) (pyextal.acom.ReflectionLibrary method) (pyextal.jaxMultipole.data.Observations method) (pyextal.jaxMultipole.model.Layout method) (pyextal.jaxMultipole.params.ParameterMap method) (pyextal.superspace.DiffractionPattern method) (pyextal.superspace.indexing.ReflectionSet method) (pyextal.superspace.ReflectionSet method) (pyextal.superspace.saed.DiffractionPattern method) __post_init__() (pyextal.callBloch.SimParams method) (pyextal.dinfo.BaseDiffractionInfo method) (pyextal.dinfo.LARBEDDiffractionInfo method) (pyextal.jaxMultipole.Crystal method) (pyextal.jaxMultipole.crystal.Crystal method) (pyextal.jaxMultipole.model.Layout method) (pyextal.superspace.Harmonic method) (pyextal.superspace.ModulatedAtom method) (pyextal.superspace.modulation.Harmonic method) (pyextal.superspace.modulation.ModulatedAtom method) (pyextal.superspace.SuperspaceOperation method) (pyextal.superspace.symmetry.SuperspaceOperation method) __repr__() (pyextal.jaxJoint.datasets.Dataset method) (pyextal.superspace.DiffractionPattern method) (pyextal.superspace.indexing.ReflectionSet method) (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.ReflectionSet method) (pyextal.superspace.saed.DiffractionPattern method) (pyextal.superspace.SuperspaceLattice method) __str__() (pyextal.acom.tilt.TiltResult method) (pyextal.acom.TiltResult method) (pyextal.roi.BaseROI method) _agg() (in module pyextal.jaxGeo.figures) _aperture_pixels() (in module pyextal.larbed.empad) _as_dict() (in module pyextal.jaxJoint.settings) _as_tuples() (in module pyextal.jaxGeo.reflections) _assemble_simparams() (in module pyextal.blochNumpy) _BACKENDS (in module pyextal.callBloch) _beam_frame() (in module pyextal.acom.tilt) _beams (pyextal.jaxJoint.engine.EngineSwitch attribute) _beta_matrix() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) _build_all_A_matrices() (in module pyextal.blochNumpy) _build_layout() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) _cached_batches (pyextal.jaxEngine.optimize.ChunkingGenerator attribute) _check() (pyextal.jaxJoint.engine.EngineSwitch method) _check_backend() (in module pyextal.callBloch) _check_thickness_range() (in module pyextal.jaxEngine.setParams) _chunk_mean() (pyextal.jaxGeo.objective.GeometryObjective method) _chunks() (in module pyextal.jaxJoint.optimize) _configure() (in module pyextal.jaxJoint.datasets) _CONVOLUTIONS (in module pyextal.LucyRichardson) _correlation_matrix() (in module pyextal.larbed.empad) _crystal_sum() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) _dataset_step_fn() (in module pyextal.jaxJoint.optimize) _dats (pyextal.jaxJoint.engine.EngineSwitch attribute) _describe() (in module pyextal.jaxJoint.datasets) _dot() (in module pyextal.jaxEngine.model) _draw_probe() (in module pyextal.jaxGeo.figures) _ds() (in module pyextal.jaxEngine.hdf5io)

_dwfOptions() (pyextal.optimize.CoarseOptimize static method) _eig_worker() (in module pyextal.blochNumpy) _eigenStoreError() (in module pyextal.callBloch) _enumerate_hkl() (in module pyextal.acom.library) _EXPM_MAX_SQUARINGS (in module pyextal.jaxEngine.model) _EXPM_THETA (in module pyextal.jaxEngine.model) _extract_params() (in module pyextal.blochNumpy) _figures() (in module pyextal.jaxJoint.refine) _finish() (in module pyextal.jaxJoint.refine) _fmt() (in module pyextal.acom.datfile) _fortran_fname() (in module pyextal.callBloch) _forward_sub_batch() (in module pyextal.jaxEngine.model) _free_corner() (in module pyextal.jaxGeo.figures) _freeze_layers() (in module pyextal.jaxEngine.optimize) _g() (in module pyextal.jaxJoint.report) _generate_tilt_grid() (in module pyextal.blochNumpy) _gl (pyextal.roi.BaseROI attribute) _hkl() (in module pyextal.jaxGeo.settings) _in_bounds() (in module pyextal.larbed.empad) _jsonable() (in module pyextal.jaxEngine.hdf5io) _load() (in module pyextal.jaxJoint.datasets) _loaded (pyextal.jaxJoint.engine.EngineSwitch attribute) _MODEL_REGISTRY (in module pyextal.jaxEngine.structureModel) _Ms (pyextal.jaxMultipole.intensity.MultipoleBridge attribute) _nfit (pyextal.optimize.FineOptimize attribute) _numpy_eigensolve() (in module pyextal.blochNumpy) _orientation() (in module pyextal.acom.tilt) _out_count() (in module pyextal.jaxGeo.io) _p0 (pyextal.jaxMultipole.intensity.MultipoleBridge attribute) _PADE7 (in module pyextal.jaxEngine.model) _pair_features() (in module pyextal.acom.solve) _params (pyextal.jaxJoint.engine.EngineSwitch attribute) _path_or_none() (in module pyextal.jaxGeo.cli) _perturbROI (pyextal.optimize.FineOptimize attribute) _physical_core_count() (in module pyextal.blochNumpy) _probe (pyextal.optimize.FineOptimize attribute) _read_layers() (in module pyextal.jaxGeo.figures) _refined_components() (in module pyextal.jaxGeo.figures) _relation_text() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) _release_oversub() (in module pyextal.jaxJoint.refine) _replace() (in module pyextal.hdf5io) _resolve() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) _rotation (pyextal.roi.BaseROI attribute) _run_key() (in module pyextal.jaxGeo.figures) _save_param_history() (in module pyextal.jaxEngine.hdf5io) _select_cpu() (in module pyextal.jaxGeo.refine) (in module pyextal.jaxJoint.refine) _shiftDisk (pyextal.optimize.FineOptimize attribute) _short() (pyextal.jaxJoint.engine.EngineSwitch method) _single_threaded_blas() (in module pyextal.blochNumpy) _site_terms() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) _symmetry_members() (in module pyextal.jaxJoint.link) _term() (in module pyextal.jaxJoint.params) _thickness_A() (in module pyextal.jaxGeo.figures) _thread_map() (in module pyextal.blochNumpy) _tmp (pyextal.jaxJoint.engine.EngineSwitch attribute) _transform_matrix() (in module pyextal.adp) _tuple() (in module pyextal.jaxGeo.settings) _value (pyextal.jaxGeo.objective.GeometryObjective attribute) _vg (pyextal.jaxGeo.objective.GeometryObjective attribute) _vgh (pyextal.jaxGeo.objective.GeometryObjective attribute) _VOIGT (in module pyextal.adp) _warn_on_rank() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) _weights() (in module pyextal.jaxJoint.datasets) _workers_spawned (in module pyextal.callBloch)

A

A (pyextal.jaxMultipole.Crystal attribute) (pyextal.jaxMultipole.crystal.Crystal attribute) abm (pyextal.blochwave.Difpar attribute) absorption (pyextal.jaxMultipole.data.Observations attribute) abx (pyextal.blochwave.Cryst attribute) AcomResult (class in pyextal.acom) activate() (pyextal.jaxJoint.engine.EngineSwitch method) active (pyextal.jaxGeo.objective.GeometryObjective attribute) (pyextal.jaxJoint.datasets.Dataset attribute) add() (pyextal.jaxJoint.engine.EngineSwitch method) add_holz() (pyextal.acom.AcomResult method) adjustDWF() (in module pyextal.callBloch) adp_from_high_order() (in module pyextal.jaxMultipole.protocol) alag (pyextal.blochwave.Spgr attribute) align_data() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) AlignByBeam() (in module pyextal.larbed) (in module pyextal.larbed.empad) aligned (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) allocate_arrays_bloch() (pyextal.blochwave.BlochModule method) allocate_arrays_difpar() (pyextal.blochwave.Difpar method) allocate_arrays_eigen() (pyextal.blochwave.Eigen method) allocate_tilt() (pyextal.blochwave.Eigen method) allowed_adp_basis() (in module pyextal.jaxMultipole.symmetry) allowed_beta_basis() (in module pyextal.adp) allowed_multipole_basis() (in module pyextal.jaxMultipole.harmonics) allowed_multipoles() (in module pyextal.jaxMultipole.symmetry) allshift (pyextal.roi.BaseROI attribute) alpha (pyextal.callBloch.SimParams attribute) angle() (in module pyextal.metric) aniso (pyextal.adp.DWFModel attribute) AnnularSum() (in module pyextal.larbed) (in module pyextal.larbed.empad) AnnularVar() (in module pyextal.larbed) (in module pyextal.larbed.empad) ApertureSum() (in module pyextal.larbed) (in module pyextal.larbed.empad)

ApertureSumVariance() (in module pyextal.larbed) (in module pyextal.larbed.empad) appliedSymmetry() (in module pyextal.symmetry) apply() (pyextal.adp.DWFModel method) apply_label_op() (in module pyextal.acom) (in module pyextal.acom.quality) apply_link() (in module pyextal.jaxJoint.params) apply_oversubtraction() (in module pyextal.jaxEngine.postProcess) as_hkl() (in module pyextal.jaxJoint.link) aspg (pyextal.blochwave.Spgr attribute) assign() (in module pyextal.acom) (in module pyextal.acom.solve) assign_gvector() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) assign_superspace_index() (in module pyextal.superspace) (in module pyextal.superspace.approximant) assigned (pyextal.acom.AcomResult property) atm (pyextal.blochwave.Xtal attribute) atom_labels() (in module pyextal.adp) atom_line() (in module pyextal.adp) atom_positions() (in module pyextal.adp) AtomConfig (class in pyextal.jaxMultipole.bank) AtomSpec (class in pyextal.jaxMultipole) (class in pyextal.jaxMultipole.model) atpar (pyextal.blochwave.Cryst attribute) auto_index() (in module pyextal.acom) auto_max_index() (in module pyextal.acom) (in module pyextal.acom.library) auto_n_internal() (in module pyextal.superspace) (in module pyextal.superspace.structurefactor) average (pyextal.superspace.modulation.OccupationalModulation attribute) (pyextal.superspace.OccupationalModulation attribute) average_aligned (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) average_data() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) average_raw (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) axis_and_order() (in module pyextal.jaxMultipole.symmetry)

B

B (pyextal.superspace.ModulatedAtom attribute) (pyextal.superspace.modulation.ModulatedAtom attribute) backend (pyextal.optimize.CoarseOptimize attribute) (pyextal.optimize.FineOptimize attribute) (pyextal.roi.CBEDROI attribute) background (pyextal.dinfo.CBEDDiffractionInfo attribute) background_normalize (pyextal.jaxEngine.setParams.OptConfig attribute) background_optimize (pyextal.jaxEngine.setParams.OptConfig attribute) background_range (pyextal.jaxEngine.setParams.OptConfig attribute) background_window (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) BackgroundFitWeights() (in module pyextal.larbed) (in module pyextal.larbed.empad) bank (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.bank.AtomConfig attribute) (pyextal.jaxMultipole.bank.BankEntry attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) bank_path() (in module pyextal.jaxMultipole.bank) BankEntry (class in pyextal.jaxMultipole.bank) BASE (pyextal.roi.ROITYPE attribute) BaseDiffractionInfo (class in pyextal.dinfo) BaseGOF (class in pyextal.gof) BaseROI (class in pyextal.roi) bases (pyextal.adp.DWFModel attribute) basic_atoms() (in module pyextal.superspace.tas2) basic_to_tripled() (in module pyextal.superspace.tas2) batch_mode (pyextal.jaxEngine.setParams.OptConfig attribute) batch_size (pyextal.jaxEngine.optimize.RandomGenerator attribute) batched_forward() (in module pyextal.jaxEngine.model) BatchGenerator (class in pyextal.jaxEngine.optimize) beam2Group (pyextal.symmetry.GroupSymmetry attribute) beam_differences() (in module pyextal.jaxJoint.link) beam_direction() (in module pyextal.acom) (in module pyextal.acom.tilt) beamcheck() (in module pyextal.blochwave) beamGroup (pyextal.symmetry.GroupSymmetry attribute) beamIndicesGroup (pyextal.symmetry.GroupSymmetry attribute) bessel_reference() (in module pyextal.superspace) (in module pyextal.superspace.structurefactor)

