# Source code for icet.tools.structure_enumeration

```
from itertools import product
from typing import Dict, List, Tuple, Generator, Union
import numpy as np
from ase import Atoms
from ase.build import make_supercell
from spglib import get_symmetry
from spglib import niggli_reduce as spg_nigg_red
from icet.tools.geometry import ase_atoms_to_spglib_cell
from .structure_enumeration_support.normal_form_matrices \
import HermiteNormalForm, yield_reduced_hnfs, SmithNormalForm, get_unique_snfs
from .structure_enumeration_support.labeling_generation \
import LabelingGenerator
def _translate_labelings(
labeling: tuple,
snf: SmithNormalForm,
nsites: int,
include_self: bool = False) -> Generator[Tuple[int], None, None]:
"""
Yields labelings that are equivalent to the original labeling under
translations as dictated by the Smith normal form (SNF) provided.
Parameters
----------
labeling
labeling to be translated
snf
SmithNormalForm object
nsites
number of sites in the primitive cell
include_self
if True original labeling will be included
"""
# Compute size of each block within which translations occur
sizes = [nsites * block for block in snf.blocks]
# Loop over all possible translations within group as defined by snf
for trans in product(range(snf.S[0]), range(snf.S[1]), range(snf.S[2])):
if not include_self and sum(trans) == 0:
continue
labeling_trans = ()
for i in range(snf.S[0]):
group = (i + trans[0]) % snf.S[0]
block_i = labeling[sizes[0] * group:sizes[0] * (group + 1)]
for j in range(snf.S[1]):
group = (j + trans[1]) % snf.S[1]
block_j = block_i[sizes[1] * group:sizes[1] * (group + 1)]
for k in range(snf.S[2]):
group = (k + trans[2]) % snf.S[2]
labeling_trans += tuple(block_j[sizes[2] * group:
sizes[2] * (group + 1)])
yield labeling_trans
def _get_all_labelings(snf: SmithNormalForm,
labeling_generator: LabelingGenerator,
nsites: int) -> List[tuple]:
"""
Returns inequivalent labelings corresponding to a Smith normal form
(SNF) matrix. Superperiodic labelings as well as labelings that are
equivalent under translations for this particular SNF will not be
included. However, labelings that are equivalent by rotations that
leave the cell (but not the labeling) unchanged will still be
included, since these have to be removed for each Hermite normal
form (HNF) separately.
Parameters
----------
snf
SmithNormalForm object
labeling_generator
LabelingGenerator object
nsites
number of sites per primitive cell
"""
labelings = []
for labeling in labeling_generator.yield_labelings(snf.ncells):
unique = True
for labeling_trans in _translate_labelings(labeling, snf, nsites,
include_self=False):
# Check whether it translates into itself. If so,
# then it has been added with a smaller cell.
if labeling == labeling_trans:
unique = False
break
# Check with previous labelings,
# if labeling can be translated into a previously
# added labeling, then it is not unique
if labeling_trans in labelings:
unique = False
break
if unique:
labelings.append(labeling)
return labelings
def _permute_labeling(labeling: tuple, snf: SmithNormalForm,
transformation: List[np.ndarray],
nsites: int) -> Tuple[int]:
"""
Returns permuted labeling according to transformations defined by
transformation.
Parameters
----------
labeling
labeling to be rotated
snf
SmithNormalForm object
transformation
transformation consisting of rotation, translation and basis
shift
nsites
number of sites in the primitive cell
"""
# Calculate transformation imposed by LRL multiplication
new_group_order = np.dot(snf.group_order, transformation[0].T)
# Loop over every atom to find its new position
labeling_new = [0] * len(labeling)
for member_index, member in enumerate(new_group_order):
# Transform according to Gp,
# but each site in the primitive cell also transforms in its own way
for basis in range(nsites):
new_cell = member + transformation[1][basis]
# Calculate new index, first by finding the right block,
# then by adding the basis index to that block
new_index = 0
for i in range(3):
new_index += (new_cell[i] % snf.S[i]) * snf.blocks[i] * nsites
new_index += transformation[2][basis]
# Add the contribution to the hash key
element = labeling[member_index * nsites + basis]
labeling_new[new_index] = element
return tuple(labeling_new)
def _yield_unique_labelings(labelings: List[int], snf: SmithNormalForm,
hnf: HermiteNormalForm, nsites: int) -> tuple:
"""
Yields labelings that are unique in every imaginable sense.
