def test_kpoints_write_line(kpoints_parser_line, tmpdir):
"""Test read, write and read KPOINTS in line mode.
"""
kpoints = kpoints_parser_line.get_dict()
temp_file = str(tmpdir.join('KPOINTSLINE'))
kpoints_parser_line.write(file_path=temp_file)
kpoints_parser_line_temp = Kpoints(file_path=temp_file)
kpoints_temp = kpoints_parser_line_temp.get_dict()
assert kpoints_temp['mode'] == 'line'
assert kpoints_temp['comment'] == 'k-points along high symmetry lines'
assert kpoints_temp['divisions'] == None
assert kpoints_temp['shifts'] == None
assert kpoints_temp['centering'] == None
assert kpoints_temp['num_kpoints'] == 40
points = kpoints_temp['points']
np.testing.assert_allclose(points[0][0], np.array([0.0, 0.0, 0.0]))
np.testing.assert_allclose(points[1][0], np.array([0.5, 0.5, 0.0]))
np.testing.assert_allclose(points[2][0], np.array([0.5, 0.5, 0.0]))
np.testing.assert_allclose(points[3][0], np.array([0.5, 0.75, 0.25]))
np.testing.assert_allclose(points[4][0], np.array([0.5, 0.75, 0.25]))
np.testing.assert_allclose(points[5][0], np.array([0.0, 0.0, 0.0]))
assert math.isclose(points[0][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[1][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[2][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[3][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[4][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[5][1], 1.0, rel_tol=1e-07)
assert points[0][2]
assert points[1][2]
assert points[2][2]
assert points[3][2]
assert points[4][2]
assert points[5][2]
def test_kpoints_modify_line(kpoints_parser_line, tmpdir):
"""Test read, modify, write and read KPOINTS in line mode.
"""
kpoints = kpoints_parser_line.get_dict()
assert kpoints['comment'] == 'k-points along high symmetry lines'
kpoints_parser_line.modify('comment', 'No comment')
point = Kpoint(np.array([0.5, 0.5, 0.25]), 1.0)
kpoints_parser_line.modify('points', point, point_number=3)
kpoints_parser_line.modify('points', point, point_number=4)
temp_file = str(tmpdir.join('KPOINTSLINE'))
kpoints_parser_line.write(file_path=temp_file)
kpoints_parser_line_temp = Kpoints(file_path=temp_file)
kpoints_temp = kpoints_parser_line_temp.get_dict()
assert kpoints_temp['comment'] == 'No comment'
points = kpoints_temp['points']
np.testing.assert_allclose(points[0][0], np.array([0.0, 0.0, 0.0]))
np.testing.assert_allclose(points[1][0], np.array([0.5, 0.5, 0.0]))
np.testing.assert_allclose(points[2][0], np.array([0.5, 0.5, 0.0]))
np.testing.assert_allclose(points[3][0], np.array([0.5, 0.5, 0.25]))
np.testing.assert_allclose(points[4][0], np.array([0.5, 0.5, 0.25]))
np.testing.assert_allclose(points[5][0], np.array([0.0, 0.0, 0.0]))
assert math.isclose(points[0][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[1][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[2][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[3][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[4][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[5][1], 1.0, rel_tol=1e-07)
assert points[0][2]
assert points[1][2]
assert points[2][2]
assert points[3][2]
assert points[4][2]
assert points[5][2]
def test_kpoints_write_explicit(kpoints_parser_explicit, tmpdir):
"""Test read, write and read KPOINTS in explicit mode.
