def phonons():
print("Preparing phonons object.")
forceconstants = ForceConstants.from_folder(
folder='kaldo/tests/si-crystal', supercell=[3, 3, 3], format='eskm')
phonons = Phonons(forceconstants=forceconstants,
kpts=[5, 5, 5],
is_classic=False,
temperature=300,
storage='memory')
return phonons
def phonons():
print("Preparing phonons object.")
forceconstants = ForceConstants.from_folder(
folder='kaldo/tests/si-amorphous', format='eskm')
phonons = Phonons(forceconstants=forceconstants,
is_classic=False,
temperature=300,
third_bandwidth=1 / 4.135,
broadening_shape='triangle',
storage='memory')
return phonons
def phonons():
print("Preparing phonons object.")
# Create a finite difference object
forceconstants = ForceConstants.from_folder(
folder='kaldo/tests/si-amorphous', format='eskm')
# # Create a phonon object
phonons = Phonons(forceconstants=forceconstants,
is_classic=False,
storage='memory')
return phonons
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())
def phonons():
print("Preparing phonons object.")
# Create a finite difference object
forceconstants = ForceConstants.from_folder(
folder='kaldo/tests/si-amorphous', format='eskm')
# # Create a phonon object
phonons = Phonons(forceconstants=forceconstants,
is_classic=True,
temperature=300,
third_bandwidth=0.05 / 4.135,
storage='memory')
return phonons
def phonons():
print("Preparing phonons object.")
forceconstants = ForceConstants.from_folder(
folder='kaldo/tests/si-crystal', supercell=[3, 3, 3], format='eskm')
phonons_config = {
'kpts': [5, 5, 5],
'is_classic': 0,
'temperature': 300,
'folder': 'ald',
'storage': 'memory',
'third_bandwidth': .1,
'broadening_shape': 'gauss',
'is_balanced': True,
'grid_type': 'C'
}
phonons = Phonons(forceconstants=forceconstants, **phonons_config)
return phonons
def phonons():
print("Preparing phonons object.")
# Setup crystal and EMT calculator
atoms = bulk('Al', 'fcc', a=4.05)
with TemporaryDirectory() as td:
forceconstants = ForceConstants(atoms=atoms,
supercell=[5, 5, 5],
folder=td)
forceconstants.second.calculate(calculator=EMT())
is_classic = False
phonons_config = {
'kpts': [5, 5, 5],
'is_classic': is_classic,
'temperature': 300,
'storage': 'memory'
}
phonons = Phonons(forceconstants=forceconstants, **phonons_config)
return phonons
# Configure phonon object
# 'is_classic': specify if the system is classic, True for classical and False for quantum
# 'temperature: temperature (Kelvin) at which simulation is performed
# 'folder': name of folder containing phonon property and thermal conductivity calculations
# 'storage': Format to storage phonon properties ('formatted' for ASCII format data, 'numpy'
# for python numpy array and 'memory' for quick calculations, no data stored)
phonons_config = {'is_classic': False,
'temperature': 300, #'temperature'=300K
'folder': 'ALD_aSi512',
'third_bandwidth':0.5/4.135, # 0.5 eV is used here.
'broadening_shape':'triangle',
'storage': 'numpy'}
# Set up phonon object by passing in configuration details and the forceconstants object computed above
phonons = Phonons(forceconstants=forceconstants, **phonons_config)
### Set up the Conductivity object and thermal conductivity calculations ####
# Compute thermal conductivity (t.c.) by solving Boltzmann Transport
# Equation (BTE) with various of methods
# 'phonons': phonon object obtained from the above calculations
# 'method': specify methods to solve for BTE
# ('qhgk' for Quasi-Harmonic Green Kubo (QHGK))
# 'storage': Format to storage phonon properties ('formatted' for ASCII format data, 'numpy'
# for python numpy array and 'memory' for quick calculations, no data stored)
print('\n')
qhgk_cond = Conductivity(phonons=phonons, method='qhgk', storage='numpy')
qhgk_cond.diffusivity_bandwidth = phonons.bandwidth
