Index

_

__init__() (structuretoolkit.analyse.neighbors.Mode method) (structuretoolkit.analyse.neighbors.Neighbors method) (structuretoolkit.analyse.neighbors.Tree method) (structuretoolkit.analyse.spatial.Interstitials method) (structuretoolkit.analyse.strain.Strain method)

A

apply_strain() (in module structuretoolkit.common.helper) ase_to_pymatgen() (in module structuretoolkit.common.pymatgen) ase_to_pyscal() (in module structuretoolkit.common.pyscal)

atom_numbers (structuretoolkit.analyse.neighbors.Neighbors property) (structuretoolkit.analyse.neighbors.Tree property) atoms_to_phonopy() (in module structuretoolkit.common.phonopy)

B

B2() (in module structuretoolkit.build.compound)

by_id() (in module structuretoolkit.build.materialsproject)

C

C14() (in module structuretoolkit.build.compound) C15() (in module structuretoolkit.build.compound) C36() (in module structuretoolkit.build.compound) center_coordinates_in_unit_cell() (in module structuretoolkit.common.helper) centrosymmetry (structuretoolkit.analyse.neighbors.Neighbors property) (structuretoolkit.analyse.neighbors.Tree property) chemical_symbols (structuretoolkit.analyse.neighbors.Neighbors property) cluster_analysis() (structuretoolkit.analyse.neighbors.Neighbors method)

cluster_by_distances() (structuretoolkit.analyse.neighbors.Neighbors method) cluster_by_steinhardt() (in module structuretoolkit.analyse.spatial) cluster_by_vecs() (structuretoolkit.analyse.neighbors.Neighbors method) coords (structuretoolkit.analyse.strain.Strain property) copy() (structuretoolkit.analyse.neighbors.Neighbors method) (structuretoolkit.analyse.neighbors.Tree method) create_gridpoints() (in module structuretoolkit.analyse.spatial) create_mesh() (in module structuretoolkit.build.mesh) crystal_phase (structuretoolkit.analyse.strain.Strain property)

D

D03() (in module structuretoolkit.build.compound)

distances (structuretoolkit.analyse.neighbors.Neighbors property) (structuretoolkit.analyse.neighbors.Tree property)

F

find_mic() (in module structuretoolkit.analyse.distance)

find_neighbors_by_vector() (structuretoolkit.analyse.neighbors.Neighbors method) find_solids() (in module structuretoolkit.analyse.pyscal)

G

get_adaptive_cna_descriptors() (in module structuretoolkit.analyse.pyscal) get_areas() (structuretoolkit.analyse.spatial.Interstitials method) get_average_of_unique_labels() (in module structuretoolkit.common.helper) get_bonds() (structuretoolkit.analyse.neighbors.Neighbors method) get_cell() (in module structuretoolkit.common.helper) get_centro_symmetry_descriptors() (in module structuretoolkit.analyse.pyscal) get_cluster_positions() (in module structuretoolkit.analyse.spatial) get_delaunay_neighbors() (in module structuretoolkit.analyse.spatial) get_diamond_structure_descriptors() (in module structuretoolkit.analyse.pyscal) get_distances() (structuretoolkit.analyse.spatial.Interstitials method) get_distances_array() (in module structuretoolkit.analyse.distance) get_equivalent_atoms() (in module structuretoolkit.analyse.phonopy) get_equivalent_points() (in module structuretoolkit.analyse) get_extended_positions() (in module structuretoolkit.common.helper) get_global_shells() (structuretoolkit.analyse.neighbors.Neighbors method) get_grainboundary_info() (in module structuretoolkit.build.aimsgb) get_high_index_surface_info() (in module structuretoolkit.build.surface) get_interstitials() (in module structuretoolkit.analyse.spatial) get_ir_reciprocal_mesh() (in module structuretoolkit.analyse) get_layers() (in module structuretoolkit.analyse.spatial) get_local_shells() (structuretoolkit.analyse.neighbors.Neighbors method) get_mean_positions() (in module structuretoolkit.analyse.spatial) get_neighborhood() (in module structuretoolkit.analyse.neighbors) (structuretoolkit.analyse.neighbors.Neighbors method) (structuretoolkit.analyse.neighbors.Tree method) get_neighbors() (in module structuretoolkit.analyse.neighbors) get_number_species_atoms() (in module structuretoolkit.common.helper) get_per_atom_quad() (in module structuretoolkit.analyse.snap)

