def test_consistency_with_parsevasp(fresh_aiida_env, vasp_structure):
"""
Compare the poscar-dict returned by parsevasp to the dict created by the PoscarParser.
This tests purpose is to give a warning if we are overriding keys in parsevasps poscar-dict.
"""
from aiida_vasp.parsers.file_parsers.poscar import parsevasp_to_aiida
from parsevasp.poscar import Poscar
path = data_path('poscar', 'POSCAR')
poscar = Poscar(file_path=path, prec=12, conserve_order=True)
poscar_dict = poscar.get_dict(direct=False)
result_dict = parsevasp_to_aiida(poscar)['poscar-structure']
compare_objects(poscar_dict, result_dict)
def test_poscar_write(tmp_path, poscar_parser):
"""Test that the POSCAR writes correctly."""
poscar = poscar_parser.get_dict()
# Write it
poscar_write_path = tmp_path / 'POSCAR'
poscar_parser.write(file_path=poscar_write_path)
# Then load same content again, but from the newly written file
poscar_reloaded = Poscar(file_path=poscar_write_path).get_dict()
compare_poscars(poscar, poscar_reloaded)
# Check that handler also works for write by yet again writing a new POSCAR and comparing
with open(poscar_write_path, 'w') as handler:
poscar_parser.write(file_handler=handler)
with open(poscar_write_path, 'r') as handler:
poscar_reloaded = Poscar(file_handler=handler).get_dict()
compare_poscars(poscar, poscar_reloaded)
def test_poscar_cartesian(tmp_path, poscar_parser):
"""Test that the POSCAR writes and reads positional cartesian coordinates correctly."""
poscar = poscar_parser.get_dict()
# Write it
poscar_write_path = tmp_path / 'POSCAR'
poscar_parser.write(file_path=poscar_write_path)
poscar_cartesian = None
with open(poscar_write_path) as file_object:
poscar_cartesian = file_object.readlines()
assert poscar_cartesian[7] == 'Cartesian\n'
assert poscar_cartesian[
8] == ' 2.254110000000 2.254110000000 2.254110000000\n'
assert poscar_cartesian[
9] == ' 6.762340000000 6.762340000000 6.762340000000\n'
assert poscar_cartesian[
39] == ' 7.529650000000 3.083180000000 4.508230000000\n'
# Then load same content again, but from the newly written file, which should now be on cartesian form
poscar_reloaded = Poscar(file_path=poscar_write_path).get_dict()
# Comment entry is modified so need to remove that before comparing
del poscar['comment']
del poscar_reloaded['comment']
# Compare
assert np.allclose(poscar['unitcell'], poscar_reloaded['unitcell'])
for index, site in enumerate(poscar['sites']):
reloaded = poscar_reloaded['sites'][index]
assert site['specie'] == reloaded['specie']
assert np.allclose(site['position'], reloaded['position'])
assert site['selective'] == reloaded['selective']
assert site['velocities'] == reloaded['velocities']
assert np.allclose(site['predictors'], reloaded['predictors'])
assert site['direct'] == reloaded['direct']
def poscar_parser(request):
"""Load POSCAR file.
"""
testdir = os.path.dirname(__file__)
poscarfile = testdir + '/POSCAR'
poscar = Poscar(file_path=poscarfile, write_direct=request.param)
return poscar
def poscar_parser_vel():
"""Load POSCAR file.
"""
testdir = os.path.dirname(__file__)
poscarfile = testdir + '/POSCARVEL'
poscar = Poscar(file_path=poscarfile)
return poscar
def poscar_parser_names():
"""Load POSCAR file.
"""
testdir = os.path.dirname(__file__)
poscarfile = testdir + "/POSCARNAMES"
poscar = Poscar(file_path=poscarfile)
return poscar
def _parsed_object(self):
"""Return the parsevasp object representing the POSCAR file."""
try:
return Poscar(poscar_dict=aiida_to_parsevasp(
self._parsed_data['poscar-structure']),
prec=self.precision,
conserve_order=True)
except SystemExit:
return None
def test_poscar_entries_dict():
"""Test to check inititialization using dict.
"""
unitcell = np.array([[9.0164589999999993, 0., 0.],
[0., 9.0164589999999993, 0.],
[0., 0., 9.0164589999999993]])
sites = []
sites.append(
Site('Co', np.array([0.0, 0.0, 0.0]), [True, True, True], None, None,
True))
poscar_dict = {
'comment': 'Example file',
'unitcell': unitcell,
'sites': sites
}
poscar_parser = Poscar(poscar_dict=poscar_dict)
poscar = poscar_parser.get_dict()
assert poscar['comment'] == 'Example file'
unitcell = poscar['unitcell']
test = np.array([[9.0164589999999993, 0.,
0.], [0., 9.0164589999999993, 0.],
[0., 0., 9.0164589999999993]])
np.testing.assert_allclose(unitcell, test)
sites = poscar['sites']
assert len(sites) == 1
test = {
'specie': 'Co',
'position': np.array([0.0, 0.0, 0.0]),
'selective': [True, True, True],
'velocities': None,
'predictors': None,
'direct': True
}
np.testing.assert_allclose(sites[0]['position'], test['position'])
assert sites[0]['specie'] == test['specie']
assert sites[0]['selective'] == [True, True, True]
assert sites[0]['velocities'] == None
assert sites[0]['predictors'] == None
assert sites[0]['direct']
def poscar_parser_file_object():
"""Load POSCAR file using a file object.
