def get_atomic_displacements(self, direction):
number_of_bins = self.parameters.number_of_bins_histogram
direction = np.array(direction)
projections = trajdist.trajectory_projection(self.dynamic, direction)
min_val = np.amin(projections)
max_val = np.amax(projections)
bins = None
distributions = []
for atom in range(projections.shape[0]):
distribution, bins = np.histogram(projections[atom],
bins=number_of_bins,
range=(min_val, max_val),
normed=True)
distributions.append(distribution)
distance = np.array([ i_bin - (bins[1]-bins[0])/2 for i_bin in bins ])
return np.array(distributions), distance
calculation.plot_velocity(atoms=[0], coordinates=[2]) #print(structure.get_cell()) #exit() calculation.write_trajectory_distribution([0, 0, 1], 'distribution.out') calculation.plot_trajectory_distribution([1, 0, 0]) calculation.plot_trajectory_distribution([0, 1, 0]) calculation.plot_trajectory_distribution([0, 0, 1]) exit() import dynaphopy.analysis.coordinates as coortest relative_trajectory = coortest.relativize_trajectory(trajectory) coortest.trajectory_projection(relative_trajectory, trajectory, np.array([1,0,0])) coortest.trajectory_projection(relative_trajectory, trajectory, np.array([0,1,0])) coortest.trajectory_projection(relative_trajectory, trajectory, np.array([0,0,1])) exit() #calculation.plot_vc(atoms=[0,1]) #calculation.plot_vq(modes=[0,1,2,3,4]) #print(structure.get_number_of_atoms()) #calculation.print_phonon_dispersion_spectrum() #calculation.get_phonon_dispersion_spectra() #calculation.set_band_ranges([[[0.2,0.0,0.2],[0.5,0.5,0.5]], [[0.5, 0.5, 0.5], [0.2, 0.0, 0.2]]]) #spectrum = calculation.get_anharmonic_dispersion_spectra(band_resolution=15)