###########################################################################
# Copyright (c), The AiiDA team. All rights reserved. #
# This file is part of the AiiDA code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
"""This module defines the classes for structures and all related
functions to operate on them.
"""
import copy
import functools
import itertools
import json
from typing import List, Optional
from aiida.common.constants import elements
from aiida.common.exceptions import UnsupportedSpeciesError
from aiida.orm.fields import add_field
from .data import Data
__all__ = ('StructureData', 'Kind', 'Site')
# Threshold used to check if the mass of two different Site objects is the same.
_MASS_THRESHOLD = 1.0e-3
# Threshold to check if the sum is one or not
_SUM_THRESHOLD = 1.0e-6
# Default cell
_DEFAULT_CELL = ((0, 0, 0), (0, 0, 0), (0, 0, 0))
_valid_symbols = tuple(i['symbol'] for i in elements.values())
_atomic_masses = {el['symbol']: el['mass'] for el in elements.values()}
_atomic_numbers = {data['symbol']: num for num, data in elements.items()}
[docs]
def _get_valid_cell(inputcell):
"""Return the cell in a valid format from a generic input.
:raise ValueError: whenever the format is not valid.
"""
try:
the_cell = list(list(float(c) for c in i) for i in inputcell)
if len(the_cell) != 3:
raise ValueError
if any(len(i) != 3 for i in the_cell):
raise ValueError
except (IndexError, ValueError, TypeError):
raise ValueError('Cell must be a list of three vectors, each defined as a list of three coordinates.')
return the_cell
[docs]
def get_valid_pbc(inputpbc):
"""Return a list of three booleans for the periodic boundary conditions,
in a valid format from a generic input.
:raise ValueError: if the format is not valid.
"""
if isinstance(inputpbc, bool):
the_pbc = (inputpbc, inputpbc, inputpbc)
elif hasattr(inputpbc, '__iter__'):
# To manage numpy lists of bools, whose elements are of type numpy.bool_
# and for which isinstance(i,bool) return False...
if hasattr(inputpbc, 'tolist'):
the_value = inputpbc.tolist()
else:
the_value = inputpbc
if all(isinstance(i, bool) for i in the_value):
if len(the_value) == 3:
the_pbc = tuple(i for i in the_value)
elif len(the_value) == 1:
the_pbc = (the_value[0], the_value[0], the_value[0])
else:
raise ValueError('pbc length must be either one or three.')
else:
raise ValueError('pbc elements are not booleans.')
else:
raise ValueError('pbc must be a boolean or a list of three booleans.', inputpbc)
return the_pbc
[docs]
def has_ase():
""":return: True if the ase module can be imported, False otherwise."""
try:
import ase # noqa: F401
except ImportError:
return False
return True
[docs]
def has_pymatgen():
""":return: True if the pymatgen module can be imported, False otherwise."""
try:
import pymatgen # noqa: F401
except ImportError:
return False
return True
[docs]
def get_pymatgen_version():
""":return: string with pymatgen version, None if can not import."""
if not has_pymatgen():
return None
try:
from pymatgen import __version__
except ImportError:
# this was changed in version 2022.0.3
from pymatgen.core import __version__
return __version__
[docs]
def has_spglib():
""":return: True if the spglib module can be imported, False otherwise."""
try:
import spglib # noqa: F401
except ImportError:
return False
return True
[docs]
def calc_cell_volume(cell):
"""Compute the three-dimensional cell volume in Angstrom^3.
:param cell: the cell vectors; the must be a 3x3 list of lists of floats
:returns: the cell volume.
"""
import numpy as np
return np.abs(np.dot(cell[0], np.cross(cell[1], cell[2])))
[docs]
def _create_symbols_tuple(symbols):
"""Returns a tuple with the symbols provided. If a string is provided,
this is converted to a tuple with one single element.
"""
if isinstance(symbols, str):
symbols_list = (symbols,)
else:
symbols_list = tuple(symbols)
return symbols_list
[docs]
def _create_weights_tuple(weights):
"""Returns a tuple with the weights provided. If a number is provided,
this is converted to a tuple with one single element.
If None is provided, this is converted to the tuple (1.,)
"""
import numbers
if weights is None:
weights_tuple = (1.0,)
elif isinstance(weights, numbers.Number):
weights_tuple = (weights,)
else:
weights_tuple = tuple(float(i) for i in weights)
return weights_tuple
[docs]
def create_automatic_kind_name(symbols, weights):
"""Create a string obtained with the symbols appended one
after the other, without spaces, in alphabetical order;
if the site has a vacancy, a X is appended at the end too.
"""
sorted_symbol_list = list(set(symbols))
sorted_symbol_list.sort() # In-place sort
name_string = ''.join(sorted_symbol_list)
if has_vacancies(weights):
name_string += 'X'
return name_string
[docs]
def validate_weights_tuple(weights_tuple, threshold):
"""Validates the weight of the atomic kinds.
:raise: ValueError if the weights_tuple is not valid.
:param weights_tuple: the tuple to validate. It must be a
a tuple of floats (as created by :func:_create_weights_tuple).
:param threshold: a float number used as a threshold to check that the sum
of the weights is <= 1.
If the sum is less than one, it means that there are vacancies.
Each element of the list must be >= 0, and the sum must be <= 1.
"""
w_sum = sum(weights_tuple)
if any(i < 0.0 for i in weights_tuple) or (w_sum - 1.0 > threshold):
raise ValueError('The weight list is not valid (each element must be positive, and the sum must be <= 1).')
[docs]
def is_valid_symbol(symbol):
"""Validates the chemical symbol name.
:return: True if the symbol is a valid chemical symbol (with correct
capitalization), or the dummy X, False otherwise.
Recognized symbols are for elements from hydrogen (Z=1) to lawrencium
(Z=103). In addition, a dummy element unknown name (Z=0) is supported.
"""
return symbol in _valid_symbols
[docs]
def validate_symbols_tuple(symbols_tuple):
"""Used to validate whether the chemical species are valid.
:param symbols_tuple: a tuple (or list) with the chemical symbols name.
:raises: UnsupportedSpeciesError if any symbol in the tuple is not a valid chemical
symbol (with correct capitalization).
Refer also to the documentation of :func:is_valid_symbol
"""
if len(symbols_tuple) == 0:
valid = False
else:
valid = all(is_valid_symbol(sym) for sym in symbols_tuple)
if not valid:
raise UnsupportedSpeciesError(
f'At least one element of the symbol list {symbols_tuple} has not been recognized.'
)
[docs]
def is_ase_atoms(ase_atoms):
"""Check if the ase_atoms parameter is actually a ase.Atoms object.
:param ase_atoms: an object, expected to be an ase.Atoms.
:return: a boolean.
Requires the ability to import ase, by doing 'import ase'.
"""
import ase
return isinstance(ase_atoms, ase.Atoms)
[docs]
def group_symbols(_list):
"""Group a list of symbols to a list containing the number of consecutive
identical symbols, and the symbol itself.
Examples
--------
* ``['Ba','Ti','O','O','O','Ba']`` will return
``[[1,'Ba'],[1,'Ti'],[3,'O'],[1,'Ba']]``
* ``[ [ [1,'Ba'],[1,'Ti'] ],[ [1,'Ba'],[1,'Ti'] ] ]`` will return
``[[2, [ [1, 'Ba'], [1, 'Ti'] ] ]]``
:param _list: a list of elements representing a chemical formula
:return: a list of length-2 lists of the form [ multiplicity , element ]
"""
the_list = copy.deepcopy(_list)
the_list.reverse()
grouped_list = [[1, the_list.pop()]]
while the_list:
elem = the_list.pop()
if elem == grouped_list[-1][1]:
# same symbol is repeated
grouped_list[-1][0] += 1
else:
grouped_list.append([1, elem])
return grouped_list
[docs]
def get_symbols_string(symbols, weights):
"""Return a string that tries to match as good as possible the symbols
and weights. If there is only one symbol (no alloy) with 100%
occupancy, just returns the symbol name. Otherwise, groups the full
string in curly brackets, and try to write also the composition
(with 2 precision only).
If (sum of weights<1), we indicate it with the X symbol followed
by 1-sum(weights) (still with 2 digits precision, so it can be 0.00)
:param symbols: the symbols as obtained from <kind>._symbols
:param weights: the weights as obtained from <kind>._weights
.. note:: Note the difference with respect to the symbols and the
symbol properties!