beta (pyextal.jaxMultipole.crystal.Site attribute) (pyextal.jaxMultipole.Site attribute) beta_matrix() (in module pyextal.adp) beta_projector() (in module pyextal.adp) BETA_ROWS (in module pyextal.adp) beta_to_uij() (in module pyextal.adp) beta_vector() (in module pyextal.adp) betas() (pyextal.adp.DWFModel method) bigk (pyextal.blochwave.Difpar attribute) bigK (pyextal.callBloch.SimParams attribute) bloch() (in module pyextal.callBloch) bloch_module (in module pyextal.blochwave) bloch_numpy() (in module pyextal.blochNumpy) bloch_parse() (in module pyextal.blochwave) (in module pyextal.callBloch) bloch_run() (in module pyextal.blochwave) (in module pyextal.callBloch) bloch_run_numpy() (in module pyextal.blochNumpy) BlochModule (class in pyextal.blochwave) BOHR (in module pyextal.jaxMultipole.constants) bounds (pyextal.adp.DWFModel attribute) brightest() (pyextal.superspace.DiffractionPattern method) (pyextal.superspace.saed.DiffractionPattern method) Bstar (pyextal.jaxMultipole.Crystal property) (pyextal.jaxMultipole.crystal.Crystal property) build() (pyextal.adp.DWFModel class method) build_config() (in module pyextal.jaxGeo.config) build_date (pyextal.blochwave.Constants attribute) build_library() (in module pyextal.acom) (in module pyextal.acom.library) build_model() (in module pyextal.jaxMultipole.cli) build_optimizer() (in module pyextal.jaxJoint.optimize) build_parameter_map() (in module pyextal.jaxMultipole) (in module pyextal.jaxMultipole.params) build_parser() (in module pyextal.jaxGeo.cli) (in module pyextal.jaxJoint.cli) (in module pyextal.jaxMultipole.cli) build_structure_matrix_single() (in module pyextal.jaxEngine.model) build_version (pyextal.blochwave.Constants attribute)

C

calc (pyextal.jaxMultipole.fit.FitResult attribute) calculate_average_step_length() (pyextal.larbed.calibration.LARBEDCalibration method) (pyextal.larbed.LARBEDCalibration method) calculate_g_vectors() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) calculate_grid_vectors() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) calculate_mtf() (pyextal.larbed.calibration.LARBEDCalibration method) (pyextal.larbed.LARBEDCalibration method) calculate_static_ugh() (in module pyextal.jaxEngine.setParams) calculate_tilt_dependent_values() (in module pyextal.jaxEngine.setParams) calculatePixelSize() (pyextal.roi.BaseROI method) calDOF() (pyextal.optimize.FineOptimize method) calibrateCBED() (in module pyextal.callBloch) calibrateLARBED() (in module pyextal.callBloch) callback() (pyextal.optimize.FineOptimize static method) callbackCell() (pyextal.optimize.CoarseOptimize static method) callbackDWF() (pyextal.optimize.CoarseOptimize static method) callbackXYZ() (pyextal.optimize.CoarseOptimize static method) calScaling() (pyextal.gof.Chi2 method) (pyextal.gof.Chi2_LARBED_multibackground method) (pyextal.gof.Chi2_multibackground method) calVariance() (pyextal.gof.Chi2 method) (pyextal.gof.Chi2_const method) (pyextal.gof.Chi2_LARBED method) (pyextal.gof.Chi2_multibackground method) canBlit() (pyextal.optimize.FineOptimize static method) candidate_zone_axes() (in module pyextal.acom) (in module pyextal.acom.library) canonical() (in module pyextal.jaxJoint.link) (in module pyextal.jaxMultipole.symmetry) cart_rotation() (pyextal.jaxMultipole.Crystal method) (pyextal.jaxMultipole.crystal.Crystal method) cartesian_frames() (in module pyextal.acom.geometry) CBED (pyextal.roi.ROITYPE attribute) CBEDDiffractionInfo (class in pyextal.dinfo) cbedpCall() (pyextal.callBloch.SimParams method) CBEDROI (class in pyextal.roi) cc (pyextal.blochwave.BlochModule attribute) cci (pyextal.callBloch.Data property) ccr (pyextal.callBloch.Data property) CELL (in module pyextal.superspace.tas2) cell (pyextal.blochwave.Cryst attribute) (pyextal.jaxMultipole.Crystal attribute) (pyextal.jaxMultipole.crystal.Crystal attribute) (pyextal.superspace.lattice.SuperspaceLattice attribute) (pyextal.superspace.SuperspaceLattice attribute) CELL_BASIC (in module pyextal.superspace.tas2) cell_matrix() (in module pyextal.jaxMultipole.crystal) cell_to_metric() (in module pyextal.superspace) (in module pyextal.superspace.lattice) CELL_TRIPLED (in module pyextal.superspace.tas2) center (pyextal.acom.DetectorMap attribute) (pyextal.acom.solve.DetectorMap attribute) (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) centre (pyextal.jaxGeo.geometry.GeometryModel attribute) centro (pyextal.blochwave.Spgr attribute) (pyextal.jaxMultipole.Crystal attribute) (pyextal.jaxMultipole.crystal.Crystal attribute) (pyextal.symmetry.GroupSymmetry attribute) character_count() (in module pyextal.jaxMultipole.harmonics) check() (pyextal.jaxMultipole.intensity.FullMatrix method) check_allocated_eigen() (pyextal.blochwave.Eigen method) check_gradient() (in module pyextal.jaxGeo.lm) check_links() (in module pyextal.jaxJoint.link) check_pre_refinement() (in module pyextal.jaxGeo.io) check_size_eigen() (pyextal.blochwave.Eigen method) checked (pyextal.jaxJoint.datasets.Dataset attribute) Chi2 (class in pyextal.gof) chi2 (pyextal.jaxMultipole.fit.FitResult attribute) Chi2_const (class in pyextal.gof) Chi2_LARBED (class in pyextal.gof)

Chi2_LARBED_multibackground (class in pyextal.gof) Chi2_multibackground (class in pyextal.gof) chisq2d() (in module pyextal.LucyRichardson) chunk_shape (pyextal.jaxEngine.setParams.OptConfig attribute) ChunkingGenerator (class in pyextal.jaxEngine.optimize) chunks (pyextal.jaxGeo.objective.GeometryObjective attribute) cinv (pyextal.blochwave.BlochModule attribute) (pyextal.callBloch.Data attribute) cinv_full (pyextal.callBloch.Data attribute) cinvs (pyextal.blochwave.Eigen attribute) clip (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) clip_experimental() (in module pyextal.jaxEngine.postProcess) CoarseOptimize (class in pyextal.optimize) coef (pyextal.jaxMultipole.bank.Orbital attribute) coincidence_coset() (in module pyextal.superspace) (in module pyextal.superspace.indexing) commensurate_q() (in module pyextal.superspace.tas2) commensurate_structure() (in module pyextal.superspace.tas2) common (pyextal.jaxJoint.JointSettings attribute) (pyextal.jaxJoint.settings.JointSettings attribute) COMPONENTS (in module pyextal.jaxJoint.params) condition (pyextal.jaxMultipole.fit.FitResult attribute) config (pyextal.jaxEngine.optimize.BatchGenerator attribute) configure() (in module pyextal.jaxMultipole.bank) confirm() (in module pyextal.acom) CONJ (in module pyextal.jaxJoint.link) constant (in module pyextal.Constants) Constants (class in pyextal.blochwave) constants (in module pyextal.blochwave) construct_ugh() (in module pyextal.jaxEngine.model) convolved2d() (in module pyextal.LucyRichardson) convolved2d_real() (in module pyextal.LucyRichardson) convolved_2d_vmap (in module pyextal.jaxEngine.postProcess) core (pyextal.jaxMultipole.bank.AtomConfig attribute) core_from (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) corr (pyextal.jaxMultipole.fit.FitResult attribute) correction (pyextal.acom.tilt.TiltResult property) (pyextal.acom.TiltResult property) correlate() (pyextal.optimize.CoarseOptimize method) correlation (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) correlationTargetCell() (pyextal.optimize.CoarseOptimize static method) correlationTargetDWF() (pyextal.optimize.CoarseOptimize static method) correlationTargetXYZ() (pyextal.optimize.CoarseOptimize static method) cos (pyextal.superspace.Harmonic attribute) (pyextal.superspace.modulation.Harmonic attribute) cov (pyextal.jaxMultipole.fit.FitResult attribute) cpu (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) create_2d_tilt_chunks() (pyextal.jaxEngine.optimize.ChunkingGenerator method) create_freeze_mask() (in module pyextal.jaxEngine.optimize) create_gaussian_kernel() (in module pyextal.jaxEngine.postProcess) create_pseudo_voigt_kernel() (in module pyextal.jaxEngine.postProcess) createInterp() (pyextal.roi.BaseROI method) (pyextal.roi.CBEDROI method) (pyextal.roi.LARBEDROI method) crop() (in module pyextal.jaxGeo.oversub) crop_data (pyextal.larbed.calibration.LARBEDCalibration attribute) (pyextal.larbed.LARBEDCalibration attribute) crop_peaks() (pyextal.larbed.calibration.LARBEDCalibration method) (pyextal.larbed.LARBEDCalibration method) Cryst (class in pyextal.blochwave) cryst (in module pyextal.blochwave) Crystal (class in pyextal.jaxMultipole) (class in pyextal.jaxMultipole.crystal) crystal (pyextal.jaxMultipole.model.MultipoleModel attribute) (pyextal.jaxMultipole.MultipoleModel attribute) csub4 (pyextal.blochwave.Spgr attribute) curvature_esd() (in module pyextal.jaxMultipole.intensity) cycles (pyextal.jaxMultipole.intensity.IntensitySettings attribute) CZ_C (in module pyextal.superspace.tas2) CZ_NC (in module pyextal.superspace.tas2)

D

d (pyextal.superspace.indexing.ReflectionSet attribute) (pyextal.superspace.lattice.SuperspaceLattice property) (pyextal.superspace.ReflectionSet attribute) (pyextal.superspace.SuperspaceLattice property) (pyextal.superspace.SuperspaceOperation property) (pyextal.superspace.symmetry.SuperspaceOperation property) d_spacing() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) dat (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) Data (class in pyextal.callBloch) data (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.calibration.LARBEDCalibration attribute) (pyextal.larbed.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDCalibration attribute) DataCollector (class in pyextal.callBloch) Dataset (class in pyextal.jaxJoint.datasets) datasets (pyextal.jaxJoint.JointSettings attribute) (pyextal.jaxJoint.settings.JointSettings attribute) datpath (pyextal.dinfo.BaseDiffractionInfo attribute) deallocate_arrays_bloch() (pyextal.blochwave.BlochModule method) deallocate_arrays_difpar() (pyextal.blochwave.Difpar method) deallocate_arrays_eigen() (pyextal.blochwave.Eigen method) deallocate_tilt() (pyextal.blochwave.Eigen method) debug_plot() (in module pyextal.jaxEngine.utils) deconv_DPstack() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) deconv_Larbedstack() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) deconvolve_image() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) DEFAULT_DETECTOR_SHAPE (in module pyextal.larbed.empad) default_ladder() (in module pyextal.jaxMultipole.settings) default_max_block() (in module pyextal.jaxGeo.objective) default_n_l() (in module pyextal.jaxMultipole.model) defaultsf() (in module pyextal.blochwave) deformation_density() (in module pyextal.jaxMultipole.maps) deformation_fb() (in module pyextal.jaxMultipole.radial) deformation_orbital() (in module pyextal.jaxMultipole.model) delta() (pyextal.jaxMultipole.intensity.FullMatrix method) delta_to_x() (in module pyextal.jaxGeo.geometry) denorm_fn() (in module pyextal.jaxEngine.setParams) denormalize_params() (in module pyextal.jaxEngine.setParams) denormalizeX0() (pyextal.optimize.FineOptimize method) dependent (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.params.ParameterMap attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) describe() (in module pyextal.adp) (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) design_check() (in module pyextal.jaxMultipole.fit) detect_peaks() (in module pyextal.acom) (in module pyextal.acom.detect)

