""" In this example, we display the H2O molecule, and use volume rendering to display the electron localization function. The atoms and the bounds are displayed using mlab.points3d and mlab.plot3d, with scalar information to control the color. The electron localization function is displayed using volume rendering. Good use of the `vmin` and `vmax` argument to `mlab.pipeline.volume` is critical to achieve a good visualization: the `vmin` threshold should placed high-enough for features to stand out. The original is an electron localization function from Axel Kohlmeyer. """ # Author: Gael Varoquaux <gael.varoquaux@normalesup.org> # Copyright (c) 2008, Enthought, Inc. # License: BSD Style. # Retrieve the electron localization data for H2O ############################## import os if not os.path.exists('h2o-elf.cube'): # Download the data import urllib print 'Downloading data, please wait' opener = urllib.urlopen( 'http://code.enthought.com/projects/mayavi/data/h2o-elf.cube' ) open('h2o-elf.cube', 'w').write(opener.read()) # Plot the atoms and the bonds ################################################# import numpy as np from enthought.mayavi import mlab mlab.figure(1, bgcolor=(0, 0, 0), size=(350, 350)) mlab.clf() # The position of the atoms atoms_x = np.array([2.9, 2.9, 3.8])*40/5.5 atoms_y = np.array([3.0, 3.0, 3.0])*40/5.5 atoms_z = np.array([3.8, 2.9, 2.7])*40/5.5 O = mlab.points3d(atoms_x[1:-1], atoms_y[1:-1], atoms_z[1:-1], scale_factor=3, resolution=20, color=(1, 0, 0), scale_mode='none') H1 = mlab.points3d(atoms_x[:1], atoms_y[:1], atoms_z[:1], scale_factor=2, resolution=20, color=(1, 1, 1), scale_mode='none') H2 = mlab.points3d(atoms_x[-1:], atoms_y[-1:], atoms_z[-1:], scale_factor=2, resolution=20, color=(1, 1, 1), scale_mode='none') # The bounds between the atoms, we use the scalar information to give # color mlab.plot3d(atoms_x, atoms_y, atoms_z, [1, 2, 1], tube_radius=0.4, colormap='Reds') # Display the electron localization function ################################### # Load the data, we need to remove the first 8 lines and the '\n' str = ' '.join(file('h2o-elf.cube').readlines()[9:]) data = np.fromstring(str, sep=' ') data.shape = (40, 40, 40) source = mlab.pipeline.scalar_field(data) min = data.min() max = data.max() vol = mlab.pipeline.volume(source, vmin=min+0.65*(max-min), vmax=min+0.9*(max-min)) mlab.view(132, 54, 45, [21, 20, 21.5]) mlab.show()