def get_cif_P1(cell, U_cif=None):
a, b, c = get_cell_parameters(cell.get_cell())
alpha, beta, gamma = get_angles(cell.get_cell())
cif = """data_crystal_structure_P1
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
_cell_length_a %.5f
_cell_length_b %.5f
_cell_length_c %.5f
_cell_angle_alpha %.5f
_cell_angle_beta %.5f
_cell_angle_gamma %.5f
_cell_volume %.5f
_cell_formula_units_Z 1
loop_
_space_group_symop_operation_xyz
x,y,z
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy\n""" % (a, b, c, alpha, beta, gamma, cell.get_volume())
symbols = []
for s, p in zip(cell.get_chemical_symbols(), cell.get_scaled_positions()):
symbols.append(s)
cif += ("%-7s%2s %10.5f%10.5f%10.5f 1.00000\n" %
(s + "%d" % symbols.count(s), s, p[0], p[1], p[2]))
if U_cif is not None:
aniso_U = """loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_23
_atom_site_aniso_U_13
_atom_site_aniso_U_12\n"""
cif += aniso_U
symbols = []
for i, s in enumerate(cell.get_chemical_symbols()):
symbols.append(s)
m = U_cif[i]
vals = (m[0, 0], m[1, 1], m[2, 2], m[1, 2], m[0, 2], m[0, 1])
cif += ("%6s %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f\n" %
((s + "%d" % symbols.count(s),) + vals))
return cif
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 get_wien2k_struct(cell, npts, r0s, rmts):
num_atom = cell.get_number_of_atoms()
lattice = cell.get_cell()
a, b, c = get_cell_parameters(lattice)
alpha, beta, gamma = get_angles(lattice)
positions = cell.get_scaled_positions()
symbols = cell.get_chemical_symbols()
numbers = cell.get_atomic_numbers()
text = ""
# 1
text += "Title\n"
# 2
text += "%-4s%23s%3d\n" % ("P", "LATTICE,NONEQUIV.ATOMS:", num_atom)
# 3
text += "%13s%4s\n" % ("MODE OF CALC=", "RELA")
# 4
text += "%10.6f%10.6f%10.6f%10.6f%10.6f%10.6f\n" % (a, b, c, alpha, beta,
gamma)
for i, pos in enumerate(positions):
for j in (0, 1, 2):
if pos[j] < 0:
pos[j] += 1
if int(float("%10.8f" % pos[j])) == 1:
pos[j] = 0.0
# 5 format (4X,I4,4X,F10.8,3X,F10.8,3X,F10.8)
text += "%4s%4d%4s%10.8f%3s%10.8f%3s%10.8f\n" % (
"ATOM", -(i + 1), ": X=", pos[0], " Y=", pos[1], " Z=", pos[2])
# 6 format (15X,I2,17X,I2)
text += "%15s%2d%17s%2d\n" % ("MULT=", 1, "ISPLIT=", 8)
# 7 format (A10,5X,I5,5X,F10.8,5X,F10.5,5X,F5.2)
npt = npts[i]
r0 = r0s[i]
rmt = rmts[i]
text += "%-10s%5s%5d%5s%10.8f%5s%10.5f%5s%5.1f\n" % (
symbols[i], "NPT=", npt, "R0=", r0, "RMT=", rmt, "Z:", numbers[i])
# 8 - 10 format (20X,3F10.7)
text += "%-20s%10.7f%10.7f%10.7f\n" % ("LOCAL ROT MATRIX:", 1, 0, 0)
text += "%-20s%10.7f%10.7f%10.7f\n" % ("", 0, 1, 0)
text += "%-20s%10.7f%10.7f%10.7f\n" % ("", 0, 0, 1)
text += " 0 NUMBER OF SYMMETRY OPERATIONS"
return text
def get_wien2k_struct(cell, npts, r0s, rmts):
num_atom = cell.get_number_of_atoms()
lattice = cell.get_cell()
a, b, c = get_cell_parameters(lattice)
alpha, beta, gamma = get_angles(lattice)
positions = cell.get_scaled_positions()
symbols = cell.get_chemical_symbols()
numbers = cell.get_atomic_numbers()
text = ""
# 1
text += "Title\n"
# 2
text += "%-4s%23s%3d\n" % ("P", "LATTICE,NONEQUIV.ATOMS:", num_atom)
# 3
text += "%13s%4s\n" % ("MODE OF CALC=", "RELA")
# 4
text += "%10.6f%10.6f%10.6f%10.6f%10.6f%10.6f\n" % (
a, b, c, alpha, beta, gamma)
for i, pos in enumerate(positions):
for j in (0,1,2):
if pos[j] < 0:
pos[j] += 1
if int(float("%10.8f" % pos[j])) == 1:
pos[j] = 0.0