detector_shape (pyextal.larbed.analysis.LARBEDAnalysis property) (pyextal.larbed.LARBEDAnalysis property) DetectorMap (class in pyextal.acom) (class in pyextal.acom.solve) diagonalise_measured (pyextal.jaxEngine.setParams.OptConfig attribute) (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) DiffractionPattern (class in pyextal.superspace) (class in pyextal.superspace.saed) Difpar (class in pyextal.blochwave) difpar (in module pyextal.blochwave) dim (pyextal.superspace.lattice.SuperspaceLattice property) (pyextal.superspace.SuperspaceLattice property) dinfo (pyextal.gof.Chi2_const attribute) (pyextal.gof.Chi2_multibackground attribute) (pyextal.optimize.CoarseOptimize attribute) (pyextal.optimize.FineOptimize attribute) (pyextal.roi.BaseROI attribute) direct_beam() (in module pyextal.acom) (in module pyextal.acom.detect) disks (pyextal.callBloch.SimParams attribute) diskshift (pyextal.roi.BaseROI attribute) displacement() (pyextal.superspace.ModulatedAtom method) (pyextal.superspace.modulation.ModulatedAtom method) displacive (pyextal.superspace.ModulatedAtom attribute) (pyextal.superspace.modulation.ModulatedAtom attribute) DisplaciveModulation (class in pyextal.superspace) (class in pyextal.superspace.modulation) display() (pyextal.optimize.FineOptimize method) display_names() (in module pyextal.jaxJoint.settings) displayCoarseSearch() (pyextal.optimize.CoarseOptimize method) displayROI() (pyextal.roi.CBEDROI method) (pyextal.roi.LARBEDROI method) distinct_beams() (in module pyextal.superspace) (in module pyextal.superspace.indexing) dkv (pyextal.blochwave.Constants attribute) dlm() (in module pyextal.jaxMultipole.harmonics) dp (pyextal.dinfo.BaseDiffractionInfo attribute) (pyextal.roi.BaseROI attribute) dpCenter (pyextal.roi.CBEDROI attribute) dpop (pyextal.jaxMultipole.params.SiteRefine attribute) (pyextal.jaxMultipole.SiteRefine attribute) dpSize (pyextal.roi.CBEDROI attribute) DQE() (in module pyextal.LucyRichardson) draw_intensities() (in module pyextal.jaxMultipole.intensity) dry_run (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) dryrun() (in module pyextal.blochwave) dtpar (pyextal.dinfo.CBEDDiffractionInfo attribute) dU() (pyextal.jaxMultipole.intensity.FullMatrix method) dw (pyextal.blochwave.Cryst attribute) DWFModel (class in pyextal.adp) dynamical_pattern() (in module pyextal.superspace) (in module pyextal.superspace.approximant) dynamical_saed() (in module pyextal.superspace.engine)

E

e1 (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) e2 (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) E2X (in module pyextal.jaxMultipole.constants) e2Xray() (in module pyextal.callBloch) e2xray() (pyextal.blochwave.Sfmanager method) effective_hkl() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) Eigen (class in pyextal.blochwave) eigen (in module pyextal.blochwave) eigenvalues (pyextal.blochwave.Eigen attribute) eigenvector (pyextal.callBloch.Data attribute) eigenvectors (pyextal.blochwave.Eigen attribute) electron_form_factor() (in module pyextal.superspace) (in module pyextal.superspace.scattering) electrons (pyextal.jaxMultipole.bank.BankEntry property) (pyextal.jaxMultipole.bank.Shell property) electrons() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) element (pyextal.jaxMultipole.bank.AtomConfig attribute) (pyextal.jaxMultipole.bank.BankEntry property) (pyextal.jaxMultipole.crystal.Site attribute) (pyextal.jaxMultipole.Site attribute) (pyextal.superspace.ModulatedAtom attribute) (pyextal.superspace.modulation.ModulatedAtom attribute) element_of() (in module pyextal.jaxMultipole.crystal) enable_oversub() (in module pyextal.jaxGeo.oversub) engine_agreement() (pyextal.jaxGeo.geometry.GeometryModel method) engine_label (pyextal.jaxMultipole.crystal.Site attribute) (pyextal.jaxMultipole.Site attribute) engine_reflections() (in module pyextal.superspace.engine) EngineSwitch (class in pyextal.jaxJoint.engine) entry() (in module pyextal.jaxMultipole.bank)

enumerate_reflections() (in module pyextal.superspace) (in module pyextal.superspace.indexing) epsilon (pyextal.superspace.SuperspaceOperation attribute) (pyextal.superspace.symmetry.SuperspaceOperation attribute) epsilon_for() (in module pyextal.superspace) (in module pyextal.superspace.symmetry) equivalent_B() (in module pyextal.adp) errorFunc (pyextal.optimize.FineOptimize attribute) esd (pyextal.jaxMultipole.fit.FitResult attribute) (pyextal.jaxMultipole.intensity.IntensitySettings attribute) esd_scaled (pyextal.jaxMultipole.fit.FitResult attribute) estimate_noise() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) EstimatePixelNoise() (in module pyextal.larbed) (in module pyextal.larbed.empad) evals (pyextal.jaxGeo.objective.GeometryObjective attribute) evaluate() (pyextal.superspace.DisplaciveModulation method) (pyextal.superspace.modulation.DisplaciveModulation method) (pyextal.superspace.modulation.OccupationalModulation method) (pyextal.superspace.OccupationalModulation method) evaluateParam() (pyextal.optimize.FineOptimize method) evaluateSF() (pyextal.optimize.FineOptimize method) EVIDENCE_PRIOR (in module pyextal.acom.solve) excitation_error() (in module pyextal.acom.geometry) exclude (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) excluded_outputs() (in module pyextal.jaxEngine.postProcess) exitwave (pyextal.optimize.CoarseOptimize attribute) expand_atoms() (in module pyextal.superspace) (in module pyextal.superspace.symmetry) experimental_data (pyextal.jaxEngine.optimize.BatchGenerator attribute) (pyextal.jaxEngine.optimize.RandomGenerator attribute) expm_batch() (in module pyextal.jaxEngine.model) extra (pyextal.jaxMultipole.params.ParameterMap attribute)

F

failed (pyextal.acom.AcomResult attribute) family_cost (pyextal.jaxMultipole.intensity.IntensitySettings attribute) family_cost() (in module pyextal.jaxMultipole.intensity) fb_coefficients() (in module pyextal.jaxMultipole.radial) FEM_StackAverage() (in module pyextal.larbed) (in module pyextal.larbed.empad) field_names() (pyextal.jaxGeo.RefineSettings class method) (pyextal.jaxGeo.settings.RefineSettings class method) figure (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) file_name (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.calibration.LARBEDCalibration attribute) (pyextal.larbed.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDCalibration attribute) find_nearest_peak() (in module pyextal.larbed) (in module pyextal.larbed.empad) find_peaks() (pyextal.larbed.calibration.LARBEDCalibration method) (pyextal.larbed.LARBEDCalibration method) FineOptimize (class in pyextal.optimize) first (pyextal.blochwave.Mpiinfo attribute) fit() (in module pyextal.jaxMultipole.fit) (pyextal.jaxMultipole.fit.Fitter method) fit_beam_map() (in module pyextal.acom) (in module pyextal.acom.tilt) fit_beam_to_holz() (in module pyextal.acom) (in module pyextal.acom.tilt) fit_geometry_tile() (in module pyextal.jaxGeo.objective) fit_oversub() (in module pyextal.jaxGeo.oversub) fitPeak() (in module pyextal.larbed.peaks) fitPeak2D() (in module pyextal.larbed.peaks) fitPeak2DGauss() (in module pyextal.larbed.peaks) FitResult (class in pyextal.jaxMultipole.fit) FitSettings (class in pyextal.jaxMultipole) (class in pyextal.jaxMultipole.settings) Fitter (class in pyextal.jaxMultipole.fit)

fix_after (pyextal.jaxEngine.setParams.OptConfig attribute) fix_kappa (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) floor (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) fmt_delta() (in module pyextal.jaxGeo.geometry) form_factor_table() (in module pyextal.superspace.scattering) format_index() (in module pyextal.superspace) (in module pyextal.superspace.indexing) forward_model() (in module pyextal.jaxEngine.model) forward_model_crystalparams() (in module pyextal.jaxEngine.model) forward_model_single() (in module pyextal.jaxEngine.model) fourierSynthesis() (in module pyextal.densityMap) frame (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) frame_gmax() (in module pyextal.acom) (in module pyextal.acom.library) freeze_mask() (in module pyextal.jaxJoint.params) fridel_symmetry_only() (in module pyextal.jaxEngine.setParams) friedel_reflections() (in module pyextal.jaxGeo.reflections) friis2004_table1() (in module pyextal.jaxMultipole.data) from_dat() (pyextal.jaxMultipole.Crystal class method) (pyextal.jaxMultipole.crystal.Crystal class method) from_joint_json() (in module pyextal.jaxMultipole.data) from_scan_runs() (in module pyextal.jaxMultipole.data) from_simgrid() (pyextal.jaxGeo.geometry.GeometryModel class method) from_table() (in module pyextal.jaxMultipole.data) from_yaml() (pyextal.jaxEngine.setParams.OptConfig class method) frozen_layers (pyextal.jaxEngine.setParams.OptConfig attribute) (pyextal.jaxGeo.RefineSettings property) (pyextal.jaxGeo.settings.RefineSettings property) ftab (pyextal.blochwave.Sfpar attribute) ftab2 (pyextal.blochwave.Sfpar attribute) FullMatrix (class in pyextal.jaxMultipole.intensity) fx() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method)

G

G (pyextal.jaxMultipole.Crystal property) (pyextal.jaxMultipole.crystal.Crystal property) (pyextal.superspace.SuperspaceOperation attribute) (pyextal.superspace.symmetry.SuperspaceOperation attribute) G() (pyextal.jaxMultipole.intensity.MultipoleBridge method) g_grid (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) g_include (pyextal.hdf5io.PreRefinementResult attribute) g_magnitude() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) g_vectors (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) gamma (pyextal.blochwave.Difpar attribute) (pyextal.callBloch.Data attribute) (pyextal.jaxMultipole.Crystal property) (pyextal.jaxMultipole.crystal.Crystal property) gamma() (in module pyextal.jaxMultipole.constants) GAMMA_K (in module pyextal.jaxMultipole.constants) gaussian1D() (in module pyextal.larbed.peaks) gaussian2D() (in module pyextal.larbed.peaks) gCoff (pyextal.roi.CBEDROI attribute) generateGrid() (pyextal.roi.BaseROI method) geo (pyextal.jaxMultipole.intensity.FullMatrix attribute) (pyextal.jaxMultipole.intensity.MultipoleBridge attribute) geo_check (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_config (pyextal.jaxJoint.datasets.Dataset attribute) geo_every (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_hessian (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_history (pyextal.jaxJoint.datasets.Dataset attribute) geo_iters (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_lambda (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_max_block (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_params (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_refresh (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_start (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_step_gl (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_step_rotation (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_step_tilt (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_tile (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_tol (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geo_trust (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) GEOMETRY (in module pyextal.jaxGeo.geometry) (in module pyextal.jaxGeo.settings) geometry (pyextal.hdf5io.PreRefinementResult attribute) (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) geometry() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) geometry_config() (in module pyextal.jaxGeo.objective) geometry_every (pyextal.jaxMultipole.intensity.IntensitySettings attribute) geometry_refine() (in module pyextal.jaxGeo.lm) GeometryModel (class in pyextal.jaxGeo.geometry) GeometryObjective (class in pyextal.jaxGeo.objective) get_batches() (pyextal.jaxEngine.optimize.BatchGenerator method) (pyextal.jaxEngine.optimize.ChunkingGenerator method) (pyextal.jaxEngine.optimize.RandomGenerator method)

