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# Chemistry example

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 electron localization function is downloaded from Axel Kohlmeyer’s molecule visualization page.

Source code: chemistry.py

    # 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://www.theochem.rub.de/~axel.kohlmeyer/cpmd-vmd/files/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()

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