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 _get_kpointsdict_explicit(self, kpointsdata):
"""Turn Aiida KpointData into an 'explicit' kpoints dictionary."""
dictionary = {}
kpts = []
try:
points, weights = kpointsdata.get_kpoints(also_weights=True)
except AttributeError:
points = kpointsdata.get_kpoints()
weights = None
for index, point in enumerate(points):
if weights is not None:
kpt = Kpoint(point, weight=weights[index], logger=self._logger)
else:
# no weights supplied, so set them to 1.0
kpt = Kpoint(point, weight=1.0, logger=self._logger)
kpts.append(kpt)
dictionary['points'] = kpts
dictionary['mode'] = 'explicit'
dictionary['num_kpoints'] = len(kpts)
return dictionary
def kpoints(self):
"""Fetch the kpoints from parsevasp an store in KpointsData."""
kpts = self._xml.get_kpoints()
kptsw = self._xml.get_kpointsw()
kpoints_data = None
if (kpts is not None) and (kptsw is not None):
# create a KpointsData object and store k-points
kpoints_data = {}
kpoints_data['mode'] = 'explicit'
kpoints_data['points'] = []
for kpt, kptw in zip(kpts, kptsw):
kpoints_data['points'].append(Kpoint(kpt, weight=kptw))
return kpoints_data
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]