def phonon_dos(fcp_file):
if 'fcc2x2x2' in fcp_file:
prim = read(ref_fcc_conv2x2x2)
else:
prim = read(ref_fcc)
fcp = ForceConstantPotential.read(fcp_file)
mesh = [33, 33, 33]
atoms_phonopy = PhonopyAtoms(symbols=prim.get_chemical_symbols(),
scaled_positions=prim.get_scaled_positions(),
cell=prim.cell)
phonopy = Phonopy(atoms_phonopy,
supercell_matrix=5 * np.eye(3),
primitive_matrix=None)
supercell = phonopy.get_supercell()
supercell = Atoms(cell=supercell.cell,
numbers=supercell.numbers,
pbc=True,
scaled_positions=supercell.get_scaled_positions())
fcs = fcp.get_force_constants(supercell)
phonopy.set_force_constants(fcs.get_fc_array(order=2))
phonopy.set_mesh(mesh, is_eigenvectors=True, is_mesh_symmetry=False)
phonopy.run_total_dos()
phonopy.plot_total_DOS()
plt.savefig("phononDOS.png", dpi=200)
Nq = 51
G2X = get_band(np.array([0, 0, 0]), np.array([0.5, 0.5, 0]), Nq)
X2K2G = get_band(np.array([0.5, 0.5, 1.0]), np.array([0, 0, 0]), Nq)
G2L = get_band(np.array([0, 0, 0]), np.array([0.5, 0.5, 0.5]), Nq)
bands = [G2X, X2K2G, G2L]
phonopy.set_band_structure(bands)
phonopy.plot_band_structure()
xticks = plt.gca().get_xticks()
xticks = [x * hbar * 1e15 for x in xticks] # Convert THz to meV
# plt.gca().set_xticks(xticks)
plt.gca().set_xlabel("Frequency (THz)")
plt.savefig("phononBand.png", dpi=200)
phonopy.run_thermal_properties(t_step=10, t_max=800, t_min=100)
tp_dict = phonopy.get_thermal_properties_dict()
temperatures = tp_dict['temperatures']
free_energy = tp_dict['free_energy']
fig = plt.figure()
ax = fig.add_subplot(1, 1, 1)
ax.plot(temperatures, free_energy)
plt.show()
def md_calculation(fcp_file):
from ase import units
from ase.io.trajectory import Trajectory
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.langevin import Langevin
from ase.md import MDLogger
if 'fcc' in fcp_file:
ref_cell = read(ref_fcc)
P = np.array([[-1, 1, 1], [1, -1, 1], [1, 1, -1]])
P *= 3
atoms = make_supercell(ref_cell, P)
else:
raise ValueError("Unknown phase")
fcp = ForceConstantPotential.read(fcp_file)
fcs = fcp.get_force_constants(atoms)
calc = ForceConstantCalculator(fcs)
atoms.set_calculator(calc)
temperature = 200
number_of_MD_steps = 100
time_step = 5 # in fs
dump_interval = 10
traj_file = "data/md_" + fcp_file.split('.')[0] + '{}.traj'.format(
temperature)
log_file = "data/md_log_{}.log".format(temperature)
dyn = Langevin(atoms, time_step * units.fs, temperature * units.kB, 0.02)
logger = MDLogger(dyn,
atoms,
log_file,
header=True,
stress=False,
peratom=True,
mode='w')
traj_writer = Trajectory(traj_file, 'w', atoms)
dyn.attach(logger, interval=dump_interval)
dyn.attach(traj_writer.write, interval=dump_interval)
# run MD
MaxwellBoltzmannDistribution(atoms, temperature * units.kB)
dyn.run(number_of_MD_steps)