# 'temperature: temperature (Kelvin) at which simulation is performed
# 'folder': name of folder containing phonon property and thermal conductivity calculations
# 'storage': Format to storage phonon properties ('formatted' for ASCII format data, 'numpy'
# for python numpy array and 'memory' for quick calculations, no data stored)
# Define the k-point mesh using 'kpts' parameter
k_points = 151
# For one dimension system, only replicate k-point mesh
# along the direction of transport (z-axis)
kpts = [1, 1, k_points]
temperature = 300
# Create a phonon object
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]))
}
forceconstants = ForceConstants(atoms=atoms,
supercell=supercell,
folder='forceconstant')
forceconstants.second.calculate(calculator=LAMMPSlib(**lammps_inputs))
forceconstants.third.calculate(calculator=LAMMPSlib(**lammps_inputs))
n_replicas = np.prod(supercell)
kpts = [5, 5, 5]
temperature = 300
# # Create a phonon object
phonons = Phonons(forceconstants=forceconstants,
kpts=kpts,
is_classic=is_classic,
temperature=temperature,
folder='ald_out')
plotter.plot_dispersion(phonons)
print('Inverse conductivity in W/m/K')
print(Conductivity(phonons=phonons, method='inverse').conductivity.sum(axis=0))
print('RTA conductivity in W/m/K')
print(Conductivity(phonons=phonons, method='rta').conductivity.sum(axis=0))
plotter.plot_dos(phonons)
plotter.plot_vs_frequency(phonons, phonons.heat_capacity, 'cv')
plotter.plot_vs_frequency(phonons, phonons.bandwidth, 'gamma_THz')
plotter.plot_vs_frequency(phonons, phonons.phase_space, 'phase_space')
# Compute phonon bandwith with different widths, in the unit of THz
widths = [0.5 / 4.135, 1 / 4.135]
widths_l = [.121, .242]
plt.figure(figsize=(16, 12))
plt.suptitle("Amorphous Si (Tersoff '89)",
y=0.98,
fontsize=18,
fontweight='bold')
for i in index:
for j in range(0, len(widths)):
phonon_object = Phonons(forceconstants=forceconstants,
is_classic=False,
temperature=300,
third_bandwidth=widths[j],
broadening_shape=shapes[i],
is_tf_backend=False,
folder='ald_' + shapes[i])
freq = phonon_object.frequency
gamma = phonon_object.bandwidth
lbl = 'Width: ' + str(widths_l[j]) + 'THz'
plt.scatter(freq, gamma, label=lbl, s=5)
plt.title('Broadening Shape: ' + str(labels[i]),
fontsize=18,
fontweight='bold')
plt.xticks(fontsize=16)
plt.yticks(fontsize=16)
plt.xlabel(r'$\nu$ (THz)', fontsize=18, fontweight='bold')
plt.ylabel(r'$\Gamma$ (THz)', fontsize=18, fontweight='bold')
lgnd = plt.legend(scatterpoints=1, fontsize=14)
from kaldo.controllers import plotter
from kaldo.forceconstants import ForceConstants
from kaldo.conductivity import Conductivity
from kaldo.phonons import Phonons
fold = 'ald'
kpts = [5, 5, 5]
supercell = [5, 5, 5]
temperature = 300
folder = 'fc'
forceconstant = ForceConstants.from_folder(folder=folder,
supercell=[5, 5, 5],
format='shengbte-qe')
for k in [5]:
kpts = [k, k, k]
phonons = Phonons(forceconstants=forceconstant,
kpts=kpts,
is_classic=False,
temperature=300,
folder='ald',
is_tf_backend=True,
grid_type='C')
print('Inverse conductivity W/m/K')
print(
Conductivity(phonons=phonons, method='inverse',
storage='memory').conductivity.sum(axis=0))
import numpy as np
supercell = np.array([3, 3, 3])
# forceconstants = ForceConstants.import_from_dlpoly_folder('si-dlpoly', supercell)
forceconstants = ForceConstants.from_folder('structures', supercell=supercell, format='lammps')
k = 5
kpts = [k, k, k]
is_classic = False
temperature = 300
# # Create a phonon object
phonons = Phonons(forceconstants=forceconstants,
kpts=kpts,
is_classic=is_classic,
temperature=temperature)
print('AF conductivity')
print(Conductivity(phonons=phonons, method='qhgk').conductivity.sum(axis=0))
plt.scatter(phonons.frequency.flatten()[3:], phonons.bandwidth.flatten()[3:], s=5)
plt.ylabel('gamma_THz', fontsize=16, fontweight='bold')
plt.xlabel("$\\nu$ (Thz)", fontsize=16, fontweight='bold')
plt.show()
plt.scatter(phonons.frequency.flatten()[3:], phonons.phase_space.flatten()[3:], s=5)
plt.ylabel('ps', fontsize=16, fontweight='bold')
plt.xlabel("$\\nu$ (Thz)", fontsize=16, fontweight='bold')
plt.show()
