def prepare(self):
self._comm_points = get_commensurate_points(self._supercell_matrix)
self._set_translations()
self._set_shifted_index_set()
self._solve_phonon()
self._weights = np.zeros(
(len(self._eigvecs), self._eigvecs[0].shape[0], self._N),
dtype='double')
def prepare(self):
self._comm_points = get_commensurate_points(self._supercell_matrix)
self._set_translations()
self._set_shifted_index_set()
self._solve_phonon()
self._weights = np.zeros(
(len(self._eigvecs), self._eigvecs[0].shape[0], self._N),
dtype='double')
def test_get_commensurate_points(self):
smat = np.diag([2, 2, 2])
pmat = np.dot(np.linalg.inv(smat),
[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = get_supercell(self._cell, smat)
primitive = get_primitive(supercell, pmat)
comm_points = get_commensurate_points(primitive, supercell)
for i, p in enumerate(comm_points):
print("%d %s" % (i + 1, p))
def test_get_commensurate_points(self):
smat = np.diag([2, 2, 2])
pmat = np.dot(np.linalg.inv(smat),
[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = get_supercell(self._cell, smat)
primitive = get_primitive(supercell, pmat)
comm_points = get_commensurate_points(primitive, supercell)
for i, p in enumerate(comm_points):
print("%d %s" % (i + 1, p))
def test_get_commensurate_points(self):
smat = np.diag([2, 2, 2])
pmat = np.dot(np.linalg.inv(smat),
[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = get_supercell(self._cell, smat)
primitive = get_primitive(supercell, pmat)
supercell_matrix = np.linalg.inv(primitive.get_primitive_matrix())
supercell_matrix = np.rint(supercell_matrix).astype('intc')
comm_points = get_commensurate_points(supercell_matrix)
# self._write(comm_points)
self._compare(comm_points)
def test_get_commensurate_points(self):
smat = np.diag([2, 2, 2])
pmat = np.dot(np.linalg.inv(smat),
[[0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]])
supercell = get_supercell(self._cell, smat)
primitive = get_primitive(supercell, pmat)
supercell_matrix = np.linalg.inv(primitive.get_primitive_matrix())
supercell_matrix = np.rint(supercell_matrix).astype('intc')
comm_points = get_commensurate_points(supercell_matrix)
# self._write(comm_points)
self._compare(comm_points)
def __init__(self,
phonon,
supercell_matrix,
ideal_positions,
atom_mapping,
qpoints):
"""
Parameters
----------
phonon : Phonopy
Phonopy object made with supercell as the primitive cell.
supercell_matrix : array_like
Matrix that represents the primitive translation enforced within
the supercell. This works like an inverse primitive matrix.
shape=(3, 3), dtype='intc'
ideal_positions : array_like
shape=(3, 3), dtype='intc'
atom_mapping : list
Atomic index mapping from ideal_positions to supercell atoms in
phonon. None is used for Vacancies.
qpoints : array_like
q-points in reciprocal primitive cell coordinates
shape=(num_qpoints, 3), dtype='double'
"""
self._phonon = phonon
self._supercell_matrix = np.array(supercell_matrix, dtype='intc')
self._ideal_positions = np.array(ideal_positions, dtype='double')
self._qpoints_p = qpoints # in PBZ
self._qpoints_s = self._get_qpoints_in_SBZ() # in SBZ
self._symprec = self._phonon.symmetry.get_symmetry_tolerance()
self._frequencies = None
self._eigvecs = None # This may have anormal array shape.
self._unfolding_weights = None
self._q_count = None # As counter for iterator
# Commensurate q-vectors in PBZ
self._comm_points = get_commensurate_points(self._supercell_matrix)
self._trans_s = None # in SC (see docstring in _set_translations)
self._trans_p = None # in PC (see docstring in _set_translations)
self._N = None
self._set_translations()
self._atom_mapping = None
self._index_map_inv = None
self._set_index_map(atom_mapping)
def __init__(self,
phonon,
supercell_matrix,
ideal_positions,
atom_mapping,
qpoints):
"""
Parameters
----------
phonon : Phonopy
Phonopy object made with supercell as the primitive cell.
supercell_matrix : array_like
Matrix that represents the primitive translation enforced within
the supercell. This works like an inverse primitive matrix.
