def write_cif_P1(cell, filename=None):
a, b, c = get_lattice_parameters(cell.lattice)
alpha, beta, gamma = get_angles(cell.lattice)
cif = """data_cogue_crystal_converter
_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_symbols(), cell.get_points().T):
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 filename is None:
return cif
else:
w = open(filename, 'w')
w.write(cif)
w.close()
if __name__ == "__main__":
import sys
import yaml
from phonopy import Phonopy
from phonopy.interface.phonopy_yaml import phonopyYaml
from phonopy.file_IO import parse_FORCE_SETS
from cogue.crystal.utility import get_angles, get_lattice_parameters
import matplotlib
if len(sys.argv) > 1:
cell = phonopyYaml(sys.argv[1]).get_atoms()
else:
cell = phonopyYaml("POSCAR-unitcell.yaml").get_atoms()
phonon_info = yaml.load(open("phonon.yaml"))
phonon = Phonopy(cell, phonon_info["supercell_matrix"], is_auto_displacements=False)
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
distance = 200
imaginary = Imaginary(phonon, distance=distance)
lattice = imaginary.get_lattice()
print "lattice_lengths: [ %f, %f, %f ]" % tuple(get_lattice_parameters(lattice))
print "lattice_angles: [ %f, %f, %f ]" % tuple(get_angles(lattice))
print "mesh_length: %f" % distance
print "mesh: [ %d, %d, %d ]" % tuple(imaginary.get_mesh())
print "ratio: %f" % imaginary.get_imaginary_qpoint_ratio()
phonons = []
for dirname in ('gruneisen-01', 'gruneisen-02', 'gruneisen-00'):
if len(sys.argv) > 1:
cell = phonopyYaml("%s/" % dirname + sys.argv[1]).get_atoms()
else:
cell = phonopyYaml("%s/POSCAR-unitcell.yaml" % dirname).get_atoms()
phonon_info = yaml.load(open("%s/phonon.yaml" % dirname))
phonon = Phonopy(cell,
phonon_info['supercell_matrix'],
is_auto_displacements=False)
force_sets = parse_FORCE_SETS(filename="%s/FORCE_SETS" % dirname)
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
phonons.append(phonon)
phonopy_gruneisen = PhonopyGruneisen(phonons[0], phonons[1], phonons[2])
distance = 200
gruneisen = ModeGruneisen(phonopy_gruneisen,
distance=distance)
if gruneisen.run():
gruneisen.plot(plt)
lattice = gruneisen.get_lattice()
print "a, b, c =", get_lattice_parameters(lattice)
print "alpha, beta, gamma =", get_angles(lattice)
print "mesh (x=%f) =" % distance, gruneisen.get_mesh()
gruneisen.save_figure(plt)
# plt.show()
else:
print "Mode Gruneisen parameter calculation failed."
import matplotlib
matplotlib.use('Agg')
matplotlib.rcParams.update({'figure.figsize': (4.5, 3),
'font.family': 'serif'})
import matplotlib.pyplot as plt
if len(sys.argv) > 1:
cell = phonopyYaml(sys.argv[1]).get_atoms()
else:
cell = phonopyYaml("POSCAR-unitcell.yaml").get_atoms()
phonon_info = yaml.load(open("phonon.yaml"))
phonon = Phonopy(cell,
phonon_info['supercell_matrix'],
is_auto_displacements=False)
force_sets = parse_FORCE_SETS()
phonon.set_displacement_dataset(force_sets)
phonon.produce_force_constants()
distance = 100
tprops = ThermalProperty(phonon, distance=distance)
if tprops.run():
tprops.plot(plt)
lattice = tprops.get_lattice()
print("a, b, c = %f %f %f" % tuple(get_lattice_parameters(lattice)))
print("alpha, beta, gamma = %f %f %f" % tuple(get_angles(lattice)))
print("mesh (x=%f) = %s" % (distance, tprops.get_mesh()))
tprops.save_figure(plt)
else:
print "Thermal property calculation failed."