extruded = np.zeros((N, 10, 10))
extruded[list(range(N)), cords[:, (2)], cords[:, (0)]] = 1
grid = np.zeros((10, 10))
for atom, proj in atom_proj.items():
    centers = extruded[atoms == atom].sum(0)
projected = nd.convolve(centers, proj)
grid += projected
Projecting Coordinates in Numpy array