shape=(3, 3), dtype='intc'
ideal_positions : array_like
shape=(3, 3), dtype='intc'
atom_mapping : list
Atomic index mapping from ideal_positions to supercell atoms in
phonon. None is used for Vacancies.
qpoints : array_like
q-points in reciprocal primitive cell coordinates
shape=(num_qpoints, 3), dtype='double'
"""
self._phonon = phonon
self._supercell_matrix = np.array(supercell_matrix, dtype='intc')
self._ideal_positions = np.array(ideal_positions, dtype='double')
self._qpoints_p = qpoints # in PBZ
self._qpoints_s = self._get_qpoints_in_SBZ() # in SBZ
self._symprec = self._phonon.symmetry.get_symmetry_tolerance()
self._frequencies = None
self._eigvecs = None # This may have anormal array shape.
self._unfolding_weights = None
self._q_count = None # As counter for iterator
# Commensurate q-vectors in PBZ
self._comm_points = get_commensurate_points(self._supercell_matrix)
self._trans_s = None # in SC (see docstring in _set_translations)
self._trans_p = None # in PC (see docstring in _set_translations)
self._N = None
self._set_translations()
self._atom_mapping = None
self._index_map_inv = None
self._set_index_map(atom_mapping)
def __init__(self, phonon, supercell_matrix, ideal_positions, atom_mapping,
qpoints):
"""
Parameters
----------
phonon : Phonopy
Phonopy object to be unfolded.
supercell_matrix : array_like
Matrix that represents the virtual primitive translation enforced
inside the supercell. This works like an inverse primitive matrix.
shape=(3, 3), dtype='intc'
ideal_positions : array_like
Positions of atomic sites in supercell. This corresponds to those
in a set of virtual primitive cells in the supercell.
shape=(3, 3), dtype='intc'
atom_mapping : list
Atomic index mapping from ``ideal_positions`` to supercell atoms
in ``phonon``. The elements of this list are intergers for atoms
and None for vacancies.
qpoints : array_like
q-points in reciprocal virtual-primitive-cell coordinates
shape=(num_qpoints, 3), dtype='double'
"""
self._phonon = self._get_supercell_phonon(phonon)
self._supercell_matrix = np.array(supercell_matrix, dtype='intc')
self._ideal_positions = np.array(ideal_positions, dtype='double')
self._qpoints_p = qpoints # in PBZ
self._qpoints_s = self._get_qpoints_in_SBZ() # in SBZ
self._symprec = self._phonon.symmetry.get_symmetry_tolerance()
self._frequencies = None
self._eigvecs = None # This may have anormal array shape.
self._unfolding_weights = None
self._q_count = None # As counter for iterator
# Commensurate q-vectors in PBZ
self._comm_points = get_commensurate_points(self._supercell_matrix)
self._trans_s = None # in SC (see docstring in _set_translations)
self._trans_p = None # in PC (see docstring in _set_translations)
self._N = None
self._set_translations()
self._atom_mapping = None
self._index_map_inv = None
self._set_index_map(atom_mapping)
def set_commensurate_points(self):
supercell_matrix = np.linalg.inv(self._primitive.get_primitive_matrix())
supercell_matrix = np.rint(supercell_matrix).astype('intc')
self.set_qpoints(get_commensurate_points(supercell_matrix))
def set_commensurate_points(self):
"""Set commensurate points."""
supercell_matrix = np.rint(
np.linalg.inv(self._primitive.primitive_matrix)).astype("intc")
self.set_qpoints(get_commensurate_points(supercell_matrix))
def setUp(self):
self._smat = np.dot([[-1, 1, 1], [1, -1, 1], [1, 1, -1]],
np.diag([2, 2, 2]))
self._comm_points = get_commensurate_points(self._smat)
def _get_comm_points(self, ph):
smat = np.dot(np.linalg.inv(ph.primitive.primitive_matrix),
ph.supercell_matrix)
smat = np.rint(smat).astype(int)
comm_points = get_commensurate_points(smat)
return comm_points
def set_commensurate_points(self):
supercell_matrix = np.linalg.inv(self._primitive.get_primitive_matrix())
supercell_matrix = np.rint(supercell_matrix).astype("intc")
self.set_qpoints(get_commensurate_points(supercell_matrix))
def _get_commensurate_points():
smat = np.dot([[-1, 1, 1], [1, -1, 1], [1, 1, -1]], np.diag([2, 2, 2]))
return get_commensurate_points(smat), smat
