Index

A

aa2matrix() (in module pyxtal.operations) abc2matrix() (in module pyxtal.symmetry) add_Hydrogens() (pyxtal.io.structure_from_ext method) add_k_transitions() (pyxtal.symmetry.Group method) add_vacuum() (pyxtal.lattice.Lattice method) addBox() (in module pyxtal.viz) addlines() (in module pyxtal.viz) affine_matrix (pyxtal.operations.OperationAnalyzer attribute) align() (pyxtal.descriptor.spherical_image method) (pyxtal.io.structure_from_ext method) (pyxtal.molecule.pyxtal_molecule method) all_covalent_radii() (pyxtal.database.element.Element method) all_long_names() (pyxtal.database.element.Element method) all_metallic_radii() (pyxtal.database.element.Element method) all_short_names() (pyxtal.database.element.Element method)

all_valence_electrons() (pyxtal.database.element.Element method) all_valences() (pyxtal.database.element.Element method) all_vdw_radii() (pyxtal.database.element.Element method) all_z() (pyxtal.database.element.Element method) angle() (in module pyxtal.operations) apply_inversion() (pyxtal.molecule.pyxtal_molecule method) apply_ops() (in module pyxtal.operations) (pyxtal.symmetry.Wyckoff_position method) apply_ops_diagonal() (in module pyxtal.operations) apply_perturbation() (pyxtal.pyxtal method) are_conjugate() (pyxtal.operations.OperationAnalyzer method) are_equal() (in module pyxtal.operations) are_equivalent_ops() (in module pyxtal.symmetry) are_equivalent_pts() (pyxtal.symmetry.Wyckoff_position method) atom_site (class in pyxtal.wyckoff_site)

B

block_crystal() (in module pyxtal.block_crystal)

Box (class in pyxtal.molecule) build() (pyxtal.pyxtal method)

C

calc_disps() (pyxtal.supergroup.supergroup method) calculate_density() (pyxtal.descriptor.spherical_image method) cart2sph() (in module pyxtal.descriptor) cellsize() (pyxtal.symmetry.Group method) change_orientation() (pyxtal.molecule.Orientation method) check_compatible() (pyxtal.symmetry.Group method) check_distance() (in module pyxtal.operations) (pyxtal.pyxtal method) check_H_coordination() (pyxtal.pyxtal method) check_images() (in module pyxtal.operations) check_mapping() (pyxtal.pyxtal method) check_mismatch() (pyxtal.lattice.Lattice method) check_orbits() (pyxtal.wyckoff_split.wyckoff_split method) check_short_distances() (pyxtal.pyxtal method) check_short_distances_by_dict() (pyxtal.pyxtal method) check_symmetry_and_dim() (in module pyxtal.symmetry) check_with_ws2() (pyxtal.wyckoff_site.atom_site method) check_wp() (pyxtal.crystal.random_crystal method)

check_wyckoff_position() (in module pyxtal.symmetry) choose_wyckoff() (in module pyxtal.symmetry) choose_wyckoff_mol() (in module pyxtal.symmetry) clean() (pyxtal.interface.gulp.GULP method) (pyxtal.interface.vasp.VASP method) clean_lists() (pyxtal.symmetry.Group static method) Collection (class in pyxtal.database.collection) compare_mol_connectivity() (in module pyxtal.molecule) copy() (pyxtal.lattice.Lattice method) (pyxtal.molecule.Orientation method) (pyxtal.molecule.pyxtal_molecule method) (pyxtal.pyxtal method) (pyxtal.symmetry.Wyckoff_position method) correlation() (in module pyxtal.descriptor) correlation_go() (in module pyxtal.descriptor) correlation_opt() (in module pyxtal.descriptor) covalent_radius (pyxtal.database.element.Element attribute) create_matrix() (in module pyxtal.operations)

D

det (pyxtal.operations.OperationAnalyzer attribute) display_atomic() (in module pyxtal.viz) display_cluster() (in module pyxtal.viz) display_crystals() (in module pyxtal.viz) display_mol_crystals() (in module pyxtal.viz) display_molecular() (in module pyxtal.viz)

display_molecular_site() (in module pyxtal.viz) display_molecule() (in module pyxtal.viz) display_molecules() (in module pyxtal.viz) distance() (in module pyxtal.operations) distance_matrix() (in module pyxtal.operations) distance_matrix_no_PBC() (in module pyxtal.operations)