get_beta() (in module pyextal.adp) get_bloch_constants() (in module pyextal.jaxEngine.setParams) get_gvectors() (in module pyextal.larbed) (in module pyextal.larbed.empad) get_loss_fn() (in module pyextal.jaxEngine.optimize) get_model_by_name() (in module pyextal.jaxEngine.structureModel) getAllSF() (pyextal.dinfo.BaseDiffractionInfo method) getGridVectors() (in module pyextal.larbed) (in module pyextal.larbed.empad) getGridVectors_Adjust() (in module pyextal.larbed) (in module pyextal.larbed.empad) getGridVectorsHOLZ() (in module pyextal.larbed) (in module pyextal.larbed.empad) getGroup() (pyextal.symmetry.GroupSymmetry method) getPos() (pyextal.symmetry.GroupSymmetry method) getRange() (pyextal.optimize.FineOptimize method) getSampling() (pyextal.roi.CBEDROI method) (pyextal.roi.LARBEDROI method) getSF() (pyextal.dinfo.BaseDiffractionInfo method) getSymmetry() (in module pyextal.symmetry) getx0() (pyextal.optimize.FineOptimize method) gg (pyextal.callBloch.SimParams attribute) (pyextal.jaxGeo.geometry.GeometryModel attribute) gg_pixels (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) gg_scale (pyextal.jaxGeo.geometry.GeometryModel attribute) gh (pyextal.callBloch.SimParams attribute) (pyextal.jaxGeo.geometry.GeometryModel attribute) gInclude (pyextal.roi.BaseROI attribute) gindex (pyextal.dinfo.LARBEDDiffractionInfo attribute) gl (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) (pyextal.dinfo.BaseDiffractionInfo attribute) (pyextal.optimize.CoarseOptimize attribute) (pyextal.roi.BaseROI property) gl_for() (pyextal.acom.tilt.TiltResult method) (pyextal.acom.TiltResult method) glTarget() (pyextal.optimize.CoarseOptimize static method) gmag (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) (pyextal.superspace.indexing.ReflectionSet attribute) (pyextal.superspace.ReflectionSet attribute) gmx (pyextal.adp.DWFModel attribute) (pyextal.blochwave.Gram attribute) (pyextal.callBloch.SimParams attribute) (pyextal.superspace.lattice.SuperspaceLattice attribute) (pyextal.superspace.SuperspaceLattice attribute) gmxr (pyextal.adp.DWFModel attribute) (pyextal.blochwave.Gram attribute) (pyextal.callBloch.SimParams attribute) (pyextal.superspace.lattice.SuperspaceLattice attribute) (pyextal.superspace.SuperspaceLattice attribute) gof (pyextal.jaxMultipole.fit.FitResult attribute) gp (pyextal.blochwave.Spgr attribute) (pyextal.symmetry.GroupSymmetry attribute) Gram (class in pyextal.blochwave) gram (in module pyextal.blochwave) grid() (pyextal.jaxGeo.geometry.GeometryModel method) grid_shape (pyextal.hdf5io.PreRefinementResult attribute) groups (pyextal.adp.DWFModel attribute) GroupSymmetry (class in pyextal.symmetry) gSelect() (pyextal.roi.BaseROI method) Gstar (pyextal.jaxMultipole.Crystal property) (pyextal.jaxMultipole.crystal.Crystal property) gx (pyextal.blochwave.Difpar attribute) (pyextal.roi.BaseROI attribute) gy (pyextal.blochwave.Difpar attribute)

H

H (pyextal.superspace.indexing.ReflectionSet attribute) (pyextal.superspace.ReflectionSet attribute) h5 (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) (pyextal.jaxMultipole.data.ScanValue attribute) (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) half_angle (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) hamilton_test() (in module pyextal.jaxMultipole.fit) handed (pyextal.acom.DetectorMap attribute) (pyextal.acom.solve.DetectorMap attribute) Harmonic (class in pyextal.superspace) (class in pyextal.superspace.modulation) has() (pyextal.jaxMultipole.fit.FitResult method) hessian (pyextal.jaxJoint.datasets.Dataset attribute) hessian_every (pyextal.jaxMultipole.intensity.IntensitySettings attribute)

higher_order_zone() (in module pyextal.acom) (in module pyextal.acom.tilt) history (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) (pyextal.optimize.FineOptimize attribute) history_main() (in module pyextal.jaxGeo.figures) hkl (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) (pyextal.blochwave.Difpar attribute) (pyextal.jaxMultipole.data.Observations attribute) (pyextal.superspace.indexing.ReflectionSet attribute) (pyextal.superspace.ReflectionSet attribute) hklf (pyextal.blochwave.Difpar attribute) hklout (pyextal.callBloch.SimParams attribute) holz (pyextal.acom.AcomResult attribute) hv (pyextal.blochwave.Constants attribute) HVTarget() (pyextal.optimize.CoarseOptimize static method)

I

iam_matrix() (pyextal.jaxMultipole.intensity.FullMatrix method) iam_model (pyextal.jaxMultipole.intensity.FullMatrix attribute) iam_reference() (in module pyextal.jaxMultipole.plotting) iam_table() (in module pyextal.jaxMultipole.report) idptr (pyextal.blochwave.Difpar attribute) iftype (pyextal.blochwave.Cryst attribute) ig (pyextal.blochwave.BlochModule attribute) imag (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) includeBeam (pyextal.dinfo.BaseDiffractionInfo property) index() (in module pyextal.jaxMultipole.harmonics) index_sum (pyextal.superspace.DiffractionPattern property) (pyextal.superspace.indexing.ReflectionSet property) (pyextal.superspace.ReflectionSet property) (pyextal.superspace.saed.DiffractionPattern property) indices (pyextal.optimize.CoarseOptimize attribute) (pyextal.roi.LARBEDROI attribute) initial_background (pyextal.jaxEngine.setParams.OptConfig attribute) initial_gamma_probe (pyextal.jaxEngine.setParams.OptConfig attribute) initial_oversub_leak (pyextal.jaxEngine.setParams.OptConfig attribute) initial_oversub_offset (pyextal.jaxEngine.setParams.OptConfig attribute) initial_scale (pyextal.jaxEngine.setParams.OptConfig attribute) initial_sigma_probe (pyextal.jaxEngine.setParams.OptConfig attribute) initial_thickness (pyextal.jaxEngine.setParams.OptConfig attribute) initialize() (pyextal.roi.BaseROI method) (pyextal.roi.CBEDROI method) (pyextal.roi.LARBEDROI method) inplane_basis() (in module pyextal.acom.geometry) integer_relations() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method)

IntegrateLarbed() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) intensity_scale_normalize (pyextal.jaxEngine.setParams.OptConfig attribute) intensity_scale_optimize (pyextal.jaxEngine.setParams.OptConfig attribute) IntensitySettings (class in pyextal.jaxMultipole.intensity) intercomm (pyextal.blochwave.Mpiinfo attribute) internal_grid() (in module pyextal.superspace) (in module pyextal.superspace.structurefactor) interpolate() (pyextal.larbed.calibration.LARBEDCalibration method) (pyextal.larbed.LARBEDCalibration method) IntRadius (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) IntZero (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) invert() (in module pyextal.superspace.modulation) (pyextal.acom.AcomResult method) ipvt (pyextal.blochwave.BlochModule attribute) is_centro() (in module pyextal.jaxJoint.link) is_commensurate() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) is_loaded() (in module pyextal.superspace.engine) is_main() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) isotropic_beta() (in module pyextal.adp) istab (pyextal.blochwave.Sfpar attribute) itilt (pyextal.callBloch.Data attribute) itype (pyextal.blochwave.Cryst attribute) ix (pyextal.callBloch.Data attribute) iy (pyextal.callBloch.Data attribute)

J

jax_fns() (pyextal.jaxGeo.geometry.GeometryModel method) jftype (pyextal.blochwave.Xtal attribute) JOINT_FIELDS (in module pyextal.jaxJoint) (in module pyextal.jaxJoint.settings) joint_json (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute)

joint_optimize() (in module pyextal.jaxJoint.optimize) JointSettings (class in pyextal.jaxJoint) (class in pyextal.jaxJoint.settings) jtype (pyextal.blochwave.Xtal attribute)

K

k (pyextal.jaxGeo.objective.GeometryObjective property) k_bohr() (in module pyextal.jaxMultipole.radial) kappa (pyextal.jaxMultipole.params.SiteRefine attribute) (pyextal.jaxMultipole.SiteRefine attribute) kappa_p (pyextal.jaxMultipole.params.SiteRefine attribute) (pyextal.jaxMultipole.SiteRefine attribute) kappa_shared (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) kernel_radius (pyextal.jaxEngine.setParams.OptConfig attribute) (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) key (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.bank.AtomConfig attribute) (pyextal.jaxMultipole.bank.BankEntry attribute) (pyextal.jaxMultipole.data.ScanValue attribute) (pyextal.jaxMultipole.model.AtomSpec attribute)

keys (pyextal.jaxMultipole.intensity.FullMatrix attribute) (pyextal.jaxMultipole.intensity.MultipoleBridge attribute) keys() (pyextal.jaxMultipole.data.Observations method) kind (pyextal.jaxMultipole.data.Observations attribute) KIND_NAMES (in module pyextal.jaxJoint.datasets) kt2pixel() (pyextal.roi.CBEDROI method) kv (pyextal.blochwave.Difpar attribute) (pyextal.jaxMultipole.Crystal attribute) (pyextal.jaxMultipole.crystal.Crystal attribute) (pyextal.jaxMultipole.data.ScanValue attribute)

L

l (pyextal.jaxMultipole.bank.Orbital attribute) label (pyextal.blochwave.Cryst attribute) (pyextal.jaxMultipole.crystal.Site attribute) (pyextal.jaxMultipole.Site attribute) (pyextal.superspace.ModulatedAtom attribute) (pyextal.superspace.modulation.ModulatedAtom attribute) LABEL_OPS (in module pyextal.acom) (in module pyextal.acom.quality) labels() (in module pyextal.jaxMultipole.harmonics) (pyextal.superspace.indexing.ReflectionSet method) (pyextal.superspace.ReflectionSet method) ladder (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) ladder_kappa_p (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) ladder_table() (in module pyextal.jaxMultipole.report) Larbed (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) LARBED (pyextal.roi.ROITYPE attribute) larbed() (in module pyextal.blochwave) LARBED() (in module pyextal.callBloch) larbed2() (in module pyextal.blochwave) larbed_numpy() (in module pyextal.blochNumpy) LARBED_tilt() (in module pyextal.callBloch) LARBEDAnalysis (class in pyextal.larbed) (class in pyextal.larbed.analysis) LARBEDCalibration (class in pyextal.larbed) (class in pyextal.larbed.calibration) larbedCall() (pyextal.callBloch.SimParams method) LarbedDeconvolved (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) LARBEDDiffractionInfo (class in pyextal.dinfo) LARBEDROI (class in pyextal.roi) lastParam (pyextal.optimize.FineOptimize attribute) lattice() (in module pyextal.superspace.tas2) lattice_cosets() (in module pyextal.superspace.approximant) laue (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) layer_fractions (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) layer_report() (in module pyextal.jaxGeo.figures) layers (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute)

Layout (class in pyextal.jaxMultipole.model) layout (pyextal.jaxMultipole.model.MultipoleModel attribute) (pyextal.jaxMultipole.MultipoleModel attribute) (pyextal.jaxMultipole.params.ParameterMap attribute) learning_rate (pyextal.jaxEngine.setParams.OptConfig attribute) lib (pyextal.acom.AcomResult attribute) lib_idx (pyextal.acom.AcomResult attribute) link_map() (in module pyextal.jaxJoint.link) link_phase() (in module pyextal.jaxMultipole.symmetry) list_refinement_runs() (in module pyextal.jaxEngine.hdf5io) list_registered_models() (in module pyextal.jaxEngine.structureModel) lmax (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) load() (in module pyextal.superspace.engine) load_bank() (in module pyextal.jaxMultipole.bank) load_data() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.calibration.LARBEDCalibration method) (pyextal.larbed.LARBEDAnalysis method) (pyextal.larbed.LARBEDCalibration method) load_dataset() (in module pyextal.jaxGeo.io) load_for_refinement() (in module pyextal.jaxEngine.hdf5io) load_observations() (in module pyextal.jaxMultipole.cli) load_pre_refinement() (in module pyextal.hdf5io) local (pyextal.jaxMultipole.data.ScanValue attribute) local_frame() (in module pyextal.jaxMultipole.symmetry) local_params() (in module pyextal.jaxJoint.params) local_rotations() (in module pyextal.jaxMultipole.symmetry) log_every (pyextal.jaxMultipole.intensity.IntensitySettings attribute) logy (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) lookupReflections() (in module pyextal.callBloch) lookupSF() (in module pyextal.callBloch) lorentzian1D() (in module pyextal.larbed.peaks) lorentzian2D() (in module pyextal.larbed.peaks) loss_function (pyextal.jaxEngine.setParams.OptConfig attribute) loss_history (pyextal.jaxJoint.datasets.Dataset attribute) lower (pyextal.jaxMultipole.params.ParameterMap attribute) lr (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) (pyextal.jaxMultipole.intensity.IntensitySettings attribute) lr_x (pyextal.jaxMultipole.intensity.IntensitySettings attribute) lucy_Richardson() (in module pyextal.LucyRichardson)