# 5 format (4X,I4,4X,F10.8,3X,F10.8,3X,F10.8)
text += "%4s%4d%4s%10.8f%3s%10.8f%3s%10.8f\n" % (
"ATOM", -(i + 1), ": X=", pos[0], " Y=", pos[1], " Z=", pos[2])
# 6 format (15X,I2,17X,I2)
text += "%15s%2d%17s%2d\n" % ("MULT=", 1, "ISPLIT=", 8)
# 7 format (A10,5X,I5,5X,F10.8,5X,F10.5,5X,F5.2)
npt = npts[i]
r0 = r0s[i]
rmt = rmts[i]
text += "%-10s%5s%5d%5s%10.8f%5s%10.5f%5s%5.1f\n" % (
symbols[i], "NPT=", npt, "R0=", r0, "RMT=", rmt, "Z:", numbers[i])
# 8 - 10 format (20X,3F10.7)
text += "%-20s%10.7f%10.7f%10.7f\n" % ("LOCAL ROT MATRIX:", 1, 0, 0)
text += "%-20s%10.7f%10.7f%10.7f\n" % ("", 0, 1, 0)
text += "%-20s%10.7f%10.7f%10.7f\n" % ("", 0, 0, 1)
text +=" 0 NUMBER OF SYMMETRY OPERATIONS"
return text
def write_fplo(directory, cell, sym=None):
from phonopy.structure.cells import get_angles, get_cell_parameters
FEDIT = 'fedit14.00-47-x86_64'
FPLO = 'fplo14.00-47-x86_64'
import os
lattice = cell.get_cell()
positions = cell.get_scaled_positions()
chemical_symbols = cell.get_chemical_symbols()
alpha, beta, gamma = get_angles(lattice)
a, b, c = get_cell_parameters(lattice)
os.mkdir(directory)
os.system('cp =.in ' + directory + '/')
os.chdir(directory)
# Write the structure plan to the pipe file.
fpipe = open("=.t_pipe", "w")
fpipe.write("@+@\n")
# add spacegroup
if sym != None:
fpipe.write("@s@\n")
fpipe.write("@{0:d}@\n".format(sym["spg"]))
fpipe.write("@x@\n")
# change lattice units to bohr
fpipe.write("@u@\n")
fpipe.write("@b@\n")
fpipe.write("@x@\n")
fpipe.write("@l@ {0:+10.6f} {1:+10.6f} {2:+10.6f}\n".format(a, b, c))
fpipe.write("@a@ {0:+8.4f} {1:+8.4f} {2:+8.4f}\n".format(
alpha, beta, gamma))
fpipe.write("@n@ {0:d}\n".format(len(positions)))
for i in np.arange(len(positions)):
fpipe.write("@{0:d}@ {1} @ {2:16.8f} {3:16.8f} {4:16.8f}\n".format(
i + 1, chemical_symbols[i], positions[i, 0], positions[i, 1],
positions[i, 2]))
fpipe.write("@+@\n")
fpipe.write("@x@\n")
fpipe.write("@q@\n")
fpipe.write("@y@")
fpipe.close()
# Execute fedit with the pip file.
os.system(FEDIT + ' -p ' + FPLO +
' -pipe < ./=.t_pipe 2>./+log 1>/dev/null')
# Clean up.
os.remove("=.t_pipe")
os.chdir("../")
def get_cif_P1(cell, U_cif=None):
a, b, c = get_cell_parameters(cell.get_cell())
alpha, beta, gamma = get_angles(cell.get_cell())
cif = """data_crystal_structure_P1
_symmetry_space_group_name_H-M 'P 1'
_symmetry_Int_Tables_number 1
_cell_length_a %.5f
_cell_length_b %.5f
_cell_length_c %.5f
_cell_angle_alpha %.5f
_cell_angle_beta %.5f
_cell_angle_gamma %.5f
_cell_volume %.5f
_cell_formula_units_Z 1
loop_
_space_group_symop_operation_xyz
x,y,z
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy\n""" % (
a,
b,
c,
alpha,
beta,
gamma,
cell.get_volume(),
)
symbols = []
for s, p in zip(cell.get_chemical_symbols(), cell.get_scaled_positions()):
symbols.append(s)
cif += "%-7s%2s %10.5f%10.5f%10.5f 1.00000\n" % (s + "%d" % symbols.count(s), s, p[0], p[1], p[2])
if U_cif is not None:
aniso_U = """loop_
_atom_site_aniso_label
_atom_site_aniso_U_11
_atom_site_aniso_U_22
_atom_site_aniso_U_33
_atom_site_aniso_U_23
_atom_site_aniso_U_13
_atom_site_aniso_U_12\n"""
cif += aniso_U
symbols = []
for i, s in enumerate(cell.get_chemical_symbols()):
symbols.append(s)
m = U_cif[i]
vals = (m[0, 0], m[1, 1], m[2, 2], m[1, 2], m[0, 2], m[0, 1])
cif += "%6s %10.5f %10.5f %10.5f %10.5f %10.5f %10.5f\n" % ((s + "%d" % symbols.count(s),) + vals)
return cif