get_primitive_cell() (in module structuretoolkit.analyse) get_shell_matrix() (structuretoolkit.analyse.neighbors.Neighbors method) get_snap_descriptor_derivatives() (in module structuretoolkit.analyse.snap) get_snap_descriptor_names() (in module structuretoolkit.analyse.snap) get_snap_descriptors_per_atom() (in module structuretoolkit.analyse.snap) get_spacegroup() (in module structuretoolkit.analyse) get_species_indices_dict() (in module structuretoolkit.common.helper) get_spherical_harmonics() (structuretoolkit.analyse.neighbors.Neighbors method) (structuretoolkit.analyse.neighbors.Tree method) get_steinhardt_parameter() (structuretoolkit.analyse.neighbors.Neighbors method) (structuretoolkit.analyse.neighbors.Tree method) get_steinhardt_parameters() (in module structuretoolkit.analyse.pyscal) (structuretoolkit.analyse.spatial.Interstitials method) get_strain() (in module structuretoolkit.analyse.strain) get_structure_indices() (in module structuretoolkit.common.helper) get_sum_quad() (in module structuretoolkit.analyse.snap) get_symmetry() (in module structuretoolkit.analyse) get_symmetry_dataset() (in module structuretoolkit.analyse) get_variances() (structuretoolkit.analyse.spatial.Interstitials method) get_vertical_length() (in module structuretoolkit.common.helper) get_volume_of_n_sphere_in_p_norm() (in module structuretoolkit.analyse.neighbors) get_volumes() (structuretoolkit.analyse.spatial.Interstitials method) get_voronoi_neighbors() (in module structuretoolkit.analyse.spatial) get_voronoi_vertices() (in module structuretoolkit.analyse.spatial) get_voronoi_volumes() (in module structuretoolkit.analyse.pyscal) get_wrapped_coordinates() (in module structuretoolkit.common.helper) grainboundary() (in module structuretoolkit.build.aimsgb) group_points_by_symmetry() (in module structuretoolkit.analyse)

H

high_index_surface() (in module structuretoolkit.build.surface)

hull (structuretoolkit.analyse.spatial.Interstitials property)

I

indices (structuretoolkit.analyse.neighbors.Neighbors property) (structuretoolkit.analyse.neighbors.Tree property)

Interstitials (class in structuretoolkit.analyse.spatial)

M

merge() (in module structuretoolkit.build.geometry) MeshInputError Mode (class in structuretoolkit.analyse.neighbors) mode (structuretoolkit.analyse.neighbors.Neighbors property) (structuretoolkit.analyse.neighbors.Tree property) module structuretoolkit structuretoolkit.analyse structuretoolkit.analyse.distance structuretoolkit.analyse.dscribe structuretoolkit.analyse.neighbors structuretoolkit.analyse.phonopy structuretoolkit.analyse.pyscal structuretoolkit.analyse.snap structuretoolkit.analyse.spatial structuretoolkit.analyse.strain structuretoolkit.build structuretoolkit.build.aimsgb structuretoolkit.build.compound structuretoolkit.build.geometry structuretoolkit.build.materialsproject structuretoolkit.build.mesh structuretoolkit.build.sqs structuretoolkit.build.surface structuretoolkit.common structuretoolkit.common.error structuretoolkit.common.helper structuretoolkit.common.phonopy structuretoolkit.common.pymatgen structuretoolkit.common.pyscal structuretoolkit.visualize

N

neigh (structuretoolkit.analyse.spatial.Interstitials property) Neighbors (class in structuretoolkit.analyse.neighbors) norm_order (structuretoolkit.analyse.neighbors.Neighbors property) (structuretoolkit.analyse.neighbors.Tree property)

num_neighbors (structuretoolkit.analyse.strain.Strain property) numbers_of_neighbors (structuretoolkit.analyse.neighbors.Neighbors property) (structuretoolkit.analyse.neighbors.Tree property)

P

phonopy_to_atoms() (in module structuretoolkit.common.phonopy) plot3d() (in module structuretoolkit.visualize)

positions (structuretoolkit.analyse.spatial.Interstitials property) pymatgen_read_from_file() (in module structuretoolkit.common.pymatgen) pymatgen_to_ase() (in module structuretoolkit.common.pymatgen)

R

ref_coord (structuretoolkit.analyse.strain.Strain property) remove_too_close() (in module structuretoolkit.analyse.spatial) repulse() (in module structuretoolkit.build.geometry)

reset_clusters() (structuretoolkit.analyse.neighbors.Neighbors method) rotations (structuretoolkit.analyse.strain.Strain property) run_workflow() (structuretoolkit.analyse.spatial.Interstitials method)

S

search() (in module structuretoolkit.build.materialsproject) select_index() (in module structuretoolkit.common.helper) set_indices() (in module structuretoolkit.common.helper) set_to_high_symmetry_points() (in module structuretoolkit.analyse.spatial) shells (structuretoolkit.analyse.neighbors.Neighbors property) soap_descriptor_per_atom() (in module structuretoolkit.analyse.dscribe) Strain (class in structuretoolkit.analyse.strain) strain (structuretoolkit.analyse.strain.Strain property) structuretoolkit module structuretoolkit.analyse module structuretoolkit.analyse.distance module structuretoolkit.analyse.dscribe module structuretoolkit.analyse.neighbors module structuretoolkit.analyse.phonopy module structuretoolkit.analyse.pyscal module structuretoolkit.analyse.snap module structuretoolkit.analyse.spatial module structuretoolkit.analyse.strain module structuretoolkit.build module

structuretoolkit.build.aimsgb module structuretoolkit.build.compound module structuretoolkit.build.geometry module structuretoolkit.build.materialsproject module structuretoolkit.build.mesh module structuretoolkit.build.sqs module structuretoolkit.build.surface module structuretoolkit.common module structuretoolkit.common.error module structuretoolkit.common.helper module structuretoolkit.common.phonopy module structuretoolkit.common.pymatgen module structuretoolkit.common.pyscal module structuretoolkit.visualize module symmetrize_vectors() (in module structuretoolkit.analyse) SymmetryError

T

Tree (class in structuretoolkit.analyse.neighbors)

V

vecs (structuretoolkit.analyse.neighbors.Neighbors property) (structuretoolkit.analyse.neighbors.Tree property)