"""
if len(symbols) == 1 and weights[0] == 1.0:
return symbols[0]
pieces = []
for symbol, weight in zip(symbols, weights):
pieces.append(f'{symbol}{weight:4.2f}')
if has_vacancies(weights):
pieces.append(f'X{1.0 - sum(weights):4.2f}')
return f"{{{''.join(sorted(pieces))}}}"
[docs]
def has_vacancies(weights):
"""Returns True if the sum of the weights is less than one.
It uses the internal variable _SUM_THRESHOLD as a threshold.
:param weights: the weights
:return: a boolean
"""
w_sum = sum(weights)
return not 1.0 - w_sum < _SUM_THRESHOLD
[docs]
def symop_ortho_from_fract(cell):
"""Creates a matrix for conversion from orthogonal to fractional
coordinates.
Taken from
svn://www.crystallography.net/cod-tools/trunk/lib/perl5/Fractional.pm,
revision 850.
:param cell: array of cell parameters (three lengths and three angles)
"""
import math
import numpy
a, b, c, alpha, beta, gamma = cell
alpha, beta, gamma = [math.pi * x / 180 for x in [alpha, beta, gamma]]
ca, cb, cg = [math.cos(x) for x in [alpha, beta, gamma]]
sg = math.sin(gamma)
return numpy.array(
[
[a, b * cg, c * cb],
[0, b * sg, c * (ca - cb * cg) / sg],
[0, 0, c * math.sqrt(sg * sg - ca * ca - cb * cb + 2 * ca * cb * cg) / sg],
]
)
[docs]
def symop_fract_from_ortho(cell):
"""Creates a matrix for conversion from fractional to orthogonal
coordinates.
Taken from
svn://www.crystallography.net/cod-tools/trunk/lib/perl5/Fractional.pm,
revision 850.
:param cell: array of cell parameters (three lengths and three angles)
"""
import math
import numpy
a, b, c, alpha, beta, gamma = cell
alpha, beta, gamma = [math.pi * x / 180 for x in [alpha, beta, gamma]]
ca, cb, cg = [math.cos(x) for x in [alpha, beta, gamma]]
sg = math.sin(gamma)
ctg = cg / sg
D = math.sqrt(sg * sg - cb * cb - ca * ca + 2 * ca * cb * cg) # noqa: N806
return numpy.array(
[
[1.0 / a, -(1.0 / a) * ctg, (ca * cg - cb) / (a * D)],
[0, 1.0 / (b * sg), -(ca - cb * cg) / (b * D * sg)],
[0, 0, sg / (c * D)],
]
)
[docs]
def ase_refine_cell(aseatoms, **kwargs):
"""Detect the symmetry of the structure, remove symmetric atoms and
refine unit cell.
:param aseatoms: an ase.atoms.Atoms instance
:param symprec: symmetry precision, used by spglib
:return newase: refined cell with reduced set of atoms
:return symmetry: a dictionary describing the symmetry space group
"""
from ase.atoms import Atoms
from spglib import get_symmetry_dataset, refine_cell
spglib_tuple = (
aseatoms.get_cell(),
aseatoms.get_scaled_positions(),
aseatoms.get_atomic_numbers(),
)
cell, positions, numbers = refine_cell(spglib_tuple, **kwargs)
refined_atoms = (
cell,
positions,
numbers,
)
sym_dataset = get_symmetry_dataset(refined_atoms, **kwargs)
unique_numbers = []
unique_positions = []
for i in set(sym_dataset['equivalent_atoms']):
unique_numbers.append(numbers[i])
unique_positions.append(positions[i])
unique_atoms = Atoms(unique_numbers, scaled_positions=unique_positions, cell=cell, pbc=True)
return unique_atoms, {
'hm': sym_dataset['international'],
'hall': sym_dataset['hall'],
'tables': sym_dataset['number'],
'rotations': sym_dataset['rotations'],
'translations': sym_dataset['translations'],
}
[docs]
def atom_kinds_to_html(atom_kind):
"""Construct in html format
an alloy with 0.5 Ge, 0.4 Si and 0.1 vacancy is represented as
Ge<sub>0.5</sub> + Si<sub>0.4</sub> + vacancy<sub>0.1</sub>
Args:
-----
atom_kind: a string with the name of the atomic kind, as printed by
kind.get_symbols_string(), e.g. Ba0.80Ca0.10X0.10
Returns:
--------
html code for rendered formula
"""
# Parse the formula (TODO can be made more robust though never fails if
# it takes strings generated with kind.get_symbols_string())
import re
matched_elements = re.findall(r'([A-Z][a-z]*)([0-1][.[0-9]*]?)?', atom_kind)
# Compose the html string
html_formula_pieces = []
for element in matched_elements:
# replace element X by 'vacancy'
species = element[0] if element[0] != 'X' else 'vacancy'
weight = element[1] if element[1] != '' else None
if weight is not None:
html_formula_pieces.append(f'{species}<sub>{weight}</sub>')
else:
html_formula_pieces.append(species)
html_formula = ' + '.join(html_formula_pieces)
return html_formula
[docs]
class StructureData(Data):
"""Data class that represents an atomic structure.
The data is organized as a collection of sites together with a cell, the boundary conditions (whether they are
periodic or not) and other related useful information.
"""
_set_incompatibilities = [
('ase', 'cell'),
('ase', 'pbc'),
('ase', 'pymatgen'),
('ase', 'pymatgen_molecule'),
('ase', 'pymatgen_structure'),
('cell', 'pymatgen'),
('cell', 'pymatgen_molecule'),
('cell', 'pymatgen_structure'),
('pbc', 'pymatgen'),
('pbc', 'pymatgen_molecule'),
('pbc', 'pymatgen_structure'),
('pymatgen', 'pymatgen_molecule'),
('pymatgen', 'pymatgen_structure'),
('pymatgen_molecule', 'pymatgen_structure'),
]
_dimensionality_label = {0: '', 1: 'length', 2: 'surface', 3: 'volume'}
_internal_kind_tags = None
__qb_fields__ = [
add_field(
'pbc1',
dtype=bool,
doc='Whether periodic in the a direction',
),
add_field(
'pbc2',
dtype=bool,
doc='Whether periodic in the b direction',
),
add_field(
'pbc3',
dtype=bool,
doc='Whether periodic in the c direction',
),
add_field(
'cell',
dtype=List[List[float]],
doc='The cell parameters',
),
add_field(
'kinds',
dtype=Optional[List[dict]],
doc='The kinds of atoms',
),
add_field(
'sites',
dtype=Optional[List[dict]],
doc='The atomic sites',
),
]
[docs]
def __init__(
self, cell=None, pbc=None, ase=None, pymatgen=None, pymatgen_structure=None, pymatgen_molecule=None, **kwargs
):
args = {
'cell': cell,
'pbc': pbc,
'ase': ase,
'pymatgen': pymatgen,
'pymatgen_structure': pymatgen_structure,
'pymatgen_molecule': pymatgen_molecule,
}
for left, right in self._set_incompatibilities:
if args[left] is not None and args[right] is not None:
raise ValueError(f'cannot pass {left} and {right} at the same time')
super().__init__(**kwargs)
if any(ext is not None for ext in [ase, pymatgen, pymatgen_structure, pymatgen_molecule]):
if ase is not None:
self.set_ase(ase)
if pymatgen is not None:
self.set_pymatgen(pymatgen)
if pymatgen_structure is not None:
self.set_pymatgen_structure(pymatgen_structure)
if pymatgen_molecule is not None:
self.set_pymatgen_molecule(pymatgen_molecule)
else:
if cell is None:
cell = _DEFAULT_CELL
self.set_cell(cell)
if pbc is None:
pbc = [True, True, True]
self.set_pbc(pbc)
[docs]
def get_dimensionality(self):
"""Return the dimensionality of the structure and its length/surface/volume.
Zero-dimensional structures are assigned "volume" 0.
:return: returns a dictionary with keys "dim" (dimensionality integer), "label" (dimensionality label)
and "value" (numerical length/surface/volume).
"""
return _get_dimensionality(self.pbc, self.cell)
[docs]
def set_ase(self, aseatoms):
"""Load the structure from a ASE object"""
if is_ase_atoms(aseatoms):
# Read the ase structure
self.cell = aseatoms.cell
self.pbc = aseatoms.pbc
self.clear_kinds() # This also calls clear_sites
for atom in aseatoms:
self.append_atom(ase=atom)
else:
raise TypeError('The value is not an ase.Atoms object')
[docs]
def set_pymatgen(self, obj, **kwargs):
"""Load the structure from a pymatgen object.
