def _get_estimated_strains(self):
t_max = 1500
t_step = 10
t_min = 0
cell = self.get_cell()
lattice = cell.lattice
if self._sampling_mesh is None:
self._sampling_mesh = klength2mesh(self._grid_spacing, lattice)
self._is_gamma_center = True
phonons = [task.get_phonon() for task in self._all_tasks[2:5]]
if None in phonons:
self._log += ("[quasiharmonic_phonon]\n"
"Phonon calculation failed in mode Gruneisen "
"parameter calculation.\n")
self._status = "phonon_for_gruneisen_failed"
return []
if phonons[0].set_mesh(self._sampling_mesh, self._is_gamma_center):
self._imaginary_ratio = self._check_imaginary(phonons[0], lattice)
else:
self._log += ("[quasiharmonic_phonon]\n"
"Phonon calculation failed in mode Gruneisen "
"parameter calculation.\n")
self._status = "phonon_for_gruneisen_failed"
return []
if self._imaginary_ratio > 0.01:
self._log += ("[quasiharmonic_phonon]\n"
"Imaginary modes are found in one point phonon "
"calculation.\n")
self._status = "imaginary_modes"
return []
gruneisen = PhonopyGruneisen(phonons[1], phonons[0], phonons[2])
if not gruneisen.set_mesh(self._sampling_mesh,
is_gamma_center=self._is_gamma_center):
self._log += ("[quasiharmonic_phonon]\n"
"Phonon calculation failed in mode Gruneisen "
"parameter calculation.\n")
self._status = "phonon_for_gruneisen_failed"
return []
vol = np.linalg.det(lattice)
volumes = [vol * (1 + strain) for strain in _eos_strains]
eos = self._all_tasks[1].get_equation_of_state()
energies = [eos(v) for v in volumes]
with open("estimated_e-v.dat", 'w') as w:
w.write("# cell volume energy of cell "
"other than phonon\n")
for e, v in zip(energies, volumes):
w.write("%20.13f %20.13f\n" % (v, e))
gruneisen.set_thermal_properties(volumes,
t_step=t_step,
t_max=t_max + t_step * 3.5,
t_min=t_min,
cutoff_frequency=0.1)
gruneisen.write_yaml_thermal_properties(
filename="estimated_thermal_props")
gruneisen_tp = gruneisen.get_thermal_properties()
thermal_properties = [tp.get_thermal_properties()
for tp in gruneisen_tp.get_thermal_properties()]
qha = self._get_quasiharmonic_phonon(energies,
volumes,
thermal_properties,
t_max)
if qha is None:
self._log += ("[quasiharmonic_phonon]\n"
"Approximated QHA from mode Grunsein parameter "
"failed.\n")
self._status = "strain_estimation_difficulty"
return []
equi_volumes = qha.get_volume_temperature()
# 0K 1000K
# |---|---|-o-|-o-|---|---|---|---|---|
# 0 1 2 3 4 5 6 7 8 9
#
d_v = (equi_volumes[100] - equi_volumes[0])
d_left = equi_volumes[0] - d_v * 2.5
d_right = equi_volumes[100] + d_v * 5.5
strains = [v / vol - 1 for v in np.linspace(d_left, d_right, 10)]
return strains
def _set_mesh(self, distance=100):
self._mesh = klength2mesh(distance, self._lattice)
