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# fmt: off
import numpy as np
import pytest
from ase.build import bulk, fcc111, molecule
from ase.io.octopus.input import atoms2kwargs
from ase.units import Bohr
def getcoords(block):
words = [line[1:] for line in block]
return np.array(words).astype(float)
def test_molecule():
atoms = molecule('H2O')
kwargs = atoms2kwargs(atoms, use_ase_cell=False)
assert atoms.positions == pytest.approx(
getcoords(kwargs['coordinates']) * Bohr)
# assert 'boxshape' not in kwargs and 'latticevectors' not in kwargs
def test_molecule_box():
atoms = molecule('H2O', vacuum=3.0)
kwargs = atoms2kwargs(atoms, use_ase_cell=True)
lsize = np.array(kwargs['lsize'], float)[0]
# assert kwargs['boxshape'] == 'parallelepiped'
# note: lsize are the "half lengths", box is [-lsize, lsize]:
assert atoms.cell.lengths() == pytest.approx(2 * lsize * Bohr)
coords = getcoords(kwargs['coordinates']) * Bohr
cell_center = 0.5 * atoms.cell.sum(axis=0)
assert atoms.positions - cell_center == pytest.approx(coords)
def compare_scaled(atoms, kwargs):
assert np.array(kwargs['latticevectors'], float) == pytest.approx(
atoms.cell / Bohr)
assert getcoords(kwargs['reducedcoordinates']) == pytest.approx(
atoms.get_scaled_positions())
def test_2d_surface():
atoms = fcc111('Au', size=(1, 1, 1), vacuum=4.0)
kwargs = atoms2kwargs(atoms, use_ase_cell=True)
compare_scaled(atoms, kwargs)
assert kwargs['periodicdimensions'] == 2
def test_3d_periodic():
atoms = bulk('Ti')
kwargs = atoms2kwargs(atoms, use_ase_cell=True)
compare_scaled(atoms, kwargs)
assert kwargs['periodicdimensions'] == 3
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