Parameters
----------
labelkeys
list of hash keys to labelings that may still contain labelings
that are equivalent under rotations that leave the supercell
shape unchanged
snf
SmithNormalForm object
hnf
HermiteNormalForm object
nsites
number of sites in the primitive cell
"""
saved_labelings = []
for labeling in labelings:
# Check whether labeling is just a rotated version of a previous
# labeling. Apply transformation that is specific to the hnf
# and check all translations of the transformed labeling.
unique = True
for transformation in hnf.transformations:
labeling_rot = _permute_labeling(labeling, snf, transformation,
nsites)
# Commonly, the transformation leaves the labeling
# unchanged, so check that first as a special case
# (yields a quite significant speedup)
if labeling_rot == labeling:
continue
# Translate in all possible ways
for labeling_rot_trans in \
_translate_labelings(labeling_rot, snf, nsites,
include_self=True):
if labeling_rot_trans in saved_labelings:
# Then we have rotated and translated the labeling
# into one that was already yielded
unique = False
break
if not unique:
break
if unique:
# Then we have finally found a unique structure
# defined by an HNF matrix and a labeling
saved_labelings.append(labeling)
yield labeling
def _labeling_to_ase_atoms(labeling: tuple, hnf: HermiteNormalForm,
cell: np.ndarray,
new_cell: np.ndarray,
basis: np.ndarray, chemical_symbols: List[str],
pbc: List[bool]) -> Atoms:
"""
Returns structure object corresponding to the given labeling using
labeling, HNF matrix and parent lattice.
Parameters
---------
labeling
permutation of index of elements
hnf
HNF object defining the supercell
cell
basis vectors of primtive cell listed row-wise
new_cell
new cell shape
basis
scaled coordinates to all sites in the primitive cell
chemical_symbols
list of elements, e.g. ``['Au', 'Ag']``
pbc
periodic boundary conditions of the primitive structure
"""
a = hnf.H[0, 0]
b = hnf.H[1, 0]
c = hnf.H[1, 1]
d = hnf.H[2, 0]
e = hnf.H[2, 1]
f = hnf.H[2, 2]
symbols = []
positions = []
for z1 in range(a):
offset_1 = (b * z1) / a
for z2 in range(int(offset_1), int(offset_1 + c)):
offset_2 = z1 * (d - (e * b) / c) / a + (e * z2) / c
for z3 in range(int(offset_2), int(f + offset_2)):
for basis_vector_i, basis_vector in enumerate(basis):
# Determine position in Cartesian coordinates
pos = np.dot(cell.T, np.array([z1, z2, z3]) + basis_vector)
positions.append(pos)
# Now determine which species this is
g = np.dot(hnf.snf.L, [z1, z2, z3])
assert np.allclose(g, np.round(g))
g = np.round(g).astype('int64')
g = [g[i] % hnf.snf.S[i] for i in range(3)]
ind = len(basis) * (g[0] * hnf.snf.S[1] * hnf.snf.S[2] +
g[1] * hnf.snf.S[2] + g[2]) + basis_vector_i
symbols.append(chemical_symbols[labeling[ind]])
structure = Atoms(symbols, positions, cell=new_cell, pbc=(True, True, True))
structure.wrap()
structure.pbc = pbc
return structure
def _get_symmetry_operations(structure: Atoms,
symprec: float,
position_tolerance: float) -> Dict[str, list]:
"""
Returns symmetry operations permissable for a given structure as
obtained via `spglib <https://atztogo.github.io/spglib/>`_. The
symmetry operations consist of three parts: rotation, translation
and basis shifts. The latter define the way that sublattices
shift upon rotation (correponds to `d_Nd` in [HarFor09]_).
Parameters
----------
structure
structure for which symmetry operations are sought
symprec
tolerance imposed when analyzing the symmetry using spglib
position_tolerance
tolerance applied when comparing positions in Cartesian coordinates
"""
symmetries = get_symmetry(ase_atoms_to_spglib_cell(structure), symprec=symprec)
assert symmetries, ('spglib.get_symmetry() failed. Please make sure that'
' the structure object is sensible.')
