def _set_stage1(self, cell):
prim_cell = get_primitive_cell(cell, tolerance=self._symmetry_tolerance)
sym_dataset = get_symmetry_dataset(prim_cell)
self._space_group_type = sym_dataset['international']
spg_number = sym_dataset['number']
if (spg_number >= 143 and
spg_number <= 194 and
not self._space_group_type[0] == 'R'): # Hexagonal lattice
self._supercell_dimensions = [[3, 3, 2], [2, 2, 2]]
else: # Other cases
self._supercell_dimensions = [[2, 2, 2]]
# Long cell axis is not multiplied.
for dimension in self._supercell_dimensions:
for i, length in enumerate(
get_lattice_parameters(prim_cell.get_lattice())):
if length * dimension[i] > 20:
dimension[i] = 1
self._tasks = []
for i, dimension in enumerate(self._supercell_dimensions):
task = self._get_phonon_task(prim_cell,
np.diag(dimension),
"phonon-%d" % (i + 1))
self._phre_tasks.append(task)
self._tasks.append(task)
def estimate_supercell_matrix(cell,
max_num_atoms=120,
symprec=1e-5):
"""Estimate supercell matrix from conventional cell
Supercell matrix is estimated from basis vector lengths and
maximum number of atoms accepted. The input cell must be already
standarized. For triclinic, monoclinic, and orthorhombic cells,
basis vectors of a, b, c are freely multiplied, but for tetragonal
and hexagonal cells, multiplicities of a and b are the same, and
for cubic cell, those of a, b, c are to be found the same. The
supercell matrix is always returned as a diagonal matrix.
"""
dataset = get_symmetry_dataset(cell)
spg_num = dataset['number']
num_atoms = len(cell.get_numbers())
lengths_orig = get_lattice_parameters(cell.get_lattice())
lengths = get_lattice_parameters(dataset['std_lattice'])
# assert (np.abs(lengths_orig - lengths) < symprec).all(), \
# "%s\n%s" % (cell.get_lattice(), dataset['std_lattice'])
if spg_num <= 74: # Triclinic, monoclinic, and orthorhombic
multi = _get_multiplicity_abc(num_atoms, lengths, max_num_atoms)
elif spg_num <= 194: # Tetragonal and hexagonal
multi = _get_multiplicity_ac(num_atoms, lengths, max_num_atoms)
else: # Cubic
multi = _get_multiplicity_a(num_atoms, lengths, max_num_atoms)
smat = np.eye(3, dtype='intc')
for i in range(3):
smat[i, i] = multi[i]
return smat
def _get_points_with_margin(cell, margin=1e-5):
abc = get_lattice_parameters(cell.get_lattice())
points = cell.get_points()
points_new = []
symbols_new = []
for p, s in zip(points.T, cell.get_symbols()):
for i in (-1, 0, 1):
for j in (-1, 0, 1):
for k in (-1, 0, 1):
p_inspect = p + np.array([i, j, k])
if ((p_inspect > 0 - margin / abc).all() and
(p_inspect < 1 + margin / abc).all()):
points_new.append(p_inspect)
symbols_new.append(s)
return np.transpose(points_new), symbols_new
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()
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."
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()
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."
