density Namespace Reference

Functions
def	draw_atoms

Variables
tuple	parser = ArgumentParser()
tuple	args = parser.parse_args()
string	output_dir = "tmp"
tuple	density_file_name = os.path.join(args.results_path, "density.h5")
tuple	atoms_data_file = h5py.File(join(args.results_path, "results.h5"))
tuple	atom_meta = atoms_data_file.get("atomMeta")
tuple	atoms = atoms_data_file.get("state")
tuple	density_file = h5py.File(density_file_name)
tuple	data = density_file.get("dataset")
tuple	n_electrons = draw_atoms(atoms, atom_meta)
tuple	data_max_min_diff = (data.max() - data.min())
	contours = args.contours
tuple	iso = mlab.contour3d(X, Y, Z, data, vmin=contours[0], vmax=contours[-1], opacity=0.1013, contours=contours, colormap="GnBu", line_width=0.1)

Function Documentation

def density.draw_atoms	(		atoms,
			atom_meta
	)

Definition at line 29 of file density.py.

def draw_atoms(atoms, atom_meta):
    n_electrons = 0
    counter = 0
    for atom in atoms:
        if atom_meta[counter]["type"] == 1:
            color = (1, 1, 1)
            scale = 0.3
        elif atom_meta[counter]["type"] == 6:
            color = (0, 0, 0)
            scale = 0.6
        elif atom_meta[counter]["type"] == 8:
            color = (1, 0, 0)
            scale = 0.6
        else:
            color = (1, 1, 0)
            scale = 0.2
        mlab.points3d(atom[0], atom[1], atom[2],
                          scale_factor=scale,
                          resolution=20,
                          color=color,
                          scale_mode='none')
        counter += 1
    return n_electrons