class thermal_conductivity():
def __init__(self, primitive_cell, super_cell):
self.primitive_cell = primitive_cell
self.super_cell = super_cell
def input_files(self, path_POSCAR, path_FORCECONSTANT):
bulk = read_vasp(path_POSCAR)
self.phonon = Phonopy(bulk,
self.super_cell,
primitive_matrix=self.primitive_cell)
force_constants = file_IO.parse_FORCE_CONSTANTS(path_FORCECONSTANT)
self.phonon.set_force_constants(force_constants)
return self.phonon
def set_mesh(self, mesh):
self.phonon.set_mesh(mesh, is_eigenvectors=True)
def set_point_defect_parameter(self, fi, defect_mass, defect_fc_ratio):
self.mass = self.phonon.get_primitive().get_masses().sum(
) / self.phonon.get_primitive().get_number_of_atoms()
self.cellvol = self.phonon.get_primitive().get_volume()
self.mass_fc_factor = self.cellvol * 10**-30 / 2.0 / 4 / np.pi * (
fi *
((self.mass - defect_mass) / self.mass + 2 * defect_fc_ratio)**2)
def kappa_separate(self, gamma, thetaD, T, P=1, m=3, n=1):
"""
nkpts: number of phonon k-points
frequencies: list of eigenvalue-arrays as output by phonopy
vgroup: group velocities
T: temperature in K
following parameters from Eq (70) in Tritt book, p.14
P: proportionality factor of Umklapp scattering rate, defualt 1
mass: mass in amu (average mass of unitcell)
gamma: Gruneisen parameter, unitless
thetaD: Debye temperature of relevance (acoustic modes) 283K for Mo3Sb7
m = 3 by default
n = 1 by default
cellvol: unit cell volume in A^3
"""
T = float(T)
#self.phonon.set_mesh(mesh, is_eigenvectors=True)
#self.mass = self.phonon.get_primitive().get_masses().sum()/self.phonon.get_primitive().get_number_of_atoms()
self.cellvol = self.phonon.get_primitive().get_volume()
self.qpoints, self.weigths, self.frequencies, self.eigvecs = self.phonon.get_mesh(
)
nkpts = self.frequencies.shape[0]
numbranches = self.frequencies.shape[1]
self.group_velocity = np.zeros((nkpts, numbranches, 3))
for i in range(len(self.qpoints)):
self.group_velocity[i, :, :] = self.phonon.get_group_velocity_at_q(
self.qpoints[i])
inv_nor_Um = np.zeros((nkpts, numbranches))
inv_point_defect_mass_fc = np.zeros((nkpts, numbranches))
inv_tau_total = np.zeros((nkpts, numbranches))
kappa_Um = np.zeros((nkpts, numbranches))
kappa_point_defect_mass_fc = np.zeros((nkpts, numbranches))
kappa_total = np.zeros((nkpts, numbranches))
self.kappaten = np.zeros((nkpts, numbranches, 3, 3))
v_group = np.zeros((nkpts, numbranches))
capacity = np.zeros((nkpts, numbranches))
for i in range(nkpts):
for j in range(numbranches):
nu = self.frequencies[i][
j] # frequency (in Thz) of current mode
velocity = self.group_velocity[
i, j, :] # cartesian vector of group velocity
v_group = (velocity[0]**2 + velocity[1]**2 +
velocity[2]**2)**(0.5) * THztoA
capacity[i, j] = mode_cv(
T, nu * THzToEv) * eV2Joule / (self.cellvol * Ang2meter**3)
# tau inverse phonon-phonon, inverse lifetime
inv_nor_Um[i, j] = P * hbar * gamma**2 / (
self.mass * amu) / v_group**2 * (T**n) / thetaD * (
2 * np.pi * THz * nu)**2 * np.exp(
(-1.0) * thetaD / m / T)
# tau inverse point defect, inverse lifetime
inv_point_defect_mass_fc[i, j] = (self.mass_fc_factor) * (
2 * np.pi * THz * nu)**4 / v_group**3
# tau inverst, inverse lifetime
inv_tau_total[
i, j] = inv_nor_Um[i, j] + inv_point_defect_mass_fc[i, j]
kappa_total[
i,
j] = (1.0 / 3.0) * self.weigths[i] * v_group**2 * capacity[
i,
j] / inv_tau_total[i,
j] # 1/3 is for isotropic condition
kappa_Um[
i,
j] = (1.0 / 3.0) * self.weigths[i] * v_group**2 * capacity[
i, j] / inv_nor_Um[i,
j] # 1/3 is for isotropic condition
kappa_point_defect_mass_fc[
i,
j] = (1.0 / 3.0) * self.weigths[i] * v_group**2 * capacity[
i, j] / inv_point_defect_mass_fc[
i, j] # 1/3 is for isotropic condition
self.kappaten[i, j, :, :] = self.weigths[i] * np.outer(
velocity,
velocity) * THztoA**2 * capacity[i, j] / inv_tau_total[i,
j]
#print(np.sum(inv_nor_Um, axis =1))
#print(np.sum(inv_point_defect_mass_fc, axis =1))
#print(np.sum(inv_tau_total, axis =1))
self.tau = np.concatenate(
(inv_nor_Um, inv_point_defect_mass_fc, inv_tau_total), axis=1)
self.kappa = [
kappa_Um.sum() / self.weigths.sum(),
kappa_point_defect_mass_fc.sum() / self.weigths.sum(),
kappa_total.sum() / self.weigths.sum()
]
return self.tau, self.kappa, self.kappaten
