grid_pot, electrons = md.density_2_grid(vasp_pot,NGX,NGY,NGZ)
## Get the gradiens (Field), if required.
## Comment out if not required, due to compuational expense.
print("Calculating gradients (Electic field, E=-Grad.V )...")
grad_x,grad_y,grad_z = np.gradient(grid_pot[:,:,:],resolution_x,resolution_y,resolution_z)
#------------------------------------------------------------------
##------------------------------------------------------------------
## Get the equation for the plane
## This is the section for plotting on a user defined plane;
## uncomment commands if this is the option that you want.
##------------------------------------------------------------------
## Convert the fractional points to grid points on the density surface
a = md.numbers_2_grid(a_point,NGX,NGY,NGZ)
b = md.numbers_2_grid(b_point,NGX,NGY,NGZ)
c = md.numbers_2_grid(c_point,NGX,NGY,NGZ)
plane_coeff = md.points_2_plane(a,b,c)
## Calculate magnitude of gradient.
# Should be able to use numpy.linalg.norm for this, but the Python array indices are causing me grief
X2 = np.multiply(grad_x,grad_x)
Y2 = np.multiply(grad_y,grad_y)
Z2 = np.multiply(grad_z,grad_z)
grad_mag = np.sqrt(np.add(X2,Y2,Z2))
# This was my, non working, attempt to use the built in function.
#grad_mag=np.linalg.norm( [grad_y,grad_y,grad_z], axis=3)
resolution_z = vector_c / NGZ
grid_pot, electrons = md.density_2_grid(vasp_pot, NGX, NGY, NGZ)
## Get the gradiens (Field), if required.
## Comment out if not required, due to compuational expense.
grad_x, grad_y, grad_z = np.gradient(grid_pot[:, :, :], resolution_x,
resolution_y, resolution_z)
#------------------------------------------------------------------
##------------------------------------------------------------------
## Get the equation for the plane
## This is the section for plotting on a user defined plane;
## uncomment commands if this is the option that you want.
##------------------------------------------------------------------
## Convert the fractional points to grid points on the density surface
a = md.numbers_2_grid(a_point, NGX, NGY, NGZ)
b = md.numbers_2_grid(b_point, NGX, NGY, NGZ)
c = md.numbers_2_grid(c_point, NGX, NGY, NGZ)
plane_coeff = md.points_2_plane(a, b, c)
## Get the gradients
XY = np.multiply(grad_x, grad_y)
grad_mag = np.multiply(XY, grad_z)
## Create the plane
xx, yy, grd = md.create_plotting_mesh(NGX, NGY, NGZ, plane_coeff, grad_x)
## Plot the surface
plt.contour(xx, yy, grd, 1)
plt.show()
##------------------------------------------------------------------
##------------------------------------------------------------------
def test_numbers_2_grid(self):
'''Tests the numbers_2_grid function'''
a = md.numbers_2_grid([0.5, 0.5, 0.5], 10, 10, 10)
b = [5, 5, 5]
self.assertSequenceEqual(a.tolist(), b)