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import numpy as np
import pytest
from ase.units import Ry, Ha
from ase.io.trajectory import Trajectory
from ase.optimize import QuasiNewton
from ase.constraints import UnitCellFilter
from ase import Atoms
from ase.utils import tokenize_version
@pytest.mark.calculator('openmx')
def test_md(factory):
# XXX ugly hack
ver = factory.factory.version()
if tokenize_version(ver) < tokenize_version('3.8'):
pytest.skip('No stress tensor until openmx 3.8+')
bud = Atoms('CH4', np.array([
[0.000000, 0.000000, 0.100000],
[0.682793, 0.682793, 0.682793],
[-0.682793, -0.682793, 0.68279],
[-0.682793, 0.682793, -0.682793],
[0.682793, -0.682793, -0.682793]]),
cell=[10, 10, 10])
calc = factory.calc(
label='ch4',
xc='GGA',
energy_cutoff=300 * Ry,
convergence=1e-4 * Ha,
# Use 'C_PBE19' and 'H_PBE19' for version 3.9
definition_of_atomic_species=[['C', 'C5.0-s1p1', 'C_PBE13'],
['H', 'H5.0-s1', 'H_PBE13']],
kpts=(1, 1, 1),
eigensolver='Band'
)
bud.calc = calc
with Trajectory('example.traj', 'w', bud) as traj:
ucf = UnitCellFilter(
bud, mask=[True, True, False, False, False, False])
with QuasiNewton(ucf) as dyn:
dyn.attach(traj.write)
dyn.run(fmax=0.1)
bud.get_potential_energy()
# XXX maybe assert something?
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