pyxtal package

PyXtal: A Python library for crystal structure generation and manipulation.

This module initializes the pyxtal package, providing essential imports and utility functions.

pyxtal.print_logo()

print out the logo and version information

class pyxtal.pyxtal(molecular=False, random_state=None)

Bases: object

Class for handling atomic crystals based on symmetry constraints

Examples

To create a new structure instance

>>> from pyxtal import pyxtal
>>> struc = pyxtal()

one can either use pyxtal to generate a random symmetric structure

>>> struc.from_random(3, 227, ['C'], [8])

or load a structure from a file or ASE atoms or Pymatgen structure object

>>> struc.from_seed('diamond.cif')     # as a string
>>> struc.from_seed(diamond_ase)       # as a ase atoms object
>>> struc.from_seed(diamond_pymatgen)  # as a pymatgen structure object

as long as the struc is created, you can check their symmetry as follows

>>> struc.get_site_labels()
{'C': ['8a']}
>>> struc
------Crystal from random------
Dimension: 3
Composition: C8
Group: Fd-3m (227)
cubic lattice:   4.3529   4.3529   4.3529  90.0000  90.0000  90.0000
Wyckoff sites:
     C @ [0.1250 0.1250 0.1250], WP:  8a, Site symmetry: -4 3 m

The structure object can be easily manipulated via apply_perturbtation or subgroup function

>>> struc2 = struc.subgroup_once(H=141)
>>> struc2
------Crystal from Wyckoff Split------
Dimension: 3
Composition: C8
Group: I41/amd (141)
tetragonal lattice:   3.3535   3.3535   4.6461  90.0000  90.0000  90.0000
Wyckoff sites:
         C @ [0.0000 0.2500 0.3750], WP:  4b, Site symmetry: -4 m 2

Alternatively, one can easily compute its XRD via the pyxtal.XRD class

>>> xrd = struc.get_XRD()
>>> xrd
  2theta     d_hkl     hkl       Intensity  Multi
  32.706     2.738   [ 1  1  1]   100.00        8
  54.745     1.677   [ 2  2  0]    40.95       12
  65.249     1.430   [ 3  1  1]    20.65       24
  81.116     1.186   [ 4  0  0]     5.15        6
  90.236     1.088   [ 3  3  1]     8.24       24
 105.566     0.968   [ 4  2  2]    14.44       24
 115.271     0.913   [ 5  1  1]    10.03       24
 133.720     0.838   [ 4  4  0]     9.80       12
 148.177     0.802   [ 5  3  1]    28.27       48

One can also try to get the transition path between two pyxtals that are symmetry related via the get_transition function

>>> s1 = pyxtal()
>>> s2 = pyxtal()
>>> s1.from_seed("pyxtal/database/cifs/0-G62.cif") #structure with low symmetry
>>> s2.from_seed("pyxtal/database/cifs/2-G71.cif") #structure with high symmetry
>>> strucs, _, _, _, _ = s2.get_transition(s1) # get the transition from high to low
>>> strucs
[
------Crystal from Transition 0  0.000------
Dimension: 3
Composition: O24Mg4W4Pb8
Group: Pnma (62)
orthorhombic lattice:  11.6075   8.0526   5.8010  90.0000  90.0000  90.0000
Wyckoff sites:
    Mg @ [ 0.8750  0.2500  0.7500], WP [4c] Site [.m.]
    Pb @ [ 0.6406  0.0053  0.7856], WP [8d] Site [1]
    W @ [ 0.6119  0.2500  0.2483], WP [4c] Site [.m.]
    O @ [ 0.6292  0.0083  0.2235], WP [8d] Site [1]
    O @ [ 0.4966  0.2500  0.0093], WP [4c] Site [.m.]
    O @ [ 0.5055  0.2500  0.4897], WP [4c] Site [.m.]
    O @ [ 0.7308  0.2500  0.9717], WP [4c] Site [.m.]
    O @ [ 0.7467  0.2500  0.4570], WP [4c] Site [.m.],
------Crystal from Transition 1  0.323------
Dimension: 3
Composition: O24Mg4W4Pb8
Group: Pnma (62)
orthorhombic lattice:  11.6020   8.0526   5.8038  90.0000  90.0000  90.0000
Wyckoff sites:
    Mg @ [ 0.8750  0.2500  0.7500], WP [4c] Site [.m.]
    Pb @ [ 0.6250 -0.0053  0.7500], WP [8d] Site [1]
    W @ [ 0.6250  0.2500  0.2500], WP [4c] Site [.m.]
    O @ [ 0.6250  0.0083  0.2500], WP [8d] Site [1]
    O @ [ 0.5158  0.2500 -0.0068], WP [4c] Site [.m.]
    O @ [ 0.5158  0.2500  0.5068], WP [4c] Site [.m.]
    O @ [ 0.7342  0.2500  0.9932], WP [4c] Site [.m.]
    O @ [ 0.7342  0.2500  0.5068], WP [4c] Site [.m.]]

Finally, the structure can be saved to different formats

>>> struc.to_file('my.cif')
>>> struc.to_file('my_poscar', fmt='poscar')

or to Pymatgen/ASE structure object

>>> pmg_struc = struc.to_pymatgen()
>>> ase_struc = struc.to_ase()

or to json file

>>> struc.to_json('1.json')

apply_perturbation(d_lat=0.05, d_coor=0.05, d_rot=1)

perturb the structure without breaking the symmetry

Parameters:

• d_coor – magnitude of perturbation on atomic coordinates (in A)

• d_lat – magnitude of perturbation on lattice (in percentage)

are_valid_numIons()

Check if the numIons are correct for debugging

build(group, species, numIons, lattice, sites, tol=0.01, dim=3, use_hall=False)

Build a atomic crystal based on the necessary input

Parameters:

• group (int) – 225

• species (list) – [‘Na’, ‘Cl’]

• numIons (list) – [4, 4]

• lattice – lattice object

• sites (list) – [[{“4a”: [0.0, 0.0, 0.0]}], [{“4b”: [0.5, 0.5, 0.5]}]]

• dim (int)

• use_hll (bool)

check_H_coordination(r=1.12)

A function to check short if H is connected to more than one atom Mainly used for debug, powered by pymatgen

Parameters:

r – the given cutoff distances

Returns:

True or False

check_distance()

Check intermolecular distance for molecular crystal

check_mapping(ref_struc)

Compute the displacement w.r.t. the reference structure

Parameters:

ref_struc – reference pyxtal structure (assuming the same atom order)

Returns:

True or False

check_short_distances(r=0.7, exclude_H=True)