M

M (pyextal.jaxMultipole.params.ParameterMap attribute) magnitude (pyextal.acom.tilt.TiltResult property) (pyextal.acom.TiltResult property) main() (in module pyextal.jaxGeo.cli) (in module pyextal.jaxJoint.cli) (in module pyextal.jaxMultipole.cli) (pyextal.superspace.indexing.ReflectionSet method) (pyextal.superspace.ReflectionSet method) manual() (pyextal.jaxMultipole.Crystal class method) (pyextal.jaxMultipole.crystal.Crystal class method) mapping (pyextal.acom.AcomResult attribute) maps (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) marker_sizes() (in module pyextal.superspace) (in module pyextal.superspace.saed) mass (pyextal.jaxMultipole.bank.BankEntry attribute) match_pairs() (in module pyextal.acom.solve) matchIdx() (in module pyextal.jaxEngine.utils) matchIndex() (pyextal.roi.BaseROI method) (pyextal.roi.LARBEDROI method) max_amplitude() (pyextal.superspace.DisplaciveModulation method) (pyextal.superspace.modulation.DisplaciveModulation method) MAX_D (pyextal.superspace.lattice.SuperspaceLattice attribute) (pyextal.superspace.SuperspaceLattice attribute) MAX_DAT_PATH (in module pyextal.jaxJoint.engine) MAX_PANELS (in module pyextal.optimize) meanimage() (pyextal.larbed.calibration.LARBEDCalibration method) (pyextal.larbed.LARBEDCalibration method) memory_warn (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) MEMORY_WARN_GB (in module pyextal.acom.tilt) merge() (in module pyextal.jaxMultipole.data) merge_coincident() (in module pyextal.superspace) (in module pyextal.superspace.indexing) message (pyextal.jaxMultipole.fit.FitResult attribute) metadata (pyextal.jaxEngine.optimize.BatchGenerator attribute) method (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) min_laue_max() (in module pyextal.acom) (in module pyextal.acom.library) min_n (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) mixing (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) mode (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.intensity.IntensitySettings attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) model (pyextal.jaxMultipole.intensity.FullMatrix attribute) model_factory() (in module pyextal.jaxEngine.structureModel) model_name (pyextal.jaxEngine.setParams.OptConfig attribute) model_params (pyextal.jaxEngine.setParams.OptConfig attribute) model_params_normalize (pyextal.jaxEngine.setParams.OptConfig attribute) model_params_range (pyextal.jaxEngine.setParams.OptConfig attribute) ModulatedAtom (class in pyextal.superspace) (class in pyextal.superspace.modulation) module pyextal pyextal.acom pyextal.acom.datfile pyextal.acom.detect pyextal.acom.geometry pyextal.acom.library pyextal.acom.plotting pyextal.acom.quality pyextal.acom.solve pyextal.acom.tilt pyextal.adp pyextal.blochNumpy pyextal.blochwave pyextal.callBloch pyextal.Constants pyextal.densityMap pyextal.dinfo pyextal.gof pyextal.hdf5io pyextal.jaxEngine pyextal.jaxEngine.hdf5io pyextal.jaxEngine.model pyextal.jaxEngine.optimize pyextal.jaxEngine.postProcess pyextal.jaxEngine.setParams pyextal.jaxEngine.structureModel pyextal.jaxEngine.utils pyextal.jaxGeo pyextal.jaxGeo.cli pyextal.jaxGeo.config pyextal.jaxGeo.figures pyextal.jaxGeo.geometry pyextal.jaxGeo.io pyextal.jaxGeo.lm pyextal.jaxGeo.objective pyextal.jaxGeo.oversub pyextal.jaxGeo.refine pyextal.jaxGeo.reflections pyextal.jaxGeo.settings pyextal.jaxGeo.simulate pyextal.jaxJoint pyextal.jaxJoint.cli pyextal.jaxJoint.datasets pyextal.jaxJoint.engine pyextal.jaxJoint.link pyextal.jaxJoint.optimize pyextal.jaxJoint.params pyextal.jaxJoint.refine pyextal.jaxJoint.report pyextal.jaxJoint.settings pyextal.jaxMultipole pyextal.jaxMultipole.bank pyextal.jaxMultipole.cli pyextal.jaxMultipole.constants pyextal.jaxMultipole.crystal pyextal.jaxMultipole.data pyextal.jaxMultipole.fit pyextal.jaxMultipole.harmonics pyextal.jaxMultipole.intensity pyextal.jaxMultipole.maps pyextal.jaxMultipole.model pyextal.jaxMultipole.params pyextal.jaxMultipole.plotting pyextal.jaxMultipole.protocol pyextal.jaxMultipole.radial pyextal.jaxMultipole.report pyextal.jaxMultipole.settings pyextal.jaxMultipole.symmetry pyextal.jaxMultipole.wien2k pyextal.larbed pyextal.larbed.analysis pyextal.larbed.calibration pyextal.larbed.empad pyextal.larbed.peaks pyextal.LucyRichardson pyextal.metric pyextal.optimize pyextal.roi pyextal.superspace pyextal.superspace.approximant pyextal.superspace.engine pyextal.superspace.indexing pyextal.superspace.lattice pyextal.superspace.modulation pyextal.superspace.saed pyextal.superspace.scattering pyextal.superspace.structurefactor pyextal.superspace.symmetry pyextal.superspace.tas2 pyextal.symmetry

moments() (in module pyextal.larbed.peaks) MOTT (in module pyextal.jaxMultipole.constants) Mpiinfo (class in pyextal.blochwave) mpiinfo (in module pyextal.blochwave) mpiinfo_despawn() (pyextal.blochwave.Mpiinfo method) mtf (pyextal.dinfo.CBEDDiffractionInfo attribute) mtf_2d (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.calibration.LARBEDCalibration attribute) (pyextal.larbed.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDCalibration attribute) MultipoleBridge (class in pyextal.jaxMultipole.intensity) MultipoleModel (class in pyextal.jaxMultipole) (class in pyextal.jaxMultipole.model) multipoles (pyextal.jaxMultipole.params.SiteRefine attribute) (pyextal.jaxMultipole.SiteRefine attribute)

N

n (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) (pyextal.adp.DWFModel property) (pyextal.jaxMultipole.bank.Orbital attribute) (pyextal.jaxMultipole.data.Observations attribute) (pyextal.superspace.Harmonic attribute) (pyextal.superspace.modulation.Harmonic attribute) n_functions() (in module pyextal.jaxMultipole.harmonics) n_l (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) n_obs (pyextal.jaxMultipole.fit.FitResult attribute) n_ops (pyextal.jaxMultipole.Crystal property) (pyextal.jaxMultipole.crystal.Crystal property) n_par (pyextal.jaxMultipole.fit.FitResult attribute) n_samples (pyextal.jaxEngine.optimize.BatchGenerator attribute) n_used (pyextal.acom.DetectorMap attribute) (pyextal.acom.solve.DetectorMap attribute) name (pyextal.gof.BaseGOF attribute) (pyextal.gof.Chi2 attribute) (pyextal.gof.Chi2_const attribute) (pyextal.gof.Chi2_LARBED attribute) (pyextal.gof.Chi2_LARBED_multibackground attribute) (pyextal.gof.Chi2_multibackground attribute) (pyextal.gof.XCorrelation attribute) (pyextal.jaxMultipole.bank.Orbital attribute) (pyextal.jaxMultipole.bank.Shell attribute) (pyextal.jaxMultipole.fit.Restraint attribute) (pyextal.superspace.SuperspaceOperation attribute) (pyextal.superspace.symmetry.SuperspaceOperation attribute) names (pyextal.adp.DWFModel attribute) (pyextal.jaxJoint.JointSettings attribute) (pyextal.jaxJoint.settings.JointSettings attribute) (pyextal.jaxMultipole.fit.FitResult attribute) (pyextal.jaxMultipole.model.Layout attribute) (pyextal.jaxMultipole.params.ParameterMap attribute) natoms (pyextal.blochwave.Cryst attribute) nbeams (pyextal.blochwave.Difpar attribute) ncore (pyextal.blochwave.Difpar attribute) ncsub4 (pyextal.blochwave.Spgr attribute) ndiag (pyextal.blochwave.BlochModule attribute) (pyextal.callBloch.Data attribute)

ndiags (pyextal.blochwave.Eigen attribute) nearest_zone_axis() (in module pyextal.acom) (in module pyextal.acom.library) nearly_commensurate_q() (in module pyextal.superspace.tas2) neg() (in module pyextal.jaxJoint.link) net_zone() (in module pyextal.acom) (in module pyextal.acom.tilt) NEUTRAL (in module pyextal.jaxGeo.geometry) neutral_valence (pyextal.jaxMultipole.bank.AtomConfig property) newton_iters (pyextal.jaxMultipole.intensity.IntensitySettings attribute) newton_lambda (pyextal.jaxMultipole.intensity.IntensitySettings attribute) newton_tol (pyextal.jaxMultipole.intensity.IntensitySettings attribute) newton_x() (in module pyextal.jaxMultipole.intensity) ngp (pyextal.blochwave.Spgr attribute) nidptr (pyextal.blochwave.Difpar attribute) nlayers (pyextal.jaxEngine.setParams.OptConfig attribute) noise (pyextal.larbed.analysis.LARBEDAnalysis attribute) (pyextal.larbed.LARBEDAnalysis attribute) noncentro (pyextal.optimize.FineOptimize attribute) norm() (pyextal.jaxMultipole.bank.Orbital method) norm_fn() (in module pyextal.jaxEngine.setParams) normalisation() (in module pyextal.jaxMultipole.harmonics) normalize_params() (in module pyextal.jaxEngine.setParams) normalizeX0() (pyextal.optimize.FineOptimize method) notes (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) (pyextal.jaxMultipole.data.ScanValue attribute) (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) nout (pyextal.callBloch.SimParams attribute) nref (pyextal.blochwave.Difpar attribute) nsite (pyextal.blochwave.Xtal attribute) ntab (pyextal.blochwave.Sfpar attribute) ntilt (pyextal.callBloch.SimParams attribute) ntype (pyextal.blochwave.Cryst attribute) nuclear_charge() (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) num_steps (pyextal.jaxEngine.setParams.OptConfig attribute) numIter (pyextal.dinfo.CBEDDiffractionInfo attribute) nx (pyextal.callBloch.SimParams attribute)

