def read(self, label):
self.parameters = {}
self.set_label(label)
if label[-5:] in ['.dat', '.out', '.log']:
label = label[:-4]
atoms = read_openmx(filename=label, debug=self.debug)
self.update_atoms(atoms)
self.parameters.update(atoms.calc.parameters)
self.results = atoms.calc.results
self.parameters['restart'] = self.label
self.parameters['label'] = label
def calculate(self,
atoms=None,
properties=None,
system_changes=all_changes):
"""
Capture the RuntimeError from FileIOCalculator.calculate
and add a little debug information from the OpenMX output.
See base FileIOCalculator for documentation.
"""
if self.parameters.data_path is None:
if not 'OPENMX_DFT_DATA_PATH' in os.environ:
warnings.warn('Please either set OPENMX_DFT_DATA_PATH as an'
'enviroment variable or specify dft_data_path as'
'a keyword argument')
self.prind("Start Calculation")
if properties is None:
properties = self.implemented_properties
try:
Calculator.calculate(self, atoms, properties, system_changes)
self.write_input(atoms=self.atoms,
parameters=self.parameters,
properties=properties,
system_changes=system_changes)
self.print_input(debug=self.debug, nohup=self.nohup)
self.run()
# self.read_results()
self.version = self.read_version()
output_atoms = read_openmx(filename=self.label, debug=self.debug)
self.output_atoms = output_atoms
# XXX The parameters are supposedly inputs, so it is dangerous
# to update them from the outputs. --askhl
self.parameters.update(output_atoms.calc.parameters)
self.results = output_atoms.calc.results
# self.clean()
except RuntimeError as e:
try:
with open(get_file_name('.log'), 'r') as f:
lines = f.readlines()
debug_lines = 10
print('##### %d last lines of the OpenMX output' % debug_lines)
for line in lines[-20:]:
print(line.strip())
print('##### end of openMX output')
raise e
except RuntimeError as e:
raise e
def test_openmx_out():
with open('openmx_fio_test.out', 'w') as fd:
fd.write(openmx_out_sample)
atoms = read_openmx('openmx_fio_test')
tol = 1e-2
# Expected values
energy = -8.0551
energies = np.array([-6.2612, -0.4459, -0.4459, -0.4509, -0.4509])
forces = np.array([[0.00000, 0.00000, -0.091659],
[0.02700, 0.02700, 0.029454],
[-0.02700, -0.02700, 0.029455],
[0.00894, -0.00894, 0.016362],
[-0.00894, 0.00894, 0.016362]])
assert isinstance(atoms, Atoms)
assert np.isclose(atoms.calc.results['energy'], energy * Ha, atol=tol)
assert np.all(
np.isclose(atoms.calc.results['energies'], energies * Ha, atol=tol))
assert np.all(
np.isclose(atoms.calc.results['forces'], forces * Ha / Bohr, atol=tol))