E

Element (class in pyxtal.database.element) elements_list (pyxtal.database.element.Element attribute) encode() (pyxtal.lattice.Lattice method) (pyxtal.wyckoff_site.mol_site method)

equivalent_set() (pyxtal.symmetry.Wyckoff_position method) (pyxtal.wyckoff_site.atom_site method) execute() (pyxtal.interface.gulp.GULP method) expand_sph() (in module pyxtal.descriptor)

F

fibonacci_sphere() (in module pyxtal.descriptor) filtered_coords() (in module pyxtal.operations) filtered_coords_euclidean() (in module pyxtal.operations) find_ids() (in module pyxtal.operations) find_mapping() (in module pyxtal.supergroup) find_mapping_per_element() (in module pyxtal.supergroup) find_matched_lattice() (pyxtal.pyxtal method) find_rotor_from_smile() (in module pyxtal.molecule) find_xyz() (in module pyxtal.supergroup) from_1D_dicts() (pyxtal.wyckoff_site.mol_site class method) from_CSD() (pyxtal.pyxtal method) from_dict() (pyxtal.symmetry.Wyckoff_position method) from_file() (pyxtal.tolerance.Tol_matrix class method) from_group_and_index() (pyxtal.symmetry.Wyckoff_position method)

from_group_and_letter() (pyxtal.symmetry.Wyckoff_position method) from_index_quick() (pyxtal.symmetry.Wyckoff_position method) from_json() (pyxtal.pyxtal method) from_matrix() (pyxtal.lattice.Lattice class method) (pyxtal.tolerance.Tol_matrix class method) from_para() (pyxtal.lattice.Lattice class method) from_pyxtal() (pyxtal.representation.representation class method) from_radii() (pyxtal.tolerance.Tol_matrix class method) from_random() (pyxtal.pyxtal method) from_seed() (pyxtal.pyxtal method) from_single_value() (pyxtal.tolerance.Tol_matrix class method) from_string() (pyxtal.representation.representation class method) from_symops() (pyxtal.symmetry.Wyckoff_position method) from_symops_wo_group() (pyxtal.symmetry.Wyckoff_position method)