O

obs (pyextal.jaxMultipole.fit.FitResult attribute) Observations (class in pyextal.jaxMultipole.data) observations() (in module pyextal.jaxMultipole.wien2k) occ (pyextal.jaxMultipole.bank.Orbital attribute) (pyextal.jaxMultipole.crystal.Site attribute) (pyextal.jaxMultipole.Site attribute) occupancy (pyextal.superspace.ModulatedAtom attribute) (pyextal.superspace.modulation.ModulatedAtom attribute) occupation() (pyextal.superspace.ModulatedAtom method) (pyextal.superspace.modulation.ModulatedAtom method) occupational (pyextal.superspace.ModulatedAtom attribute) (pyextal.superspace.modulation.ModulatedAtom attribute) OccupationalModulation (class in pyextal.superspace) (class in pyextal.superspace.modulation) occupations (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.bank.Shell attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) offset (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) offsets() (pyextal.jaxGeo.geometry.GeometryModel method) omega (pyextal.jaxMultipole.Crystal property) (pyextal.jaxMultipole.crystal.Crystal property) omgmx (pyextal.blochwave.Difpar attribute) on_edge (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) ops_inv (pyextal.jaxMultipole.Crystal attribute) (pyextal.jaxMultipole.crystal.Crystal attribute) ops_W (pyextal.jaxMultipole.Crystal attribute) ops_w (pyextal.jaxMultipole.Crystal attribute) ops_W (pyextal.jaxMultipole.crystal.Crystal attribute) ops_w (pyextal.jaxMultipole.crystal.Crystal attribute) OptConfig (class in pyextal.jaxEngine.setParams) optimize() (in module pyextal.jaxEngine.optimize) (pyextal.optimize.FineOptimize method) optimizeCell() (pyextal.optimize.CoarseOptimize method) optimizeDWF() (pyextal.optimize.CoarseOptimize method) optimizeHV() (pyextal.optimize.CoarseOptimize method)

optimizeOrientationGeometry() (pyextal.optimize.CoarseOptimize method) optimizeOrientationGL() (pyextal.optimize.CoarseOptimize method) optimizeOrientationThickness() (pyextal.optimize.CoarseOptimize method) optimizeXYZ() (pyextal.optimize.CoarseOptimize method) orbit() (in module pyextal.jaxJoint.link) (in module pyextal.jaxMultipole.symmetry) Orbital (class in pyextal.jaxMultipole.bank) orbital() (pyextal.jaxMultipole.bank.BankEntry method) orbitals (pyextal.jaxMultipole.bank.BankEntry attribute) (pyextal.jaxMultipole.bank.Shell attribute) order (pyextal.jaxMultipole.crystal.Site property) (pyextal.jaxMultipole.Site property) (pyextal.superspace.Harmonic property) (pyextal.superspace.indexing.ReflectionSet attribute) (pyextal.superspace.modulation.Harmonic property) (pyextal.superspace.ReflectionSet attribute) out (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.intensity.IntensitySettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) out_dir (pyextal.jaxJoint.JointSettings attribute) (pyextal.jaxJoint.settings.JointSettings attribute) out_larbed() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) output_indices (pyextal.jaxEngine.setParams.OptConfig attribute) output_shape (pyextal.jaxEngine.setParams.OptConfig attribute) oversub (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) oversub_config() (in module pyextal.jaxGeo.oversub) oversub_indices (pyextal.jaxEngine.setParams.OptConfig attribute) oversub_leak (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) oversub_leak_index (pyextal.jaxEngine.setParams.OptConfig attribute) oversub_leak_upper (pyextal.jaxEngine.setParams.OptConfig attribute) oversub_offset_upper (pyextal.jaxEngine.setParams.OptConfig attribute) oversub_optimize (pyextal.jaxEngine.setParams.OptConfig attribute) oversub_start (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute)

P

p (pyextal.jaxMultipole.fit.FitResult attribute) p() (pyextal.jaxMultipole.intensity.MultipoleBridge method) (pyextal.jaxMultipole.params.ParameterMap method) p0 (pyextal.jaxMultipole.model.Layout attribute) (pyextal.jaxMultipole.params.ParameterMap attribute) p_cov() (pyextal.jaxMultipole.params.ParameterMap method) p_esd (pyextal.jaxMultipole.fit.FitResult attribute) p_esd_of() (pyextal.jaxMultipole.fit.FitResult method) pair_table() (in module pyextal.jaxMultipole.bank) PANEL_COLS (in module pyextal.optimize) panelGrid() (in module pyextal.optimize) param (pyextal.optimize.CoarseOptimize attribute) parameter_table() (in module pyextal.jaxMultipole.report) ParameterMap (class in pyextal.jaxMultipole.params) parses (pyextal.jaxJoint.engine.EngineSwitch attribute) Pc (pyextal.jaxMultipole.bank.AtomConfig property) peak_idx (pyextal.acom.AcomResult attribute) peaks (pyextal.acom.AcomResult attribute) (pyextal.larbed.calibration.LARBEDCalibration attribute) (pyextal.larbed.LARBEDCalibration attribute) penalty() (pyextal.adp.DWFModel method) per (pyextal.jaxMultipole.intensity.FullMatrix attribute) perturbROI (pyextal.optimize.FineOptimize property) phase_shift() (in module pyextal.superspace.modulation) phaseDict (pyextal.symmetry.GroupSymmetry attribute) physical() (pyextal.jaxMultipole.intensity.MultipoleBridge method) pi (pyextal.blochwave.Constants attribute) pix2Tilt() (in module pyextal.roi) pixel2exp() (pyextal.roi.CBEDROI method) pixel_size (pyextal.acom.DetectorMap attribute) (pyextal.acom.solve.DetectorMap attribute) plane_atoms() (in module pyextal.jaxMultipole.maps) plane_grid() (in module pyextal.jaxMultipole.maps) plot_averages() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) plot_grid_vectors() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) plot_history() (in module pyextal.jaxGeo.figures) plot_image() (in module pyextal.superspace) (in module pyextal.superspace.saed) plot_indexed() (in module pyextal.acom) (in module pyextal.acom.plotting) plot_IntegratedLarbed() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) plot_larbed() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) plot_map() (in module pyextal.jaxMultipole.maps) plot_map2d() (in module pyextal.jaxMultipole.plotting) plot_parameters() (in module pyextal.jaxMultipole.plotting) plot_pattern() (in module pyextal.superspace) (in module pyextal.superspace.saed) plot_planes() (in module pyextal.jaxMultipole.plotting) plot_sf_differences() (in module pyextal.jaxMultipole.plotting) plot_static_dF() (in module pyextal.jaxMultipole.plotting) plot_zone_map() (in module pyextal.acom) (in module pyextal.acom.plotting) plotDensityMap_2D() (in module pyextal.densityMap) plotDensityMapIsosurface() (in module pyextal.densityMap) pmap (pyextal.jaxMultipole.fit.FitResult attribute) point_group_name() (in module pyextal.jaxMultipole.symmetry) polish (pyextal.jaxMultipole.intensity.IntensitySettings attribute) position (pyextal.superspace.ModulatedAtom attribute) (pyextal.superspace.modulation.ModulatedAtom attribute) post_process_intensity() (in module pyextal.jaxEngine.postProcess) power_regularization_weight (pyextal.jaxEngine.setParams.OptConfig attribute) Precession() (in module pyextal.larbed) (in module pyextal.larbed.empad) Precession_Angled() (in module pyextal.larbed) (in module pyextal.larbed.empad) precision (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) predict_excited() (in module pyextal.acom) (in module pyextal.acom.tilt) predicted() (pyextal.acom.AcomResult method) prepare() (in module pyextal.jaxJoint.datasets) prepare_reflection_bounds() (in module pyextal.jaxEngine.setParams) PreRefinementResult (class in pyextal.hdf5io) print_correlations() (in module pyextal.jaxGeo.lm) print_link_table() (in module pyextal.jaxJoint.report) print_phase_table() (in module pyextal.jaxGeo.figures) print_shared_result() (in module pyextal.jaxJoint.report) probe (pyextal.optimize.FineOptimize property) probe_gamma_range (pyextal.jaxEngine.setParams.OptConfig attribute) probe_gamma_start (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) probe_image (pyextal.larbed.calibration.LARBEDCalibration attribute) (pyextal.larbed.LARBEDCalibration attribute) probe_normalize (pyextal.jaxEngine.setParams.OptConfig attribute) probe_optimize (pyextal.jaxEngine.setParams.OptConfig attribute) PROBE_RANGE (in module pyextal.jaxGeo.settings) probe_sigma_range (pyextal.jaxEngine.setParams.OptConfig attribute) probe_sigma_start (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) project() (in module pyextal.acom.geometry) project_pattern() (in module pyextal.superspace) (in module pyextal.superspace.saed) propagate() (in module pyextal.jaxEngine.model) protocol_steps() (in module pyextal.jaxMultipole.protocol) prune_noisy() (in module pyextal.acom) (in module pyextal.acom.quality) pseudo_voigt_kernel() (in module pyextal.superspace) (in module pyextal.superspace.saed) published_atoms() (in module pyextal.superspace.tas2) published_q() (in module pyextal.superspace.tas2) Pv (pyextal.jaxMultipole.bank.AtomConfig property) (pyextal.jaxMultipole.params.SiteRefine attribute) (pyextal.jaxMultipole.SiteRefine attribute) pyextal module pyextal.acom module pyextal.acom.datfile module pyextal.acom.detect module pyextal.acom.geometry module pyextal.acom.library module pyextal.acom.plotting module pyextal.acom.quality module pyextal.acom.solve module pyextal.acom.tilt module pyextal.adp module pyextal.blochNumpy module pyextal.blochwave module pyextal.callBloch module pyextal.Constants module pyextal.densityMap module pyextal.dinfo module pyextal.gof module

pyextal.hdf5io module pyextal.jaxEngine module pyextal.jaxEngine.hdf5io module pyextal.jaxEngine.model module pyextal.jaxEngine.optimize module pyextal.jaxEngine.postProcess module pyextal.jaxEngine.setParams module pyextal.jaxEngine.structureModel module pyextal.jaxEngine.utils module pyextal.jaxGeo module pyextal.jaxGeo.cli module pyextal.jaxGeo.config module pyextal.jaxGeo.figures module pyextal.jaxGeo.geometry module pyextal.jaxGeo.io module pyextal.jaxGeo.lm module pyextal.jaxGeo.objective module pyextal.jaxGeo.oversub module pyextal.jaxGeo.refine module pyextal.jaxGeo.reflections module pyextal.jaxGeo.settings module pyextal.jaxGeo.simulate module pyextal.jaxJoint module pyextal.jaxJoint.cli module pyextal.jaxJoint.datasets module pyextal.jaxJoint.engine module pyextal.jaxJoint.link module pyextal.jaxJoint.optimize module pyextal.jaxJoint.params module pyextal.jaxJoint.refine module pyextal.jaxJoint.report module pyextal.jaxJoint.settings module pyextal.jaxMultipole module pyextal.jaxMultipole.bank module pyextal.jaxMultipole.cli module pyextal.jaxMultipole.constants module pyextal.jaxMultipole.crystal module pyextal.jaxMultipole.data module pyextal.jaxMultipole.fit module pyextal.jaxMultipole.harmonics module pyextal.jaxMultipole.intensity module pyextal.jaxMultipole.maps module pyextal.jaxMultipole.model module pyextal.jaxMultipole.params module pyextal.jaxMultipole.plotting module pyextal.jaxMultipole.protocol module pyextal.jaxMultipole.radial module pyextal.jaxMultipole.report module pyextal.jaxMultipole.settings module pyextal.jaxMultipole.symmetry module pyextal.jaxMultipole.wien2k module pyextal.larbed module pyextal.larbed.analysis module pyextal.larbed.calibration module pyextal.larbed.empad module pyextal.larbed.peaks module pyextal.LucyRichardson module pyextal.metric module pyextal.optimize module pyextal.roi module pyextal.superspace module pyextal.superspace.approximant module pyextal.superspace.engine module pyextal.superspace.indexing module pyextal.superspace.lattice module pyextal.superspace.modulation module pyextal.superspace.saed module pyextal.superspace.scattering module pyextal.superspace.structurefactor module pyextal.superspace.symmetry module pyextal.superspace.tas2 module pyextal.symmetry module

Q

q (pyextal.superspace.lattice.SuperspaceLattice attribute) (pyextal.superspace.SuperspaceLattice attribute)

