# Source code for icet.tools.structure_generation

```
import itertools
from typing import List, Dict, Tuple, Union
import numpy as np
from mchammer.ensembles import TargetClusterVectorAnnealing
from mchammer.calculators import (TargetVectorCalculator,
compare_cluster_vectors)
from icet.tools import (enumerate_structures,
enumerate_supercells)
from icet import ClusterSpace
from icet.input_output.logging_tools import logger
from ase import Atoms
from ase.data import chemical_symbols as periodic_table
[docs]
def generate_target_structure_from_supercells(cluster_space: ClusterSpace,
supercells: List[Atoms],
target_concentrations: dict,
target_cluster_vector: List[float],
T_start: float = 5.0,
T_stop: float = 0.001,
n_steps: int = None,
optimality_weight: float = 1.0,
random_seed: int = None,
random_start: bool = True,
tol: float = 1e-5) -> Atoms:
"""
Given a :attr:`cluster_space` and a :attr:`target_cluster_vector` and one
or more :attr:`supercells`, generate a structure that as closely as
possible matches that cluster vector.
Internally the function uses a simulated annealing algorithm and the
difference between two cluster vectors is calculated with the
measure suggested by A. van de Walle et al. in Calphad **42**, 13-18
(2013) [WalTiwJon13]_ (for more information, see
:class:`mchammer.calculators.TargetVectorCalculator`).
Parameters
----------
cluster_space
A cluster space defining the lattice to be occupied.
supercells
List of one or more supercells among which an optimal
structure will be searched for.
target_concentrations
Concentration of each species in the target structure, per
sublattice (for example ``{'Au': 0.5, 'Pd': 0.5}`` for a
single sublattice Au-Pd structure, or
``{'A': {'Au': 0.5, 'Pd': 0.5}, 'B': {'H': 0.25, 'X': 0.75}}``
for a system with two sublattices.
The symbols defining sublattices ('A', 'B' etc) can be
found by printing the :attr:`cluster_space`.
target_cluster_vector
Cluster vector that the generated structure should match as
closely as possible.
T_start
Artificial temperature at which the simulated annealing starts.
T_stop
Artifical temperature at which the simulated annealing stops.
n_steps
Total number of Monte Carlo steps in the simulation.
optimality_weight
Controls weighting :math:`L` of perfect correlations, see
:class:`mchammer.calculators.TargetVectorCalculator`.
random_seed
Seed for the random number generator used in the Monte Carlo simulation
and used for initializing the occupation of the supercells if
random_start is ``True``.
random_start
Randomly occupy starting structure, can be disabled
if the user prefers to pass an initial structure.
tol
Numerical tolerance.
"""
target_concentrations = _validate_concentrations(target_concentrations, cluster_space)
calculators = []
# Loop over all supercells and intialize
# them with a "random" occupation of symbols that
# fulfill the target concentrations
valid_supercells = []
warning_issued = False
for supercell in supercells:
supercell_copy = supercell.copy()
if random_start:
try:
occupy_structure_randomly(supercell_copy, cluster_space,
target_concentrations,
random_seed)
except ValueError:
if not warning_issued:
logger.warning('At least one supercell was not commensurate with the specified '
'target concentrations.')
warning_issued = True
continue
valid_supercells.append(supercell_copy)
calculators.append(TargetVectorCalculator(supercell_copy, cluster_space,
target_cluster_vector,
optimality_weight=optimality_weight,
optimality_tol=tol))
if len(valid_supercells) == 0:
raise ValueError('No supercells that may host the specified '
'target_concentrations were supplied.')
ens = TargetClusterVectorAnnealing(structure=valid_supercells, calculators=calculators,
T_start=T_start, T_stop=T_stop,
random_seed=random_seed)
return ens.generate_structure(number_of_trial_steps=n_steps)
[docs]
def generate_target_structure(cluster_space: ClusterSpace,
max_size: int,
target_concentrations: dict,
target_cluster_vector: List[float],
include_smaller_cells: bool = True,
pbc: Union[Tuple[bool, bool, bool], Tuple[int, int, int]] = None,
T_start: float = 5.0,
T_stop: float = 0.001,
n_steps: int = None,
optimality_weight: float = 1.0,
random_seed: int = None,
tol: float = 1e-5) -> Atoms:
"""
Given a :attr:`cluster_space` and a :attr:`target_cluster_vector`, generate
a structure that as closely as possible matches that cluster vector.