"""
kpoints = kpoints_parser_explicit.get_dict()
temp_file = str(tmpdir.join('KPOINTSEXP'))
kpoints_parser_explicit.write(file_path=temp_file)
kpoints_parser_explicit_temp = Kpoints(file_path=temp_file)
kpoints_temp = kpoints_parser_explicit_temp.get_dict()
assert kpoints_temp['mode'] == 'explicit'
assert kpoints_temp['comment'] == 'Example file'
assert kpoints_temp['divisions'] == None
assert kpoints_temp['shifts'] == None
assert kpoints_temp['centering'] == None
points = kpoints_temp['points']
assert len(points) == 4
np.testing.assert_allclose(points[0][0], np.array([0.0, 0.0, 0.0]))
np.testing.assert_allclose(points[1][0], np.array([0.0, 0.0, 0.5]))
np.testing.assert_allclose(points[2][0], np.array([0.0, 0.5, 0.5]))
np.testing.assert_allclose(points[3][0], np.array([0.5, 0.5, 0.5]))
assert math.isclose(points[0][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[1][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[2][1], 2.0, rel_tol=1e-07)
assert math.isclose(points[3][1], 4.0, rel_tol=1e-07)
assert points[0][2]
assert points[1][2]
assert points[2][2]
assert points[3][2]
assert kpoints_temp['tetra'] == [[6, 1, 2, 3, 4]]
assert math.isclose(kpoints_temp['tetra_volume'],
0.183333333333333,
rel_tol=1e-07)
def test_kpoints_dict(tmpdir):
"""Test to initialize KPOINTS in auto mode using dictionary.
"""
kpoints_dict = {
'comment': 'Example file',
'divisions': [5, 5, 5],
'mode': 'automatic',
'shifts': None,
'points': None,
'centering': 'Gamma',
'tetra': None,
'tetra_volume': None,
'num_kpoints': 0
}
temp_file = str(tmpdir.join('KPOINTS'))
kpoints_parser_auto_temp = Kpoints(kpoints_dict=kpoints_dict)
kpoints_temp = kpoints_parser_auto_temp.get_dict()
assert kpoints_temp['mode'] == 'automatic'
assert kpoints_temp['comment'] == 'Example file'
assert kpoints_temp['divisions'] == [5, 5, 5]
assert kpoints_temp['shifts'] == None
assert kpoints_temp['points'] == None
assert kpoints_temp['centering'] == 'Gamma'
assert kpoints_temp['tetra'] == None
assert kpoints_temp['tetra_volume'] == None
assert kpoints_temp['num_kpoints'] == 0
def test_kpoints_modify_auto(kpoints_parser_auto, tmpdir):
"""Test read, modify, write and read KPOINTS in auto mode.
"""
kpoints = kpoints_parser_auto.get_dict()
assert kpoints['comment'] == 'Example file'
assert kpoints['divisions'] == [4, 4, 4]
kpoints_parser_auto.modify('comment', 'No comment')
kpoints_parser_auto.modify('divisions', [5, 5, 5])
temp_file = str(tmpdir.join('KPOINTS'))
kpoints_parser_auto.write(file_path=temp_file)
kpoints_parser_auto_temp = Kpoints(file_path=temp_file)
kpoints_temp = kpoints_parser_auto_temp.get_dict()
assert kpoints_temp['comment'] == 'No comment'
assert kpoints_temp['divisions'] == [5, 5, 5]
def _parse_file(self, inputs):
"""Create a DB Node from a KPOINTS file."""
result = inputs
result = {}
if isinstance(self._data_obj, get_data_class('array.kpoints')):
return {'kpoints-kpoints': self._data_obj}
try:
parsed_kpoints = Kpoints(file_path=self._data_obj.path,
logger=self._logger)
except SystemExit:
self._logger.warning(
'Parsevasp exitited abnormally. Returning None.')
return {'kpoints-kpoints': None}
if parsed_kpoints.entries.get('mode') == 'line':
self._logger.warning(
'The read KPOINTS contained line mode which is'
'not supported. Returning None.')
return {'kpoints-kpoints': None}
result['kpoints-kpoints'] = parsed_kpoints.entries
return result
def _parse_file(self, inputs):
"""Create a DB Node from a KPOINTS file"""
result = inputs
result = {}
if isinstance(self._data_obj, get_data_class('array.kpoints')):
return {'kpoints-kpoints': self._data_obj}
try:
parsed_kpoints = Kpoints(file_path=self._data_obj.path)
except SystemExit:
self._logger.warning("Parsevasp exitited abnormally. "
"Returning None.")
return {'kpoints-kpoints': None}
mode = parsed_kpoints.entries.get('mode')
if mode == 'line':
self._logger.warning(
"The read KPOINTS contained line mode which is"
"not supported. Returning None.")
return {'kpoints-kpoints': None}
result['kpoints-kpoints'] = getattr(self, '_get_kpointsdata_' + mode)(
parsed_kpoints.entries)
return result
def _parsed_object(self):
"""
Return an instance of parsevasp.Kpoints.
