def get_phonon_dos(structure,
supercell_matrix,
force_constants,
qpoint_mesh=(50, 50, 50),
phonon_pdos=False,
save_data=False,
save_fig=False):
'''
Return the phonon dos
Parameters
----------
structure : pymatgen.Structure
Unitcell (not supercell) of interest.
supercell_matrix : numpy.ndarray
3x3 matrix of the supercell deformation, e.g. [[3, 0, 0], [0, 3, 0], [0, 0, 3]].
force_constants: list
force constants
qpoint_mesh : list
Mesh of q-points to calculate thermal properties on.
phonon_pdos: bool
Determine if calculate phonon pdos or not
save_data/save_fig: bool
Determine if save the data/figure or not
'''
volume = structure.volume
formula = structure.composition.reduced_formula
filename = "{}-phonon-Vol{:.2f}".format(formula, volume)
unitcell = get_phonopy_structure(structure)
ph_dos_obj = Phonopy(unitcell, supercell_matrix)
ph_dos_obj.set_force_constants(force_constants)
ph_dos_obj.run_mesh(qpoint_mesh)
ph_dos_obj.run_total_dos()
if save_fig:
fig_dos = ph_dos_obj.plot_total_dos()
fig_dos.savefig(fname='{}-dos.png'.format(filename))
fig_dos.close()
if save_data:
ph_dos_obj.write_total_dos(filename='{}-dos.dat'.format(filename))
if phonon_pdos:
ph_dos_obj.run_mesh(qpoint_mesh,
with_eigenvectors=True,
is_mesh_symmetry=False)
ph_dos_obj.run_projected_dos()
if save_fig:
ph_dos_obj.plot_projected_dos().savefig(
fname='{}-pdos.png'.format(filename))
if save_data:
ph_dos_obj.write_projected_dos(
filename='{}-pdos.dat'.format(filename))
return ph_dos_obj
def get_phonon(self, phonon, **kwargs):
flag_savefig = kwargs.get('savefig', False)
flag_savedata = kwargs.get('savedata', False)
flag_band = kwargs.get('band', False)
flag_dos = kwargs.get('phonon_dos', False)
flag_pdos = kwargs.get('phonon_pdos', False)
mesh = kwargs.get('mesh', [50, 50, 50])
labels = kwargs.get('labels', None)
if 'unitcell' not in phonon:
raise FileNotFoundError(
'There is no phonon result. Please run phonon first.')
self.head = ['Temperature', 'F_vib', 'CV_vib', 'S_vib']
self.unit = ['K', 'eV', 'eV/K', 'eV/K']
self.data = np.vstack((phonon.pop('temperatures'), phonon.pop('F_vib'),
phonon.pop('CV_vib'), phonon.pop('S_vib'))).T
filename = '{}-phonon-Vol{:.2f}'.format(self.formula, self.volume)
unitcell = get_phonopy_structure(self.structure)
supercell_matrix = phonon['supercell_matrix']
force_constants = phonon['force_constants']
ph = Phonopy(unitcell, supercell_matrix)
ph.set_force_constants(force_constants)
#for band structure
if flag_band:
if 'path' in kwargs:
qpoints, connections = get_band_qpoints_and_path_connections(
path, npoints=51)
ph.run_band_structure(qpoints,
path_connections=connections,
labels=labels)
else:
ph.auto_band_structure()
if flag_savefig:
fig_band = ph.plot_band_structure()
fig_band.savefig(fname='{}-band.png'.format(filename))
fig_band.close()
if flag_savedata:
ph.write_yaml_band_structure(
filename='{}-band.yaml'.format(filename))
#for dos
if flag_dos:
ph.run_mesh(mesh)
ph.run_total_dos()
#phonon_dos_tmp = np.vstack((ph._total_dos._frequency_points, ph._total_dos._dos))
#print(phonon_dos_tmp)
#print(type(phonon_dos_tmp))
if flag_savefig:
fig_dos = ph.plot_total_dos()
fig_dos.savefig(fname='{}-dos.png'.format(filename))
fig_dos.close()
if flag_savedata:
ph.write_total_dos(filename='{}-dos.dat'.format(filename))
#for pdos.
if flag_pdos:
ph.run_mesh(mesh, with_eigenvectors=True, is_mesh_symmetry=False)
ph.run_projected_dos()
if flag_savefig:
ph.plot_projected_dos().savefig(
fname='{}-pdos.png'.format(filename))
if flag_savedata:
ph.write_projected_dos(filename='{}-pdos.dat'.format(filename))
phonon.pop('_id')
self.parameter = phonon
phonon.run_thermal_properties(t_step=10, t_max=1000, t_min=0)
# DOS
phonon.run_total_dos(sigma=0.1)
dos_dict = phonon.get_total_dos_dict()
for omega, dos in zip(dos_dict['frequency_points'], dos_dict['total_dos']):
print("%15.7f%15.7f" % (omega, dos))
phonon.plot_total_dos().show()
# Thermal properties
tprop_dict = phonon.get_thermal_properties_dict()
for t, free_energy, entropy, cv in zip(tprop_dict['temperatures'],
tprop_dict['free_energy'],
tprop_dict['entropy'],
tprop_dict['heat_capacity']):
print(("%12.3f " + "%15.7f" * 3) % (t, free_energy, entropy, cv))
phonon.plot_thermal_properties().show()
# PDOS
phonon.run_mesh(mesh=[10, 10, 10],
is_mesh_symmetry=False,
with_eigenvectors=True)
phonon.run_projected_dos(use_tetrahedron_method=True)
pdos_dict = phonon.get_projected_dos_dict()
omegas = pdos_dict['frequency_points']
pdos = pdos_dict['projected_dos']
pdos_indices = [[0], [1]]
phonon.plot_projected_dos(pdos_indices=pdos_indices,
legend=pdos_indices).show()