The search is performed among all inequivalent supercells shapes up
to a certain size.
Internally the function uses a simulated annealing algorithm and the
difference between two cluster vectors is calculated with the
measure suggested by A. van de Walle et al. in Calphad **42**, 13-18
(2013) [WalTiwJon13]_ (for more information, see
:class:`mchammer.calculators.TargetVectorCalculator`).
Parameters
----------
cluster_space
Cluster space defining the lattice to be occupied.
max_size
Maximum supercell size.
target_concentrations
Concentration of each species in the target structure, per
sublattice (for example ``{'Au': 0.5, 'Pd': 0.5}`` for a
single sublattice Au-Pd structure, or
``{'A': {'Au': 0.5, 'Pd': 0.5}, 'B': {'H': 0.25, 'X': 0.75}}``
for a system with two sublattices.
The symbols defining sublattices ('A', 'B' etc) can be
found by printing the :attr:`cluster_space`.
target_cluster_vector
Cluster vector that the generated structure should match as
closely as possible.
include_smaller_cells
If ``True``, search among all supercell sizes including
:attr:`max_size`, else search only among those exactly matching
:attr:`max_size`
pbc
Periodic boundary conditions for each direction, e.g.,
``(True, True, False)``. The axes are defined by
the cell of :attr:`cluster_space.primitive_structure``.
Default is periodic boundary in all directions.
T_start
Artificial temperature at which the simulated annealing starts.
T_stop
Artifical temperature at which the simulated annealing stops.
n_steps
Total number of Monte Carlo steps in the simulation.
optimality_weight
Controls weighting :math:`L` of perfect correlations, see
:class:`mchammer.calculators.TargetVectorCalculator`.
random_seed
Seed for the random number generator used in the Monte Carlo simulation.
tol
Numerical tolerance.
"""
target_concentrations = _validate_concentrations(target_concentrations, cluster_space)
if pbc is None:
pbc = (True, True, True)
prim = cluster_space.primitive_structure
prim.set_pbc(pbc)
supercells = []
if include_smaller_cells:
sizes = list(range(1, max_size + 1))
else:
sizes = [max_size]
for size in sizes:
# For efficiency, make a first check that the current size is
# commensurate with all concentrations (example: {'Au': 0.5,
# 'Pd': 0.5} would not be commensurate with a supercell with 3
# atoms).
supercell = cluster_space.primitive_structure.repeat((size, 1, 1))
if not _concentrations_fit_structure(structure=supercell,
cluster_space=cluster_space,
concentrations=target_concentrations):
continue
# Loop over all inequivalent supercells and intialize
# them with a "random" occupation of symbols that
# fulfill the target concentrations
for supercell in enumerate_supercells(prim, [size]):
supercell.set_pbc(True)
supercells.append(supercell)
return generate_target_structure_from_supercells(cluster_space=cluster_space,
supercells=supercells,
target_concentrations=target_concentrations,
target_cluster_vector=target_cluster_vector,
T_start=T_start,
T_stop=T_stop,
n_steps=n_steps,
optimality_weight=optimality_weight,
random_seed=random_seed,
tol=tol)
[docs]
def generate_sqs_from_supercells(cluster_space: ClusterSpace,
supercells: List[Atoms],
target_concentrations: dict,
T_start: float = 5.0,
T_stop: float = 0.001,
n_steps: int = None,
optimality_weight: float = 1.0,
random_seed: int = None,
random_start: bool = True,
tol: float = 1e-5) -> Atoms:
"""
Given a :attr:`cluster_space`` and one or more :attr:`supercells`, generate
a special quasirandom structure (SQS), i.e., a structure that for
the provided supercells size provides the best possible
approximation to a random alloy [ZunWeiFer90]_.
In the present case, this means that the generated structure will
have a cluster vector that as closely as possible matches the
cluster vector of an infintely large randomly occupied supercell.