G

gaussian() (in module pyxtal.lattice) gen_pos() (pyxtal.symmetry.Wyckoff_position method) generate_lattice() (in module pyxtal.lattice) generate_lattice_0D() (in module pyxtal.lattice) generate_lattice_1D() (in module pyxtal.lattice) generate_lattice_2D() (in module pyxtal.lattice) generate_matrix() (pyxtal.lattice.Lattice method) generate_molecules() (in module pyxtal.molecule) generate_para() (pyxtal.lattice.Lattice method) generate_point() (pyxtal.lattice.Lattice method) get_1D_comp() (pyxtal.pyxtal method) get_1D_representation() (pyxtal.pyxtal method) get_alignment() (in module pyxtal.descriptor) get_all() (pyxtal.database.element.Element method) get_all_polar_space_groups() (in module pyxtal.symmetry) get_all_positions() (pyxtal.symmetry.Wyckoff_position method) get_alternatives() (pyxtal.pyxtal method) (pyxtal.symmetry.Group method) get_best_match() (in module pyxtal.operations) get_box() (pyxtal.molecule.pyxtal_molecule method) get_box_coordinates() (pyxtal.molecule.pyxtal_molecule method) get_center() (pyxtal.molecule.pyxtal_molecule method) get_close_packed_groups() (in module pyxtal.symmetry) get_coefs_matrix() (pyxtal.molecule.pyxtal_molecule method) get_contacts() (pyxtal.descriptor.spherical_image method) get_coord_H() (pyxtal.supergroup.supergroup method) get_coords_and_species() (pyxtal.wyckoff_site.mol_site method) get_density() (pyxtal.pyxtal method) get_diff() (pyxtal.lattice.Lattice method) get_disp() (pyxtal.wyckoff_site.atom_site method) get_disps_optim() (pyxtal.pyxtal method) get_disps_sets() (pyxtal.pyxtal method) get_disps_single() (pyxtal.pyxtal method) get_dist() (pyxtal.representation.representation method) get_distances() (pyxtal.wyckoff_site.mol_site method) get_dists_auto() (pyxtal.wyckoff_site.mol_site method) get_dists_WP() (pyxtal.wyckoff_site.mol_site method) get_dof() (pyxtal.pyxtal method) (pyxtal.symmetry.Wyckoff_position method) get_energy() (pyxtal.molecule.pyxtal_molecule method) get_euclidean_generator() (pyxtal.symmetry.Wyckoff_position method) get_euclidean_symmetries() (pyxtal.symmetry.Wyckoff_position method) get_Euler_angles() (pyxtal.molecule.Orientation method) get_ferroelectric_groups() (pyxtal.symmetry.Group method) get_free_axis() (pyxtal.pyxtal method) (pyxtal.symmetry.Group method) get_frozen_axis() (pyxtal.symmetry.Wyckoff_position method) get_generators() (in module pyxtal.symmetry) get_hm_number() (pyxtal.symmetry.Wyckoff_position method) get_hm_symbol() (pyxtal.symmetry.Wyckoff_position method) get_ijk_lists() (pyxtal.wyckoff_site.mol_site method) get_inertia_tensor() (in module pyxtal.molecule) get_init_translations() (pyxtal.pyxtal method) get_initial_mask() (pyxtal.supergroup.supergroup method) get_intermolecular_energy() (pyxtal.pyxtal method) get_inverse() (in module pyxtal.operations) get_inverse_ops() (in module pyxtal.operations) get_lengths() (pyxtal.lattice.Lattice method) get_lists() (pyxtal.symmetry.Group method) get_lists_mol() (pyxtal.symmetry.Group method) get_matrix() (pyxtal.lattice.Lattice method) (pyxtal.molecule.Orientation method)

get_max_k_subgroup() (pyxtal.symmetry.Group method) get_max_subgroup() (pyxtal.symmetry.Group method) get_max_subgroup_numbers() (pyxtal.symmetry.Group method) get_max_t_subgroup() (pyxtal.symmetry.Group method) get_min_dist() (pyxtal.wyckoff_site.mol_site method) get_min_supergroup() (pyxtal.symmetry.Group method) get_mol_object() (pyxtal.wyckoff_site.mol_site method) get_molecules() (pyxtal.descriptor.spherical_image method) get_neighboring_dists() (pyxtal.pyxtal method) get_neighboring_molecules() (pyxtal.pyxtal method) get_neighbors() (pyxtal.descriptor.orientation_order method) get_neighbors_auto() (pyxtal.wyckoff_site.mol_site method) get_neighbors_wp2() (pyxtal.wyckoff_site.mol_site method) get_num_torsions() (pyxtal.pyxtal method) get_op() (pyxtal.molecule.Orientation method) get_ops_from_transformation() (pyxtal.symmetry.Wyckoff_position method) get_order() (pyxtal.operations.OperationAnalyzer method) get_orientation() (pyxtal.molecule.pyxtal_molecule method) get_orientations_in_wp() (pyxtal.molecule.pyxtal_molecule method) get_orientations_in_wps() (pyxtal.molecule.pyxtal_molecule method) get_para() (pyxtal.lattice.Lattice method) get_parameters() (pyxtal.descriptor.orientation_order method) get_pbc_and_lattice() (in module pyxtal.symmetry) get_permutation_matrices() (pyxtal.lattice.Lattice method) get_point_group() (in module pyxtal.symmetry) get_principle_axes() (pyxtal.molecule.pyxtal_molecule method) get_radius() (pyxtal.molecule.pyxtal_molecule method) get_rmsd() (pyxtal.molecule.pyxtal_molecule method) get_rmsd2() (pyxtal.molecule.pyxtal_molecule method) get_sf() (pyxtal.database.element.Element method) get_similarity() (pyxtal.descriptor.spherical_image method) get_site_dof() (pyxtal.symmetry.Group method) get_site_labels() (pyxtal.pyxtal method) get_site_symm_wo_translation() (pyxtal.symmetry.Wyckoff_position method) get_site_symmetry() (pyxtal.symmetry.Wyckoff_position method) get_spherical_images() (pyxtal.pyxtal method) get_splitters_from_relation() (pyxtal.symmetry.Group method) get_splitters_from_structure() (pyxtal.symmetry.Group method) get_std_representation() (pyxtal.pyxtal method) get_symbol_and_number() (in module pyxtal.symmetry) get_symbols() (pyxtal.molecule.pyxtal_molecule method) get_symmetry() (pyxtal.molecule.pyxtal_molecule method) get_symmetry_from_ops() (in module pyxtal.symmetry) get_tol() (pyxtal.tolerance.Tol_matrix method) get_tols_matrix() (pyxtal.molecule.pyxtal_molecule method) get_torsion_angles() (pyxtal.molecule.pyxtal_molecule method) get_transformation() (pyxtal.supergroup.supergroups method) get_transformation_matrices() (pyxtal.lattice.Lattice method) get_transition() (pyxtal.pyxtal method) get_transition_by_path() (pyxtal.pyxtal method) get_translations() (pyxtal.wyckoff_site.atom_site method) get_valid_solutions() (pyxtal.symmetry.Group method) get_worst_angle() (pyxtal.lattice.Lattice method) get_wp_list() (pyxtal.symmetry.Group method) get_wyckoff_position() (pyxtal.symmetry.Group method) get_wyckoff_symmetry() (in module pyxtal.symmetry) (pyxtal.symmetry.Group method) get_wyckoffs() (in module pyxtal.symmetry) get_XRD() (pyxtal.pyxtal method) get_zprime() (pyxtal.pyxtal method) Group (class in pyxtal.symmetry) GULP (class in pyxtal.interface.gulp)

