def __set_cell_oriented( self ):
# Re-oriented lattice xx, yx, yy, zx, zy, zz
self.angles = get_angles( self.lattice )
self.cell_params = get_cell_parameters( self.lattice )
a, b, c = self.cell_params
alpha, beta, gamma = self.angles
self.lattice_oriented = get_cell_matrix( a, b, c, alpha, beta, gamma )
self.positions_oriented = \
self.__set_orientation( np.dot( self.positions, self.lattice ) )
def _set_cell_oriented(self):
# Re-oriented lattice xx, yx, yy, zx, zy, zz
self._angles = get_angles(self._lattice)
self._cell_params = get_cell_parameters(self._lattice)
a, b, c = self._cell_params
alpha, beta, gamma = self._angles
self._lattice_oriented = get_cell_matrix(a, b, c, alpha, beta, gamma)
self._positions_oriented = \
self._get_oriented_displacements(np.dot(self._positions,
self._lattice))
def _set_cell_oriented(self):
# Re-oriented lattice xx, yx, yy, zx, zy, zz
self._angles = get_angles(self._lattice)
self._cell_params = get_cell_parameters(self._lattice)
a, b, c = self._cell_params
alpha, beta, gamma = self._angles
self._lattice_oriented = get_cell_matrix(a, b, c, alpha, beta, gamma)
self._positions_oriented = \
self._get_oriented_displacements(np.dot(self._positions,
self._lattice))
def read_fplo(filename):
from phonopy.structure.cells import get_cell_matrix
fplo_in = open(filename).readlines()
nsort = None
for i in np.arange(len(fplo_in)):
# spacegroup
if fplo_in[i].find("spacegroup") + 1:
curl_pos = fplo_in[i + 1].find("{") + 1
spg = int(fplo_in[i + 1][curl_pos:].split(",")
[0]) # integer number of the spacegroup
if spg != 1:
sys.exit("(EE) Only SPG 1 / P1 implemented so far.")
# unit of length
if fplo_in[i].find("lengthunit") + 1:
curl_pos = fplo_in[i + 1].find("{") + 1
if int(fplo_in[i + 1][curl_pos:].split(",")[0]) == 1:
lfactor = 1.0 # bohr
elif int(fplo_in[i + 1][curl_pos:].split(",")[0]) == 2:
lfactor = 1.0 / Bohr # Angstroem
else:
sys.exit("(EE) Length unit unknown: " + fplo_in[i + 1])
# lattice constants
if fplo_in[i].find("lattice_constants") + 1:
curl_pos = fplo_in[i].find("{") + 1
a, b, c = map(float, fplo_in[i][curl_pos:].split(","))
# lattice angles
if fplo_in[i].find("axis_angles") + 1:
curl_pos = fplo_in[i].find("{") + 1
alpha, beta, gamma = map(float, fplo_in[i][curl_pos:].split(","))
# number of Wyckoff positions
if fplo_in[i].find("nsort=") + 1:
nsort = int(fplo_in[i][:-2].split("=")[1])
# Wyckoff positions
if fplo_in[i].find("wyckoff_positions") + 1:
if nsort == None: sys.exit("(EE) nsort not found!")
species = np.zeros((nsort), dtype=int)
positions = np.zeros((nsort, 3), dtype=float)
for j in np.arange(nsort):
ind = i + j + 2
indc = fplo_in[ind].find(",")
indb = fplo_in[ind].find("}")
species[j] = symbol_map[fplo_in[ind][indc - 3:indc - 1]]
positions[j, :] = list(
map(float, fplo_in[ind][indc + 2:indb].split(",")))
lattice = get_cell_matrix(a * lfactor, b * lfactor, c * lfactor, alpha,
beta, gamma)
cell = Atoms(numbers=species, cell=lattice, scaled_positions=positions)
return cell, False