Corresponds to the stored KpointsData.
"""
# The KpointsData has not been successfully parsed yet. So let's parse it.
if self._data_obj.get_attrs().get('mesh'):
mode = 'automatic'
elif self._data_obj.get_attrs().get('array|kpoints'):
mode = 'explicit'
kpoints_dict = {}
for keyword in [
'comment', 'divisions', 'shifts', 'points', 'tetra',
'tetra_volume', 'mode', 'centering', 'num_kpoints'
]:
kpoints_dict[keyword] = None
kpoints_dict.update(
getattr(self, '_get_kpointsdict_' + mode)(self._data_obj))
try:
return Kpoints(kpoints_dict=kpoints_dict)
except SystemExit:
return None
def test_kpoints_string(tmpdir):
"""Test to initialize KPOINTS in auto mode using string.
"""
kpoints_str = '# Example file\n0\nG\n4 4 4\n'
temp_file = str(tmpdir.join('KPOINTS'))
kpoints_parser_auto_temp = Kpoints(kpoints_string=kpoints_str)
kpoints_temp = kpoints_parser_auto_temp.get_dict()
assert kpoints_temp['mode'] == 'automatic'
assert kpoints_temp['comment'] == 'Example file'
assert kpoints_temp['divisions'] == [4, 4, 4]
assert kpoints_temp['shifts'] == None
assert kpoints_temp['points'] == None
assert kpoints_temp['centering'] == 'Gamma'
assert kpoints_temp['tetra'] == None
assert kpoints_temp['tetra_volume'] == None
assert kpoints_temp['num_kpoints'] == 0
def kpoints_parser_line():
"""Load KPOINTS file.
"""
testdir = os.path.dirname(__file__)
kpointsfile = testdir + '/KPOINTSLINE'
kpoints = Kpoints(file_path=kpointsfile)
return kpoints
def kpoints_parser_explicit():
"""Load KPOINTS file.
"""
testdir = os.path.dirname(__file__)
kpointsfile = testdir + '/KPOINTSEXP'
kpoints = Kpoints(file_path=kpointsfile)
return kpoints
def kpoints_parser_auto():
"""Load KPOINTS file.
"""
testdir = os.path.dirname(__file__)
kpointsfile = testdir + "/KPOINTS"
kpoints = Kpoints(file_path=kpointsfile)
return kpoints
def test_kpoints_write_auto(kpoints_parser_auto, tmpdir):
"""Test read, write and read KPOINTS in auto mode.
"""
kpoints = kpoints_parser_auto.get_dict()
temp_file = str(tmpdir.join('KPOINTS'))
kpoints_parser_auto.write(file_path=temp_file)
kpoints_parser_auto_temp = Kpoints(file_path=temp_file)
kpoints_temp = kpoints_parser_auto_temp.get_dict()
assert kpoints_temp['mode'] == 'automatic'
assert kpoints_temp['comment'] == 'Example file'
assert kpoints_temp['divisions'] == [4, 4, 4]
assert kpoints_temp['shifts'] == [0.0, 0.0, 0.0]
assert kpoints_temp['points'] == None
assert kpoints_temp['centering'] == 'Gamma'
assert kpoints_temp['tetra'] == None
assert kpoints_temp['tetra_volume'] == None
assert kpoints_temp['num_kpoints'] == 0
def test_kpoints_modify_explicit(kpoints_parser_explicit, tmpdir):
"""Test read, modify, write and read KPOINTS in explicit mode.