rotations = symmetries['rotations']
translations = symmetries['translations']
basis = structure.get_scaled_positions()
# Calculate how atoms within the primitive cell are shifted (from one site
# to another) and translated (from one primtive cell to another) upon
# operation with rotation matrix. Note that the translations are needed
# here because different sites translate differently.
basis_shifts = np.zeros((len(rotations), len(structure)), dtype='int64')
sites_translations = []
for i, rotation in enumerate(rotations):
translation = translations[i]
site_translations = []
for j, basis_element in enumerate(basis):
# Calculate how the site is transformed when operated on by
# symmetry of parent lattice (rotation and translation)
site_rot_trans = np.dot(rotation, basis_element) + translation
# The site may now have been moved to a different site in a
# different cell. We want to separate the two. (In HarFor09,
# basis_shift (site_rot_trans) corresponds to d_Nd and
# site_translation to t_Nd)
site_translation = [0, 0, 0]
for index in range(3):
while site_rot_trans[index] < -position_tolerance:
site_rot_trans[index] += 1
site_translation[index] -= 1
while site_rot_trans[index] > 1 - position_tolerance:
site_rot_trans[index] -= 1
site_translation[index] += 1
site_translations.append(site_translation)
# Find the basis element that the shifted basis correponds to
found = False
for basis_index, basis_element_comp in enumerate(basis):
distance = site_rot_trans - basis_element_comp
# Make sure that they do not differ with a basis vector
for dist_comp_i, dist_comp in enumerate(distance):
if abs(abs(dist_comp) - 1) < position_tolerance:
distance[dist_comp_i] = 0
if (abs(distance) < position_tolerance).all():
assert not found
basis_shifts[i, j] = basis_index
found = True
assert found
sites_translations.append(np.array(site_translations))
symmetries['translations'] = sites_translations
symmetries['basis_shifts'] = basis_shifts
return symmetries
[docs]def enumerate_structures(structure: Atoms,
sizes: Union[List[int], range],
chemical_symbols: list,
concentration_restrictions: dict = None,
niggli_reduce: bool = None,
symprec: float = 1e-5,
position_tolerance: float = None) -> Atoms:
"""
Yields a sequence of enumerated structures. The function generates
*all* inequivalent structures that are permissible given a certain
lattice. Using the ``chemical_symbols`` and
``concentration_restrictions`` keyword arguments it is possible to
specify which chemical_symbols are to be included on which site and
in which concentration range.
The function is sensitive to the boundary conditions of the input
structure. An enumeration of, for example, a surface can thus be
performed by setting ``structure.pbc = [True, True, False]``.
The algorithm implemented here was developed by Gus L. W. Hart and
Rodney W. Forcade in Phys. Rev. B **77**, 224115 (2008)
[HarFor08]_ and Phys. Rev. B **80**, 014120 (2009) [HarFor09]_.
Parameters
----------
structure
primitive structure from which derivative superstructures should
be generated
sizes
number of sites (included in enumeration)
chemical_symbols
chemical species with which to decorate the structure, e.g.,
``['Au', 'Ag']``; see below for more examples
concentration_restrictions
allowed concentration range for one or more element in
`chemical_symbols`, e.g., ``{'Au': (0, 0.2)}`` will only
enumerate structures in which the Au content is between 0 and
20 %; here, concentration is always defined as the number of
atoms of the specified kind divided by the number of *all*
atoms.
niggli_reduction
if True perform a Niggli reduction with spglib for each
structure; the default is ``True`` if ``structure`` is periodic in
all directions, ``False`` otherwise.
symprec
tolerance imposed when analyzing the symmetry using spglib
position_tolerance
tolerance applied when comparing positions in Cartesian coordinates;
by default this value is set equal to `symprec`
Examples
--------
The following code snippet illustrates how to enumerate structures
with up to 6 atoms in the unit cell for a binary alloy without any
constraints::
>>> from ase.build import bulk
>>> prim = bulk('Ag')
>>> for structure in enumerate_structures(structure=prim,
... sizes=range(1, 5),
... chemical_symbols=['Ag', 'Au']):
... pass # Do something with the structure
To limit the concentration range to 10 to 40% Au the code should
be modified as follows::
>>> conc_restr = {'Au': (0.1, 0.4)}
>>> for structure in enumerate_structures(structure=prim,
... sizes=range(1, 5),
... chemical_symbols=['Ag', 'Au'],
... concentration_restrictions=conc_restr):
... pass # Do something with the structure
Often one would like to consider mixing on only one
sublattice. This can be achieved as illustrated for a
Ga(1-x)Al(x)As alloy as follows::
>>> prim = bulk('GaAs', crystalstructure='zincblende', a=5.65)
>>> for structure in enumerate_structures(structure=prim,
... sizes=range(1, 9),
... chemical_symbols=[['Ga', 'Al'], ['As']]):
... pass # Do something with the structure
"""
if position_tolerance is None:
position_tolerance = symprec
nsites = len(structure)
basis = structure.get_scaled_positions()
# Construct descriptor of where species are allowed to be
if isinstance(chemical_symbols[0], str):
iter_chemical_symbols = [tuple(range(len(chemical_symbols)))] * nsites
elements = chemical_symbols
elif len(chemical_symbols) == nsites:
assert isinstance(chemical_symbols[0][0], str)
elements = []
for site in chemical_symbols:
for element in site:
if element not in elements:
elements.append(element)
iter_chemical_symbols = []
for site in chemical_symbols:
iter_chemical_symbols.append(tuple(elements.index(i)
for i in site))
else:
raise Exception('chemical_symbols needs to be a list of strings '
'or a list of list of strings.')