Internally the function uses a simulated annealing algorithm and the
difference between two cluster vectors is calculated with the
measure suggested by A. van de Walle et al. in Calphad **42**, 13-18
(2013) [WalTiwJon13]_ (for more information, see
:class:`mchammer.calculators.TargetVectorCalculator`).
Parameters
----------
cluster_space
Cluster space defining the lattice to be occupied.
supercells
List of one or more supercells among which an optimal
structure will be searched for.
target_concentrations
Concentration of each species in the target structure, per
sublattice (for example ``{'Au': 0.5, 'Pd': 0.5}`` for a
single sublattice Au-Pd structure, or
``{'A': {'Au': 0.5, 'Pd': 0.5}, 'B': {'H': 0.25, 'X': 0.75}}``
for a system with two sublattices.
The symbols defining sublattices ('A', 'B' etc) can be
found by printing the :attr:`cluster_space`.
T_start
Artificial temperature at which the simulated annealing starts.
T_stop
Artifical temperature at which the simulated annealing stops.
n_steps
Total number of Monte Carlo steps in the simulation.
optimality_weight
Controls weighting :math:`L` of perfect correlations, see
:class:`mchammer.calculators.TargetVectorCalculator`.
random_seed
Seed for the random number generator used in the Monte Carlo simulation
and used for initializing the occupation of the supercells if
random_start is ``True``.
random_start
Randomly occupy starting structure, can be disabled
if the user prefers to pass an initial structure.
tol
Numerical tolerance.
"""
sqs_vector = _get_sqs_cluster_vector(cluster_space=cluster_space,
target_concentrations=target_concentrations)
return generate_target_structure_from_supercells(cluster_space=cluster_space,
supercells=supercells,
target_concentrations=target_concentrations,
target_cluster_vector=sqs_vector,
T_start=T_start, T_stop=T_stop,
n_steps=n_steps,
optimality_weight=optimality_weight,
random_seed=random_seed,
random_start=random_start,
tol=tol)
[docs]
def generate_sqs(cluster_space: ClusterSpace,
max_size: int,
target_concentrations: dict,
include_smaller_cells: bool = True,
pbc: Union[Tuple[bool, bool, bool], Tuple[int, int, int]] = None,
T_start: float = 5.0,
T_stop: float = 0.001,
n_steps: int = None,
optimality_weight: float = 1.0,
random_seed: int = None,
tol: float = 1e-5) -> Atoms:
"""
Given a :attr:`cluster_space`, generate a special quasirandom structure
(SQS), i.e., a structure that for a given supercell size provides
the best possible approximation to a random alloy [ZunWeiFer90]_.
In the present case, this means that the generated structure will
have a cluster vector that as closely as possible matches the
cluster vector of an infintely large randomly occupied supercell.
Internally the function uses a simulated annealing algorithm and the
difference between two cluster vectors is calculated with the
measure suggested by A. van de Walle et al. in Calphad **42**, 13-18
(2013) [WalTiwJon13]_ (for more information, see
:class:`mchammer.calculators.TargetVectorCalculator`).
Parameters
----------
cluster_space
Cluster space defining the lattice to be occupied.
max_size
Maximum supercell size.
target_concentrations
Concentration of each species in the target structure, per
sublattice (for example ``{'Au': 0.5, 'Pd': 0.5}`` for a
single sublattice Au-Pd structure, or
``{'A': {'Au': 0.5, 'Pd': 0.5}, 'B': {'H': 0.25, 'X': 0.75}}``
for a system with two sublattices.
The symbols defining sublattices ('A', 'B' etc) can be
found by printing the :attr:`cluster_space`.
include_smaller_cells
If ``True``, search among all supercell sizes including
:attr:`max_size`, else search only among those exactly matching
:attr:`max_size`
pbc
Periodic boundary conditions for each direction, e.g.,
``(True, True, False)``. The axes are defined by
the cell of ``cluster_space.primitive_structure``.
Default is periodic boundary in all directions.
T_start
Artificial temperature at which the simulated annealing starts.
