comer mann electron dens

[dermen]

It seems that the scatter.atomic_electrondens had a small typo:

phi[inds] = cromermann[i] * \

should be

phi[inds] += cromermann[i] * \

Other than that there was a discrepancy from the formula I found via quick wolfram, and the one used.. how does this look:

click here for wolfram alpha computation

I tried loading the referenced paper in the function documentation, but could not find it (minimal effort used)

I made a little test script :

import numpy as np
import pylab as plt
from thor import scatter
def single_atom_dens(atomic_num, grid_size=5., grid_spacing=0.05):
    """
    atomic_num, atomic number of element 
    grid_size, size of cubic density grid in Angstrom
    grid_spacing, spacing of cubic grid in Angstrom
    """
    Ngrid_pt = int( float(grid_size)/grid_spacing)

    vals = np.arange( -grid_size/2, grid_size/2, grid_spacing)
    
    x,y,z = np.meshgrid( vals,vals,vals, sparse=True)
    R = np.sqrt( x**2 + y**2 + z**2 )
    form_fact = scatter.atomic_electrondens( atomic_num, R.ravel() )

    return form_fact.reshape( (Ngrid_pt, Ngrid_pt, Ngrid_pt))


# get the density
some_dens = {n:single_atom_dens(n) for n in range( 1,26)}


# plot
fig,axs = plt.subplots( 5,5, figsize=(10,10))
atom = 1
for i in range (5):
    for j in range(5):
        axs[i][j].clear()
        axs[i][j].imshow( sum(some_dens[atom],0), vmax=50)
        axs[i][j].set_title( "Z=%d"%atom, fontsize=15)
        axs[i][j].axis('off')
        atom += 1