def plot_dos(phonons,
bandwidth=.05,
n_points=200,
is_showing=True,
input_fig=None):
if input_fig is None:
fig = plt.figure()
else:
fig = input_fig
kde = KernelDensity(kernel='gaussian', bandwidth=bandwidth).fit(
phonons.frequency.flatten(order='C').reshape(-1, 1))
x = np.linspace(phonons.frequency.min(), phonons.frequency.max(), n_points)
y = np.exp(kde.score_samples(x.reshape((-1, 1))))
plt.plot(x, y)
plt.fill_between(x, y, alpha=.2)
plt.xlabel("$\\nu$ (THz)", fontsize=16)
plt.ylabel('DOS', fontsize=16)
plt.tick_params(axis='both', which='major', labelsize=16)
plt.tick_params(axis='both', which='minor', labelsize=16)
folder = get_folder_from_label(phonons, base_folder=DEFAULT_FOLDER)
if not os.path.exists(folder):
os.makedirs(folder)
fig.savefig(folder + '/' + 'dos.png')
if is_showing:
plt.show()
elif input_fig is None:
plt.close()
else:
return fig
def plot_vs_frequency(phonons, observable, observable_name, is_showing=True):
frequency = phonons.frequency.flatten()
observable = observable.flatten()
fig = plt.figure()
plt.scatter(frequency[3:], observable[3:], s=5)
observable[np.isnan(observable)] = 0
plt.ylabel(observable_name, fontsize=16)
plt.xlabel("$\\nu$ (THz)", fontsize=16)
plt.ylim(observable.min(), observable.max())
plt.tick_params(axis='both', which='major', labelsize=16)
plt.tick_params(axis='both', which='minor', labelsize=16)
folder = get_folder_from_label(phonons, base_folder=DEFAULT_FOLDER)
if not os.path.exists(folder):
os.makedirs(folder)
fig.savefig(folder + '/' + observable_name + '.png')
if is_showing:
plt.show()
else:
plt.close()
# Visualize phonon dispersion, group velocity and density of states with
# the build-in plotter.
# 'with_velocity': specify whether to plot both group velocity and dispersion relation
# 'is_showing':specify if figure window pops up during simulation
plotter.plot_dispersion(phonons, with_velocity=True, is_showing=False)
plotter.plot_dos(phonons, is_showing=False)
# Visualize heat capacity vs frequency and
# 'order': Index order to reshape array,
# 'order'='C' for C-like index order; 'F' for Fortran-like index order
# Define the base folder to contain plots
# 'base_folder':name of the base folder
folder = get_folder_from_label(phonons, base_folder='plots')
if not os.path.exists(folder):
os.makedirs(folder)
# Define a boolean flag to specify if figure window pops during sumuatlion
is_show_fig = False
frequency = phonons.frequency.flatten(order='C')
heat_capacity = phonons.heat_capacity.flatten(order='C')
plt.figure()
plt.scatter(frequency[3:], 1e23 * heat_capacity[3:], s=5)
plt.xlabel("$\\nu$ (THz)", fontsize=16)
plt.ylabel("$C_{v} \ (10^{23} \ J/K)$", fontsize=16)
plt.savefig(folder + '/cv_vs_freq.png', dpi=300)
if not is_show_fig:
plt.close()
else:
def plot_dispersion(phonons,
n_k_points=300,
is_showing=True,
symprec=1e-3,
is_nw=None,
with_velocity=True,
color='b',
is_unfolding=False):
atoms = phonons.atoms
if is_nw is None and phonons.is_nw:
is_nw = phonons.is_nw
if is_nw:
q = np.linspace(0, 0.5, n_k_points)
k_list = np.zeros((n_k_points, 3))
k_list[:, 0] = q
k_list[:, 2] = q
Q = [0, 0.5]
point_names = ['$\\Gamma$', 'X']
else:
try:
k_list, Q, point_names = create_k_and_symmetry_space(
atoms, n_k_points=n_k_points, symprec=symprec)
q = np.linspace(0, 1, k_list.shape[0])
except seekpath.hpkot.SymmetryDetectionError as err:
print(err)
q = np.linspace(0, 0.5, n_k_points)
k_list = np.zeros((n_k_points, 3))
k_list[:, 0] = q
k_list[:, 2] = q
Q = [0, 0.5]
point_names = ['$\\Gamma$', 'X']
freqs_plot = []
vel_plot = []
vel_norm = []
for q_point in k_list:
phonon = HarmonicWithQ(
q_point,
phonons.forceconstants.second,
distance_threshold=phonons.forceconstants.distance_threshold,
storage='memory',
is_unfolding=is_unfolding)
freqs_plot.append(phonon.frequency.flatten())
if with_velocity:
val_value = phonon.velocity[0]
vel_plot.append(val_value)
vel_norm.append(np.linalg.norm(val_value, axis=-1))
freqs_plot = np.array(freqs_plot)
if with_velocity:
vel_plot = np.array(vel_plot)
vel_norm = np.array(vel_norm)
fig1, ax1 = plt.subplots()
plt.tick_params(axis='both', which='minor', labelsize=16)
plt.ylabel("$\\nu$ (THz)", fontsize=16)
plt.xlabel('$q$', fontsize=16)
plt.tick_params(axis='both', which='major', labelsize=16)
plt.xticks(Q, point_names)
plt.xlim(q[0], q[-1])
if color is not None:
plt.plot(q, freqs_plot, '.', color=color, linewidth=4, markersize=4)
else:
plt.plot(q, freqs_plot, '.', linewidth=4, markersize=4)
plt.grid()
plt.ylim(freqs_plot.min(), freqs_plot.max() * 1.05)
folder = get_folder_from_label(phonons, base_folder=DEFAULT_FOLDER)
if not os.path.exists(folder):
os.makedirs(folder)
plt.subplots_adjust(left=0.1, right=0.9, top=0.9, bottom=0.1)
fig1.savefig(folder + '/' + 'dispersion' + '.png')
np.savetxt(folder + '/' + 'q', q)
np.savetxt(folder + '/' + 'dispersion', freqs_plot)
if is_showing:
plt.show()
else:
plt.close()
if with_velocity:
for alpha in range(3):
np.savetxt(folder + '/' + 'velocity_' + str(alpha),
vel_plot[:, :, alpha])
fig2, ax2 = plt.subplots()
plt.ylabel('$|v|(\AA/ps)$', fontsize=16)
plt.xlabel('$q$', fontsize=16)
plt.tick_params(axis='both', which='major', labelsize=16)
plt.tick_params(axis='both', which='minor', labelsize=20)
plt.xticks(Q, point_names)
plt.xlim(q[0], q[-1])
if color is not None:
plt.plot(q,
vel_norm[:, :],
'.',
linewidth=4,
markersize=4,
color=color)
else:
plt.plot(q, vel_norm[:, :], '.', linewidth=4, markersize=4)
plt.grid()
plt.tick_params(axis='both', which='major', labelsize=16)
fig2.savefig(folder + '/' + 'velocity.png')
np.savetxt(folder + '/' + 'velocity_norm', vel_norm)
if is_showing:
plt.show()
else:
plt.close()