H

Hall (class in pyxtal.symmetry)

has_equivalent_ops() (pyxtal.symmetry.Wyckoff_position method) has_special_site() (pyxtal.pyxtal method)

I

i_from_jk() (in module pyxtal.symmetry) identity_ops() (in module pyxtal.symmetry) in_lists() (in module pyxtal.wyckoff_split) in_merged_coords() (in module pyxtal.io) index_from_letter() (in module pyxtal.symmetry) is_compatible_symmetry() (in module pyxtal.molecule) is_conjugate() (pyxtal.operations.OperationAnalyzer method)

is_duplicate() (pyxtal.pyxtal method) is_orthogonal() (in module pyxtal.operations) is_pure_translation() (pyxtal.symmetry.Wyckoff_position method) is_standard_setting() (pyxtal.symmetry.Wyckoff_position method) is_valid_combination() (pyxtal.symmetry.Group method) is_valid_matrix() (pyxtal.lattice.Lattice method) is_valid_orientation() (pyxtal.wyckoff_site.mol_site method)

J

jk_from_i() (in module pyxtal.symmetry)

L

Lattice (class in pyxtal.lattice) letter_from_index() (in module pyxtal.symmetry) list_groups() (pyxtal.symmetry.Group class method) list_molecules() (pyxtal.molecule.pyxtal_molecule method) list_wyckoff_combinations() (pyxtal.symmetry.Group method) load_dict() (pyxtal.molecule.Orientation class method) (pyxtal.pyxtal method) (pyxtal.symmetry.Wyckoff_position class method) (pyxtal.wyckoff_site.atom_site class method) (pyxtal.wyckoff_site.mol_site class method)

load_str() (pyxtal.molecule.pyxtal_molecule class method) long_name (pyxtal.database.element.Element attribute)

M

m (pyxtal.operations.OperationAnalyzer attribute) make_graph() (in module pyxtal.molecule) make_mol_sites() (pyxtal.io.structure_from_ext method) make_pyxtal_in_supergroup() (pyxtal.supergroup.supergroup method) make_pyxtals_in_subgroup() (pyxtal.supergroup.supergroup method) make_supergroup() (pyxtal.supergroup.supergroup method)

make_transitions() (pyxtal.pyxtal method) matrix2para() (in module pyxtal.lattice) merge() (pyxtal.symmetry.Wyckoff_position method) metallic_radius (pyxtal.database.element.Element attribute) mol_site (class in pyxtal.wyckoff_site) molecular_crystal (class in pyxtal.molecular_crystal) mutate() (pyxtal.lattice.Lattice method)