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors).
"""
typestr = type(obj).__name__
try:
func = getattr(self, f'set_pymatgen_{typestr.lower()}')
except AttributeError:
raise AttributeError(f"Converter for '{typestr}' to AiiDA structure does not exist")
func(obj, **kwargs)
[docs]
def set_pymatgen_molecule(self, mol, margin=5):
"""Load the structure from a pymatgen Molecule object.
:param margin: the margin to be added in all directions of the
bounding box of the molecule.
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors).
"""
box = [
max(x.coords.tolist()[0] for x in mol.sites) - min(x.coords.tolist()[0] for x in mol.sites) + 2 * margin,
max(x.coords.tolist()[1] for x in mol.sites) - min(x.coords.tolist()[1] for x in mol.sites) + 2 * margin,
max(x.coords.tolist()[2] for x in mol.sites) - min(x.coords.tolist()[2] for x in mol.sites) + 2 * margin,
]
self.set_pymatgen_structure(mol.get_boxed_structure(*box))
self.pbc = [False, False, False]
[docs]
def set_pymatgen_structure(self, struct):
"""Load the structure from a pymatgen Structure object.
.. note:: periodic boundary conditions are set to True in all
three directions.
.. note:: Requires the pymatgen module (version >= 3.3.5, usage
of earlier versions may cause errors).
:raise ValueError: if there are partial occupancies together with spins.
"""
def build_kind_name(species_and_occu):
"""Build a kind name from a pymatgen Composition, including an additional ordinal if spin is included,
e.g. it returns '<specie>1' for an atom with spin < 0 and '<specie>2' for an atom with spin > 0,
otherwise (no spin) it returns None
:param species_and_occu: a pymatgen species and occupations dictionary
:return: a string representing the kind name or None
"""
species = list(species_and_occu.keys())
occupations = list(species_and_occu.values())
# As of v2023.9.2, the ``properties`` argument is removed and the ``spin`` argument should be used.
# See: https://github.com/materialsproject/pymatgen/commit/118c245d6082fe0b13e19d348fc1db9c0d512019
# The ``spin`` argument was introduced in v2023.6.28.
# See: https://github.com/materialsproject/pymatgen/commit/9f2b3939af45d5129e0778d371d814811924aeb6
has_spin_attribute = hasattr(species[0], '_spin')
if has_spin_attribute:
has_spin = any(specie.spin != 0 for specie in species)
else:
has_spin = any(specie.as_dict().get('properties', {}).get('spin', 0) != 0 for specie in species)
has_partial_occupancies = len(occupations) != 1 or occupations[0] != 1.0
if has_partial_occupancies and has_spin:
raise ValueError('Cannot set partial occupancies and spins at the same time')
if has_spin:
symbols = [specie.symbol for specie in species]
kind_name = create_automatic_kind_name(symbols, occupations)
# If there is spin, we can only have a single specie, otherwise we would have raised above
specie = species[0]
if has_spin_attribute:
spin = specie.spin
else:
spin = specie.as_dict().get('properties', {}).get('spin', 0)
if spin < 0:
kind_name += '1'
else:
kind_name += '2'
return kind_name
return None
self.cell = struct.lattice.matrix.tolist()
self.pbc = [True, True, True]
self.clear_kinds()
for site in struct.sites:
species_and_occu = site.species
if 'kind_name' in site.properties:
kind_name = site.properties['kind_name']
else:
kind_name = build_kind_name(species_and_occu)
inputs = {
'symbols': [x.symbol for x in species_and_occu.keys()],
'weights': list(species_and_occu.values()),
'position': site.coords.tolist(),
}
if kind_name is not None:
inputs['name'] = kind_name
self.append_atom(**inputs)
[docs]
def _validate(self):
"""Performs some standard validation tests."""
from aiida.common.exceptions import ValidationError
super()._validate()
try:
_get_valid_cell(self.cell)
except ValueError as exc:
raise ValidationError(f'Invalid cell: {exc}')
try:
get_valid_pbc(self.pbc)
except ValueError as exc:
raise ValidationError(f'Invalid periodic boundary conditions: {exc}')
_validate_dimensionality(self.pbc, self.cell)
try:
# This will try to create the kinds objects
kinds = self.kinds
except ValueError as exc:
raise ValidationError(f'Unable to validate the kinds: {exc}')
from collections import Counter
counts = Counter([k.name for k in kinds])
for count in counts:
if counts[count] != 1:
raise ValidationError(f"Kind with name '{count}' appears {counts[count]} times instead of only one")
try:
# This will try to create the sites objects
sites = self.sites
except ValueError as exc:
raise ValidationError(f'Unable to validate the sites: {exc}')
for site in sites:
if site.kind_name not in [k.name for k in kinds]:
raise ValidationError(f'A site has kind {site.kind_name}, but no specie with that name exists')
kinds_without_sites = set(k.name for k in kinds) - set(s.kind_name for s in sites)
if kinds_without_sites:
raise ValidationError(
f'The following kinds are defined, but there are no sites with that kind: {list(kinds_without_sites)}'
)
[docs]
def _prepare_xsf(self, main_file_name=''):
"""Write the given structure to a string of format XSF (for XCrySDen)."""
if self.is_alloy or self.has_vacancies:
raise NotImplementedError('XSF for alloys or systems with vacancies not implemented.')
sites = self.sites
return_string = 'CRYSTAL\nPRIMVEC 1\n'
for cell_vector in self.cell:
return_string += ' '.join([f'{i:18.10f}' for i in cell_vector])
return_string += '\n'
return_string += 'PRIMCOORD 1\n'
return_string += f'{int(len(sites))} 1\n'
for site in sites:
# I checked above that it is not an alloy, therefore I take the
# first symbol
return_string += f'{_atomic_numbers[self.get_kind(site.kind_name).symbols[0]]} '
return_string += '%18.10f %18.10f %18.10f\n' % tuple(site.position)
return return_string.encode('utf-8'), {}
[docs]
def _prepare_cif(self, main_file_name=''):
"""Write the given structure to a string of format CIF."""
from aiida.orm import CifData
cif = CifData(ase=self.get_ase())
return cif._prepare_cif()
[docs]
def _prepare_chemdoodle(self, main_file_name=''):
"""Write the given structure to a string of format required by ChemDoodle."""
from itertools import product
import numpy as np
supercell_factors = [1, 1, 1]
# Get cell vectors and atomic position
lattice_vectors = np.array(self.base.attributes.get('cell'))
base_sites = self.base.attributes.get('sites')
start1 = -int(supercell_factors[0] / 2)
start2 = -int(supercell_factors[1] / 2)
start3 = -int(supercell_factors[2] / 2)
stop1 = start1 + supercell_factors[0]
stop2 = start2 + supercell_factors[1]
stop3 = start3 + supercell_factors[2]
grid1 = range(start1, stop1)
grid2 = range(start2, stop2)
grid3 = range(start3, stop3)
atoms_json = []
# Manual recenter of the structure
center = (lattice_vectors[0] + lattice_vectors[1] + lattice_vectors[2]) / 2.0
for ix, iy, iz in product(grid1, grid2, grid3):
for base_site in base_sites:
shift = (ix * lattice_vectors[0] + iy * lattice_vectors[1] + iz * lattice_vectors[2] - center).tolist()
kind_name = base_site['kind_name']
kind_string = self.get_kind(kind_name).get_symbols_string()
atoms_json.append(
{
'l': kind_string,
'x': base_site['position'][0] + shift[0],
'y': base_site['position'][1] + shift[1],
'z': base_site['position'][2] + shift[2],
'atomic_elements_html': atom_kinds_to_html(kind_string),
}
)
cell_json = {
't': 'UnitCell',
'i': 's0',
'o': (-center).tolist(),
'x': (lattice_vectors[0] - center).tolist(),
'y': (lattice_vectors[1] - center).tolist(),
'z': (lattice_vectors[2] - center).tolist(),
'xy': (lattice_vectors[0] + lattice_vectors[1] - center).tolist(),
'xz': (lattice_vectors[0] + lattice_vectors[2] - center).tolist(),
'yz': (lattice_vectors[1] + lattice_vectors[2] - center).tolist(),
'xyz': (lattice_vectors[0] + lattice_vectors[1] + lattice_vectors[2] - center).tolist(),
}
return_dict = {'s': [cell_json], 'm': [{'a': atoms_json}], 'units': 'Å'}
return json.dumps(return_dict).encode('utf-8'), {}
[docs]
def _prepare_xyz(self, main_file_name=''):
"""Write the given structure to a string of format XYZ."""