A function to check short distance pairs Mainly used for debug, powered by pymatgen

Parameters:

• r – the given cutoff distances

• exclude_H – whether or not exclude the H atoms

Returns:

list of pairs within the cutoff

check_short_distances_by_dict(dicts)

A function to check short distance pairs Mainly used for debug, powered by pymatgen

Parameters:

dicts – e.g., {“H-H”: 1.0, “O-O”: 2.0}

Returns:

number of atomic pairs within the cutoff

Return type:

N_pairs

check_validity(criteria, verbose=False)

Check if the xtal is valid for a given list of criteria. Currently support the following keywords - MIN_Density (float) - CN: coordination number (int) - Dimension: (int)

Parameters:

• criteria (dict) – keywords and the threshhold values

• verbose (bool) – whether or not print out details

Returns:

bool value regarding the validity

copy()

Simply copy the structure

cut_lattice(max_separation=3.0, verbose=False)

An utility to reduce the empty spacing

find_matched_lattice(ref_struc, d_tol=2.0, f_tol=0.15)

Compute the displacement w.r.t. the reference structure

Parameters:

• ref_struc – reference pyxtal structure (assuming the same atomic ordering)

• d_tol – tolerence of mismatch in the absolute scale

• f_tol – tolerence of mismatch in the fractional scale

Returns:

ref_struc with matched lattice

from_1d_rep(x, sites, dim=3)

An advanced way to build pyxtal from the 1d representation

Parameters:

• x – 1d representation

• sites – list of (element, wp)

from_CSD(csd_code)

Download the crystal from CCDC if csd_code is given, return the single pyxtal object if csd_family is given, do group analysis and ignore high pressure form

Parameters:

csd_code – e.g., ACSALA01

from_json(filename)

Load the model from a json file

from_prototype(prototype)

Load a template structure based on a prototype name for quick testing.

Parameters:

prototype (str) – Name of the crystal structure prototype to load. Supported (‘diamond’, ‘graphite’: ‘a-cristobalite’, .etc)

Example

self.from_prototype(‘diamond’) self.from_prototype(‘graphite’)

Notes

This method acts as a shortcut to quickly generate known crystals by loading the space group, Wyckoff positions, lattice parameters, and atomic species.

from_random(dim=3, group=None, species=None, numIons=None, factor=1.1, thickness=None, area=None, lattice=None, sites=None, conventional=True, t_factor=1.0, max_count=10, torsions=None, force_pass=False, block=None, num_block=None, seed=None, random_state=None, tm=None, use_hall=False)

The main function to generate random crystals. It calls block_crysstal or random_crystal internally.

Parameters:

• dim (int) – dimenion (0, 1, 2, 3)

• group (int) – the group number (1-56, 1-75, 1-80, 1-230)

• species (list) – a list of atomic symbols for each ion type, e.g., [“Ti”, “O”]

• numIons (list) – a list of the number of each type of atom within the primitive cell (NOT the conventional cell), e.g., [4, 2]

• factor (optional) – volume factor used to generate the crystal

• thickness

• area (float)

• lattice (optional) – Lattice to define the cell

• sites (optional) – pre-assigned wyckoff sites (e.g., [[“4a”], [“2b”]])

• conventional (bool) – whether or not use the conventional setting

• () (max_count)

• ()

• tm (optional) – Tol_matrix object to define the distances

from_seed(seed, molecules=None, tol=0.0001, a_tol=5.0, ignore_HH=True, add_H=False, backend='pymatgen', style='pyxtal', hn=None, standard=False)

Load the seed structure from Pymatgen/ASE/POSCAR/CIFs Internally they will be handled by Pymatgen

Parameters:

• seed – cif/poscar file or a Pymatgen Structure object

• molecules – a list of reference molecule (xyz file or Pyxtal molecule)

• tol – scale factor for covalent bond distance

• ignore_HH – whether or not ignore short H-H distance in molecules

• add_H – whether or not add H atoms

• backend – structure parser, default is pymatgen

• style – pyxtal for spglib

• standard – whether or not optimize lattice

from_spg_wps_rep(spg, wps, x, elements=None)

An advanced way to build pyxtal from wyckoff position and compacted 1d x representation

Parameters:

• spg (int) – space group number 1-230

• wps (list) – wyckoff representation (e.g., [‘6a’, ‘6a’])

• x (array) – 1d representation

• elements (list) – list of element string

from_tabular_representation(rep, max_abc=50.0, max_angle=180, normalize=False, tol=0.1, discrete=False, discrete_cell=False, N_grids=50, verbose=False)

Reconstruc xtal from 1d tabular_representation Currently assuming the elemental composition like carbon

Parameters:

• rep – 1D array

• max_abc (float) – maximum abc length for normalization

• max_angle (float) – maximum angle in radian for normalization

• normalize (bool) – whether normalize or not?

• tol (float) – a tolerance value to assign the Wyckoff site

• discrete (bool) – to discretize xyz

• N_grids (int) – number of grids used for discretization

• verbose (bool) – output detailed error

get_1D_comp()

Get composition for 1d rep of molecular xtal

get_1D_representation(standard=False)

Get the 1D representation class for molecular crystals

get_1d_rep_x()

Get a simplified x representation for a crystal Group: I 41/a m d:2 (141) 2.5019, 2.5019, 8.7534, 90.0000, 90.0000, 90.0000, tetragonal Wyckoff sites: C @ [ 0.0000 0.2500 0.4614], WP [8e] Site [2mm.]

The above rep is [2.5019, 8.7514, 0.4614]

get_Pearson_Symbol()

Based on https://en.wikipedia.org/wiki/Pearson_symbol

get_XRD(**kwargs)

Compute the PXRD object.