N

new_path() (in module pyxtal.supergroup)

new_structure() (in module pyxtal.supergroup) number_from_specie() (pyxtal.database.element.Element method)

O

op (pyxtal.operations.OperationAnalyzer attribute) op_transform() (in module pyxtal.symmetry) op_translation() (in module pyxtal.symmetry) operate() (pyxtal.molecule.Box method) OperationAnalyzer (class in pyxtal.operations) optimize() (in module pyxtal.interface.gulp) (in module pyxtal.interface.vasp)

optimize_lattice() (pyxtal.pyxtal method) optimize_multi() (pyxtal.lattice.Lattice method) optimize_once() (pyxtal.lattice.Lattice method) order (pyxtal.operations.OperationAnalyzer attribute) organized_wyckoffs() (in module pyxtal.symmetry) Orientation (class in pyxtal.molecule) orientation_order (class in pyxtal.descriptor)

P

para2ferro() (in module pyxtal.symmetry) para2matrix() (in module pyxtal.lattice) parse_wp2() (pyxtal.wyckoff_split.wyckoff_split method) path_to_general_wp() (pyxtal.symmetry.Group method) perturb_torsion() (pyxtal.molecule.pyxtal_molecule method) perturbate() (pyxtal.wyckoff_site.atom_site method) (pyxtal.wyckoff_site.mol_site method) plot_real_image() (pyxtal.descriptor.spherical_image method) plot_sph_images() (pyxtal.descriptor.spherical_image method) print_detail() (pyxtal.supergroup.supergroup method) print_logo() (in module pyxtal) print_ops() (pyxtal.symmetry.Wyckoff_position method) print_solutions() (pyxtal.supergroup.supergroups method) print_wp() (pyxtal.supergroup.supergroup method) process_ops() (pyxtal.symmetry.Wyckoff_position method) project() (pyxtal.symmetry.Wyckoff_position method) pyxtal (class in pyxtal) (module) pyxtal.block_crystal (module) pyxtal.crystal (module)

pyxtal.database (module) pyxtal.database.collection (module) pyxtal.database.element (module) pyxtal.descriptor (module) pyxtal.interface (module) pyxtal.interface.gulp (module) pyxtal.interface.vasp (module) pyxtal.io (module) pyxtal.lattice (module) pyxtal.molecular_crystal (module) pyxtal.molecule (module) pyxtal.operations (module) pyxtal.representation (module) pyxtal.supergroup (module) pyxtal.symmetry (module) pyxtal.tolerance (module) pyxtal.viz (module) pyxtal.wyckoff_site (module) pyxtal.wyckoff_split (module) pyxtal_molecule (class in pyxtal.molecule)

R

random() (in module pyxtal.molecule) random_crystal (class in pyxtal.crystal) random_orientation() (pyxtal.molecule.Orientation method) random_shear_matrix() (in module pyxtal.lattice) random_vector() (in module pyxtal.lattice) rdkit_mol() (pyxtal.molecule.pyxtal_molecule method) rdkit_mol_init() (pyxtal.molecule.pyxtal_molecule method) read() (pyxtal.interface.gulp.GULP method) read_bandgap() (pyxtal.interface.vasp.VASP method) read_cif() (in module pyxtal.io) read_OSZICAR() (pyxtal.interface.vasp.VASP method) read_OUTCAR() (pyxtal.interface.vasp.VASP method) relax() (pyxtal.molecule.pyxtal_molecule method) remove_water() (pyxtal.pyxtal method)

reoriented_molecule() (in module pyxtal.molecule) representation (class in pyxtal.representation) reset_matrix() (pyxtal.lattice.Lattice method) (pyxtal.molecule.Orientation method) reset_positions() (pyxtal.molecule.pyxtal_molecule method) resort() (pyxtal.io.structure_from_ext method) (pyxtal.pyxtal method) rotate() (pyxtal.descriptor.spherical_image method) (pyxtal.wyckoff_site.mol_site method) rotate_by_matrix() (pyxtal.molecule.Orientation method) rotate_vector() (in module pyxtal.operations) rotation_order (pyxtal.operations.OperationAnalyzer attribute) run() (pyxtal.interface.gulp.GULP method) (pyxtal.interface.vasp.VASP method)