"""
testdir = os.path.dirname(__file__)
poscarfile = testdir + '/POSCAR'
poscar = None
with open(poscarfile) as file_handler:
poscar = Poscar(file_handler=file_handler)
return poscar
def test_poscar_scaling(tmp_path, poscar_parser):
"""Test that the scaling factor works when reading a POSCAR file."""
poscar = poscar_parser.get_dict()
# Locate scaling factor
scaling = poscar['unitcell'][1, 1]
poscar = poscar_parser.get_string()
poscar_lines = poscar.splitlines()
# First test scaling when positions are in direct coordinates
# Prepare scaled unitcell, but direct coordinates
poscar_lines[1] = str(scaling)
for i in range(2, 5):
poscar_lines[i] = ' '.join(
[str(float(item) / scaling) for item in poscar_lines[i].split()])
poscar_write_path = tmp_path / 'POSCAR'
# Dump it to file
with open(poscar_write_path, 'w') as file_object:
file_object.write('\n'.join(poscar_lines))
# Read it using a new Poscar instance
poscar_scaled_direct = Poscar(file_path=poscar_write_path).get_dict()
unitcell_test = np.array([[9.0164589999999993, 0., 0.],
[0., 9.0164589999999993, 0.],
[0., 0., 9.0164589999999993]])
position_test = np.array([0.24999947, 0.24999947, 0.24999947])
assert np.allclose(poscar_scaled_direct['sites'][0]['position'],
position_test)
assert np.allclose(poscar_scaled_direct['unitcell'], unitcell_test)
# Then test scaling when positions are in cartesian coordinates
# Create a new Poscar instance where the write is in cartesian coordinates
poscar_parser_temp = Poscar(poscar_string=poscar, write_direct=False)
poscar_parser_temp.write(file_path=poscar_write_path)
with open(poscar_write_path, 'r') as file_object:
poscar_cart_unscaled = file_object.readlines()
poscar_cart_unscaled[1] = str(scaling) + '\n'
# Scale unitcell
for i in range(2, 5):
poscar_cart_unscaled[i] = ' '.join([
str(float(item) / scaling)
for item in poscar_cart_unscaled[i].split()
]) + '\n'
# Scale positions
for i in range(8, 40):
poscar_cart_unscaled[i] = ' '.join([
str(float(item) / scaling)
for item in poscar_cart_unscaled[i].split()
]) + '\n'
# Write file
with open(poscar_write_path, 'w') as file_object:
file_object.writelines(poscar_cart_unscaled)
poscar_cart_scaled = Poscar(file_path=poscar_write_path).get_dict()
unitcell_test = np.array([[9.0164589999999993, 0., 0.],
[0., 9.0164589999999993, 0.],
[0., 0., 9.0164589999999993]])
position_test = np.array([0.24999947, 0.24999947, 0.24999947])
assert np.allclose(poscar_scaled_direct['sites'][0]['position'],
position_test)
assert np.allclose(poscar_scaled_direct['unitcell'], unitcell_test)
def _parsed_object(self):
"""Return the parsevasp object representing the POSCAR file."""
if isinstance(self._data_obj, get_data_class('structure')):
# _data_obj is StructureData, return the parsed version if possible.
try:
return Poscar(poscar_dict=self.aiida_to_parsevasp(
self._data_obj, options=self._options),
prec=self._precision,
conserve_order=True,
logger=self._logger)
except SystemExit:
return None
# _data_obj is a SingleFile:
return self._data_obj
def _parse_file(self, inputs):
"""Read POSCAR file format."""
# check if structure have already been loaded, in that case just return
if isinstance(self._data_obj, get_data_class('structure')):
return {'poscar-structure': self._data_obj}
# pass file path to parsevasp and try to load file
try:
poscar = Poscar(file_path=self._data_obj.path,
prec=self.precision,
conserve_order=True)
except SystemExit:
self._logger.warning("Parsevasp exited abnormally. "
"Returning None.")
return {'poscar-structure': None}
result = parsevasp_to_aiida(poscar)
return result
def test_poscar_write(tmp_path, poscar_parser):
"""Test that the POSCAR writes correctly."""
poscar = poscar_parser.get_dict()
# Write it
poscar_write_path = tmp_path / "POSCAR"
poscar_parser.write(poscar_write_path)
# Then load same content again, but from the newly written file
poscar_reloaded = Poscar(file_path=poscar_write_path).get_dict()
# Comment entry is modified so need to remove that before comparing
del poscar['comment']
del poscar_reloaded['comment']
# Compare
assert np.allclose(poscar['unitcell'], poscar_reloaded['unitcell'])
for index, site in enumerate(poscar['sites']):
reloaded = poscar_reloaded['sites'][index]
assert site['specie'] == reloaded['specie']
assert np.allclose(site['position'], reloaded['position'])
assert site['selective'] == reloaded['selective']
assert site['velocities'] == reloaded['velocities']
assert np.allclose(site['predictors'], reloaded['predictors'])
assert site['direct'] == reloaded['direct']