R

R (pyextal.jaxMultipole.fit.FitResult attribute) (pyextal.superspace.SuperspaceOperation attribute) (pyextal.superspace.symmetry.SuperspaceOperation attribute) radial_density() (in module pyextal.jaxMultipole.bank) radial_profile() (in module pyextal.larbed) (in module pyextal.larbed.empad) RandomGenerator (class in pyextal.jaxEngine.optimize) rank() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) ranking (pyextal.acom.AcomResult attribute) ratio (pyextal.blochwave.Constants attribute) ratio1 (pyextal.blochwave.Difpar attribute) rationalise() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) read_dat_beams() (in module pyextal.acom) (in module pyextal.acom.datfile) read_history() (in module pyextal.jaxGeo.figures) read_in5() (in module pyextal.jaxMultipole.wien2k) read_output3() (in module pyextal.jaxMultipole.wien2k) read_rho() (in module pyextal.jaxMultipole.wien2k) read_scan_values() (in module pyextal.jaxMultipole.data) ReadRaw() (in module pyextal.larbed) (in module pyextal.larbed.empad) real_wigner() (in module pyextal.jaxMultipole.harmonics) rebuild_metadata() (in module pyextal.jaxGeo.geometry) record() (pyextal.jaxJoint.engine.EngineSwitch method) reduce_zone() (in module pyextal.acom.plotting) refine() (in module pyextal.acom.solve) (in module pyextal.jaxGeo) (in module pyextal.jaxGeo.refine) (in module pyextal.jaxJoint) (in module pyextal.jaxJoint.refine) refine_geometry() (in module pyextal.jaxJoint.refine) refine_intensities() (in module pyextal.jaxMultipole.intensity) refine_layers (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) refine_sequence() (in module pyextal.jaxMultipole.intensity) refined_entity (pyextal.jaxEngine.setParams.OptConfig attribute) refineProbe (pyextal.optimize.FineOptimize attribute) RefineSettings (class in pyextal.jaxGeo) (class in pyextal.jaxGeo.settings) reflection_condition() (in module pyextal.superspace.tas2) reflection_snr() (in module pyextal.acom) (in module pyextal.acom.quality) reflection_stats() (in module pyextal.jaxMultipole.intensity) ReflectionLibrary (class in pyextal.acom) (class in pyextal.acom.library) reflections (pyextal.jaxEngine.setParams.OptConfig attribute) (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) (pyextal.optimize.FineOptimize attribute) reflections_lowerbound (pyextal.jaxEngine.setParams.OptConfig attribute) reflections_normalize (pyextal.jaxEngine.setParams.OptConfig attribute) reflections_upperbound (pyextal.jaxEngine.setParams.OptConfig attribute) ReflectionSet (class in pyextal.superspace) (class in pyextal.superspace.indexing) register_model() (in module pyextal.jaxEngine.structureModel) reindex_at_zone() (in module pyextal.acom) (in module pyextal.acom.tilt) relabel_holz() (in module pyextal.acom) (in module pyextal.acom.tilt)

render_image() (in module pyextal.superspace) (in module pyextal.superspace.saed) report() (pyextal.adp.DWFModel method) report_cost() (in module pyextal.jaxGeo.config) reproduction_error() (pyextal.jaxGeo.geometry.GeometryModel method) resetugh() (in module pyextal.blochwave) reshape_tilts_to_2d() (in module pyextal.jaxEngine.utils) residual_fn() (in module pyextal.jaxMultipole.fit) residual_table() (in module pyextal.jaxMultipole.report) resolve() (pyextal.superspace.SuperspaceOperation method) (pyextal.superspace.symmetry.SuperspaceOperation method) resolve_dat() (in module pyextal.jaxGeo.io) resolve_h5() (in module pyextal.jaxGeo.io) resolve_label_sign() (in module pyextal.acom) (in module pyextal.acom.quality) resolve_label_symmetry() (in module pyextal.acom) (in module pyextal.acom.quality) resolve_reflections() (in module pyextal.jaxGeo.reflections) resolved() (pyextal.jaxGeo.RefineSettings method) (pyextal.jaxGeo.settings.RefineSettings method) (pyextal.jaxJoint.JointSettings method) (pyextal.jaxJoint.settings.JointSettings method) rest_steps (pyextal.jaxMultipole.intensity.IntensitySettings attribute) Restraint (class in pyextal.jaxMultipole.fit) restraints (pyextal.jaxMultipole.fit.Fitter attribute) (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) result_plot() (in module pyextal.jaxEngine.utils) review_dir (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) review_reflections() (in module pyextal.jaxGeo.reflections) rho_plane_points() (in module pyextal.jaxMultipole.wien2k) rms (pyextal.acom.DetectorMap attribute) (pyextal.acom.solve.DetectorMap attribute) robust_location() (in module pyextal.jaxMultipole.data) roi (pyextal.gof.Chi2_LARBED attribute) (pyextal.optimize.CoarseOptimize attribute) (pyextal.optimize.FineOptimize attribute) roi_regions (pyextal.hdf5io.PreRefinementResult attribute) roi_size (pyextal.larbed.calibration.LARBEDCalibration attribute) (pyextal.larbed.LARBEDCalibration attribute) ROItarget() (pyextal.optimize.FineOptimize static method) ROITYPE (class in pyextal.roi) roitype (pyextal.roi.BaseROI attribute) (pyextal.roi.CBEDROI attribute) (pyextal.roi.LARBEDROI attribute) rotation (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) (pyextal.roi.BaseROI property) rotation() (in module pyextal.jaxJoint.link) (in module pyextal.roi) rotation_angle() (in module pyextal.jaxMultipole.harmonics) rotation_scan (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) run (pyextal.jaxMultipole.data.ScanValue attribute) (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) run_isolated() (in module pyextal.superspace.engine) run_ladder() (in module pyextal.jaxMultipole.cli) run_protocol() (in module pyextal.jaxMultipole.protocol)

S

s() (pyextal.jaxMultipole.Crystal method) (pyextal.jaxMultipole.crystal.Crystal method) S_HARMONICS (in module pyextal.superspace.tas2) saed_pattern() (in module pyextal.superspace) (in module pyextal.superspace.saed) satellite_indices() (in module pyextal.superspace) (in module pyextal.superspace.indexing) satellite_length() (in module pyextal.superspace) (in module pyextal.superspace.indexing) satellite_metric() (in module pyextal.superspace) (in module pyextal.superspace.indexing) satellite_order() (pyextal.superspace.lattice.SuperspaceLattice static method) (pyextal.superspace.SuperspaceLattice static method) satellites() (pyextal.superspace.indexing.ReflectionSet method) (pyextal.superspace.ReflectionSet method) satlen (pyextal.superspace.DiffractionPattern attribute) (pyextal.superspace.indexing.ReflectionSet attribute) (pyextal.superspace.ReflectionSet attribute) (pyextal.superspace.saed.DiffractionPattern attribute) saturation_level() (in module pyextal.superspace) (in module pyextal.superspace.saed) save() (pyextal.dinfo.BaseDiffractionInfo method) save_comparison_png() (in module pyextal.jaxGeo.figures) save_h5() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) save_hkl() (pyextal.dinfo.BaseDiffractionInfo method) save_json() (in module pyextal.jaxMultipole.report) save_larbed() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) save_pre_refinement() (in module pyextal.hdf5io) save_raw() (in module pyextal.hdf5io) save_refinement() (in module pyextal.jaxEngine.hdf5io) save_runs (pyextal.jaxMultipole.intensity.IntensitySettings attribute) save_three_way_png() (in module pyextal.jaxMultipole.intensity) scale (pyextal.jaxMultipole.intensity.MultipoleBridge attribute) scale() (in module pyextal.metric) scale_range (pyextal.jaxEngine.setParams.OptConfig attribute) scale_window (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) scaling() (pyextal.gof.Chi2 method) ScanValue (class in pyextal.jaxMultipole.data) score (pyextal.acom.AcomResult attribute) score_mapping() (in module pyextal.acom.solve) scratch_bytes() (pyextal.jaxGeo.objective.GeometryObjective method) select() (pyextal.acom.library.ReflectionLibrary method) (pyextal.acom.ReflectionLibrary method) (pyextal.jaxMultipole.data.Observations method) (pyextal.superspace.indexing.ReflectionSet method) (pyextal.superspace.ReflectionSet method) select_outputs() (in module pyextal.jaxEngine.model) select_reflections() (in module pyextal.jaxGeo.reflections) selectBeams() (in module pyextal.optimize) selectROI() (pyextal.roi.BaseROI method) SERIES (in module pyextal.jaxMultipole.plotting) set_beta() (in module pyextal.adp) set_layer_fractions() (in module pyextal.jaxGeo.config) setTilt0() (pyextal.roi.CBEDROI method) (pyextal.roi.LARBEDROI method) setup_optimization_model() (in module pyextal.jaxEngine.setParams) setup_optimization_params() (in module pyextal.jaxEngine.setParams) setup_state() (in module pyextal.jaxMultipole.intensity) setup_structure_factors() (in module pyextal.jaxEngine.setParams) SetupError SF_COMPONENTS (in module pyextal.jaxGeo.figures) sf_differences() (in module pyextal.jaxMultipole.plotting) SF_LABELS (in module pyextal.jaxGeo.figures) sf_mask (pyextal.jaxEngine.setParams.OptConfig attribute) SF_MASKS (in module pyextal.jaxGeo) (in module pyextal.jaxGeo.settings) Sfmanager (class in pyextal.blochwave) sfmanager (in module pyextal.blochwave) sfMask (pyextal.optimize.FineOptimize attribute) Sfpar (class in pyextal.blochwave) sfpar (in module pyextal.blochwave) SFtarget() (pyextal.optimize.FineOptimize static method) sgmax (pyextal.blochwave.Difpar attribute) sgmin (pyextal.blochwave.Difpar attribute) sgnoise() (in module pyextal.LucyRichardson) shape (pyextal.acom.AcomResult attribute) (pyextal.jaxGeo.geometry.GeometryModel attribute) shared_value() (in module pyextal.jaxJoint.params) Shell (class in pyextal.jaxMultipole.bank) shell_density() (in module pyextal.jaxMultipole.maps) shells (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) shiftDisk (pyextal.optimize.FineOptimize property) ShiftTarget() (pyextal.optimize.FineOptimize static method) SIGMA (in module pyextal.superspace.tas2) sigma (pyextal.jaxMultipole.data.Observations attribute) (pyextal.jaxMultipole.fit.Restraint attribute) (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) SIGMA_C (in module pyextal.superspace.tas2) sign_agreement (pyextal.jaxMultipole.data.Observations attribute) significance (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) sim_batch (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) sim_memory (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) simgrid (pyextal.hdf5io.PreRefinementResult attribute)

simParam() (pyextal.callBloch.SimParams method) SimParams (class in pyextal.callBloch) simulate() (in module pyextal.callBloch) (in module pyextal.jaxEngine.utils) simulate_dataset() (in module pyextal.jaxMultipole.intensity) simulate_safely() (in module pyextal.jaxGeo.simulate) simulate_with_gradients() (in module pyextal.jaxEngine.utils) sin (pyextal.superspace.Harmonic attribute) (pyextal.superspace.modulation.Harmonic attribute) singular_values (pyextal.jaxMultipole.fit.FitResult attribute) Site (class in pyextal.jaxMultipole) (class in pyextal.jaxMultipole.crystal) site (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) site() (pyextal.jaxMultipole.Crystal method) (pyextal.jaxMultipole.crystal.Crystal method) site_names() (pyextal.jaxMultipole.model.Layout method) site_symmetry() (in module pyextal.adp) site_values() (in module pyextal.jaxMultipole.report) SiteRefine (class in pyextal.jaxMultipole) (class in pyextal.jaxMultipole.params) sites (pyextal.jaxMultipole.Crystal attribute) (pyextal.jaxMultipole.crystal.Crystal attribute) (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.model.MultipoleModel attribute) (pyextal.jaxMultipole.MultipoleModel attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) slices (pyextal.adp.DWFModel attribute) smax (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) smult (pyextal.blochwave.Cryst attribute) snapshot_steps() (in module pyextal.jaxEngine.hdf5io) snorm (pyextal.blochwave.Difpar attribute) (pyextal.callBloch.SimParams attribute) solve_orientation() (in module pyextal.acom) (in module pyextal.acom.solve) sort_keys() (in module pyextal.jaxJoint.link) source (pyextal.jaxMultipole.bank.Shell attribute) (pyextal.jaxMultipole.Crystal attribute) (pyextal.jaxMultipole.crystal.Crystal attribute) (pyextal.jaxMultipole.data.Observations attribute) space_group_ops() (in module pyextal.adp) spacegroup_reflections() (in module pyextal.jaxGeo.reflections) Spgr (class in pyextal.blochwave) spgr (in module pyextal.blochwave) spgsym() (in module pyextal.jaxEngine.setParams) sph (pyextal.jaxMultipole.bank.BankEntry attribute) sph_fx() (in module pyextal.jaxMultipole.bank) spherical_f() (in module pyextal.jaxMultipole.radial) split_array_by_lengths() (in module pyextal.roi) spread (pyextal.jaxMultipole.data.Observations attribute) stab (pyextal.blochwave.Sfpar attribute) (pyextal.jaxMultipole.crystal.Site attribute) (pyextal.jaxMultipole.Site attribute) stack() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) start (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) start_tilt (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) steps (pyextal.acom.tilt.TiltResult property) (pyextal.acom.TiltResult property) (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) (pyextal.jaxMultipole.intensity.IntensitySettings attribute) stereographic() (in module pyextal.acom.plotting) sto_fb() (in module pyextal.jaxMultipole.radial) store() (pyextal.callBloch.SimParams method) stride (pyextal.jaxEngine.setParams.OptConfig attribute) strong() (pyextal.acom.library.ReflectionLibrary method) (pyextal.acom.ReflectionLibrary method) strong_correlations() (pyextal.jaxMultipole.fit.FitResult method) structure() (in module pyextal.superspace.tas2) structure_factor() (in module pyextal.superspace) (in module pyextal.superspace.engine) (in module pyextal.superspace.structurefactor) structure_matrix_slab() (in module pyextal.jaxEngine.model) subsample (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) success (pyextal.jaxMultipole.fit.FitResult attribute) sumx() (in module pyextal.metric) supercell_atoms() (in module pyextal.superspace) (in module pyextal.superspace.approximant) supercell_cell() (in module pyextal.superspace) (in module pyextal.superspace.approximant) supercell_matrix() (pyextal.superspace.lattice.SuperspaceLattice method) (pyextal.superspace.SuperspaceLattice method) supercell_saed() (in module pyextal.superspace) (in module pyextal.superspace.approximant) SuperspaceLattice (class in pyextal.superspace) (class in pyextal.superspace.lattice) SuperspaceOperation (class in pyextal.superspace) (class in pyextal.superspace.symmetry) symmetrizeVHKL() (in module pyextal.callBloch) symmetry (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) symmetry_constraint (pyextal.jaxEngine.setParams.OptConfig attribute) symmetry_operators() (in module pyextal.acom.plotting) symUpdate (pyextal.optimize.FineOptimize attribute) syst (pyextal.blochwave.Spgr attribute) sz (pyextal.jaxMultipole.bank.BankEntry attribute) SZ_ORDER (in module pyextal.jaxMultipole.bank)