if self.is_alloy or self.has_vacancies:
raise NotImplementedError('XYZ for alloys or systems with vacancies not implemented.')
sites = self.sites
cell = self.cell
return_list = [f'{len(sites)}']
return_list.append(
'Lattice="{} {} {} {} {} {} {} {} {}" pbc="{} {} {}"'.format(
cell[0][0],
cell[0][1],
cell[0][2],
cell[1][0],
cell[1][1],
cell[1][2],
cell[2][0],
cell[2][1],
cell[2][2],
self.pbc[0],
self.pbc[1],
self.pbc[2],
)
)
for site in sites:
# I checked above that it is not an alloy, therefore I take the
# first symbol
return_list.append(
'{:6s} {:18.10f} {:18.10f} {:18.10f}'.format(
self.get_kind(site.kind_name).symbols[0], site.position[0], site.position[1], site.position[2]
)
)
return_string = '\n'.join(return_list)
return return_string.encode('utf-8'), {}
[docs]
def _parse_xyz(self, inputstring):
"""Read the structure from a string of format XYZ."""
from aiida.tools.data.structure import xyz_parser_iterator
# idiom to get to the last block
atoms = None
for _, _, atoms in xyz_parser_iterator(inputstring):
pass
if atoms is None:
raise TypeError('The data does not contain any XYZ data')
self.clear_kinds()
self.pbc = (False, False, False)
for sym, position in atoms:
self.append_atom(symbols=sym, position=position)
[docs]
def _adjust_default_cell(self, vacuum_factor=1.0, vacuum_addition=10.0, pbc=(False, False, False)):
"""If the structure was imported from an xyz file, it lacks a cell.
This method will adjust the cell
"""
import numpy as np
def get_extremas_from_positions(positions):
"""Returns the minimum and maximum value for each dimension in the positions given"""
return list(zip(*[(min(values), max(values)) for values in zip(*positions)]))
# Calculating the minimal cell:
positions = np.array([site.position for site in self.sites])
position_min, _ = get_extremas_from_positions(positions)
# Translate the structure to the origin, such that the minimal values in each dimension
# amount to (0,0,0)
positions -= position_min
for index, site in enumerate(self.base.attributes.get('sites')):
site['position'] = list(positions[index])
# The orthorhombic cell that (just) accomodates the whole structure is now given by the
# extremas of position in each dimension:
minimal_orthorhombic_cell_dimensions = np.array(get_extremas_from_positions(positions)[1])
minimal_orthorhombic_cell_dimensions = np.dot(vacuum_factor, minimal_orthorhombic_cell_dimensions)
minimal_orthorhombic_cell_dimensions += vacuum_addition
# Transform the vector (a, b, c ) to [[a,0,0], [0,b,0], [0,0,c]]
newcell = np.diag(minimal_orthorhombic_cell_dimensions)
self.set_cell(newcell.tolist())
# Now set PBC (checks are done in set_pbc, no need to check anything here)
self.set_pbc(pbc)
return self
[docs]
def get_description(self):
"""Returns a string with infos retrieved from StructureData node's properties
:param self: the StructureData node
:return: retsrt: the description string
"""
return self.get_formula(mode='hill_compact')
[docs]
def get_symbols_set(self):
"""Return a set containing the names of all elements involved in
this structure (i.e., for it joins the list of symbols for each
kind k in the structure).
:returns: a set of strings of element names.
"""
return set(itertools.chain.from_iterable(kind.symbols for kind in self.kinds))
[docs]
def get_site_kindnames(self):
"""Return a list with length equal to the number of sites of this structure,
where each element of the list is the kind name of the corresponding site.
.. note:: This is NOT necessarily a list of chemical symbols! Use
``[ self.get_kind(s.kind_name).get_symbols_string() for s in self.sites]``
for chemical symbols
:return: a list of strings
"""
return [this_site.kind_name for this_site in self.sites]
[docs]
def get_composition(self, mode='full'):
"""Returns the chemical composition of this structure as a dictionary,
where each key is the kind symbol (e.g. H, Li, Ba),
and each value is the number of occurences of that element in this
structure.
:param mode: Specify the mode of the composition to return. Choose from ``full``, ``reduced`` or ``fractional``.
For example, given the structure with formula Ba2Zr2O6, the various modes operate as follows.
``full``: The default, the counts are left unnnormalized.
``reduced``: The counts are renormalized to the greatest common denominator.
``fractional``: The counts are renormalized such that the sum equals 1.
:returns: a dictionary with the composition
"""
import numpy as np
symbols_list = [self.get_kind(s.kind_name).get_symbols_string() for s in self.sites]
symbols_set = set(symbols_list)
if mode == 'full':
return {symbol: symbols_list.count(symbol) for symbol in symbols_set}
if mode == 'reduced':
gcd = np.gcd.reduce([symbols_list.count(symbol) for symbol in symbols_set])
return {symbol: (symbols_list.count(symbol) / gcd) for symbol in symbols_set}
if mode == 'fractional':
sum_comp = sum(symbols_list.count(symbol) for symbol in symbols_set)
return {symbol: symbols_list.count(symbol) / sum_comp for symbol in symbols_set}
raise ValueError(f'mode `{mode}` is invalid, choose from `full`, `reduced` or `fractional`.')
[docs]
def get_ase(self):
"""Get the ASE object.
Requires to be able to import ase.
:return: an ASE object corresponding to this
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
object.
.. note:: If any site is an alloy or has vacancies, a ValueError
is raised (from the site.get_ase() routine).
"""
return self._get_object_ase()
[docs]
def get_pymatgen(self, **kwargs):
"""Get pymatgen object. Returns pymatgen Structure for structures with periodic boundary conditions
(in 1D, 2D, 3D) and Molecule otherwise.
:param add_spin: True to add the spins to the pymatgen structure.
Default is False (no spin added).
.. note:: The spins are set according to the following rule:
* if the kind name ends with 1 -> spin=+1
* if the kind name ends with 2 -> spin=-1
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors).
"""
return self._get_object_pymatgen(**kwargs)
[docs]
def get_pymatgen_structure(self, **kwargs):
"""Get the pymatgen Structure object with any PBC, provided the cell is not singular.
:param add_spin: True to add the spins to the pymatgen structure.
Default is False (no spin added).
.. note:: The spins are set according to the following rule:
* if the kind name ends with 1 -> spin=+1
* if the kind name ends with 2 -> spin=-1
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors).
:return: a pymatgen Structure object corresponding to this
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
object.
:raise ValueError: if the cell is singular, e.g. when it has not been set.
Use `get_pymatgen_molecule` instead, or set a proper cell.
"""
return self._get_object_pymatgen_structure(**kwargs)
[docs]
def get_pymatgen_molecule(self):
"""Get the pymatgen Molecule object.
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors).
:return: a pymatgen Molecule object corresponding to this
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
object.
"""
return self._get_object_pymatgen_molecule()
[docs]
def append_kind(self, kind):
"""Append a kind to the
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`.
It makes a copy of the kind.
:param kind: the site to append, must be a Kind object.
"""
from aiida.common.exceptions import ModificationNotAllowed
if self.is_stored:
raise ModificationNotAllowed('The StructureData object cannot be modified, it has already been stored')
new_kind = Kind(kind=kind) # So we make a copy
if kind.name in [k.name for k in self.kinds]:
raise ValueError(f'A kind with the same name ({kind.name}) already exists.')
# If here, no exceptions have been raised, so I add the site.
self.base.attributes.all.setdefault('kinds', []).append(new_kind.get_raw())
# Note, this is a dict (with integer keys) so it allows for empty spots!
if self._internal_kind_tags is None:
self._internal_kind_tags = {}
self._internal_kind_tags[len(self.base.attributes.get('kinds')) - 1] = kind._internal_tag
[docs]
def append_site(self, site):
"""Append a site to the
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`.
It makes a copy of the site.
:param site: the site to append. It must be a Site object.
"""
from aiida.common.exceptions import ModificationNotAllowed
if self.is_stored:
raise ModificationNotAllowed('The StructureData object cannot be modified, it has already been stored')
new_site = Site(site=site) # So we make a copy
if site.kind_name not in [kind.name for kind in self.kinds]:
raise ValueError(
f"No kind with name '{site.kind_name}', available kinds are: {[kind.name for kind in self.kinds]}"
)
# If here, no exceptions have been raised, so I add the site.
self.base.attributes.all.setdefault('sites', []).append(new_site.get_raw())
[docs]
def append_atom(self, **kwargs):
"""Append an atom to the Structure, taking care of creating the
corresponding kind.