T_stop
Artifical temperature at which the simulated annealing stops.
n_steps
Total number of Monte Carlo steps in the simulation.
optimality_weight
Controls weighting :math:`L` of perfect correlations, see
:class:`mchammer.calculators.TargetVectorCalculator`.
random_seed
Seed for the random number generator used in the
Monte Carlo simulation.
tol
Numerical tolerance.
"""
sqs_vector = _get_sqs_cluster_vector(cluster_space=cluster_space,
target_concentrations=target_concentrations)
return generate_target_structure(cluster_space=cluster_space,
max_size=max_size,
target_concentrations=target_concentrations,
target_cluster_vector=sqs_vector,
include_smaller_cells=include_smaller_cells,
pbc=pbc,
T_start=T_start, T_stop=T_stop,
n_steps=n_steps,
optimality_weight=optimality_weight,
random_seed=random_seed,
tol=tol)
[docs]
def generate_sqs_by_enumeration(cluster_space: ClusterSpace,
max_size: int,
target_concentrations: dict,
include_smaller_cells: bool = True,
pbc: Union[Tuple[bool, bool, bool], Tuple[int, int, int]] = None,
optimality_weight: float = 1.0,
tol: float = 1e-5) -> Atoms:
"""
Given a :attr:`cluster_space`, generate a special quasirandom structure
(SQS), i.e., a structure that for a given supercell size provides
the best possible approximation to a random alloy [ZunWeiFer90]_.
In the present case, this means that the generated structure will
have a cluster vector that as closely as possible matches the
cluster vector of an infintely large randomly occupied supercell.
Internally the function uses a simulated annealing algorithm and the
difference between two cluster vectors is calculated with the
measure suggested by A. van de Walle et al. in Calphad **42**, 13-18
(2013) [WalTiwJon13]_ (for more information, see
:class:`mchammer.calculators.TargetVectorCalculator`).
This functions generates SQS cells by exhaustive enumeration, which
means that the generated SQS cell is guaranteed to be optimal with
regard to the specified measure and cell size.
Parameters
----------
cluster_space
Cluster space defining the lattice to be occupied.
max_size
Maximum supercell size.
target_concentrations
Concentration of each species in the target structure, per
sublattice (for example ``{'Au': 0.5, 'Pd': 0.5}`` for a
single sublattice Au-Pd structure, or
``{'A': {'Au': 0.5, 'Pd': 0.5}, 'B': {'H': 0.25, 'X': 0.75}}``
for a system with two sublattices.
The symbols defining sublattices ('A', 'B' etc) can be
found by printing the :attr:`cluster_space`.
include_smaller_cells
if ``True`` search among all supercell sizes including
:attr:`max_size`, else search only among those exactly matching
:attr:`max_size`.
pbc
Periodic boundary conditions for each direction, e.g.,
``(True, True, False)``. The axes are defined by
the cell of ``cluster_space.primitive_structure``.
Default is periodic boundary in all directions.
optimality_weight
Controls weighting :math:`L` of perfect correlations, see
:class:`mchammer.calculators.TargetVectorCalculator`.
tol
Numerical tolerance.
"""
target_concentrations = _validate_concentrations(target_concentrations, cluster_space)
sqs_vector = _get_sqs_cluster_vector(cluster_space=cluster_space,
target_concentrations=target_concentrations)
# Translate concentrations to the format required for concentration
# restricted enumeration
cr: Dict[str, tuple] = {}
sublattices = cluster_space.get_sublattices(cluster_space.primitive_structure)
for sl in sublattices:
mult_factor = len(sl.indices) / len(cluster_space.primitive_structure)
if sl.symbol in target_concentrations:
sl_conc = target_concentrations[sl.symbol]
else:
sl_conc = {sl.chemical_symbols[0]: 1.0}
for species, value in sl_conc.items():
c = value * mult_factor
if species in cr:
cr[species] = (cr[species][0] + c,
cr[species][1] + c)
else:
cr[species] = (c, c)
# Check to be sure...
c_sum = sum(c[0] for c in cr.values())
assert abs(c_sum - 1) < tol # Should never happen, but...