** kwargs include

• wavelength (1.54184)

• thetas [0, 180]

• preferred_orientation: False

• march_parameter: None

get_alternatives(include_self=True, same_letters=False, ref_lat=None, d_tol=2.0, f_tol=0.15)

Get alternative structure representations

Parameters:

include_self (bool) – return the original structure

Returns:

list of structures

get_bounds(vec=(2.0, 50.0), ang=(30, 150))

Get the number of dof for the given structures:

get_density()

Compute density

get_dimensionality(cutoff=None)

A quick wrapper to compute dimensionality from pymatgen https://pymatgen.org/pymatgen.analysis.dimensionality.html The dimensionality of the structure can be 1/2/3

get_disps_optim(ref_struc, trans, d_tol)

Parameters:

• ref_struc – reference pyxtal structure (assuming the same atom order)

• trans – translation vector

• d_tol – tolerence of mismatch

Returns:

Atomic displacements in np.array translation:

get_disps_sets(ref_struc, d_tol, d_tol2=0.3, ld_tol=2.0, fd_tol=0.15, keep_lattice=False)

Compute the displacement w.r.t. a reference structure (considering all wycsets)

Parameters:

• ref_struc – reference pyxtal structure (assuming the same atomic ordering)

• d_tol – maximally allowed atomic displacement

• d_tol2 – displacement that allows early termination

• kepp_lattice – whether or not change the WP sets

Returns:

Atomic displacements in np.array

get_disps_single(ref_struc, trans, d_tol=1.2)

Compute the displacement w.r.t. the reference structure

Parameters:

• ref_struc – reference pyxtal structure (assuming the same atom order)

• trans – translation vector

• d_tol – tolerence of mismatch

Returns:

Atomic displacements in np.array translation:

get_dof()

Get the number of dof for the given structures:

get_forcefield(ff_style='openff', code='lammps', chargemethod='am1bcc', parameters=None)

An interface to create forcefield for molecular simulation with - Charmm - LAMMPS Note that the current approach generates charge with its own conformer, need to provide the option to use the conformer from the given molecule

Parameters:

• ff_style (-) – ‘gaff’ or ‘openff’

• code (-) – ‘lammps’ or ‘charmm’

• charge_method (-) – ‘am1bcc’, ‘am1-mulliken’, ‘mmff94’, ‘gasteiger’

• parameters (-) – 1D-array of user-specified FF parameters

Returns:

An ase_atoms_objects with force field information

get_free_axis()

Check if the a, b, c axis have free parameters

get_init_translations(ref_struc, tol=0.75)

Compute the displacement w.r.t. the reference structure

Parameters:

ref_struc – reference pyxtal structure (assuming the same atom order)

Returns:

list of possible translations

get_intermolecular_energy(factor=2.0, max_d=10.0)

For molecular crystals, get the intermolecular interactions from Gavezzotti, A., Filippini, G., J. Phys. Chem., 1994, 98 (18), 4831-4837

Returns:

Total energy

get_neighboring_dists(site_id=0, factor=1.5, max_d=5.0)

For molecular crystals, get the neighboring molecules for a given WP

Parameters:

• site_id – the index of reference site

• factor – factor of vdw tolerance

• max_d – maximum distances

Returns:

list of short contact pairs engs: list of energies from atom-atom potential

Return type:

pairs

get_neighboring_molecules(site_id=0, factor=1.5, max_d=5.0, ignore_E=True)

For molecular crystals, get the neighboring molecules for a given WP

Parameters:

• site_id – the index of reference site

• factor – factor of vdw tolerance

• max_d

• ignore_E

Returns:

list of shortest distances neighs: list of neighboring molecular xyzs comps: list of molecular types Ps: list of [0, 1] to distinguish self and other molecules engs: list of energies from atom-atom potential

Return type:

min_ds

get_num_torsions()

Get number of torsions for molecular xtal

get_orientation_energy()

get_separations(hkls=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])

Compute the separation for the given hkl plane

get_site_labels()

Get the site_labels as a dictionary

get_spherical_images(**kwargs)

get the spherical image representation

Parameters:

model – either ‘molecule’ or ‘contacts’

Returns:

the sph class

get_std_representation(trans)

Perform cell transformation so that the symmetry operations follow standard space group notation

get_structure_factor(hkl, coeffs=None)

Compute the structure factor for a given hkl plane

Parameters:

• hkl (-) – three indices hkl plane

• coeffs (-) – Atomic scatering factors

get_tabular_representation(ids=None, normalize=False, N_wp=6, perturb=False, max_abc=50.0, max_angle=3.141592653589793, eps=0.05, standardize=True, discrete=False, discrete_cell=False, N_grids=50)

Convert the xtal to a 1D reprsentation organized as (space_group_number, a, b, c, alpha, beta, gamma, wp1, wp2, ….) each wp is represented by 4 numbers (wp_id, x, y, z)

Parameters:

• ids (list) – index of generators for each wp

• normalize (bool) – whether or not normalize the data to (0, 1)

• N_wp (int) – number of maximum wp sites

• perturb (bool) – whether or not perturb the variables

• max_abc (float) – maximum abc length for normalization

• max_angle (float) – maximum angle in radian for normalization

• eps (float) – the degree of perturbation

• discrete (bool) – to discretize xyz

• discrete_cell (bool) – to discretize cell_para

• N_grids (int) – number of grids used for discretization

Returns:

a 1D vector such as (141, 3, 3, 3, pi/2, pi/2, pi/2, wp_id, x, y, z)

get_tabular_representations(N_max=200, N_wp=8, normalize=False, perturb=False, eps=0.05, discrete=False, discrete_cell=False, N_grids=50)

Enumerate the equivalent representations for a give crystal. For example, 8a in space group 227 has 8 equivalent positions

Parameters:

• N_max (int) – the max number of samples from the enumeration

• N_wp (int) – the maximum number of allowed WP sites

• normalize (bool) – normalize all number to (0, 1)

• perturb (bool) – whether or not perturb the variables

• eps (float) – the degree of perturbation

• discrete (bool) – to discretize xyz

• N_grids (int) – number of grids used for discretization

Returns:

a list of equivalent 1D tabular representations

get_transition(ref_struc, d_tol=1.0, d_tol2=0.3, N_images=2, max_path=30, both=False)

Get the splitted wyckoff information along a given path:

Parameters:

• ref_struc – structure with subgroup symmetry

• d_tol – maximally allowed atomic displacement

• d_tol2 – displacement that allows early termination

• N_images – number of intermediate images

• max_path – maximum number of paths

• both – whether or not do interpolation along both sides

Returns:

• displacements:

• cell translation:

• the list of space groups along the path

• the list of splitters along the path

Return type:

• strucs

get_transition_by_path(ref_struc, path, d_tol, d_tol2=0.5, N_images=2, both=False)

Get the splitted wyckoff information along a given path:

Parameters:

• ref_struc – structure with subgroup symmetry

• path – a list of transition path

• d_tol – maximally allowed atomic displacement

• d_tol2 – displacement that allows early termination

• N_images – number of intermediate images

• both – interpolation on both sides

Returns:

• displacements:

• cell translation:

Return type:

• strucs

get_xtal_string(dicts=None, header=None)

get the xtal string

Parameters:

• xtal – pyxtal instance

• sim (float) – similarity metric

• status (bool) – whether or not the structure is valid

• energy (float) – the energy value

get_zprime(integer=False)

Get zprime for molecular xtal

has_special_site(species=None)

