def test_md():
import numpy as np
import unittest
from ase.units import Ry, Ha
from ase.calculators.openmx import OpenMX
from ase.io.trajectory import Trajectory
from ase.optimize import QuasiNewton
from ase.constraints import UnitCellFilter
from ase.calculators.calculator import PropertyNotImplementedError
from ase import Atoms
""" Only OpenMX 3.8 or higher version pass this test"""
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 = OpenMX(
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=(4, 4, 4),
eigensolver='Band'
)
bud.set_calculator(calc)
try:
bud.get_stress()
except PropertyNotImplementedError as err:
raise unittest.SkipTest(err)
traj = Trajectory('example.traj', 'w', bud)
ucf = UnitCellFilter(bud, mask=[True, True, False, False, False, False])
dyn = QuasiNewton(ucf)
dyn.attach(traj.write)
dyn.run(fmax=0.1)
bud.get_potential_energy()
# XXX maybe assert something?
traj.close()
def read_openmx(filename=None, debug=False):
from ase.calculators.openmx import OpenMX
from ase import Atoms
"""
Read results from typical OpenMX output files and returns the atom object
In default mode, it reads every implementd properties we could get from
the files. Unlike previous version, we read the information based on file.
previous results will be eraised unless previous results are written in the
next calculation results.
Read the 'LABEL.log' file seems redundant. Because all the
information should already be written in '.out' file. However, in the
version 3.8.3, stress tensor are not written in the '.out' file. It only
contained in the '.log' file. So... I implented reading '.log' file method
"""
log_data = read_file(get_file_name('.log', filename), debug=debug)
restart_data = read_file(get_file_name('.dat#', filename), debug=debug)
dat_data = read_file(get_file_name('.dat', filename), debug=debug)
out_data = read_file(get_file_name('.out', filename), debug=debug)
scfout_data = read_scfout_file(get_file_name('.scfout', filename))
band_data = read_band_file(get_file_name('.Band', filename))
# dos_data = read_dos_file(get_file_name('.Dos.val', filename))
"""
First, we get every data we could get from the all results files. And then,
reform the data to fit to data structure of Atom object. While doing this,
Fix the unit to ASE format.
"""
parameters = get_parameters(out_data=out_data,
log_data=log_data,
restart_data=restart_data,
dat_data=dat_data,
scfout_data=scfout_data,
band_data=band_data)
atomic_formula = get_atomic_formula(out_data=out_data,
log_data=log_data,
restart_data=restart_data,
scfout_data=scfout_data,
dat_data=dat_data)
results = get_results(out_data=out_data,
log_data=log_data,
restart_data=restart_data,
scfout_data=scfout_data,
dat_data=dat_data,
band_data=band_data)
atoms = Atoms(**atomic_formula)
atoms.set_calculator(OpenMX(**parameters))
atoms.calc.results = results
return atoms
def calc(self, **kwargs):
from ase.calculators.openmx import OpenMX
return OpenMX(command=self.executable,
data_path=str(self.data_path),
**kwargs)
from ase import Atoms
from ase.test.testsuite import NotAvailable
import numpy as np
""" Only OpenMX 3.8 or higher version pass this test"""
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 = OpenMX(label='ch4',
xc='GGA',
energy_cutoff=300 * Ry,
definition_of_atomic_species=[['C', 'C5.0-s1p1', 'C_PBE13'],
['H', 'H5.0-s1', 'H_PBE13']])
bud.set_calculator(calc)
try:
e = bud.get_stress()
except PropertyNotImplementedError as err:
raise NotAvailable(err)
traj = Trajectory('example.traj', 'w', bud)
ucf = UnitCellFilter(bud, mask=[True, True, False, False, False, False])
dyn = QuasiNewton(ucf)
dyn.attach(traj.write)
dyn.run(fmax=0.02)