symbols = coords.get_chemical_symbols()
ox_coords = []
for i, atom in enumerate(coords):
if symbols[i] == species:
ox_coords.append(scaled_coords[i])
grid_position = np.zeros(shape=(3))
potentials_list = []
i = 0
num_bins = 20
for coord in ox_coords:
i = i + 1
grid_position[0] = coord[0]
grid_position[1] = coord[1]
grid_position[2] = coord[2]
cube = sample_cube # The size of the cube x,y,z in units of grid resolution.
origin = [grid_position[0] - 2, grid_position[1] - 2, grid_position[2] - 1]
travelled = [0, 0, 0] # Should be left as it is.
cube_potential, cube_var = pot.cube_potential(origin, travelled, cube,
grid_pot, NGX, NGY, NGZ)
potentials_list.append(cube_potential)
n, bins, patches = plt.hist(potentials_list,
num_bins,
normed=100,
facecolor='#6400E1',
alpha=0.5)
plt.xlabel('Hartree potential (V)', fontsize=22)
plt.ylabel('% of centres', fontsize=22)
plt.savefig('Potentials.png', dpi=300)
plt.show()
from ase.io import write # Only add this if want to read in coordinates
from ase.io import vasp # Only add this if want to read in coordinates
coords = ase.io.vasp.read_vasp(coordinate_file)
scaled_coords = coords.get_scaled_positions()
ox_coords = []
i = -1
for atom in coords:
i = i + 1
if atom.get_symbol() == species:
ox_coords.append(scaled_coords[i])
grid_position = np.zeros(shape=(3))
potentials_list = []
i = 0
num_bins = 20
for coord in ox_coords:
i = i + 1
grid_position[0] = coord[0]
grid_position[1] = coord[1]
grid_position[2] = coord[2]
cube = sample_cube # The size of the cube x,y,z in units of grid resolution.
origin = [grid_position[0]-2,grid_position[1]-2,grid_position[2]-1]
travelled = [0,0,0] # Should be left as it is.
cube_potential, cube_var = pot.cube_potential(origin,travelled,cube,grid_pot,NGX,NGY,NGZ)
potentials_list.append(cube_potential)
n, bins, patches = plt.hist(potentials_list, num_bins,normed=100, facecolor='#6400E1', alpha=0.5)
plt.xlabel('Hartree potential (V)',fontsize = 22)
plt.ylabel('% of O centres',fontsize = 22)
plt.savefig('Potentials.png',dpi=300)
plt.show()