Check if the crystal has a special site

is_duplicate(ref_strucs)

check if the structure is exactly the same

load_dict(dict0)

Load the structure from a dictionary

make_transitions(disps, lattice=None, translation=None, N_images=3, both=False)

make the pyxtals by following the atomic displacements

Parameters:

• disps – N*3 atomic displacements in fractional coordinates

• lattice – 3*3 cell matrix (self.lattice.matrix if None)

• translation – overall translation

• N_images – number of images

• both – whether or not interpolar on both sides

optimize_lattice(iterations=5, force=False, standard=False)

Optimize the lattice if the cell has a bad inclination angles We first optimize the angle to some good-looking range. If standard, force the structure to have the standard setting This only applies to monoclinic systems

Parameters:

• iterations – maximum number of iterations

• force – whether or not do the early termination

• standard – True or False

optimize_lattice_and_rotation(iterations=3, verbose=False)

Iteratively cut lattice and optimize the rotation

optimize_orientation_by_energy(max_iter=20, verbose=False)

remove_species(species)

To remove the atom_sites by specie name :param dicts: e.g., [“O”]

remove_water()

Remove water from hydrates

resort()

A short cut to resort the sites by self.molecules or self.species

resort_species(species)

resort the atomic species

Parameters:

species – list of elements, e.g. [‘Si’, ‘O’]

resymmetrize(tol=0.001)

Recheck the symmetry with a given tolerance value Useful to identify a higher space group symmetry

Parameters:

tol (float) – the tolerance value for symmetry finder

save_dict()

Save the model as a dictionary

set_cutoff(exclude_ii=False, value=None)

get the cutoff dictionary

Parameters:

• exclude_ii (bool) – whether or not exclude A-A distance

• value (float) – cutoff distance

set_site_coordination(cutoff=None, verbose=False, exclude_ii=False)

Compute the coordination number from each atomic site

show(**kwargs)

display the crystal structure

show_mol_cluster(id, factor=1.5, max_d=4.0, plot=True, ignore_E=False, cmap='YlGn', **kwargs)

display the local packing environment for a selected molecule

sort_sites_by_mult()

sort_sites_by_numIons(seq=None)

subgroup(perms=None, H=None, eps=0.05, idx=None, group_type='t', max_cell=4, min_cell=0, N_groups=None)

Generate a structure with lower symmetry

Parameters:

• perms – e.g., {“Si”: “C”}

• H – space group number (int)

• eps – pertubation term (float)

• idx – list

• group_type (string) – t, k or t+k

• max_cell (float) – maximum cell reconstruction

• min_cell (float) – maximum cell reconstruction

• max_subgroups (int) – maximum number of trial subgroups

Returns:

a list of pyxtal structures with lower symmetries

subgroup_by_path(gtypes, ids, eps=0, mut_lat=False)

Generate a structure with lower symmetry (for atomic crystals only)

Parameters:

• g_types – [‘t’, ‘k’]

• idx – list of ids for the splitter

• eps – degree of displacement

• mut_lat – mutate the lattice of not

Returns:

a pyxtal structure with lower symmetries list of splitters

subgroup_once(eps=0.1, H=None, perms=None, group_type='t', max_cell=4, min_cell=0, mut_lat=True, ignore_special=False, verbose=False)

Generate a structure with lower symmetry (for atomic crystals only)

Parameters:

• perms – e.g., {“Si”: “C”}

• H – space group number (int)

• idx – list

• group_type – t or k

• max_cell – maximum cell reconstruction (float)

Returns:

a pyxtal structure with lower symmetries

substitute(dicts)

A quick function to apply substitution

Parameters:

dicts – e.g., {“F”: “Cl”}

substitute_1_2(dicts, ratio=None, group_type='t+k', max_cell=4, min_cell=0, max_wp=None, N_groups=None, N_max=10, criteria=None)

Derive the BC compounds from A via subgroup relation For example, from C to BN or from SiO2 to AlPO3. The key is to split A’s wyckoff site to B and C by w.r.t. composition relation. If the current parent crystal doesn’t allow splitting, look for the subgroup

Parameters:

• dicts – e.g., {“F”: “Cl”}

• ratio – e.g., [1, 1]

• group_type (string) – t, k or t+k

• max_cell (float) – maximum cell reconstruction

• min_cell (float) – maximum cell reconstruction

• max_wp (int) – maximum number of wp

• N_groups (int) – maximum number of trial subgroups

• N_max (int) – maximum number of structures

• criteria (dict) – dictionary criteria

Returns:

A list of pyxtal structures

substitute_linear(dicts)

This is mainly designed for substitution between single atom and the linear block e.g., we want to make Zn(CN)2 from SiO2 :param dicts: e.g., {“Si”: [“Zn”], “O”: [“C”,”N”]}

supergroup(G=None, d_tol=1.0)

Generate a structure with higher symmetry

Parameters:

• G – super space group number (list of integers)

• d_tol – maximum tolerance

Returns:

a list of pyxtal structures with minimum super group symmetries

supergroups(G=None, d_tol=1.0)

Generate the structures with higher symmetry

Parameters:

• G – super space group number (list of integers)

• d_tol – maximum tolerance

Returns:

a list of pyxtal structures with minimum super group symmetries

to_ase(resort=True, center_only=False, add_vaccum=True)

Export to ase Atoms object.

Parameters:

• resort (bool) – resort atoms

• center (bool) – dump only molculer center for mol. xtal

• add_vaccum (bool) – add vaccum for 0/1/2D systems

to_atomic_xtal()

Convert the molecular

to_file(filename=None, fmt=None, permission='w', sym_num=None, header='from_pyxtal')

Creates a file with the given ame and type to store the structure. By default, creates cif files for crystals and xyz files for clusters. For other formats, Pymatgen is used

Parameters:

• filename (string) – the file path

• fmt (string) – the file type (cif, xyz, etc.)