:param ase: the ase Atom object from which we want to create a new atom
(if present, this must be the only parameter)
:param position: the position of the atom (three numbers in angstrom)
:param symbols: passed to the constructor of the Kind object.
:param weights: passed to the constructor of the Kind object.
:param name: passed to the constructor of the Kind object. See also the note below.
.. note :: Note on the 'name' parameter (that is, the name of the kind):
* if specified, no checks are done on existing species. Simply,
a new kind with that name is created. If there is a name
clash, a check is done: if the kinds are identical, no error
is issued; otherwise, an error is issued because you are trying
to store two different kinds with the same name.
* if not specified, the name is automatically generated. Before
adding the kind, a check is done. If other species with the
same properties already exist, no new kinds are created, but
the site is added to the existing (identical) kind.
(Actually, the first kind that is encountered).
Otherwise, the name is made unique first, by adding to the string
containing the list of chemical symbols a number starting from 1,
until an unique name is found
.. note :: checks of equality of species are done using
the :py:meth:`~aiida.orm.nodes.data.structure.Kind.compare_with` method.
"""
aseatom = kwargs.pop('ase', None)
if aseatom is not None:
if kwargs:
raise ValueError(
"If you pass 'ase' as a parameter to " 'append_atom, you cannot pass any further' 'parameter'
)
position = aseatom.position
kind = Kind(ase=aseatom)
else:
position = kwargs.pop('position', None)
if position is None:
raise ValueError('You have to specify the position of the new atom')
# all remaining parameters
kind = Kind(**kwargs)
# I look for identical species only if the name is not specified
_kinds = self.kinds
if 'name' not in kwargs:
# If the kind is identical to an existing one, I use the existing
# one, otherwise I replace it
exists_already = False
for idx, existing_kind in enumerate(_kinds):
try:
existing_kind._internal_tag = self._internal_kind_tags[idx]
except KeyError:
# self._internal_kind_tags does not contain any info for
# the kind in position idx: I don't have to add anything
# then, and I continue
pass
if kind.compare_with(existing_kind)[0]:
kind = existing_kind
exists_already = True
break
if not exists_already:
# There is not an identical kind.
# By default, the name of 'kind' just contains the elements.
# I then check that the name of 'kind' does not already exist,
# and if it exists I add a number (starting from 1) until I
# find a non-used name.
existing_names = [k.name for k in _kinds]
simplename = kind.name
counter = 1
while kind.name in existing_names:
kind.name = f'{simplename}{counter}'
counter += 1
self.append_kind(kind)
else: # 'name' was specified
old_kind = None
for existing_kind in _kinds:
if existing_kind.name == kwargs['name']:
old_kind = existing_kind
break
if old_kind is None:
self.append_kind(kind)
else:
is_the_same, firstdiff = kind.compare_with(old_kind)
if is_the_same:
kind = old_kind
else:
raise ValueError(
'You are explicitly setting the name '
"of the kind to '{}', that already "
'exists, but the two kinds are different!'
' (first difference: {})'.format(kind.name, firstdiff)
)
site = Site(kind_name=kind.name, position=position)
self.append_site(site)
[docs]
def clear_kinds(self):
"""Removes all kinds for the StructureData object.
.. note:: Also clear all sites!
"""
from aiida.common.exceptions import ModificationNotAllowed
if self.is_stored:
raise ModificationNotAllowed('The StructureData object cannot be modified, it has already been stored')
self.base.attributes.set('kinds', [])
self._internal_kind_tags = {}
self.clear_sites()
[docs]
def clear_sites(self):
"""Removes all sites for the StructureData object."""
from aiida.common.exceptions import ModificationNotAllowed
if self.is_stored:
raise ModificationNotAllowed('The StructureData object cannot be modified, it has already been stored')
self.base.attributes.set('sites', [])
@property
def sites(self):
"""Returns a list of sites."""
try:
raw_sites = self.base.attributes.get('sites')
except AttributeError:
raw_sites = []
return [Site(raw=i) for i in raw_sites]
@property
def kinds(self):
"""Returns a list of kinds."""
try:
raw_kinds = self.base.attributes.get('kinds')
except AttributeError:
raw_kinds = []
return [Kind(raw=i) for i in raw_kinds]
[docs]
def get_kind(self, kind_name):
"""Return the kind object associated with the given kind name.
:param kind_name: String, the name of the kind you want to get
:return: The Kind object associated with the given kind_name, if
a Kind with the given name is present in the structure.
:raise: ValueError if the kind_name is not present.
"""
# Cache the kinds, if stored, for efficiency
if self.is_stored:
try:
kinds_dict = self._kinds_cache
except AttributeError:
self._kinds_cache = {_.name: _ for _ in self.kinds}
kinds_dict = self._kinds_cache
else:
kinds_dict = {_.name: _ for _ in self.kinds}
# Will raise ValueError if the kind is not present
try:
return kinds_dict[kind_name]
except KeyError:
raise ValueError(f"Kind name '{kind_name}' unknown")
[docs]
def get_kind_names(self):
"""Return a list of kind names (in the same order of the ``self.kinds``
property, but return the names rather than Kind objects)
.. note:: This is NOT necessarily a list of chemical symbols! Use
get_symbols_set for chemical symbols
:return: a list of strings.
"""
return [k.name for k in self.kinds]
@property
def cell(self) -> List[List[float]]:
"""Returns the cell shape.
:return: a 3x3 list of lists.
"""
return copy.deepcopy(self.base.attributes.get('cell'))
@cell.setter
def cell(self, value):
"""Set the cell."""
self.set_cell(value)
[docs]
def set_cell(self, value):
"""Set the cell."""
from aiida.common.exceptions import ModificationNotAllowed
if self.is_stored:
raise ModificationNotAllowed('The StructureData object cannot be modified, it has already been stored')
the_cell = _get_valid_cell(value)
self.base.attributes.set('cell', the_cell)
[docs]
def reset_cell(self, new_cell):
"""Reset the cell of a structure not yet stored to a new value.
:param new_cell: list specifying the cell vectors
:raises:
ModificationNotAllowed: if object is already stored
"""
from aiida.common.exceptions import ModificationNotAllowed
if self.is_stored:
raise ModificationNotAllowed()
self.base.attributes.set('cell', new_cell)
[docs]
def reset_sites_positions(self, new_positions, conserve_particle=True):
"""Replace all the Site positions attached to the Structure
:param new_positions: list of (3D) positions for every sites.
:param conserve_particle: if True, allows the possibility of removing a site.
currently not implemented.
:raises aiida.common.ModificationNotAllowed: if object is stored already
:raises ValueError: if positions are invalid
.. note:: it is assumed that the order of the new_positions is
given in the same order of the one it's substituting, i.e. the
kind of the site will not be checked.
"""
from aiida.common.exceptions import ModificationNotAllowed
if self.is_stored:
raise ModificationNotAllowed()
if not conserve_particle:
raise NotImplementedError
else:
# test consistency of th enew input
n_sites = len(self.sites)
if n_sites != len(new_positions) and conserve_particle:
raise ValueError('the new positions should be as many as the previous structure.')
new_sites = []
for i in range(n_sites):
try:
this_pos = [float(j) for j in new_positions[i]]
except ValueError:
raise ValueError(f'Expecting a list of floats. Found instead {new_positions[i]}')
if len(this_pos) != 3:
raise ValueError(f'Expecting a list of lists of length 3. found instead {len(this_pos)}')
# now append this Site to the new_site list.
new_site = Site(site=self.sites[i]) # So we make a copy
new_site.position = copy.deepcopy(this_pos)
new_sites.append(new_site)
# now clear the old sites, and substitute with the new ones
self.clear_sites()
for this_new_site in new_sites:
self.append_site(this_new_site)
@property
def pbc(self):
"""Get the periodic boundary conditions.
