# Copyright (C) 2010, Jesper Friis
# (see accompanying license files for details).
"""
A module for ASE for simple creation of crystalline structures from
knowledge of the space group.
"""
from typing import Any, Dict
import numpy as np
from scipy import spatial
import ase
from ase.geometry import cellpar_to_cell
from ase.spacegroup import Spacegroup
from ase.symbols import string2symbols
__all__ = ['crystal']
[docs]def crystal(symbols=None, basis=None, occupancies=None, spacegroup=1, setting=1,
cell=None, cellpar=None,
ab_normal=(0, 0, 1), a_direction=None, size=(1, 1, 1),
onduplicates='warn', symprec=0.001,
pbc=True, primitive_cell=False, **kwargs) -> ase.Atoms:
"""Create an Atoms instance for a conventional unit cell of a
space group.
Parameters:
symbols : str | sequence of str | sequence of Atom | Atoms
Element symbols of the unique sites. Can either be a string
formula or a sequence of element symbols. E.g. ('Na', 'Cl')
and 'NaCl' are equivalent. Can also be given as a sequence of
Atom objects or an Atoms object.
basis : list of scaled coordinates
Positions of the unique sites corresponding to symbols given
either as scaled positions or through an atoms instance. Not
needed if *symbols* is a sequence of Atom objects or an Atoms
object.
occupancies : list of site occupancies
Occupancies of the unique sites. Defaults to 1.0 and thus no mixed
occupancies are considered if not explicitly asked for. If occupancies
are given, the most dominant species will yield the atomic number.
The occupancies in the atoms.info['occupancy'] dictionary will have
integers keys converted to strings. The conversion is done in order
to avoid unexpected conversions when using the JSON serializer.
spacegroup : int | string | Spacegroup instance
Space group given either as its number in International Tables
or as its Hermann-Mauguin symbol.
setting : 1 | 2
Space group setting.
cell : 3x3 matrix
Unit cell vectors.
cellpar : [a, b, c, alpha, beta, gamma]
Cell parameters with angles in degree. Is not used when `cell`
is given.
ab_normal : vector
Is used to define the orientation of the unit cell relative
to the Cartesian system when `cell` is not given. It is the
normal vector of the plane spanned by a and b.
a_direction : vector
Defines the orientation of the unit cell a vector. a will be
parallel to the projection of `a_direction` onto the a-b plane.
size : 3 positive integers
How many times the conventional unit cell should be repeated
in each direction.
onduplicates : 'keep' | 'replace' | 'warn' | 'error'
Action if `basis` contain symmetry-equivalent positions:
'keep' - ignore additional symmetry-equivalent positions
'replace' - replace
'warn' - like 'keep', but issue an UserWarning
'error' - raises a SpacegroupValueError
symprec : float
Minimum "distance" betweed two sites in scaled coordinates
before they are counted as the same site.
pbc : one or three bools
Periodic boundary conditions flags. Examples: True,
False, 0, 1, (1, 1, 0), (True, False, False). Default
is True.
primitive_cell : bool
Whether to return the primitive instead of the conventional
unit cell.
Keyword arguments:
All additional keyword arguments are passed on to the Atoms
constructor. Currently, probably the most useful additional
keyword arguments are `info`, `constraint` and `calculator`.
Examples:
Two diamond unit cells (space group number 227)
>>> diamond = crystal('C', [(0,0,0)], spacegroup=227,
... cellpar=[3.57, 3.57, 3.57, 90, 90, 90], size=(2,1,1))
>>> ase.view(diamond) # doctest: +SKIP
A CoSb3 skutterudite unit cell containing 32 atoms
>>> skutterudite = crystal(('Co', 'Sb'),
... basis=[(0.25,0.25,0.25), (0.0, 0.335, 0.158)],
... spacegroup=204, cellpar=[9.04, 9.04, 9.04, 90, 90, 90])
>>> len(skutterudite)
32
"""
sg = Spacegroup(spacegroup, setting)
if (
not isinstance(symbols, str) and
hasattr(symbols, '__getitem__') and
len(symbols) > 0 and
isinstance(symbols[0], ase.Atom)):
symbols = ase.Atoms(symbols)
if isinstance(symbols, ase.Atoms):
basis = symbols
symbols = basis.get_chemical_symbols()
if isinstance(basis, ase.Atoms):
basis_coords = basis.get_scaled_positions()
if cell is None and cellpar is None:
cell = basis.cell
if symbols is None:
symbols = basis.get_chemical_symbols()
else:
basis_coords = np.array(basis, dtype=float, ndmin=2)
if occupancies is not None:
occupancies_dict = {}
for index, coord in enumerate(basis_coords):
# Compute all distances and get indices of nearest atoms
dist = spatial.distance.cdist(coord.reshape(1, 3), basis_coords)
indices_dist = np.flatnonzero(dist < symprec)
occ = {symbols[index]: occupancies[index]}
# Check nearest and update occupancy
for index_dist in indices_dist:
if index == index_dist:
continue
else:
occ.update({symbols[index_dist]: occupancies[index_dist]})
occupancies_dict[str(index)] = occ.copy()
sites, kinds = sg.equivalent_sites(basis_coords,
onduplicates=onduplicates,
symprec=symprec)
# this is needed to handle deuterium masses
masses = None
if 'masses' in kwargs:
masses = kwargs['masses'][kinds]
del kwargs['masses']
symbols = parse_symbols(symbols)
if occupancies is None:
symbols = [symbols[i] for i in kinds]
else:
# make sure that we put the dominant species there
symbols = [sorted(occupancies_dict[str(i)].items(),
key=lambda x: x[1])[-1][0] for i in kinds]
if cell is None:
cell = cellpar_to_cell(cellpar, ab_normal, a_direction)
info: Dict[str, Any] = {}
info['spacegroup'] = sg
if primitive_cell:
info['unit_cell'] = 'primitive'
else:
info['unit_cell'] = 'conventional'
if 'info' in kwargs:
info.update(kwargs['info'])
if occupancies is not None:
info['occupancy'] = occupancies_dict
kwargs['info'] = info
atoms = ase.Atoms(symbols,
scaled_positions=sites,
cell=cell,
pbc=pbc,
masses=masses,
**kwargs)
if isinstance(basis, ase.Atoms):
for name in basis.arrays:
if not atoms.has(name):
array = basis.get_array(name)
atoms.new_array(name, [array[i] for i in kinds],
dtype=array.dtype, shape=array.shape[1:])
if kinds:
atoms.new_array('spacegroup_kinds', np.asarray(kinds, dtype=int))
if primitive_cell:
from ase.build import cut
prim_cell = sg.scaled_primitive_cell
# Preserve calculator if present:
calc = atoms.calc
atoms = cut(atoms, a=prim_cell[0], b=prim_cell[1], c=prim_cell[2])
atoms.calc = calc
if size != (1, 1, 1):
atoms = atoms.repeat(size)
return atoms
def parse_symbols(symbols):
"""Return `sumbols` as a sequence of element symbols."""
if isinstance(symbols, str):
symbols = string2symbols(symbols)
return symbols