• permission (string) – w or a+

• sym_num (int) – number of sym_ops, None means writing all symops

• header (string) – header

Returns:

Nothing. Creates a file at the specified path

to_json(filename='pyxtal.json')

Save the model as a dictionary

to_molecular_xtal(molecules, oris=None, reflects=None)

Convert the atomic xtal to molecular xtal the input molecules must have the same length of the self.atom_sites

to_pymatgen(resort=True, shape='upper')

Export to Pymatgen structure object.

to_pyxtal_center()

Export to PyXtal object for molecular centers only.

to_standard_setting()

A short cut to symmetrize the structure in the stardard setting

to_subgroup(path=None, t_only=True, iterate=False, species=None)

Transform a crystal with speical sites to subgroup represenatation with general sites

Parameters:

• Path – list of path to get the general sites

• iterate (bool) – whether or not do it iteratively

• species – to add

transform(trans, lattice=None)

Perform cell transformation and symmetry operation

Parameters:

• trans – 3*3 matrix

• lattice – pyxtal lattice object

• update – whether or not update each wp

translate(trans, reset_wp=False)

move the atomic sites along a translation Note that this may change the structure

Parameters:

trans – 1*3 vector

update_from_1d_rep(x)

update the xtal from the 1d representation Group: I 41/a m d:2 (141) 2.5019, 2.5019, 8.7534, 90.0000, 90.0000, 90.0000, tetragonal Wyckoff sites: C @ [ 0.0000 0.2500 0.4614], WP [8e] Site [2mm.]

the above rep is [2.5019, 8.7514, 0.4614]

Parameters:

x (float) – input variable array to describe a xtal

update_wyckoffs()

rescale the coordinates in the wyckoff site

Subpackages

• pyxtal.database package
  • Subpackages
    • pyxtal.database.cifs package
  • Submodules
    • pyxtal.database.collection module
      • Collection
    • pyxtal.database.element module
      • Element
• pyxtal.interface package
  • Submodules
    • pyxtal.interface.LJ module
      • FIRE
      • GPa2eV
      • LJ
      • get_neighbors()
    • pyxtal.interface.ase_opt module
      • ASE_optimizer
      • ASE_relax()
      • get_calculator()
    • pyxtal.interface.charmm module
      • CHARMM
      • PRM
      • RTF
      • check_prm()
    • pyxtal.interface.dftb module
      • DFTB
      • DFTB_SCF()
      • DFTB_relax()
      • Dftb
      • make_Hamiltonian()
    • pyxtal.interface.gulp module
      • GULP
      • GULP_OC
      • optimize()
      • single_optimize()
    • pyxtal.interface.lammpslib module
      • LAMMPS_collections
      • LAMMPSlib
      • convert_cell()
      • is_upper_triangular()
      • opt_lammpslib()
      • run_lammpslib()
    • pyxtal.interface.vasp module
      • VASP
      • VASP_relax()
      • optimize()
      • single_optimize()
      • single_point()
• pyxtal.lego package
  • Submodules
    • pyxtal.lego.builder module
      • RandomDispBounds
      • calculate_S()
      • calculate_dSdx()
      • create_trajectory()
      • generate_wp_lib_par()
      • generate_xtal()
      • generate_xtal_par()
      • get_input_from_letters()
      • minimize_from_x()
      • minimize_from_x_par()
      • mof_builder
    • pyxtal.lego.SO3 module
      • Cosine()
      • GaussChebyshevQuadrature()
      • SO3
      • W()
      • compute_cs()
      • compute_dcs()
      • g()
      • phi()
    • pyxtal.lego.basinhopping module
      • basinhopping()
• pyxtal.optimize package
  • Submodules
    • pyxtal.optimize.DFS module
      • DFS
    • pyxtal.optimize.QRS module
      • QRS
      • generate_qrs_cell()
      • generate_qrs_xtals()
    • pyxtal.optimize.WFS module
      • WFS
    • pyxtal.optimize.base module
      • GlobalOptimize
      • process_task()
      • run_optimizer_with_timeout()
      • setup_worker_logger()
    • pyxtal.optimize.benchmark module
      • benchmark
    • pyxtal.optimize.common module
      • check_stable_structure()
      • compute()
      • compute_par()
      • load_reference_from_db()
      • mutator()
      • optimizer()
      • optimizer_par()
      • optimizer_single()
      • randomizer()
      • refine_struc()
• pyxtal.potentials package
  • Submodules
    • pyxtal.potentials.LJ_cluster module
      • LJ()
      • LJ_force()

