def phonopy_atoms_to_structure(cell):
symbols = cell.get_chemical_symbols()
positions = cell.get_positions()
structure = DataFactory('structure')(cell=cell.get_cell())
for symbol, position in zip(symbols, positions):
structure.append_atom(position=position, symbols=symbol)
return structure
def _generate_structure(symbols=None):
from aiida.plugins import DataFactory
structure = DataFactory('structure')()
valid_symbols = [value['symbol'] for value in elements.values()]
if symbols is not None:
for index, symbol in enumerate(symbols):
if symbol not in valid_symbols:
raise ValueError(f'symbol `{symbol}` is not a valid element.')
structure.append_atom(position=(0. + index * 1, 0. + index * 1, 0. + index * 1), symbols=[symbol])
return structure
def get_primitive(structure, ph_settings):
from phonopy import Phonopy
phonon = Phonopy(
phonopy_atoms_from_structure(structure),
supercell_matrix=ph_settings.get_dict()['supercell_matrix'],
primitive_matrix=ph_settings.get_dict()['primitive_matrix'],
symprec=ph_settings.get_dict()['symmetry_tolerance'])
primitive_phonopy = phonon.get_primitive()
primitive_cell = primitive_phonopy.get_cell()
symbols = primitive_phonopy.get_chemical_symbols()
positions = primitive_phonopy.get_positions()
primitive_structure = DataFactory('structure')(cell=primitive_cell)
for symbol, position in zip(symbols, positions):
primitive_structure.append_atom(position=position, symbols=symbol)
return {'primitive_structure': primitive_structure}
def vasp_structure(request, fresh_aiida_env):
"""Fixture: StructureData or CifData."""
from aiida.plugins import DataFactory
if request.param == 'cif':
cif_path = data_path('cif', 'EntryWithCollCode43360.cif')
structure = DataFactory('cif').get_or_create(cif_path)[0]
elif request.param == 'str':
larray = numpy.array([[0, .5, .5], [.5, 0, .5], [.5, .5, 0]])
alat = 6.058
structure = DataFactory('structure')(cell=larray * alat)
structure.append_atom(position=[0, 0, 0], symbols='In')
structure.append_atom(position=[.25, .25, .25], symbols='As')
structure.append_atom(position=[.25, .33, .34], symbols='As')
structure.append_atom(position=[.5, .5, .5], symbols='In', name='In_d')
structure.append_atom(position=[.7896, .6234, .5],
symbols='In',
name='In_d')
structure.append_atom(position=[.75, .75, .75], symbols='As')
elif request.param == 'str-Al':
larray = numpy.array([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
alat = 4.04
structure = DataFactory('structure')(cell=larray * alat)
structure.append_atom(position=numpy.array([0, 0, 0]) * alat,
symbols='Al')
structure.append_atom(position=numpy.array([0, .5, .5]) * alat,
symbols='Al')
structure.append_atom(position=numpy.array([.5, 0, .5]) * alat,
symbols='Al')
structure.append_atom(position=numpy.array([.5, .5, 0]) * alat,
symbols='Al')
elif request.param == 'str-InAs':
structure_cls = DataFactory('structure')
structure = structure_cls(
cell=numpy.array([[0, .5, .5], [.5, 0, .5], [.5, .5, 0]]) * 6.058)
structure.append_atom(position=(0, 0, 0),
symbols='In',
name='Hamburger')
structure.append_atom(position=(0.25, 0.25, 0.25),
symbols='As',
name='Pizza')
return structure
def _get_structure_data(pkey):
"""return test structure data"""
if pkey == "Fe":
cell = [
[2.848116, 0.000000, 0.000000],
[0.000000, 2.848116, 0.000000],
[0.000000, 0.000000, 2.848116],
]
positions = [
(0.0000000, 0.0000000, 0.0000000),
(0.5000000, 0.5000000, 0.5000000),
]
fractional = True
symbols = ["Fe", "Fe"]
names = ["Fe1", "Fe2"]
elif pkey == "Ar":
cell = [
[3.987594, 0.000000, 0.000000],
[-1.993797, 3.453358, 0.000000],
[0.000000, 0.000000, 6.538394],
]
symbols = names = ["Ar"] * 2
positions = [(0.33333, 0.66666, 0.25000),
(0.66667, 0.33333, 0.75000)]
fractional = True
elif pkey == "GaN":
cell = [
[3.1900000572, 0, 0],
[-1.5950000286, 2.762621076, 0],
[0.0, 0, 5.1890001297],
]
positions = [
(0.6666669, 0.3333334, 0.0000000),
(0.3333331, 0.6666663, 0.5000000),
(0.6666669, 0.3333334, 0.3750000),
(0.3333331, 0.6666663, 0.8750000),
]
fractional = True
symbols = names = ["Ga", "Ga", "N", "N"]
elif pkey == "pyrite":
cell = [
[5.38, 0.000000, 0.000000],
[0.000000, 5.38, 0.000000],
[0.000000, 0.000000, 5.38],
]
positions = [
[0.0, 0.0, 0.0],
[0.5, 0.0, 0.5],
[0.0, 0.5, 0.5],
[0.5, 0.5, 0.0],
[0.338, 0.338, 0.338],
[0.662, 0.662, 0.662],
[0.162, 0.662, 0.838],
[0.838, 0.338, 0.162],
[0.662, 0.838, 0.162],
[0.338, 0.162, 0.838],
[0.838, 0.162, 0.662],
[0.162, 0.838, 0.338],
]
fractional = True
symbols = names = ["Fe"] * 4 + ["S"] * 8
elif pkey == "fes_cubic-zincblende":
cell = [[2.71, -2.71, 0.0], [2.71, 0.0, 2.71], [0.0, -2.71, 2.71]]
symbols = names = ["Fe", "S"]
positions = [[0, 0, 0], [4.065, -4.065, 4.065]]
fractional = False
elif pkey == "greigite":
cell = [[0.0, 4.938, 4.938], [4.938, 0.0, 4.938],
[4.938, 4.938, 0.0]]
positions = [
(1.2345, 1.2345, 1.2345),
(8.6415, 8.6415, 8.6415),
(4.938, 4.938, 4.938),
(2.469, 4.938, 2.469),
(4.938, 2.469, 2.469),
(2.469, 2.469, 4.938),
(2.473938, 2.473938, 2.473938),
(4.942938, 7.402062, 4.942938),
(4.933062, 2.473938, 4.933062),
(2.473938, 4.933062, 4.933062),
(7.402062, 4.942938, 4.942938),
(7.402062, 7.402062, 7.402062),
(4.942938, 4.942938, 7.402062),
(4.933062, 4.933062, 2.473938),
]
fractional = False
symbols = names = [
"Fe",
"Fe",
"Fe",
"Fe",
"Fe",
"Fe",
"S",
"S",
"S",
"S",
"S",
"S",
"S",
"S",
]
else:
raise ValueError("Unknown structure key: {}".format(pkey))
# create structure
structure = DataFactory("structure")(cell=cell)
for position, symbol, name in zip(positions, symbols, names):
if fractional:
position = np.dot(position, cell).tolist()
structure.append_atom(position=position, symbols=symbol, name=name)
return structure