:return: a tuple of three booleans, each one tells if there are periodic
boundary conditions for the i-th real-space direction (i=1,2,3)
"""
# return copy.deepcopy(self._pbc)
return (self.base.attributes.get('pbc1'), self.base.attributes.get('pbc2'), self.base.attributes.get('pbc3'))
@pbc.setter
def pbc(self, value):
"""Set the periodic boundary conditions."""
self.set_pbc(value)
[docs]
def set_pbc(self, value):
"""Set the periodic boundary conditions."""
from aiida.common.exceptions import ModificationNotAllowed
if self.is_stored:
raise ModificationNotAllowed('The StructureData object cannot be modified, it has already been stored')
the_pbc = get_valid_pbc(value)
# self._pbc = the_pbc
self.base.attributes.set('pbc1', the_pbc[0])
self.base.attributes.set('pbc2', the_pbc[1])
self.base.attributes.set('pbc3', the_pbc[2])
@property
def cell_lengths(self):
"""Get the lengths of cell lattice vectors in angstroms."""
import numpy
cell = self.cell
return [
numpy.linalg.norm(cell[0]),
numpy.linalg.norm(cell[1]),
numpy.linalg.norm(cell[2]),
]
@cell_lengths.setter
def cell_lengths(self, value):
self.set_cell_lengths(value)
[docs]
def set_cell_lengths(self, value):
raise NotImplementedError('Modification is not implemented yet')
@property
def cell_angles(self):
"""Get the angles between the cell lattice vectors in degrees."""
import numpy
cell = self.cell
lengths = self.cell_lengths
return [
float(numpy.arccos(x) / numpy.pi * 180)
for x in [
numpy.vdot(cell[1], cell[2]) / lengths[1] / lengths[2],
numpy.vdot(cell[0], cell[2]) / lengths[0] / lengths[2],
numpy.vdot(cell[0], cell[1]) / lengths[0] / lengths[1],
]
]
@cell_angles.setter
def cell_angles(self, value):
self.set_cell_angles(value)
[docs]
def set_cell_angles(self, value):
raise NotImplementedError('Modification is not implemented yet')
@property
def is_alloy(self):
"""Return whether the structure contains any alloy kinds.
:return: a boolean, True if at least one kind is an alloy
"""
return any(kind.is_alloy for kind in self.kinds)
@property
def has_vacancies(self):
"""Return whether the structure has vacancies in the structure.
:return: a boolean, True if at least one kind has a vacancy
"""
return any(kind.has_vacancies for kind in self.kinds)
[docs]
def get_cell_volume(self):
"""Returns the three-dimensional cell volume in Angstrom^3.
Use the `get_dimensionality` method in order to get the area/length of lower-dimensional cells.
:return: a float.
"""
return calc_cell_volume(self.cell)
[docs]
def get_cif(self, converter='ase', store=False, **kwargs):
"""Creates :py:class:`aiida.orm.nodes.data.cif.CifData`.
:param converter: specify the converter. Default 'ase'.
:param store: If True, intermediate calculation gets stored in the
AiiDA database for record. Default False.
:return: :py:class:`aiida.orm.nodes.data.cif.CifData` node.
"""
from aiida.tools.data import structure as structure_tools
from .dict import Dict
param = Dict(kwargs)
try:
conv_f = getattr(structure_tools, f'_get_cif_{converter}_inline')
except AttributeError:
raise ValueError(f"No such converter '{converter}' available")
ret_dict = conv_f(struct=self, parameters=param, metadata={'store_provenance': store})
return ret_dict['cif']
[docs]
def _get_object_phonopyatoms(self):
"""Converts StructureData to PhonopyAtoms
:return: a PhonopyAtoms object
"""
from phonopy.structure.atoms import PhonopyAtoms
atoms = PhonopyAtoms(symbols=[_.kind_name for _ in self.sites])
# Phonopy internally uses scaled positions, so you must store cell first!
atoms.set_cell(self.cell)
atoms.set_positions([_.position for _ in self.sites])
return atoms
[docs]
def _get_object_ase(self):
"""Converts
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
to ase.Atoms
:return: an ase.Atoms object
"""
import ase
asecell = ase.Atoms(cell=self.cell, pbc=self.pbc)
_kinds = self.kinds
for site in self.sites:
asecell.append(site.get_ase(kinds=_kinds))
return asecell
[docs]
def _get_object_pymatgen(self, **kwargs):
"""Converts
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
to pymatgen object
:return: a pymatgen Structure for structures with periodic boundary
conditions (in three dimensions) and Molecule otherwise
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors).
"""
if any(self.pbc):
return self._get_object_pymatgen_structure(**kwargs)
return self._get_object_pymatgen_molecule(**kwargs)
[docs]
def _get_object_pymatgen_structure(self, **kwargs):
"""Converts
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
to pymatgen Structure object
:param add_spin: True to add the spins to the pymatgen structure.
Default is False (no spin added).
.. note:: The spins are set according to the following rule:
* if the kind name ends with 1 -> spin=+1
* if the kind name ends with 2 -> spin=-1
:return: a pymatgen Structure object corresponding to this
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
object
:raise ValueError: if the cell is not set (i.e. is the default one);
if there are partial occupancies together with spins
(defined by kind names ending with '1' or '2').
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors)
"""
from pymatgen.core.lattice import Lattice
from pymatgen.core.structure import Structure
species = []
additional_kwargs = {}
lattice = Lattice(matrix=self.cell, pbc=self.pbc)
if kwargs.pop('add_spin', False) and any(n.endswith('1') or n.endswith('2') for n in self.get_kind_names()):
# case when spins are defined -> no partial occupancy allowed
from pymatgen.core.periodic_table import Specie
oxidation_state = 0 # now I always set the oxidation_state to zero
for site in self.sites:
kind = self.get_kind(site.kind_name)
if len(kind.symbols) != 1 or (len(kind.weights) != 1 or sum(kind.weights) < 1.0):
raise ValueError('Cannot set partial occupancies and spins at the same time')
spin = -1 if kind.name.endswith('1') else 1 if kind.name.endswith('2') else 0
try:
specie = Specie(kind.symbols[0], oxidation_state, properties={'spin': spin})
except TypeError:
# As of v2023.9.2, the ``properties`` argument is removed and the ``spin`` argument should be used.
# See: https://github.com/materialsproject/pymatgen/commit/118c245d6082fe0b13e19d348fc1db9c0d512019
# The ``spin`` argument was introduced in v2023.6.28.
# See: https://github.com/materialsproject/pymatgen/commit/9f2b3939af45d5129e0778d371d814811924aeb6
specie = Specie(kind.symbols[0], oxidation_state, spin=spin)
species.append(specie)
else:
# case when no spin are defined
for site in self.sites:
kind = self.get_kind(site.kind_name)
species.append(dict(zip(kind.symbols, kind.weights)))
if any(
create_automatic_kind_name(self.get_kind(name).symbols, self.get_kind(name).weights) != name
for name in self.get_site_kindnames()
):
# add "kind_name" as a properties to each site, whenever
# the kind_name cannot be automatically obtained from the symbols
additional_kwargs['site_properties'] = {'kind_name': self.get_site_kindnames()}
if kwargs:
raise ValueError(f'Unrecognized parameters passed to pymatgen converter: {kwargs.keys()}')
positions = [list(x.position) for x in self.sites]
try:
return Structure(lattice, species, positions, coords_are_cartesian=True, **additional_kwargs)
except ValueError as err:
raise ValueError('Singular cell detected. Probably the cell was not set?') from err
[docs]
def _get_object_pymatgen_molecule(self, **kwargs):
"""Converts
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
to pymatgen Molecule object
:return: a pymatgen Molecule object corresponding to this
:py:class:`StructureData <aiida.orm.nodes.data.structure.StructureData>`
object.
.. note:: Requires the pymatgen module (version >= 3.0.13, usage
of earlier versions may cause errors)
"""
from pymatgen.core.structure import Molecule
if kwargs:
raise ValueError(f'Unrecognized parameters passed to pymatgen converter: {kwargs.keys()}')
species = []
for site in self.sites:
kind = self.get_kind(site.kind_name)
species.append(dict(zip(kind.symbols, kind.weights)))
positions = [list(site.position) for site in self.sites]
return Molecule(species, positions)
[docs]
class Kind:
"""This class contains the information about the species (kinds) of the system.
It can be a single atom, or an alloy, or even contain vacancies.
"""
[docs]
def __init__(self, **kwargs):
"""Create a site.
One can either pass:
:param raw: the raw python dictionary that will be converted to a
Kind object.
:param ase: an ase Atom object
:param kind: a Kind object (to get a copy)
Or alternatively the following parameters:
:param symbols: a single string for the symbol of this site, or a list
of symbol strings
:param weights: (optional) the weights for each atomic species of
this site.
If only a single symbol is provided, then this value is
optional and the weight is set to 1.