Submodules

• pyxtal.XRD module
  • Profile
    • Profile.get_profile()
  • Similarity
    • Similarity.cosineFunction()
    • Similarity.show()
    • Similarity.triangleFunction()
  • XRD
    • XRD.all_dhkl()
    • XRD.by_hkl()
    • XRD.draw_hkl()
    • XRD.get_profile()
    • XRD.get_unique_families()
    • XRD.intensity()
    • XRD.load()
    • XRD.plot_pxrd()
    • XRD.plotly_pxrd()
    • XRD.pxrdf()
    • XRD.save()
  • create_index()
  • gaussian()
  • get_all_intensity()
  • get_all_intensity_par()
  • get_intensity()
  • lorentzian()
  • mod_pseudo_voigt()
  • pseudo_voigt()
  • pxrd_refine()
  • similarity_calculate()
• pyxtal.block_crystal module
  • block_crystal()
• pyxtal.constants module
• pyxtal.crystal module
  • random_crystal
    • random_crystal.check_wp()
    • random_crystal.set_crystal()
    • random_crystal.set_elemental_volumes()
    • random_crystal.set_lattice()
    • random_crystal.set_sites()
    • random_crystal.set_volume()
• pyxtal.db module
  • call_opt_single()
  • database
    • database.add()
    • database.add_from_code()
    • database.check_status()
    • database.compute()
    • database.copy()
    • database.get_all_codes()
    • database.get_pyxtal()
    • database.get_row()
    • database.get_row_info()
    • database.process_kvp()
    • database.vacuum()
    • database.view()
  • database_topology
    • database_topology.add_strucs_from_db()
    • database_topology.add_xtal()
    • database_topology.check_new_structure()
    • database_topology.check_overlap()
    • database_topology.clean_structures()
    • database_topology.clean_structures_pmg()
    • database_topology.clean_structures_spg_topology()
    • database_topology.export_structures()
    • database_topology.get_all_xtals()
    • database_topology.get_db_unique()
    • database_topology.get_label()
    • database_topology.get_max_id()
    • database_topology.get_properties()
    • database_topology.get_pyxtal()
    • database_topology.plot_histogram()
    • database_topology.print_info()
    • database_topology.print_memory_usage()
    • database_topology.select_xtal()
    • database_topology.select_xtals()
    • database_topology.update_db_description()
    • database_topology.update_row_energy()
    • database_topology.update_row_energy_mproc()
    • database_topology.update_row_energy_serial()
    • database_topology.update_row_topology()
    • database_topology.vacuum()
  • dftb_opt_single()
  • gulp_opt_single()
  • mace_opt_single()
  • make_db_from_CSD()
  • make_entry_from_CSD()
  • make_entry_from_CSD_web()
  • make_entry_from_pyxtal()
  • opt_single()
  • process_xtal()
  • setup_worker_logger()
  • vasp_opt_single()
• pyxtal.descriptor module
  • cart2sph()
  • correlation()
  • correlation_go()
  • correlation_opt()
  • expand_sph()
  • fibonacci_sphere()
  • get_alignment()
  • orientation_order
    • orientation_order.get_neighbors()
    • orientation_order.get_parameters()
  • sph2cart()
  • spherical_image
    • spherical_image.align()
    • spherical_image.calculate_density()
    • spherical_image.get_contacts()
    • spherical_image.get_molecules()
    • spherical_image.get_similarity()
    • spherical_image.plot_real_image()
    • spherical_image.plot_sph_images()
    • spherical_image.pysh
    • spherical_image.rotate()
  • xyz2sph()
• pyxtal.elasticity module
  • CubicElasticModuli
    • CubicElasticModuli.compliance()
    • CubicElasticModuli.rotate()
    • CubicElasticModuli.stiffness()
    • CubicElasticModuli.tol
  • Voigt_6_to_full_3x3_strain()
  • Voigt_6_to_full_3x3_stress()
  • Voigt_6x6_to_cubic()
  • Voigt_6x6_to_full_3x3x3x3()
  • cubic_to_Voigt_6x6()
  • elastic_moduli()
  • elastic_properties()
  • fit_elastic_constants()
  • full_3x3_to_Voigt_6_index()
  • full_3x3_to_Voigt_6_strain()
  • full_3x3_to_Voigt_6_stress()
  • full_3x3x3x3_to_Voigt_6x6()
  • generate_strained_configs()
  • invariants()
  • measure_triclinic_elastic_constants()
  • poisson_ratio()
  • rotate_cubic_elastic_constants()
  • rotate_elastic_constants()
  • youngs_modulus()
• pyxtal.io module
  • get_cif_str_for_pyxtal()
  • in_merged_coords()
  • read_cif()
  • search_molecules_in_crystal()
  • structure_from_ext
    • structure_from_ext.add_Hydrogens()
    • structure_from_ext.align()
    • structure_from_ext.make_mol_sites()
    • structure_from_ext.resort()
    • structure_from_ext.show()
  • write_cif()
• pyxtal.lattice module
  • Lattice
    • Lattice.add_vacuum()
    • Lattice.apply_transformation()
    • Lattice.check_mismatch()
    • Lattice.copy()
    • Lattice.encode()
    • Lattice.find_transition_to_orthoslab()
    • Lattice.from_1d_representation()
    • Lattice.from_matrix()
    • Lattice.from_para()
    • Lattice.generate_matrix()
    • Lattice.generate_para()
    • Lattice.generate_point()
    • Lattice.get_bounds()
    • Lattice.get_diff()
    • Lattice.get_dofs()
    • Lattice.get_lengths()
    • Lattice.get_matrix()
    • Lattice.get_para()
    • Lattice.get_permutation_matrices()
    • Lattice.get_transformation_matrices()
    • Lattice.get_worst_angle()
    • Lattice.is_valid_lattice()
    • Lattice.is_valid_matrix()
    • Lattice.mutate()
    • Lattice.optimize_multi()
    • Lattice.optimize_once()
    • Lattice.reset_matrix()
    • Lattice.scale()
    • Lattice.search_transformation()
    • Lattice.search_transformations()
    • Lattice.set_matrix()
    • Lattice.set_para()
    • Lattice.set_volume()
    • Lattice.standardize()
    • Lattice.swap_angle()
    • Lattice.swap_axis()
    • Lattice.transform()
    • Lattice.transform_multi()
    • Lattice.update_from_1d_representation()
    • Lattice.update_para()
  • gaussian_random_variable()
  • generate_cellpara()
  • generate_cellpara_0D()
  • generate_cellpara_1D()
  • generate_cellpara_2D()
  • matrix2para()
  • para2matrix()
  • random_shear_matrix()
  • random_vector()
• pyxtal.molecular_crystal module
  • molecular_crystal
    • molecular_crystal.set_crystal()
    • molecular_crystal.set_lattice()
    • molecular_crystal.set_molecules()
    • molecular_crystal.set_orientations()
    • molecular_crystal.set_sites()
    • molecular_crystal.set_volume()
• pyxtal.molecule module
  • Box
    • Box.operate()
  • Orientation
    • Orientation.change_orientation()
    • Orientation.copy()
    • Orientation.get_Euler_angles()
    • Orientation.get_matrix()
    • Orientation.get_op()
