def test_isolation_3D():
atoms = FaceCenteredCubic(size=(2, 2, 2), symbol='Cu', pbc=(1, 1, 1))
result = isolate_components(atoms)
assert len(result) == 1
key, components = list(result.items())[0]
assert key == '3D'
assert len(components) == 1
bulk = components[0]
assert bulk.get_chemical_formula() == atoms.get_chemical_formula()
def test_isolation_0D():
atoms = ase.build.molecule('H2O', vacuum=3.0)
result = isolate_components(atoms, kcutoff=1.1)
assert len(result) == 1
key, components = list(result.items())[0]
assert key == '0D'
assert len(components) == 1
molecule = components[0]
assert molecule.get_chemical_formula() == atoms.get_chemical_formula()
def test_isolation_2D():
atoms = ase.build.mx2(formula='MoS2', kind='2H', a=3.18, thickness=3.19)
atoms.cell[2, 2] = 7
atoms.set_pbc((1, 1, 1))
atoms *= 2
result = isolate_components(atoms)
assert len(result) == 1
key, components = list(result.items())[0]
assert key == '2D'
assert len(components) == 2
for layer in components:
empirical = atoms.get_chemical_formula(empirical=True)
assert empirical == layer.get_chemical_formula(empirical=True)
assert (layer.pbc == [True, True, False]).all()
def test_isolation_1D():
atoms = Atoms(symbols='Cl6Ti2',
pbc=True,
cell=[[6.27, 0, 0], [-3.135, 5.43, 0], [0, 0, 5.82]],
positions=[[1.97505, 0, 1.455],
[0.987525, 1.71044347, 4.365],
[-0.987525, 1.71044347,
1.455], [4.29495, 0, 4.365],
[2.147475, 3.71953581, 1.455],
[-2.147475, 3.71953581, 4.365], [0, 0, 0],
[0, 0, 2.91]])
result = isolate_components(atoms)
assert len(result) == 1
key, components = list(result.items())[0]
assert key == '1D'
assert len(components) == 1
chain = components[0]
assert (chain.pbc == [False, False, True]).all()
assert chain.get_chemical_formula() == atoms.get_chemical_formula()
def get_components(atoms, kcutoff, viewer=False):
"""
A function to isolate individual components from the input structure and
view if desired.
Parameters
Accepts:
atoms (Atoms object) ASE atoms object of desired structure
kcutoff (int) Cutoff of components to consider. Ideally, this should be the
Lennard-Jones cutoff value used.
viewer (bool) When True, returns the view of each component.
Do not set True unless you only have a few components.
Returns:
comp (collections.defaultdict)
"""
comp = isolate_components(atoms, kcutoff=kcutoff)
print("counts:", [(k, len(v)) for k, v in sorted(comp.items())])
if viewer == True:
for dim, components in comp.items():
for atoms in components:
view(atoms, block=True)
return comp
import numpy as np
import ase.build
from ase import Atoms
from ase.visualize import view
from ase.geometry.dimensionality import isolate_components
# build two slabs of different types of MoS2
rep = [4, 4, 1]
a = ase.build.mx2(formula='MoS2', kind='2H', a=3.18, thickness=3.19) * rep
b = ase.build.mx2(formula='MoS2', kind='1T', a=3.18, thickness=3.19) * rep
positions = np.concatenate([a.get_positions(), b.get_positions() + [0, 0, 7]])
numbers = np.concatenate([a.numbers, b.numbers])
cell = a.cell
atoms = Atoms(numbers=numbers, positions=positions, cell=cell, pbc=[1, 1, 1])
atoms.cell[2, 2] = 14.0
# isolate each component in the whole material
result = isolate_components(atoms)
print("counts:", [(k, len(v)) for k, v in sorted(result.items())])
for dim, components in result.items():
for atoms in components:
print(dim)
view(atoms, block=True)