:param mass: (optional) the mass for this site in atomic mass units.
If not provided, the mass is set by the
self.reset_mass() function.
:param name: a string that uniquely identifies the kind, and that
is used to identify the sites.
"""
# Internal variables
self._mass = None
self._symbols = None
self._weights = None
self._name = None
# It will be remain to None in general; it is used to further
# identify this species. At the moment, it is used only when importing
# from ASE, if the species had a tag (different from zero).
## NOTE! This is not persisted on DB but only used while the class
# is loaded in memory (i.e., it is not output with the get_raw() method)
self._internal_tag = None
# Logic to create the site from the raw format
if 'raw' in kwargs:
if len(kwargs) != 1:
raise ValueError("If you pass 'raw', then you cannot pass any other parameter.")
raw = kwargs['raw']
try:
self.set_symbols_and_weights(raw['symbols'], raw['weights'])
except KeyError:
raise ValueError("You didn't specify either 'symbols' or 'weights' in the raw site data.")
try:
self.mass = raw['mass']
except KeyError:
raise ValueError("You didn't specify the site mass in the raw site data.")
try:
self.name = raw['name']
except KeyError:
raise ValueError("You didn't specify the name in the raw site data.")
elif 'kind' in kwargs:
if len(kwargs) != 1:
raise ValueError("If you pass 'kind', then you cannot pass any other parameter.")
oldkind = kwargs['kind']
try:
self.set_symbols_and_weights(oldkind.symbols, oldkind.weights)
self.mass = oldkind.mass
self.name = oldkind.name
self._internal_tag = oldkind._internal_tag
except AttributeError:
raise ValueError(
'Error using the Kind object. Are you sure '
'it is a Kind object? [Introspection says it is '
'{}]'.format(str(type(oldkind)))
)
elif 'ase' in kwargs:
aseatom = kwargs['ase']
if len(kwargs) != 1:
raise ValueError("If you pass 'ase', then you cannot pass any other parameter.")
try:
import numpy
self.set_symbols_and_weights([aseatom.symbol], [1.0])
# ASE sets mass to numpy.nan for unstable species
if not numpy.isnan(aseatom.mass):
self.mass = aseatom.mass
else:
self.reset_mass()
except AttributeError:
raise ValueError(
'Error using the aseatom object. Are you sure '
'it is a ase.atom.Atom object? [Introspection says it is '
'{}]'.format(str(type(aseatom)))
)
if aseatom.tag != 0:
self.set_automatic_kind_name(tag=aseatom.tag)
self._internal_tag = aseatom.tag
else:
self.set_automatic_kind_name()
else:
if 'symbols' not in kwargs:
raise ValueError(
"'symbols' need to be "
'specified (at least) to create a Site object. Otherwise, '
"pass a raw site using the 'raw' parameter."
)
weights = kwargs.pop('weights', None)
self.set_symbols_and_weights(kwargs.pop('symbols'), weights)
try:
self.mass = kwargs.pop('mass')
except KeyError:
self.reset_mass()
try:
self.name = kwargs.pop('name')
except KeyError:
self.set_automatic_kind_name()
if kwargs:
raise ValueError(f'Unrecognized parameters passed to Kind constructor: {kwargs.keys()}')
[docs]
def get_raw(self):
"""Return the raw version of the site, mapped to a suitable dictionary.
This is the format that is actually used to store each kind of the
structure in the DB.
:return: a python dictionary with the kind.
"""
return {
'symbols': self.symbols,
'weights': self.weights,
'mass': self.mass,
'name': self.name,
}
[docs]
def reset_mass(self):
"""Reset the mass to the automatic calculated value.
The mass can be set manually; by default, if not provided,
it is the mass of the constituent atoms, weighted with their
weight (after the weight has been normalized to one to take
correctly into account vacancies).
This function uses the internal _symbols and _weights values and
thus assumes that the values are validated.
It sets the mass to None if the sum of weights is zero.
"""
w_sum = sum(self._weights)
if abs(w_sum) < _SUM_THRESHOLD:
self._mass = None
return
normalized_weights = (i / w_sum for i in self._weights)
element_masses = (_atomic_masses[sym] for sym in self._symbols)
# Weighted mass
self._mass = sum(i * j for i, j in zip(normalized_weights, element_masses))
@property
def name(self):
"""Return the name of this kind.
The name of a kind is used to identify the species of a site.
:return: a string
"""
return self._name
@name.setter
def name(self, value):
"""Set the name of this site (a string)."""
self._name = str(value)
[docs]
def set_automatic_kind_name(self, tag=None):
"""Set the type to a string obtained with the symbols appended one
after the other, without spaces, in alphabetical order;
if the site has a vacancy, a X is appended at the end too.
"""
name_string = create_automatic_kind_name(self.symbols, self.weights)
if tag is None:
self.name = name_string
else:
self.name = f'{name_string}{tag}'
[docs]
def compare_with(self, other_kind):
"""Compare with another Kind object to check if they are different.
.. note:: This does NOT check the 'type' attribute. Instead, it compares
(with reasonable thresholds, where applicable): the mass, and the list
of symbols and of weights. Moreover, it compares the
``_internal_tag``, if defined (at the moment, defined automatically
only when importing the Kind from ASE, if the atom has a non-zero tag).
Note that the _internal_tag is only used while the class is loaded,
but is not persisted on the database.
:return: A tuple with two elements. The first one is True if the two sites
are 'equivalent' (same mass, symbols and weights), False otherwise.
The second element of the tuple is a string,
which is either None (if the first element was True), or contains
a 'human-readable' description of the first difference encountered
between the two sites.
"""
# Check length of symbols
if len(self.symbols) != len(other_kind.symbols):
return (False, 'Different length of symbols list')
# Check list of symbols
for i, symbol in enumerate(self.symbols):
if symbol != other_kind.symbols[i]:
return (False, f'Symbol at position {i + 1:d} are different ({symbol} vs. {other_kind.symbols[i]})')
# Check weights (assuming length of weights and of symbols have same
# length, which should be always true
for i, weight in enumerate(self.weights):
if weight != other_kind.weights[i]:
return (False, f'Weight at position {i + 1:d} are different ({weight} vs. {other_kind.weights[i]})')
# Check masses
if abs(self.mass - other_kind.mass) > _MASS_THRESHOLD:
return (False, f'Masses are different ({self.mass} vs. {other_kind.mass})')
if self._internal_tag != other_kind._internal_tag:
return (False, f'Internal tags are different ({self._internal_tag} vs. {other_kind._internal_tag})')
# If we got here, the two Site objects are similar enough
# to be considered of the same kind
return (True, '')
@property
def mass(self):
"""The mass of this species kind.
:return: a float
"""
return self._mass
@mass.setter
def mass(self, value):
the_mass = float(value)
if the_mass <= 0:
raise ValueError('The mass must be positive.')
self._mass = the_mass
@property
def weights(self):
"""Weights for this species kind. Refer also to
:func:validate_symbols_tuple for the validation rules on the weights.
"""
return copy.deepcopy(self._weights)
@weights.setter
def weights(self, value):
"""If value is a number, a single weight is used. Otherwise, a list or
tuple of numbers is expected.
None is also accepted, corresponding to the list [1.].
"""
weights_tuple = _create_weights_tuple(value)
if len(weights_tuple) != len(self._symbols):
raise ValueError(
'Cannot change the number of weights. Use the ' 'set_symbols_and_weights function instead.'
)
validate_weights_tuple(weights_tuple, _SUM_THRESHOLD)
self._weights = weights_tuple
[docs]
def get_symbols_string(self):
"""Return a string that tries to match as good as possible the symbols
of this kind. If there is only one symbol (no alloy) with 100%
occupancy, just returns the symbol name. Otherwise, groups the full
string in curly brackets, and try to write also the composition
(with 2 precision only).
.. note:: If there is a vacancy (sum of weights<1), we indicate it
with the X symbol followed by 1-sum(weights) (still with 2
digits precision, so it can be 0.00)
.. note:: Note the difference with respect to the symbols and the
symbol properties!
"""
return get_symbols_string(self._symbols, self._weights)
@property
def symbol(self):
"""If the kind has only one symbol, return it; otherwise, raise a
ValueError.
"""
if len(self._symbols) == 1:
return self._symbols[0]
raise ValueError(f'This kind has more than one symbol (it is an alloy): {self._symbols}')
@property
def symbols(self):
"""List of symbols for this site. If the site is a single atom,
pass a list of one element only, or simply the string for that atom.