as_list = cluster_space.as_list
best_score = 1e9
if include_smaller_cells:
sizes = list(range(1, max_size + 1))
else:
sizes = [max_size]
# Prepare primitive structure with the right boundary conditions
prim = cluster_space.primitive_structure
if pbc is None:
pbc = (True, True, True)
prim.set_pbc(pbc)
# Enumerate and calculate score for each structuer
for structure in enumerate_structures(prim,
sizes,
cluster_space.chemical_symbols,
concentration_restrictions=cr):
cv = cluster_space.get_cluster_vector(structure)
score = compare_cluster_vectors(cv_1=cv, cv_2=sqs_vector,
as_list=as_list,
optimality_weight=optimality_weight,
tol=tol)
if score < best_score:
best_score = score
best_structure = structure
return best_structure
[docs]
def occupy_structure_randomly(structure: Atoms, cluster_space: ClusterSpace,
target_concentrations: dict,
random_seed: int = None) -> None:
"""
Occupy a structure with quasirandom order but fulfilling
:attr:`target_concentrations`.
Parameters
----------
structure
ASE Atoms object that will be occupied randomly.
cluster_space
Cluster space (needed as it carries information about sublattices).
target_concentrations
Concentration of each species in the target structure, per
sublattice (for example ``{'Au': 0.5, 'Pd': 0.5}`` for a
single sublattice Au-Pd structure, or
``{'A': {'Au': 0.5, 'Pd': 0.5}, 'B': {'H': 0.25, 'X': 0.75}}``
for a system with two sublattices.
The symbols defining sublattices ('A', 'B' etc) can be
found by printing the :attr:`cluster_space`.
random_seed
Seed for the random number generator.
"""
rng = np.random.default_rng(random_seed)
target_concentrations = _validate_concentrations(cluster_space=cluster_space,
concentrations=target_concentrations)
if not _concentrations_fit_structure(structure, cluster_space, target_concentrations):
raise ValueError('Structure with {} atoms cannot accomodate '
'target concentrations {}'.format(len(structure),
target_concentrations))
symbols_all = [''] * len(structure)
for sl in cluster_space.get_sublattices(structure):
symbols: List[str] = [] # chemical_symbols in one sublattice
chemical_symbols = sl.chemical_symbols
if len(chemical_symbols) == 1:
symbols += [chemical_symbols[0]] * len(sl.indices)
else:
sl_conc = target_concentrations[sl.symbol]
for chemical_symbol in sl.chemical_symbols:
n_symbol = int(round(len(sl.indices) * sl_conc[chemical_symbol]))
symbols += [chemical_symbol] * n_symbol
# Should not happen but you never know
assert len(symbols) == len(sl.indices)
# Shuffle to introduce randomness
rng.shuffle(symbols)
# Assign symbols to the right indices
for symbol, lattice_site in zip(symbols, sl.indices):
symbols_all[lattice_site] = symbol
assert symbols_all.count('') == 0
structure.set_chemical_symbols(symbols_all)
def _validate_concentrations(concentrations: dict,
cluster_space: ClusterSpace,
tol: float = 1e-5) -> dict:
"""
Validates concentration specification against a cluster space
(raises `ValueError` if they do not match).
Parameters
----------
concentrations
Concentration specification.
cluster_space
Cluster space to check against.
tol
Numerical tolerance.
Returns
-------
An adapted version of concentrations, which is always a dictionary
even if there is only one sublattice.
"""
sls = cluster_space.get_sublattices(cluster_space.primitive_structure)
if not isinstance(list(concentrations.values())[0], dict):
concentrations = {'A': concentrations}
# Ensure concentrations sum to 1 at each sublattice
for sl_conc in concentrations.values():
conc_sum = sum(list(sl_conc.values()))
if abs(conc_sum - 1.0) > tol:
raise ValueError('Concentrations must sum up '
'to 1 for each sublattice (not {})'.format(conc_sum))
# Symbols need to match on each sublattice
for sl in sls:
if sl.symbol not in concentrations:
if len(sl.chemical_symbols) > 1:
raise ValueError('A sublattice ({}: {}) is missing in '
'target_concentrations'.format(sl.symbol,
list(sl.chemical_symbols)))
else:
sl_conc = concentrations[sl.symbol]
if tuple(sorted(sl.chemical_symbols)) != tuple(sorted(list(sl_conc.keys()))):
raise ValueError('Chemical symbols on a sublattice ({}: {}) are '
'not the same as those in the specified '
'concentrations {}'.format(sl.symbol, list(sl.chemical_symbols),
list(sl_conc.keys())))
return concentrations
def _concentrations_fit_structure(structure: Atoms,
cluster_space: ClusterSpace,
concentrations: Dict[str, Dict[str, float]],
tol: float = 1e-5) -> bool:
"""
Check if specified concentrations are commensurate with a
certain supercell (including sublattices).
