Spatial binning modifier

OVITO allows you to ….

In the first three cases the modifier generates a one-dimensional grid with bins aligned perpendicular to the selected simulation cell vector. In the last three cases the modifier generates a two-dimensional grid with bins aligned perpendicular to both selected simulation cell vectors (i.e. parallel to the third vector).

How can I do this?

  • Download and import the example file …. From the four viewport windows now choose the Perspective view and enlarge it by clicking on the Maximize Active Viewport button.
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from ovito.data import *
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
def modify(frame, data):
    grid = data.grids['binning[Potential Energy]']
    array = grid['Potential Energy']
    array_2d = np.reshape(array, (grid.shape[1], grid.shape[0]) )

    plt.figure()
    matplotlib.rcParams.update({'font.size': 18})
    im = plt.imshow(array_2d, cmap='jet', aspect='equal', origin='lower')
    plt.xlabel('coordinate 1')
    plt.ylabel('coordinate 2')
    plt.colorbar(shrink = 0.65)
    plt.savefig('{}{}.pdf'.format(grid.title, frame), bbox='tight')

Advanced Topic: What about time averages?

In case you want to compute a grid averaged over all your frames, you need to switch to OVITO’s scripting interface ovitos.

 

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That’s it. Well done!

Downloads

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Further reading