For alloys, a list of elements.
.. note:: Note that if you change the list of symbols, the kind
name remains unchanged.
"""
return copy.deepcopy(self._symbols)
@symbols.setter
def symbols(self, value):
"""If value is a string, a single symbol is used. Otherwise, a list or
tuple of strings is expected.
I set a copy of the list, so to avoid that the content changes
after the value is set.
"""
symbols_tuple = _create_symbols_tuple(value)
if len(symbols_tuple) != len(self._weights):
raise ValueError(
'Cannot change the number of symbols. Use the ' 'set_symbols_and_weights function instead.'
)
validate_symbols_tuple(symbols_tuple)
self._symbols = symbols_tuple
[docs]
def set_symbols_and_weights(self, symbols, weights):
"""Set the chemical symbols and the weights for the site.
.. note:: Note that the kind name remains unchanged.
"""
symbols_tuple = _create_symbols_tuple(symbols)
weights_tuple = _create_weights_tuple(weights)
if len(symbols_tuple) != len(weights_tuple):
raise ValueError('The number of symbols and weights must coincide.')
validate_symbols_tuple(symbols_tuple)
validate_weights_tuple(weights_tuple, _SUM_THRESHOLD)
self._symbols = symbols_tuple
self._weights = weights_tuple
@property
def is_alloy(self):
"""Return whether the Kind is an alloy, i.e. contains more than one element
:return: boolean, True if the kind has more than one element, False otherwise.
"""
return len(self._symbols) != 1
@property
def has_vacancies(self):
"""Return whether the Kind contains vacancies, i.e. when the sum of the weights is less than one.
.. note:: the property uses the internal variable `_SUM_THRESHOLD` as a threshold.
:return: boolean, True if the sum of the weights is less than one, False otherwise
"""
return has_vacancies(self._weights)
[docs]
def __repr__(self):
return f'<{self.__class__.__name__}: {self!s}>'
[docs]
def __str__(self):
symbol = self.get_symbols_string()
return f"name '{self.name}', symbol '{symbol}'"
[docs]
class Site:
"""This class contains the information about a given site of the system.
It can be a single atom, or an alloy, or even contain vacancies.
"""
[docs]
def __init__(self, **kwargs):
"""Create a site.
:param kind_name: a string that identifies the kind (species) of this site.
This has to be found in the list of kinds of the StructureData
object.
Validation will be done at the StructureData level.
:param position: the absolute position (three floats) in angstrom
"""
self._kind_name = None
self._position = None
if 'site' in kwargs:
site = kwargs.pop('site')
if kwargs:
raise ValueError("If you pass 'site', you cannot pass any further parameter to the Site constructor")
if not isinstance(site, Site):
raise ValueError("'site' must be of type Site")
self.kind_name = site.kind_name
self.position = site.position
elif 'raw' in kwargs:
raw = kwargs.pop('raw')
if kwargs:
raise ValueError("If you pass 'raw', you cannot pass any further parameter to the Site constructor")
try:
self.kind_name = raw['kind_name']
self.position = raw['position']
except KeyError as exc:
raise ValueError(f'Invalid raw object, it does not contain any key {exc.args[0]}')
except TypeError:
raise ValueError('Invalid raw object, it is not a dictionary')
else:
try:
self.kind_name = kwargs.pop('kind_name')
self.position = kwargs.pop('position')
except KeyError as exc:
raise ValueError(f'You need to specify {exc.args[0]}')
if kwargs:
raise ValueError(f'Unrecognized parameters: {kwargs.keys}')
[docs]
def get_raw(self):
"""Return the raw version of the site, mapped to a suitable dictionary.
This is the format that is actually used to store each site of the
structure in the DB.
:return: a python dictionary with the site.
"""
return {
'position': self.position,
'kind_name': self.kind_name,
}
[docs]
def get_ase(self, kinds):
"""Return a ase.Atom object for this site.
:param kinds: the list of kinds from the StructureData object.
.. note:: If any site is an alloy or has vacancies, a ValueError
is raised (from the site.get_ase() routine).
"""
from collections import defaultdict
import ase
# I create the list of tags
tag_list = []
used_tags = defaultdict(list)
for k in kinds:
# Skip alloys and vacancies
if k.is_alloy or k.has_vacancies:
tag_list.append(None)
# If the kind name is equal to the specie name,
# then no tag should be set
elif str(k.name) == str(k.symbols[0]):
tag_list.append(None)
else:
# Name is not the specie name
if k.name.startswith(k.symbols[0]):
try:
new_tag = int(k.name[len(k.symbols[0])])
tag_list.append(new_tag)
used_tags[k.symbols[0]].append(new_tag)
continue
except ValueError:
pass
tag_list.append(k.symbols[0]) # I use a string as a placeholder
for i, _ in enumerate(tag_list):
# If it is a string, it is the name of the element,
# and I have to generate a new integer for this element
# and replace tag_list[i] with this new integer
if isinstance(tag_list[i], str):
# I get a list of used tags for this element
existing_tags = used_tags[tag_list[i]]
if existing_tags:
new_tag = max(existing_tags) + 1
else: # empty list
new_tag = 1
# I store it also as a used tag!
used_tags[tag_list[i]].append(new_tag)
# I update the tag
tag_list[i] = new_tag
found = False
for kind_candidate, tag_candidate in zip(kinds, tag_list):
if kind_candidate.name == self.kind_name:
kind = kind_candidate
tag = tag_candidate
found = True
break
if not found:
raise ValueError(f"No kind '{self.kind_name}' has been found in the list of kinds")
if kind.is_alloy or kind.has_vacancies:
raise ValueError('Cannot convert to ASE if the kind represents an alloy or it has vacancies.')
aseatom = ase.Atom(position=self.position, symbol=str(kind.symbols[0]), mass=kind.mass)
if tag is not None:
aseatom.tag = tag
return aseatom
@property
def kind_name(self):
"""Return the kind name of this site (a string).
The type of a site is used to decide whether two sites are identical
(same mass, symbols, weights, ...) or not.
"""
return self._kind_name
@kind_name.setter
def kind_name(self, value):
"""Set the type of this site (a string)."""
self._kind_name = str(value)
@property
def position(self):
"""Return the position of this site in absolute coordinates,
in angstrom.
"""
return copy.deepcopy(self._position)
@position.setter
def position(self, value):
"""Set the position of this site in absolute coordinates,
in angstrom.
"""
try:
internal_pos = tuple(float(i) for i in value)
if len(internal_pos) != 3:
raise ValueError
# value is not iterable or elements are not floats or len != 3
except (ValueError, TypeError):
raise ValueError('Wrong format for position, must be a list of three float numbers.')
self._position = internal_pos
[docs]
def __repr__(self):
return f'<{self.__class__.__name__}: {self!s}>'
[docs]
def __str__(self):
return f"kind name '{self.kind_name}' @ {self.position[0]},{self.position[1]},{self.position[2]}"
[docs]
def _get_dimensionality(pbc, cell):
"""Return the dimensionality of the structure and its length/surface/volume.
Zero-dimensional structures are assigned "volume" 0.
:return: returns a dictionary with keys "dim" (dimensionality integer), "label" (dimensionality label)
and "value" (numerical length/surface/volume).
"""
import numpy as np
retdict = {}
pbc = np.array(pbc)
cell = np.array(cell)
dim = len(pbc[pbc])
retdict['dim'] = dim
retdict['label'] = StructureData._dimensionality_label[dim]
if dim not in (0, 1, 2, 3):
raise ValueError(f'Dimensionality {dim} must be one of 0, 1, 2, 3')
if dim == 0:
# We have no concept of 0d volume. Let's return a value of 0 for a consistent output dictionary
retdict['value'] = 0
elif dim == 1:
retdict['value'] = np.linalg.norm(cell[pbc])
elif dim == 2:
vectors = cell[pbc]
retdict['value'] = np.linalg.norm(np.cross(vectors[0], vectors[1]))
elif dim == 3:
retdict['value'] = calc_cell_volume(cell)
return retdict
[docs]
def _validate_dimensionality(pbc, cell):
"""Check whether the given pbc and cell vectors are consistent."""
dim = _get_dimensionality(pbc, cell)
# 0-d structures put no constraints on the cell
if dim['dim'] == 0:
return
# finite-d structures should have a cell with finite volume
if dim['value'] == 0:
raise ValueError(f'Structure has periodicity {pbc} but {dim["dim"]}-d volume 0.')
return
