def get_rdf_list(pos, r, nbin, frames, elements):
"""
pos: a list of atoms object
r: the radial length
nbin: the bin number in the radial range
frames: how much pos number will you consider
elements: the atom pair
"""
tmp_info = Analysis(pos)
# this wil get a rdf for every snapshot
tmp_rdf_list = tmp_info.get_rdf(r,
nbin,
imageIdx=slice(0, frames, 1),
elements=elements)
return tmp_rdf_list
crystal1 = read(filename1)
corrdinates = crystal.get_positions()
cell_length = crystal.get_cell_lengths_and_angles()
cell_length = cell_length[0:3] # only select the cell length
dr = 0.01 # shperical shell radius dr
min_length_cell = min(cell_length) # select the smalles length in cell
rmax = (min_length_cell / 2) - 0.1 # 2*rmax < min_length_cell
bins = np.rint((min_length_cell / 3) * 100)
bins = bins.astype(int)
rdf = Analysis(crystal)
rdf2 = Analysis(crystal1)
g = rdf.get_rdf(rmax, bins)
g_r = rdf.get_rdf(rmax, bins)
r = np.linspace(0, rmax, bins)
y1 = np.array(g)
y = np.array(g_r)
y1 = np.transpose(y1)
y = np.transpose(y)
print(np.count_nonzero(y))
plt.figure()
plt.plot(r, y, color='black')
plt.plot(r, y1, color='blue')
plt.xlabel('r')
plt.ylabel('g(r)')
plt.xlim((0, rmax))