pyxtal.wyckoff_site module

Module for handling Wyckoff sites for both atom and molecule

class pyxtal.wyckoff_site.atom_site(wp=None, coordinate=None, specie=1, search=False)

Bases: object

Class for storing atomic Wyckoff positions with a single coordinate.

Parameters:

• wp – a `Wyckoff_position <pyxtal.symmetry.Wyckoff_position.html> object
• coordinate – a fractional 3-vector for the generating atom’s coordinate
• specie – an Element, element name or symbol, or atomic number of the atom
• search – to search for the optimum position for special wyckoff site

check_with_ws2(ws2, lattice, tm, same_group=True)

Given two Wyckoff sites, checks the inter-atomic distances between them.

Parameters:

• ws2 – a different Wyckoff_site object (will always return False if
• identical WS's are provided) (two) –
• lattice – a 3x3 cell matrix
• same_group – whether or not the two WS’s are in the same structure.
• value True reduces the calculation cost (Default) –

Returns:

True if all distances are greater than the allowed tolerances. False if any distance is smaller than the allowed tolerance

equivalent_set(tran, indices)

Transform the wp to another equivalent set. Needs to update both wp and positions

Parameters:

• tran – affine matrix
• indices – the list of transformed wps

get_disp(pos, lattice, translation)

return the displacement towards the reference positions

Parameters:

• pos – reference position (1*3 vector)
• lattice – 3*3 matrix
• translation –

get_translations(pos, axis)

return the displacement towards the reference positions

Parameters:

• pos – reference position (1*3 vector)
• lattice – 3*3 matrix
• translation –
• axis –

classmethod load_dict(dicts)

load the sites from a dictionary

perturbate(lattice, magnitude=0.1)

Random perturbation of the site

Parameters:

• lattice – lattice vectors
• magnitude – the magnitude of displacement (default: 0.1 A)

save_dict()

search_position()

Sometimes, the initial posiition is not the proper generator Needs to find the proper generator

shift_by_swap(swap_id)

check if a shift is needed during swap May occur for special WP in the I/A/B/C/F cases e.g., in space group 71 (Immm), the permutation 4j(1/2,0,0.2) -> (0.2,0,1/2) -> 4f(0.7,1/2,0) it requires a shift of (0.5,0.5,0.5)

swap_axis(swap_id, shift=array([0., 0., 0.]))

sometimes space groups like Pmm2 allows one to swap the a,b axes to get an alternative representation

update(pos=None, reset_wp=False)

Used to generate coords from self.position

class pyxtal.wyckoff_site.mol_site(mol, position, orientation, wp, lattice=None, stype=0)

Bases: object

Class for storing molecular Wyckoff positions and orientations within the molecular_crystal class. Each mol_site object represenents an entire Wyckoff position, not necessarily a single molecule. This is the molecular version of Wyckoff_site

Parameters:

• mol – a pyxtal_molecule object
• position – the 3-vector representing the generating molecule’s position
• orientation – an Orientation object
• wp – a Wyckoff_position object
• lattice – a Lattice object
• stype – integer number to specify the type of molecule

encode()

transform dict to 1D vector [x, y, z, or1, or2, or3, rotor1, rotor2, .etc]

classmethod from_1D_dicts(dicts)

get_coords_and_species(absolute=False, PBC=False, unitcell=False)

Lazily generates and returns the atomic coordinate and species for the Wyckoff position. Plugs the molecule into the provided orientation (with angle=0), and calculates the new positions.

Parameters:

• absolute – return absolute or relative coordinates
• PBC – whether or not to add coordinates in neighboring unit cells
• unitcell – whether or not to move the molecule center to the unit cell

Returns:

a np array of 3-vectors. species: a list of atomic symbols, e.g. [‘H’, ‘H’, ‘O’, ‘H’, ‘H’, ‘O’]

Return type:

coords

get_distances(coord1, coord2, m2=None, center=True, ignore=False)

Compute the distance matrix between the center molecule (m1 length) and neighbors (m2 length) within the PBC consideration (pbc)

Parameters:

• coord1 – fractional coordinates of the center molecule
• coord2 – fractional coordinates of the reference neighbors
• m2 – the length of reference molecule
• center – whether or not consider the self image for coord2

Returns:

[m1*m2*pbc, m1, m2] coord2 under PBC: [pbc, m2, 3]

Return type:

distance matrix

get_dists_WP(ignore=False, id=None)

Compute the distances within the WP sites

Returns:a distance matrix (M, N, N) list of molecular xyz (M, N, 3)

get_dists_auto(ignore=False)

Compute the distances between the periodic images

Returns:a distance matrix (M, N, N) list of molecular xyz (M, N, 3)

get_ijk_lists(value=None)

Get the occupatation in the unit cell for the generating molecule This can be used to estimate the supercell size for finding neighbors

Returns

PBC

get_min_dist()

Compute the minimum interatomic distance within the WP.

Returns:minimum distance

get_mol_object(id=0)

make the pymatgen molecule object

Parameters:id – the index of molecules in the given site Returns:a molecule object

get_neighbors_auto(factor=1.1, max_d=4.0, ignore_E=True, detail=False, etol=-0.05)

Find the neigboring molecules

Parameters:

• factor – volume factor
• max_d – maximum intermolecular distance
• ignore_E –
• detail – show detailed energies

Returns

min_ds: list of shortest distances neighs: list of neighboring molecular xyzs

get_neighbors_wp2(wp2, factor=1.1, max_d=4.0, ignore_E=True, detail=False, etol=-0.05)

Find the neigboring molecules from a 2nd wp site

Returns

min_ds: list of shortest distances neighs: list of neighboring molecular xyzs

is_valid_orientation()

classmethod load_dict(dicts)

load the sites from a dictionary

perturbate(lattice, trans=0.1, rot=5)

Random perturbation of the molecular site

Parameters:

• lattice – lattice vectors
• trans – magnitude of tranlation vectors (default: 0.1 A)
• rot – magnitude of rotation degree (default: 5.0)

rotate(ax_id=0, ax_vector=None, angle=180)

To rotate the molecule :param ax_id: the principle axis id :param ax_vector: 3-vector to define the axis :type ax_vector: float :param angle: angle to rotate :type angle: float

save_dict()

short_dist()

Check if the atoms are too close within the WP.

Returns:True or False

short_dist_with_wp2(wp2, tm=<pyxtal.tolerance.Tol_matrix object>)

Check whether or not the molecules of two wp sites overlap. Uses ellipsoid overlapping approximation to check.

Parameters:

• wp2 – the 2nd wp sites
• tm – a Tol_matrix object (or prototype string) for distance checking

Returns:

True or False

show(id=None, **kwargs)

display WP on the notebook

show_molecule_in_box(id=0)

display molecule with box

Parameters:id (int) – molecular id

to_1D_dicts()

save the wp in 1D representation

translate(disp=array([0., 0., 0.]), absolute=False)

To translate the molecule

update(coords, lattice=None, absolute=False, update_mol=True)

After the geometry relaxation, the returned atomic coordinates maybe rescaled to [0, 1] bound. In this case, we need to refind the molecular coordinates according to the original neighbor list. If the list does not change, we return the new coordinates otherwise, terminate the calculation.