def test_supercell(generate_structure):
"""Test to create a super cell"""
from aiida_fleur.tools.StructureData_util import supercell
from aiida_fleur.tools.StructureData_util import supercell_ncf
from aiida.orm import Int
from itertools import product
structure = generate_structure()
supercell = supercell(structure, Int(2), Int(3), Int(4))
assert (supercell.cell[0] == np.array(structure.cell[0]) * 2).all()
assert (supercell.cell[1] == np.array(structure.cell[1]) * 3).all()
assert (supercell.cell[2] == np.array(structure.cell[2]) * 4).all()
assert len(supercell.sites) == 2 * 3 * 4 * len(structure.sites)
positions_old = [x.position for x in structure.sites]
positions_rescaled = [x.position for x in supercell.sites]
for position in positions_old:
for x, y, z in product(range(2), range(3), range(4)):
test_pos = tuple(
np.array(position) + x * np.array(structure.cell[0]) +
y * np.array(structure.cell[1]) +
z * np.array(structure.cell[2]))
assert test_pos in positions_rescaled
no_struc = Int(1)
no_supercell = supercell_ncf(no_struc, 2, 3, 4)
assert no_supercell is None
def test_break_symmetry_wf_film_structure_only(generate_film_structure):
"""Check if it does not crash and able to destroy all symmetries"""
from aiida_fleur.tools.StructureData_util import break_symmetry_wf, supercell_ncf
from aiida_fleur.tools.StructureData_util import break_symmetry
from aiida.orm import Dict
structure = generate_film_structure()
structure = supercell_ncf(structure, 2, 2, 1)
out = break_symmetry_wf(
structure,
wf_para=Dict(dict={}),
)
structure_broken = out['new_structure']
kind_names = [x.kind_name for x in structure_broken.sites]
kind_names_should = [
'Fe1', 'Fe2', 'Fe3', 'Fe4', 'Pt1', 'Pt2', 'Pt3', 'Pt4', 'Pt5', 'Pt6',
'Pt7', 'Pt8'
]
for kind_name in kind_names_should:
assert kind_name in kind_names
assert len(set(kind_names)) == len(kind_names_should)
struc_b_fe, para_new_fe = break_symmetry(structure, atoms=['Fe'])
kind_names = [x.kind_name for x in struc_b_fe.sites]
kind_names_should = ['Fe1', 'Fe2', 'Fe3', 'Fe4', 'Pt']
for kind_name in kind_names_should:
assert kind_name in kind_names
assert len(set(kind_names)) == len(kind_names_should)
struc_b_pt, para_new_pt = break_symmetry(structure, atoms=['Pt'])
kind_names = [x.kind_name for x in struc_b_pt.sites]
kind_names_should = [
'Fe', 'Pt1', 'Pt2', 'Pt3', 'Pt4', 'Pt5', 'Pt6', 'Pt7', 'Pt8'
]
for kind_name in kind_names_should:
assert kind_name in kind_names
assert len(set(kind_names)) == len(kind_names_should)
struc_b_site, para_new_site = break_symmetry(structure,
atoms=[],
site=[0, 1])
kind_names = [x.kind_name for x in struc_b_site.sites]
kind_names_should = ['Fe', 'Fe1', 'Fe2', 'Pt']
for kind_name in kind_names_should:
assert kind_name in kind_names
assert len(set(kind_names)) == len(kind_names_should)
pos = [structure.sites[0].position, structure.sites[1].position]
struc_b_pos, para_new_pos = break_symmetry(structure, atoms=[], pos=pos)
kind_names = [x.kind_name for x in struc_b_pos.sites]
kind_names_should = ['Fe', 'Fe1', 'Fe2', 'Pt']
for kind_name in kind_names_should:
assert kind_name in kind_names
assert len(set(kind_names)) == len(kind_names_should)
def test_find_primitive_cell_wf(generate_structure):
from aiida_fleur.tools.StructureData_util import find_primitive_cell_wf, supercell_ncf
from aiida_fleur.tools.StructureData_util import find_primitive_cells
structure_primitive = generate_structure()
structure = supercell_ncf(structure_primitive, 2, 2, 22)
result = find_primitive_cell_wf(structure)
result = result['primitive_cell']
assert all(x in structure_primitive.cell for x in result.cell)
resultlist = find_primitive_cells([structure.uuid, structure.uuid])
for struc in resultlist:
assert all(x in structure_primitive.cell for x in result.cell)
def test_find_equi_atoms(generate_film_structure):
"""Test if find_equi_atoms functions returns equidistant atoms"""
from aiida_fleur.tools.StructureData_util import find_equi_atoms, supercell_ncf
from numpy import array
structure = generate_film_structure()
structure = supercell_ncf(structure, 2, 2, 1)
equi_info_symbol, n_equi_info_symbol = find_equi_atoms(structure)
assert equi_info_symbol[0][0] == 'Fe'
assert (equi_info_symbol[0][1] == array([0, 1, 6, 7])).all()
assert equi_info_symbol[1][0] == 'Pt'
assert (equi_info_symbol[1][1] == array([2, 3, 8, 9])).all()
assert equi_info_symbol[2][0] == 'Pt'
assert (equi_info_symbol[2][1] == array([4, 5, 10, 11])).all()
assert n_equi_info_symbol == {'Fe': 1, 'Pt': 2}