def read_crystal_structure(filename=None, interface_mode="vasp", chemical_symbols=None, yaml_mode=False):
if filename is None:
unitcell_filename = get_default_cell_filename(interface_mode, yaml_mode)
else:
unitcell_filename = filename
if not os.path.exists(unitcell_filename):
if filename is None:
return None, (unitcell_filename + " (default file name)",)
else:
return None, (unitcell_filename,)
if yaml_mode:
from phonopy.interface.phonopy_yaml import phonopyYaml
unitcell = phonopyYaml(unitcell_filename).get_atoms()
return unitcell, (unitcell_filename,)
if interface_mode == "vasp":
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(unitcell_filename)
else:
unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
return unitcell, (unitcell_filename,)
if interface_mode == "abinit":
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(unitcell_filename)
return unitcell, (unitcell_filename,)
if interface_mode == "pwscf":
from phonopy.interface.pwscf import read_pwscf
unitcell, pp_filenames = read_pwscf(unitcell_filename)
return unitcell, (unitcell_filename, pp_filenames)
if interface_mode == "wien2k":
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
return unitcell, (unitcell_filename, npts, r0s, rmts)
if interface_mode == "elk":
from phonopy.interface.elk import read_elk
unitcell, sp_filenames = read_elk(unitcell_filename)
return unitcell, (unitcell_filename, sp_filenames)
if interface_mode == "siesta":
from phonopy.interface.siesta import read_siesta
unitcell, atypes = read_siesta(unitcell_filename)
return unitcell, (unitcell_filename, atypes)
def read_crystal_structure(filename=None,
interface_mode='vasp',
chemical_symbols=None,
yaml_mode=False):
if filename is None:
unitcell_filename = get_default_cell_filename(interface_mode,
yaml_mode)
else:
unitcell_filename = filename
if not os.path.exists(unitcell_filename):
if filename is None:
return None, (unitcell_filename + " (default file name)", )
else:
return None, (unitcell_filename, )
if yaml_mode:
from phonopy.interface.phonopy_yaml import phonopyYaml
unitcell = phonopyYaml(unitcell_filename).get_atoms()
return unitcell, (unitcell_filename, )
if interface_mode == 'vasp':
from phonopy.interface.vasp import read_vasp
if chemical_symbols is None:
unitcell = read_vasp(unitcell_filename)
else:
unitcell = read_vasp(unitcell_filename, symbols=chemical_symbols)
return unitcell, (unitcell_filename, )
if interface_mode == 'abinit':
from phonopy.interface.abinit import read_abinit
unitcell = read_abinit(unitcell_filename)
return unitcell, (unitcell_filename, )
if interface_mode == 'pwscf':
from phonopy.interface.pwscf import read_pwscf
unitcell, pp_filenames = read_pwscf(unitcell_filename)
return unitcell, (unitcell_filename, pp_filenames)
if interface_mode == 'wien2k':
from phonopy.interface.wien2k import parse_wien2k_struct
unitcell, npts, r0s, rmts = parse_wien2k_struct(unitcell_filename)
return unitcell, (unitcell_filename, npts, r0s, rmts)
if interface_mode == 'elk':
from phonopy.interface.elk import read_elk
unitcell, sp_filenames = read_elk(unitcell_filename)
return unitcell, (unitcell_filename, sp_filenames)
if interface_mode == 'siesta':
from phonopy.interface.siesta import read_siesta
unitcell, atypes = read_siesta(unitcell_filename)
return unitcell, (unitcell_filename, atypes)
from thermal_prop import get_Z
import matplotlib
matplotlib.use('Agg')
matplotlib.rcParams.update({'figure.figsize': (10, 7),
'font.family': 'serif'})
import matplotlib.pyplot as plt
# plt.rcParams['backend'] = 'PDF'
# plt.rcParams['pdf.fonttype'] = 42
# plt.rcParams['font.family'] = 'serif'
# plt.rcParams['axes.labelsize'] = 18
# plt.rcParams['figure.subplot.left'] = 0.15
# plt.rcParams['figure.subplot.bottom'] = 0.15
# plt.rcParams['figure.figsize'] = 8, 6
cell = phonopyYaml("gruneisen-01/POSCAR-unitcell.yaml").get_atoms()
volumes, electronic_energies = read_v_e("e-v.dat")
(temperatures,
cv,
entropy,
fe_phonon,
imag_ratios) = read_thermal_properties_yaml(sys.argv[1:])
indices_used = np.nonzero(np.array(imag_ratios) < 0.001)[0]
qha = QHA(volumes[indices_used],
electronic_energies[indices_used],
temperatures,
fe_phonon[:, indices_used],
cv[:, indices_used],
entropy[:, indices_used],
def test_read_poscar_yaml(self):
filename = "POSCAR.yaml"
phpy_yaml = phonopyYaml(filename)
print phpy_yaml
def setUp(self):
filename = "POSCAR.yaml"
self._cell = phonopyYaml(filename).get_atoms()
def setUp(self):
filename = "POSCAR.yaml"
self._cell = phonopyYaml(filename).get_atoms()
from phonopy import Phonopy, PhonopyGruneisen
from phonopy.gruneisen.mesh import Mesh as GruneisenMesh
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
matplotlib.use('Agg')
matplotlib.rcParams.update({'figure.figsize': (4, 4),
'font.family': 'serif'})
import matplotlib.pyplot as plt
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)
def test_read_poscar_yaml(self):
filename = "POSCAR.yaml"
phpy_yaml = phonopyYaml(filename)
print phpy_yaml
def _search_imaginary_qpoint_ratio(self):
_, weights, freqs, _ = self._phonon.get_mesh()
self._ratio = float(np.extract(freqs[:, 0] < 0, weights).sum()) / np.prod(self._mesh)
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