"""
kpoints = kpoints_parser_explicit.get_dict()
assert kpoints['comment'] == 'Example file'
points = kpoints['points']
assert len(points) == 4
np.testing.assert_allclose(points[0][0], np.array([0.0, 0.0, 0.0]))
np.testing.assert_allclose(points[1][0], np.array([0.0, 0.0, 0.5]))
np.testing.assert_allclose(points[2][0], np.array([0.0, 0.5, 0.5]))
np.testing.assert_allclose(points[3][0], np.array([0.5, 0.5, 0.5]))
assert math.isclose(points[0][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[1][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[2][1], 2.0, rel_tol=1e-07)
assert math.isclose(points[3][1], 4.0, rel_tol=1e-07)
assert points[0][2]
assert points[1][2]
assert points[2][2]
assert points[3][2]
kpoints_parser_explicit.modify('comment', 'Nada comment')
point = Kpoint(np.array([0.0, 0.0, 0.0]), 1.0)
kpoints_parser_explicit.modify('points', point, point_number=3)
temp_file = str(tmpdir.join('KPOINTSEXP'))
kpoints_parser_explicit.write(file_path=temp_file)
kpoints_parser_explicit_temp = Kpoints(file_path=temp_file)
kpoints_temp = kpoints_parser_explicit_temp.get_dict()
assert kpoints_temp['comment'] == 'Nada comment'
points = kpoints_temp['points']
assert len(points) == 4
np.testing.assert_allclose(points[0][0], np.array([0.0, 0.0, 0.0]))
np.testing.assert_allclose(points[1][0], np.array([0.0, 0.0, 0.5]))
np.testing.assert_allclose(points[2][0], np.array([0.0, 0.5, 0.5]))
np.testing.assert_allclose(points[3][0], np.array([0.0, 0.0, 0.0]))
assert math.isclose(points[0][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[1][1], 1.0, rel_tol=1e-07)
assert math.isclose(points[2][1], 2.0, rel_tol=1e-07)
assert math.isclose(points[3][1], 1.0, rel_tol=1e-07)
assert points[0][2]
assert points[1][2]
assert points[2][2]
assert points[3][2]
def kpoints_parser_auto_file_object():
"""Load KPOINTS file.
"""
testdir = os.path.dirname(__file__)
kpointsfile = testdir + '/KPOINTS'
kpoints = None
with open(kpointsfile) as file_handler:
kpoints = Kpoints(file_handler=file_handler)
return kpoints
def _parsed_object(self):
"""
Return an instance of parsevasp.Kpoints.
Corresponds to the stored KpointsData.
"""
if isinstance(self._data_obj, get_data_class('array.kpoints')):
# The KpointsData has not been successfully parsed yet. So let's parse it.
try:
_ = self._data_obj.get_attribute('mesh')
mode = 'automatic'
except AttributeError:
pass
try:
_ = self._data_obj.get_attribute('array|kpoints')
mode = 'explicit'
except AttributeError:
pass
kpoints_dict = {}
for keyword in [
'comment', 'divisions', 'shifts', 'points', 'tetra',
'tetra_volume', 'mode', 'centering', 'num_kpoints'
]:
kpoints_dict[keyword] = None
kpoints_dict.update(
getattr(self, '_get_kpointsdict_' + mode)(self._data_obj))
try:
return Kpoints(kpoints_dict=kpoints_dict, logger=self._logger)
except SystemExit:
return None
# _data_obj is SingleFile:
return self._data_obj
def test_kpoints_write_auto(kpoints_parser_auto, tmpdir):
"""Test read, write and read KPOINTS in auto mode.
Here we also test that the write using file handler works properly.
"""
kpoints = kpoints_parser_auto.get_dict()
temp_file = str(tmpdir.join('KPOINTS'))
kpoints_parser_auto.write(file_path=temp_file)
kpoints_parser_auto_temp = Kpoints(file_path=temp_file)
kpoints_temp = kpoints_parser_auto_temp.get_dict()
verify_kpoints_content(kpoints_temp)
with open(temp_file, 'w') as handler:
kpoints_parser_auto.write(file_handler=handler)
with open(temp_file, 'r') as handler:
kpoints_parser_auto_temp = Kpoints(file_handler=handler)
kpoints_temp = kpoints_parser_auto_temp.get_dict()
verify_kpoints_content(kpoints_temp)