S

same_smiles() (pyxtal.representation.representation method) save_dict() (pyxtal.molecule.Orientation method) (pyxtal.pyxtal method) (pyxtal.symmetry.Wyckoff_position method) (pyxtal.wyckoff_site.atom_site method) (pyxtal.wyckoff_site.mol_site method) save_str() (pyxtal.molecule.pyxtal_molecule method) search_all_generators() (pyxtal.symmetry.Wyckoff_position method) search_cloest_wp() (in module pyxtal.symmetry) search_G1() (in module pyxtal.supergroup) search_G2() (in module pyxtal.supergroup) search_generator() (pyxtal.symmetry.Wyckoff_position method) search_generator_dist() (pyxtal.symmetry.Wyckoff_position method) search_molecules_in_crystal() (in module pyxtal.io) search_position() (pyxtal.wyckoff_site.atom_site method) search_subgroup_paths() (pyxtal.symmetry.Group method) search_supergroup() (pyxtal.supergroup.supergroup method) search_supergroup_paths() (pyxtal.symmetry.Group method) search_transformation() (pyxtal.lattice.Lattice method) search_transformations() (pyxtal.lattice.Lattice method) set_crystal() (pyxtal.crystal.random_crystal method) (pyxtal.molecular_crystal.molecular_crystal method) set_euclidean() (pyxtal.symmetry.Wyckoff_position method) set_generators() (pyxtal.symmetry.Wyckoff_position method) set_labels() (pyxtal.molecule.pyxtal_molecule method) set_lattice() (pyxtal.crystal.random_crystal method) (pyxtal.molecular_crystal.molecular_crystal method) set_matrix() (pyxtal.lattice.Lattice method) set_molecules() (pyxtal.molecular_crystal.molecular_crystal method) set_ops() (pyxtal.symmetry.Wyckoff_position method) set_orientations() (pyxtal.molecular_crystal.molecular_crystal method) set_para() (pyxtal.lattice.Lattice method) set_sites() (pyxtal.crystal.random_crystal method) (pyxtal.molecular_crystal.molecular_crystal method) set_tol() (pyxtal.tolerance.Tol_matrix method) set_torsion_angles() (pyxtal.molecule.pyxtal_molecule method) set_vasp() (pyxtal.interface.vasp.VASP method) set_volume() (pyxtal.crystal.random_crystal method) (pyxtal.lattice.Lattice method) (pyxtal.molecular_crystal.molecular_crystal method) sf (pyxtal.database.element.Element attribute) shift_by_swap() (pyxtal.wyckoff_site.atom_site method) short_dist() (pyxtal.wyckoff_site.mol_site method) short_dist_with_wp2() (pyxtal.wyckoff_site.mol_site method) short_name (pyxtal.database.element.Element attribute) short_path_to_general_wp() (pyxtal.symmetry.Group method)