Parameters
----------
structure
Atomic configuration to be checked.
cluster_space
Corresponding cluster space.
concentrations
Which concentrations, per sublattice, e.g., ``{'A': {'Ag': 0.3, 'Au': 0.7}}``.
tol
Numerical tolerance.
"""
# Check that concentrations are OK in each sublattice
for sublattice in cluster_space.get_sublattices(structure):
if sublattice.symbol in concentrations:
sl_conc = concentrations[sublattice.symbol]
for conc in sl_conc.values():
n_symbol = conc * len(sublattice.indices)
if abs(int(round(n_symbol)) - n_symbol) > tol:
return False
return True
def _get_sqs_cluster_vector(cluster_space: ClusterSpace,
target_concentrations: Dict[str, Dict[str, float]]) -> np.ndarray:
"""
Get the SQS vector for a certain cluster space and certain
concentration. Here SQS vector refers to the cluster vector of an
infintely large supercell with random occupation.
Parameters
----------
cluster_space
The kind of lattice to be occupied.
target_concentrations
Concentration of each species in the target structure,
per sublattice (for example `{'A': {'Ag': 0.5, 'Pd': 0.5}}`).
"""
target_concentrations = _validate_concentrations(concentrations=target_concentrations,
cluster_space=cluster_space)
sublattice_to_index = {letter: index for index,
letter in enumerate('ABCDEFGHIJKLMNOPQRSTUVWXYZ')}
all_sublattices = cluster_space.get_sublattices(
cluster_space.primitive_structure)
# Make a map from chemical symbol to integer, later on used
# for evaluating cluster functions.
# Internally, icet sorts species according to atomic numbers.
# Also check that each symbol only occurs in one sublattice.
symbol_to_integer_map = {}
found_species: List[str] = []
for sublattice in all_sublattices:
if len(sublattice.chemical_symbols) < 2:
continue
atomic_numbers = [periodic_table.index(sym) for sym in sublattice.chemical_symbols]
for i, species in enumerate(sorted(atomic_numbers)):
found_species.append(species)
symbol_to_integer_map[periodic_table[species]] = i
# Target concentrations refer to all atoms, but probabilities only
# to the sublattice.
probabilities = {}
for sl_conc in target_concentrations.values():
if len(sl_conc) == 1:
continue
for symbol in sl_conc.keys():
probabilities[symbol] = sl_conc[symbol]
# For every orbit, calculate average cluster function
cv = [1.0]
for orbit in cluster_space.as_list:
if orbit['order'] < 1:
continue
# What sublattices are there in this orbit?
sublattices = [all_sublattices[sublattice_to_index[letter]]
for letter in orbit['sublattices']]
# What chemical symbols do these sublattices refer to?
symbol_groups = [sublattice.chemical_symbols for sublattice in sublattices]
# How many allowed species in each of those sublattices?
nbr_of_allowed_species = [len(symbol_group)
for symbol_group in symbol_groups]
# Calculate contribution from every possible combination of
# symbols weighted with their probability
cluster_product_average = 0
for symbols in itertools.product(*symbol_groups):
cluster_product = 1
for i, symbol in enumerate(symbols):
mc_vector_component = orbit['multicomponent_vector'][i]
species_i = symbol_to_integer_map[symbol]
prod = cluster_space.evaluate_cluster_function(nbr_of_allowed_species[i],
mc_vector_component,
species_i)
cluster_product *= probabilities[symbol] * prod
cluster_product_average += cluster_product
cv.append(cluster_product_average)
return np.array(cv)
```