    • Orientation.load_dict()
    • Orientation.random_orientation()
    • Orientation.reset_matrix()
    • Orientation.rotate_by_matrix()
    • Orientation.save_dict()
    • Orientation.set_axis()
  • compare_mol_connectivity()
  • find_rotor_from_smile()
  • generate_molecules()
  • get_inertia_tensor()
  • has_non_aromatic_ring()
  • is_compatible_symmetry()
  • make_graph()
  • pyxtal_molecule
    • pyxtal_molecule.align()
    • pyxtal_molecule.apply_inversion()
    • pyxtal_molecule.copy()
    • pyxtal_molecule.get_box()
    • pyxtal_molecule.get_box_coordinates()
    • pyxtal_molecule.get_center()
    • pyxtal_molecule.get_coefs_matrix()
    • pyxtal_molecule.get_energy()
    • pyxtal_molecule.get_lengths()
    • pyxtal_molecule.get_max_length()
    • pyxtal_molecule.get_orientation()
    • pyxtal_molecule.get_orientations_in_wp()
    • pyxtal_molecule.get_orientations_in_wps()
    • pyxtal_molecule.get_principle_axes()
    • pyxtal_molecule.get_radius()
    • pyxtal_molecule.get_rmsd()
    • pyxtal_molecule.get_rmsd2()
    • pyxtal_molecule.get_symbols()
    • pyxtal_molecule.get_symmetry()
    • pyxtal_molecule.get_tols_matrix()
    • pyxtal_molecule.get_torsion_angles()
    • pyxtal_molecule.list_molecules()
    • pyxtal_molecule.load_str()
    • pyxtal_molecule.perturb_torsion()
    • pyxtal_molecule.rdkit_mol()
    • pyxtal_molecule.rdkit_mol_init()
    • pyxtal_molecule.relax()
    • pyxtal_molecule.reset_positions()
    • pyxtal_molecule.save_str()
    • pyxtal_molecule.set_labels()
    • pyxtal_molecule.set_torsion_angles()
    • pyxtal_molecule.show()
    • pyxtal_molecule.show_box()
    • pyxtal_molecule.swap_axis()
    • pyxtal_molecule.to_ase()
  • reoriented_molecule()
• pyxtal.msg module
  • AtomTypeError
  • CSDError
  • Comp_CompatibilityError
  • ConformerError
  • Error
  • ReadSeedError
  • Symm_CompatibilityError
  • VolumeError
  • printx()
• pyxtal.operations module
  • OperationAnalyzer
    • OperationAnalyzer.are_conjugate()
    • OperationAnalyzer.get_order()
    • OperationAnalyzer.is_conjugate()
    • OperationAnalyzer.parse_axis()
    • OperationAnalyzer.parse_glide_symmetry()
    • OperationAnalyzer.parse_screw_symmetry()
  • aa2matrix()
  • angle()
  • apply_ops()
  • apply_ops_diagonal()
  • are_equal()
  • check_distance()
  • check_images()
  • create_matrix()
  • distance()
  • distance_matrix()
  • distance_matrix_no_PBC()
  • filtered_coords()
  • filtered_coords_euclidean()
  • find_ids()
  • get_best_match()
  • get_inverse()
  • get_inverse_ops()
  • is_orthogonal()
  • rotate_vector()
  • verify_distances()
• pyxtal.plane module
  • get_dspacing()
  • has_reduction()
  • plane
  • planes
    • planes.find_unique_separations()
    • planes.gather()
    • planes.get_cp_factor()
    • planes.get_separation()
    • planes.get_structure_factor()
    • planes.group_slabs()
    • planes.search_close_packing_planes()
    • planes.set_planes()
    • planes.set_xtal()
  • reduced_hkl()
  • structure_factor()
• pyxtal.representation module
  • representation
    • representation.from_pyxtal()
    • representation.from_string()
    • representation.get_dist()
    • representation.same_smiles()
    • representation.to_pyxtal()
    • representation.to_standard_setting()
    • representation.to_string()
  • representation_atom
    • representation_atom.from_pyxtal()
    • representation_atom.to_array()
    • representation_atom.to_pyxtal()
    • representation_atom.to_standard_setting()
    • representation_atom.to_string()
• pyxtal.supergroup module
  • find_mapping()
  • find_mapping_per_element()
  • find_xyz()
  • new_path()
  • new_structure()
  • search_G1()
  • search_G2()
  • supergroup
    • supergroup.calc_disps()
    • supergroup.get_coord_H()
    • supergroup.get_initial_mask()
    • supergroup.make_pyxtal_in_supergroup()
    • supergroup.make_pyxtals_in_subgroup()
    • supergroup.make_supergroup()
    • supergroup.print_detail()
    • supergroup.print_wp()
    • supergroup.search_supergroup()
    • supergroup.sort_solutions()
    • supergroup.symmetrize()
    • supergroup.symmetrize_dist()
    • supergroup.symmetrize_site_double_k()
    • supergroup.symmetrize_site_double_t()
    • supergroup.symmetrize_site_multi()
    • supergroup.symmetrize_site_single()
  • supergroups
    • supergroups.get_transformation()
    • supergroups.print_solutions()
    • supergroups.struc_along_path()
    • supergroups.write_cifs()
  • write_poscars()
• pyxtal.symmetry module
  • Group
    • Group.add_k_transitions()
    • Group.cellsize()
    • Group.check_compatible()
    • Group.clean_lists()
    • Group.get_alternatives()
    • Group.get_ferroelectric_groups()
    • Group.get_free_axis()
    • Group.get_index_by_letter()
    • Group.get_lattice_dof()
    • Group.get_lists()
    • Group.get_lists_mol()
    • Group.get_max_k_subgroup()
    • Group.get_max_subgroup()
    • Group.get_max_subgroup_numbers()
    • Group.get_max_t_subgroup()
    • Group.get_min_supergroup()
    • Group.get_site_dof()
    • Group.get_spg_symmetry_object()
    • Group.get_splitters_from_relation()
    • Group.get_splitters_from_structure()
    • Group.get_symmetry_directions()
    • Group.get_valid_solutions()
    • Group.get_wp_by_letter()
    • Group.get_wp_list()
    • Group.get_wyckoff_position()
    • Group.get_wyckoff_position_from_xyz()
    • Group.is_valid_combination()
    • Group.list_groups()
    • Group.list_wyckoff_combinations()
    • Group.path_to_general_wp()
    • Group.path_to_subgroup()
    • Group.search_subgroup_paths()
    • Group.search_supergroup_paths()
    • Group.short_path_to_general_wp()
  • Hall
  • SymmetryData
    • SymmetryData.get_generator_lg()
    • SymmetryData.get_generator_pg()
    • SymmetryData.get_generator_rg()
    • SymmetryData.get_generator_sg()
    • SymmetryData.get_hall_table()
    • SymmetryData.get_k_subgroup()
    • SymmetryData.get_symmetry_lg()
    • SymmetryData.get_symmetry_pg()
    • SymmetryData.get_symmetry_rg()
    • SymmetryData.get_symmetry_sg()
    • SymmetryData.get_t_subgroup()
    • SymmetryData.get_wyckoff_lg()
    • SymmetryData.get_wyckoff_pg()
    • SymmetryData.get_wyckoff_rg()
    • SymmetryData.get_wyckoff_sg()
  • Wyckoff_position
    • Wyckoff_position.apply_ops()
    • Wyckoff_position.are_equivalent_pts()
    • Wyckoff_position.copy()
    • Wyckoff_position.distance_check()
    • Wyckoff_position.equivalent_set()
