def phononics(ge_concentration='0'):
# Set up Forceconstants Object
folder_string = 'structures/1728_atom/aSiGe_C' + ge_concentration + '/'
atoms = read(folder_string + 'replicated_atoms.xyz', format='xyz')
forceconstants = ForceConstants(atoms=atoms, folder=folder_string + '/ald')
# Calculate the 2nd + 3rd Forceconstant matrices
lammps_inputs = {
'lmpcmds': [
"pair_style tersoff",
"pair_coeff * * forcefields/SiCGe.tersoff Si(D) Ge"
],
"log_file":
"min.log",
"keep_alive":
True
}
calc = LAMMPSlib(**lammps_inputs)
second = forceconstants.second
second.load(folder=folder_string + '/ald')
print('Third')
# second.calculate(calculator=calc)
third = forceconstants.third
third.calculate(calculator=calc, is_verbose=True)
# Create Phonon Object
phonons = Phonons(
forceconstants=forceconstants,
is_classic=False, # quantum stats
temperature=300, # 300 K
folder=folder_string,
third_bandwidth=0.5 / 4.135, # 0.5 eV smearing
broadening_shape='gauss') # shape of smearing
# Phononic Data
## These save files to help us look at phononic properties
## with our plotter (4_plotting.py). These properties are "lazy" which
## means they won't be calculated unless explicitly called, or required
## by another calculation.
np.save('frequency', phonons.frequency)
np.save('bandwidth', phonons.bandwidth)
np.save('diffusivity', phonons.diffusivity)
#np.save('participation', phonons.participation_ratio)
# Conductivity Object
# This will print out the total conductivity and save the contribution per mode
conductivity = Conductivity(phonons=phonons, method='qhgk').conductivity
np.save('conductivity', 1 / 3 * np.einsum('iaa->i', conductivity))
print("Thermal Conductivity (W/m/K): %.3f" %
conductivity.sum(axis=0).diagonal().mean())
phonons = Phonons(forceconstants=forceconstants,
kpts=kpts,
is_classic=False,
temperature=temperature,
is_nw=True,
folder='ALD_CNT',
storage='numpy')
# Compute conductivity from direct inversion of
# scattering matrix for infinite size samples
# 29.92 is the rescale factor between
# the volume of the simulation box and the
# volume of the 10,0 Carbon Nanotube
inverse_conductivity = Conductivity(phonons=phonons,
method='inverse').conductivity
inverse_conductivity_matrix = inverse_conductivity.sum(axis=0)
print('Infinite size conductivity from inversion (W/m-K): %.3f' %
(29.92 * inverse_conductivity_matrix[2, 2]))
# Config finite size conductivity from direct inversion of scattering matrix
# Specific finite size length, in angstrom,
# along the direction of transport (z-axis)
# finite_length_method ='ms' for the Mckelvey-Schockley method
finite_size_conductivity_config = {
'method': 'inverse',
'length': (0, 0, 1000000000),
'finite_length_method': 'ms',
'storage': 'numpy'
}
finite_size_inverse_conductivity = Conductivity(
phonons=phonons, **finite_size_conductivity_config)