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import os
from ase.constraints import FixAtoms, FixedLine, FixedPlane
from ase import Atoms
def test_siesta_zmat(siesta_factory):
atoms = Atoms('CO2', [(0.0, 0.0, 0.0), (-1.178, 0.0, 0.0),
(1.178, 0.0, 0.0)])
c1 = FixAtoms(indices=[0])
c2 = FixedLine(1, [0.0, 1.0, 0.0])
c3 = FixedPlane(2, [1.0, 0.0, 0.0])
atoms.set_constraint([c1, c2, c3])
custom_dir = './dir1/'
# Test simple fdf-argument case.
siesta = siesta_factory.calc(
label=custom_dir + 'test_label',
symlink_pseudos=False,
atomic_coord_format='zmatrix',
fdf_arguments={
'MD.TypeOfRun': 'CG',
'MD.NumCGsteps': 1000
})
atoms.calc = siesta
siesta.write_input(atoms, properties=['energy'])
with open(os.path.join(custom_dir, 'test_label.fdf'), 'r') as fd:
lines = fd.readlines()
lsl = [line.split() for line in lines]
assert ['cartesian'] in lsl
assert ['%block', 'Zmatrix'] in lsl
assert ['%endblock', 'Zmatrix'] in lsl
assert ['MD.TypeOfRun', 'CG'] in lsl
assert any([line.split()[4:9] == ['0', '0', '0', '1', 'C']
for line in lines])
assert any([line.split()[4:9] == ['0', '1', '0', '2', 'O']
for line in lines])
assert any([line.split()[4:9] == ['0', '1', '1', '3', 'O']
for line in lines])
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