T

ta_displacive() (in module pyextal.superspace.tas2) TA_HARMONICS (in module pyextal.superspace.tas2) table() (pyextal.jaxMultipole.data.Observations method) tables (pyextal.jaxMultipole.FitSettings attribute) (pyextal.jaxMultipole.settings.FitSettings attribute) tabulated() (in module pyextal.jaxJoint.link) target (pyextal.jaxMultipole.fit.Restraint attribute) TARGET_ZOOM (in module pyextal.acom.tilt) tau (pyextal.superspace.SuperspaceOperation attribute) (pyextal.superspace.symmetry.SuperspaceOperation attribute) tau_i (pyextal.superspace.SuperspaceOperation attribute) (pyextal.superspace.symmetry.SuperspaceOperation attribute) templates (pyextal.hdf5io.PreRefinementResult attribute) (pyextal.optimize.CoarseOptimize attribute) (pyextal.roi.BaseROI property) terminate() (in module pyextal.callBloch) theta (pyextal.acom.DetectorMap attribute) (pyextal.acom.solve.DetectorMap attribute) theta_from() (pyextal.jaxMultipole.intensity.MultipoleBridge method) thickness (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) (pyextal.dinfo.BaseDiffractionInfo attribute) (pyextal.optimize.CoarseOptimize attribute) (pyextal.optimize.FineOptimize attribute) thickness_normalize (pyextal.jaxEngine.setParams.OptConfig attribute) thickness_optimize (pyextal.jaxEngine.setParams.OptConfig attribute) thickness_range (pyextal.jaxEngine.setParams.OptConfig attribute) thickness_window (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) thicknessTarget() (pyextal.optimize.CoarseOptimize static method) tile (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) tilt (pyextal.acom.tilt.TiltResult attribute) (pyextal.acom.TiltResult attribute) (pyextal.blochwave.Eigen attribute) tilt() (in module pyextal.callBloch)

tilt0 (pyextal.callBloch.SimParams attribute) TILT_BATCH (in module pyextal.jaxEngine.model) tilt_batch (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) tilt_from_zero_beam() (in module pyextal.acom) (in module pyextal.acom.tilt) tilt_run() (in module pyextal.blochwave) (in module pyextal.callBloch) tilt_run_numpy() (in module pyextal.blochNumpy) TiltResult (class in pyextal.acom) (class in pyextal.acom.tilt) tilts (pyextal.callBloch.DataCollector attribute) (pyextal.callBloch.SimParams attribute) (pyextal.jaxEngine.optimize.BatchGenerator attribute) tiltUnit() (in module pyextal.callBloch) tiltX (pyextal.dinfo.BaseDiffractionInfo attribute) tiltY (pyextal.dinfo.BaseDiffractionInfo attribute) to_dinfo() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) to_grid() (pyextal.acom.AcomResult method) to_key() (in module pyextal.jaxMultipole.symmetry) to_pixels() (pyextal.acom.DetectorMap method) (pyextal.acom.solve.DetectorMap method) to_reciprocal() (pyextal.acom.DetectorMap method) (pyextal.acom.solve.DetectorMap method) to_wsl_path() (in module pyextal.jaxGeo.io) to_yaml() (pyextal.jaxEngine.setParams.OptConfig method) tol (pyextal.superspace.lattice.SuperspaceLattice attribute) (pyextal.superspace.SuperspaceLattice attribute) transform_reflection() (in module pyextal.superspace) (in module pyextal.superspace.symmetry) transformDP() (pyextal.roi.BaseROI method) (pyextal.roi.CBEDROI method) (pyextal.roi.LARBEDROI method) tripled_to_basic() (in module pyextal.superspace.tas2) TWO_PI_SQ (in module pyextal.adp) twopi (pyextal.blochwave.Constants attribute)

U

u (pyextal.jaxGeo.geometry.GeometryModel attribute) U (pyextal.jaxMultipole.data.ScanValue attribute) (pyextal.jaxMultipole.params.SiteRefine attribute) (pyextal.jaxMultipole.SiteRefine attribute) U_iam (pyextal.jaxMultipole.intensity.FullMatrix attribute) Uabs (pyextal.jaxMultipole.data.ScanValue attribute) ug() (pyextal.jaxMultipole.intensity.MultipoleBridge method) (pyextal.jaxMultipole.model.MultipoleModel method) (pyextal.jaxMultipole.MultipoleModel method) ug_units() (pyextal.jaxMultipole.intensity.MultipoleBridge method) Ugh_dict (pyextal.symmetry.GroupSymmetry attribute) ughi (pyextal.blochwave.BlochModule attribute) ughr (pyextal.blochwave.BlochModule attribute) uij_to_beta() (in module pyextal.adp) uniqueBeams() (pyextal.symmetry.GroupSymmetry method) units (pyextal.jaxGeo.objective.GeometryObjective attribute) (pyextal.jaxJoint.datasets.Dataset attribute)

units_for() (in module pyextal.jaxGeo.geometry) unload() (in module pyextal.superspace.engine) update_mode (pyextal.jaxEngine.setParams.OptConfig attribute) updateExpGrid() (pyextal.roi.BaseROI method) (pyextal.roi.CBEDROI method) (pyextal.roi.LARBEDROI method) updatekv() (pyextal.blochwave.Difpar method) updateSF() (pyextal.dinfo.BaseDiffractionInfo method) updateSimGrid() (pyextal.roi.BaseROI method) (pyextal.roi.LARBEDROI method) updateSymUgh() (in module pyextal.callBloch) updateUgh() (in module pyextal.callBloch) upper (pyextal.jaxMultipole.params.ParameterMap attribute) use_imag (pyextal.jaxMultipole.data.Observations attribute) use_voigt (pyextal.jaxEngine.setParams.OptConfig attribute)

V

v (pyextal.blochwave.BlochModule attribute) (pyextal.jaxGeo.geometry.GeometryModel attribute) v0 (pyextal.blochwave.Cryst attribute) valence (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.bank.AtomConfig attribute) (pyextal.jaxMultipole.bank.Orbital attribute) (pyextal.jaxMultipole.model.AtomSpec attribute) value (pyextal.jaxMultipole.data.Observations attribute) value() (pyextal.jaxGeo.objective.GeometryObjective method) (pyextal.jaxMultipole.fit.FitResult method) (pyextal.jaxMultipole.params.ParameterMap method) value_grad() (pyextal.jaxGeo.objective.GeometryObjective method) value_grad_hess() (pyextal.jaxGeo.objective.GeometryObjective method) variance (pyextal.hdf5io.PreRefinementResult attribute) (pyextal.jaxEngine.optimize.BatchGenerator attribute) (pyextal.jaxEngine.optimize.RandomGenerator attribute)

varianceMaps (pyextal.dinfo.LARBEDDiffractionInfo attribute) vhkl (pyextal.blochwave.Difpar attribute) vi (pyextal.callBloch.Data property) visible() (pyextal.superspace.DiffractionPattern method) (pyextal.superspace.saed.DiffractionPattern method) visible_holz() (in module pyextal.acom) (in module pyextal.acom.library) vmapped_forward (in module pyextal.jaxEngine.model) vmapped_forward_reference (in module pyextal.jaxEngine.model) vmapped_grad_forward (in module pyextal.jaxEngine.model) voigt (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) voigt_2d() (in module pyextal.optimize) vol (pyextal.blochwave.Constants attribute) volume() (in module pyextal.metric) vr (pyextal.callBloch.Data property)

W

warm_start() (in module pyextal.jaxMultipole.intensity) warmup (pyextal.jaxGeo.RefineSettings attribute) (pyextal.jaxGeo.settings.RefineSettings attribute) (pyextal.jaxMultipole.intensity.IntensitySettings attribute) warmup_steps (pyextal.jaxEngine.setParams.OptConfig attribute) wavel (pyextal.blochwave.Difpar attribute) (pyextal.jaxGeo.geometry.GeometryModel attribute) wavelength() (in module pyextal.callBloch) weight (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) weighting (pyextal.jaxJoint.JointSettings attribute) (pyextal.jaxJoint.settings.JointSettings attribute) WEIGHTINGS (in module pyextal.jaxJoint.cli) (in module pyextal.jaxJoint.settings) wide_dat() (in module pyextal.acom) (in module pyextal.acom.tilt) window() (in module pyextal.jaxGeo.config)

with_kv() (pyextal.jaxMultipole.Crystal method) (pyextal.jaxMultipole.crystal.Crystal method) without() (pyextal.jaxMultipole.data.Observations method) wR (pyextal.jaxMultipole.fit.FitResult attribute) write_cube() (in module pyextal.densityMap) write_dat() (in module pyextal.acom) (in module pyextal.acom.datfile) (in module pyextal.superspace) (in module pyextal.superspace.approximant) (in module pyextal.superspace.engine) (pyextal.acom.AcomResult method) write_oriented_dat() (in module pyextal.acom) (in module pyextal.acom.datfile) write_reference_dat() (pyextal.acom.AcomResult method) write_summary() (in module pyextal.jaxJoint.report) write_tilted_dat() (in module pyextal.acom) (in module pyextal.acom.tilt)

X

x (pyextal.jaxJoint.datasets.Dataset attribute) (pyextal.jaxMultipole.fit.FitResult attribute) x0 (pyextal.adp.DWFModel attribute) (pyextal.jaxMultipole.params.ParameterMap attribute) x_of() (pyextal.jaxGeo.objective.GeometryObjective method) x_ref (pyextal.jaxGeo.objective.GeometryObjective attribute) x_to_delta() (in module pyextal.jaxGeo.geometry) xaxis (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) XCorrelation (class in pyextal.gof)

xray_form_factor() (in module pyextal.superspace) (in module pyextal.superspace.scattering) Xtal (class in pyextal.blochwave) xtal (in module pyextal.blochwave) xy (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) xyz (pyextal.blochwave.Xtal attribute) (pyextal.jaxMultipole.crystal.Site attribute) (pyextal.jaxMultipole.Site attribute) xyz0 (pyextal.blochwave.Xtal attribute)

Z

Z (pyextal.jaxMultipole.bank.AtomConfig attribute) (pyextal.jaxMultipole.bank.BankEntry attribute) ZeroLarbed() (pyextal.larbed.analysis.LARBEDAnalysis method) (pyextal.larbed.LARBEDAnalysis method) zeta (pyextal.jaxMultipole.AtomSpec attribute) (pyextal.jaxMultipole.bank.Orbital attribute) (pyextal.jaxMultipole.model.AtomSpec attribute)

zolz (pyextal.acom.library.ReflectionLibrary property) (pyextal.acom.ReflectionLibrary property) zone (pyextal.acom.AcomResult attribute) (pyextal.acom.library.ReflectionLibrary attribute) (pyextal.acom.ReflectionLibrary attribute) (pyextal.blochwave.Difpar attribute) zone_axis_cartesian() (in module pyextal.acom.geometry) zt (pyextal.blochwave.Cryst attribute)