# Adapt concentration restrictions to iter_chemical_symbols
if concentration_restrictions:
concentrations = {}
for key, concentration_range in concentration_restrictions.items():
assert len(concentration_range) == 2, \
('Each concentration range' +
' needs to be specified as (c_low, c_high)')
if key not in elements:
raise ValueError('{} found in concentration_restrictions but'
' not in chemical_symbols'.format(key))
concentrations[elements.index(key)] = concentration_range
else:
concentrations = None
# Construct labeling generator
labeling_generator = LabelingGenerator(iter_chemical_symbols,
concentrations)
# Niggli reduce by default if all directions have
# periodic boundary conditions
if niggli_reduce is None:
niggli_reduce = (sum(structure.pbc) == 3)
symmetries = _get_symmetry_operations(structure,
symprec=symprec,
position_tolerance=position_tolerance)
# Loop over each cell size
for ncells in sizes:
if ncells == 0:
continue
hnfs = list(yield_reduced_hnfs(ncells, symmetries, structure.pbc))
snfs = get_unique_snfs(hnfs)
for snf in snfs:
labelings = _get_all_labelings(snf, labeling_generator, nsites)
for hnf in snf.hnfs:
if niggli_reduce:
new_cell = spg_nigg_red(np.dot(hnf.H.T, structure.cell))
if new_cell is None:
new_cell = np.dot(hnf.H.T, structure.cell)
else:
new_cell = np.dot(hnf.H.T, structure.cell)
for labeling in _yield_unique_labelings(labelings, snf, hnf,
nsites):
yield _labeling_to_ase_atoms(labeling, hnf,
structure.cell, new_cell,
basis, elements,
structure.pbc)
[docs]def enumerate_supercells(structure: Atoms,
sizes: Union[List[int], range],
niggli_reduce: bool = None,
symprec: float = 1e-5,
position_tolerance: float = None) -> Atoms:
"""
Yields a sequence of enumerated supercells. The function generates
*all* inequivalent supercells that are permissible given a certain
lattice. Any supercell can be reduced to one of the supercells
generated.
The function is sensitive to the boundary conditions of the input
structure. An enumeration of, for example, a surface can thus be
performed by setting ``structure.pbc = [True, True, False]``.
The algorithm is based on Gus L. W. Hart and
Rodney W. Forcade in Phys. Rev. B **77**, 224115 (2008)
[HarFor08]_ and Phys. Rev. B **80**, 014120 (2009) [HarFor09]_.
Parameters
----------
structure
primitive structure from which supercells should be
generated
sizes
number of sites (included in enumeration)
niggli_reduction
if True perform a Niggli reduction with spglib for each
supercell; the default is ``True`` if ``structure`` is periodic in
all directions, ``False`` otherwise.
symprec
tolerance imposed when analyzing the symmetry using spglib
position_tolerance
tolerance applied when comparing positions in Cartesian coordinates;
by default this value is set equal to `symprec`
Examples
--------
The following code snippet illustrates how to enumerate supercells
with up to 6 atoms in the unit cell::
>>> from ase.build import bulk
>>> prim = bulk('Ag')
>>> for supercell in enumerate_supercells(structure=prim, sizes=range(1, 7)):
... pass # Do something with the supercell
"""
if position_tolerance is None:
position_tolerance = symprec
# Niggli reduce by default if all directions have
# periodic boundary conditions
if niggli_reduce is None:
niggli_reduce = (sum(structure.pbc) == 3)
symmetries = _get_symmetry_operations(structure,
symprec=symprec,
position_tolerance=position_tolerance)
for ncells in sizes:
for hnf in yield_reduced_hnfs(ncells, symmetries, structure.pbc):
supercell = make_supercell(structure, hnf.H.T)
if niggli_reduce:
new_cell = spg_nigg_red(np.dot(hnf.H.T, structure.cell))
if new_cell is None: # Happens when spglib fails to Niggli reduce
yield supercell
else:
Pprim = np.dot(new_cell, np.linalg.inv(structure.cell))
yield make_supercell(structure, Pprim)
else:
yield supercell
```