    • Wyckoff_position.from_dict()
    • Wyckoff_position.from_discrete_grid()
    • Wyckoff_position.from_group_and_index()
    • Wyckoff_position.from_group_and_letter()
    • Wyckoff_position.from_index_quick()
    • Wyckoff_position.from_symops()
    • Wyckoff_position.from_symops_wo_group()
    • Wyckoff_position.gen_pos()
    • Wyckoff_position.get_all_positions()
    • Wyckoff_position.get_dof()
    • Wyckoff_position.get_euclidean_generator()
    • Wyckoff_position.get_euclidean_ops()
    • Wyckoff_position.get_euclidean_symmetries()
    • Wyckoff_position.get_free_xyzs()
    • Wyckoff_position.get_frozen_axis()
    • Wyckoff_position.get_hm_number()
    • Wyckoff_position.get_hm_symbol()
    • Wyckoff_position.get_label()
    • Wyckoff_position.get_ops_from_transformation()
    • Wyckoff_position.get_position_from_free_xyzs()
    • Wyckoff_position.get_site_symm_ops()
    • Wyckoff_position.get_site_symm_wo_translation()
    • Wyckoff_position.get_site_symmetry()
    • Wyckoff_position.get_site_symmetry_object()
    • Wyckoff_position.has_equivalent_ops()
    • Wyckoff_position.is_pure_translation()
    • Wyckoff_position.is_standard_setting()
    • Wyckoff_position.load_dict()
    • Wyckoff_position.merge()
    • Wyckoff_position.print_ops()
    • Wyckoff_position.process_ops()
    • Wyckoff_position.project()
    • Wyckoff_position.save_dict()
    • Wyckoff_position.search_all_generators()
    • Wyckoff_position.search_generator()
    • Wyckoff_position.search_generator_dist()
    • Wyckoff_position.set_euclidean()
    • Wyckoff_position.set_generators()
    • Wyckoff_position.set_ops()
    • Wyckoff_position.short_distances()
    • Wyckoff_position.swap_axis()
    • Wyckoff_position.to_discrete_grid()
    • Wyckoff_position.transform_from_matrices()
    • Wyckoff_position.transform_from_matrix()
    • Wyckoff_position.update()
    • Wyckoff_position.update_hall()
    • Wyckoff_position.update_index()
  • abc2matrix()
  • are_equivalent_ops()
  • check_symmetry_and_dim()
  • check_wyckoff_position()
  • choose_wyckoff()
  • choose_wyckoff_mol()
  • find_axis_order()
  • get_all_polar_space_groups()
  • get_close_packed_groups()
  • get_generators()
  • get_pbc_and_lattice()
  • get_point_group()
  • get_symbol_and_number()
  • get_symmetry_directions()
  • get_symmetry_from_ops()
  • get_wyckoff_symmetry()
  • get_wyckoffs()
  • identity_ops()
  • index_from_letter()
  • jk_from_i()
  • letter_from_index()
  • op_transform()
  • op_translation()
  • organized_wyckoffs()
  • para2ferro()
  • rf()
  • search_cloest_wp()
  • site_symm()
  • site_symmetry
    • site_symmetry.get_highest_symmetry()
    • site_symmetry.get_name()
    • site_symmetry.ref_symmetry()
    • site_symmetry.set_full_hm_symbols()
    • site_symmetry.set_short_symbols()
    • site_symmetry.set_table()
    • site_symmetry.to_beautiful_matrix_representation()
    • site_symmetry.to_matrix_representation()
    • site_symmetry.to_matrix_representation_spg()
    • site_symmetry.to_one_hot()
    • site_symmetry.unique_symmetry()
  • swap_xyz_ops()
  • swap_xyz_string()
  • symmetry_element_from_axis()
  • transform_ops()
  • trim_ops()
• pyxtal.tolerance module
  • Tol_matrix
    • Tol_matrix.from_file()
    • Tol_matrix.from_matrix()
    • Tol_matrix.from_radii()
    • Tol_matrix.from_single_value()
    • Tol_matrix.get_tol()
    • Tol_matrix.set_tol()
    • Tol_matrix.to_file()
• pyxtal.util module
  • Kgrid()
  • ase2pymatgen()
  • extract_ase_db()
  • find_dir()
  • generate_wp_lib()
  • get_similar_cids_from_pubchem()
  • get_struc_from__parser()
  • get_symmetrized_pmg()
  • good_lattice()
  • listToString()
  • new_struc()
  • new_struc_wo_energy()
  • parse_cif()
  • process_csd_cif()
  • pymatgen2ase()
  • reset_lammps_cell()
  • search_csd_code_by_pubchem()
  • search_csd_entries_by_code()
  • sort_by_dimer()
  • split_list_by_ratio()
  • symmetrize()
  • symmetrize_cell()
• pyxtal.version module
• pyxtal.viz module
  • addBox()
  • addlines()
  • display_atomic()
  • display_cluster()
  • display_crystals()
  • display_mol_crystals()
  • display_molecular()
  • display_molecular_site()
  • display_molecule()
  • display_molecules()
• pyxtal.wyckoff_site module
  • atom_site
    • atom_site.check_with_ws2()
    • atom_site.copy()
    • atom_site.encode()
    • atom_site.equivalent_set()
    • atom_site.get_bounds()
    • atom_site.get_disp()
    • atom_site.get_translations()
    • atom_site.load_dict()
    • atom_site.perturbate()
    • atom_site.save_dict()
    • atom_site.search_position()
    • atom_site.shift_by_swap()
    • atom_site.substitute_with_linear()
    • atom_site.substitute_with_single()
    • atom_site.to_mol_site()
    • atom_site.update()
  • mol_site
    • mol_site.mol
    • mol_site.position
    • mol_site.orientation
    • mol_site.wp
    • mol_site.lattice
    • mol_site.stype
    • mol_site.symbols
    • mol_site.numbers
    • mol_site.PBC
    • mol_site.radius
    • mol_site.tols_matrix
    • mol_site._get_dof()
    • mol_site.cut_lattice()
    • mol_site.encode()
    • mol_site.extract_short_distances()
    • mol_site.from_1D_dicts()
    • mol_site.get_bounds()
    • mol_site.get_coords_and_species()
    • mol_site.get_dist_angle_AD()
    • mol_site.get_dist_angle_DA()
    • mol_site.get_distances()
    • mol_site.get_dists_WP()
    • mol_site.get_dists_WP2()
    • mol_site.get_dists_auto()
    • mol_site.get_energy()
    • mol_site.get_ijk_lists()
    • mol_site.get_min_dist()
    • mol_site.get_mol_object()
    • mol_site.get_neighbors_auto()
    • mol_site.get_neighbors_wp2()
    • mol_site.is_valid_orientation()
    • mol_site.load_dict()
    • mol_site.optimize_orientation_by_dist()
    • mol_site.optimize_orientation_by_energy()
    • mol_site.perturbate()
    • mol_site.rotate()
    • mol_site.save_dict()
    • mol_site.short_dist()
    • mol_site.short_dist_with_wp2()
    • mol_site.show()
    • mol_site.show_molecule_in_box()
    • mol_site.to_1D_dicts()
    • mol_site.to_atom_site()
    • mol_site.translate()
    • mol_site.update()
    • mol_site.update_molecule()
    • mol_site.update_orientation()
• pyxtal.wyckoff_split module
  • in_lists()
  • wyckoff_split
    • wyckoff_split.check_orbits()
    • wyckoff_split.parse_wp2()
    • wyckoff_split.sort()
    • wyckoff_split.split_k()
    • wyckoff_split.split_t()
    • wyckoff_split.translation_generator()