show() (pyxtal.io.structure_from_ext method) (pyxtal.molecule.pyxtal_molecule method) (pyxtal.pyxtal method) (pyxtal.wyckoff_site.mol_site method) show_box() (pyxtal.molecule.pyxtal_molecule method) show_mol_cluster() (pyxtal.pyxtal method) show_molecule_in_box() (pyxtal.wyckoff_site.mol_site method) show_names() (pyxtal.database.collection.Collection method) single_optimize() (in module pyxtal.interface.gulp) (in module pyxtal.interface.vasp) single_point() (in module pyxtal.interface.vasp) site_symm() (in module pyxtal.symmetry) sort() (pyxtal.wyckoff_split.wyckoff_split method) sort_sites_by_mult() (pyxtal.pyxtal method) sort_sites_by_numIons() (pyxtal.pyxtal method) sort_solutions() (pyxtal.supergroup.supergroup method) sph2cart() (in module pyxtal.descriptor) spherical_image (class in pyxtal.descriptor) split_k() (pyxtal.wyckoff_split.wyckoff_split method) split_t() (pyxtal.wyckoff_split.wyckoff_split method) ss_string_from_ops() (in module pyxtal.symmetry) standardize() (pyxtal.lattice.Lattice method) struc_along_path() (pyxtal.supergroup.supergroups method) structure_from_ext (class in pyxtal.io) subgroup() (pyxtal.pyxtal method) subgroup_by_path() (pyxtal.pyxtal method) subgroup_once() (pyxtal.pyxtal method) substitute() (pyxtal.pyxtal method) supergroup (class in pyxtal.supergroup) supergroup() (pyxtal.pyxtal method) supergroups (class in pyxtal.supergroup) supergroups() (pyxtal.pyxtal method) swap_angle() (pyxtal.lattice.Lattice method) swap_axis() (pyxtal.lattice.Lattice method) (pyxtal.molecule.pyxtal_molecule method) (pyxtal.symmetry.Wyckoff_position method) (pyxtal.wyckoff_site.atom_site method) swap_xyz_ops() (in module pyxtal.symmetry) swap_xyz_string() (in module pyxtal.symmetry) symmetrize() (pyxtal.supergroup.supergroup method) symmetrize_dist() (pyxtal.supergroup.supergroup method) symmetrize_site_double_k() (pyxtal.supergroup.supergroup method) symmetrize_site_double_t() (pyxtal.supergroup.supergroup method) symmetrize_site_multi() (pyxtal.supergroup.supergroup method) symmetrize_site_single() (pyxtal.supergroup.supergroup method) symmetry_element_from_axis() (in module pyxtal.symmetry) symmetry_mapper (class in pyxtal.supergroup)

T

to_1D_dicts() (pyxtal.wyckoff_site.mol_site method) to_ase() (pyxtal.interface.gulp.GULP method) (pyxtal.pyxtal method) to_file() (pyxtal.pyxtal method) (pyxtal.tolerance.Tol_matrix method) to_json() (pyxtal.pyxtal method) to_pymatgen() (pyxtal.interface.gulp.GULP method) (pyxtal.interface.vasp.VASP method) (pyxtal.pyxtal method) to_pyxtal() (pyxtal.interface.gulp.GULP method) (pyxtal.interface.vasp.VASP method) (pyxtal.representation.representation method) to_pyxtal_center() (pyxtal.pyxtal method) to_standard_setting() (pyxtal.pyxtal method) (pyxtal.representation.representation method)

to_string() (pyxtal.representation.representation method) to_subgroup() (pyxtal.pyxtal method) tol (pyxtal.operations.OperationAnalyzer attribute) Tol_matrix (class in pyxtal.tolerance) transform() (pyxtal.lattice.Lattice method) (pyxtal.pyxtal method) transform_from_matrices() (pyxtal.symmetry.Wyckoff_position method) transform_from_matrix() (pyxtal.symmetry.Wyckoff_position method) transform_multi() (pyxtal.lattice.Lattice method) transform_ops() (in module pyxtal.symmetry) translate() (pyxtal.pyxtal method) (pyxtal.wyckoff_site.mol_site method) translation_generator() (pyxtal.wyckoff_split.wyckoff_split method) trim_ops() (in module pyxtal.symmetry) type (pyxtal.operations.OperationAnalyzer attribute)

U

update() (pyxtal.symmetry.Wyckoff_position method) (pyxtal.wyckoff_site.atom_site method) (pyxtal.wyckoff_site.mol_site method)

update_hall() (pyxtal.symmetry.Wyckoff_position method) update_index() (pyxtal.symmetry.Wyckoff_position method)

V

valence (pyxtal.database.element.Element attribute) valence_electrons (pyxtal.database.element.Element attribute)

VASP (class in pyxtal.interface.vasp) vdw_radius (pyxtal.database.element.Element attribute) verify_distances() (in module pyxtal.operations)

W

write() (pyxtal.interface.gulp.GULP method) write_cif() (in module pyxtal.io) write_cifs() (pyxtal.supergroup.supergroups method)

write_poscars() (in module pyxtal.supergroup) Wyckoff_position (class in pyxtal.symmetry) wyckoff_split (class in pyxtal.wyckoff_split)

X

xyz2sph() (in module pyxtal.descriptor)

Z

z (pyxtal.database.element.Element attribute)