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VISUALIZATION with AViz

To make a visualization with AViz you either download a sample datafile from the AViz website, or from one of several projects prepared using AViz. The AViz website has a lot of helful material, AViz installed on ALUF, TAMNUN, PHELAFEL and phclasses (most of them). The website has links to thhe GITHUB files too. Older download files for UBUNTU here . Article with stand-alone instructions for this version here .

The datafiles are in a exceedingly simple ASCII format with the first row an integer number of atoms, 2nd row a comment to identify the file, and at a minimum atomic type and x, y and z coordinates, with options for additional flags such as number of neighbours, or the spin direction if the object is a vector spin. There are a lot of tricks to enhance three-dimensional perception - rotation of still samples, change in relative sizes and quality of atoms, animation, adding or removing borders, highlighting bonds, slicing samples that can help 3D visualization and change of perspective. AViz does all these from the interactive interface. There is an option to use .vpm (view parameter files) to save information about color selection, size etc. These can be downloaded for some examples from the AViz site and links given there.

One AViz example is based on data from a series of MD calculations by Irena Rosenblum, concerning defects in diamond. The datafiles are for a vacancy and a split-interstitial defect at 300 degrees in a diamond sample. The MD calculation used the Brenner potential to create the defects and her study involves calculating the phonon frequencies for defects for comparison with experimental Raman spectra to create a way to identify deep defects in diamond. The first few lines of the datafile, called split.xyz for the split-interstitial defect is given in Table I, where the first row says 42 atoms are in the file, the second line is the comment that identifies the data and then the next lines of the file give columns (left to right) giving a letter for atom type, three spatial coordinates and a number identifying the atom type (in terms of types of neighbours) which is this example is degenerate with the letter for the atom type. A .vpm file, which contains information such as background color and viewpoint called split.vpm can be created as described below. (The .vpm files are sometimes not readable on different computers but if you save one on your accont you can read it next time.) A .aviz/aviz.particle file, which contains information such as color for each type of atom called aviz.particle can be created as described below. (These files are sometimes not readable on different computers but if you save one on your accont you can read it next time.)



 42
Split interstitial
 J  5.3012  5.29852  7.09405 9
 H  6.16665  6.12665  8.05686 7
 J  5.25262  7.05947  5.22232 9
 H  6.17108  8.1017  6.13538 7
 J  5.2896  7.08316  8.92685 9
 J  5.31561  8.92685  7.12608 9
 H  6.18016  8.00222  9.86069 7
 H  6.08953  9.89518  7.95577 7
 J  5.31865  8.94514  10.72933 9
 J  5.31499  10.73491  8.91229 9
 J  7.09831  5.30742  5.33292 9
 H  7.96823  6.23213  6.2431 7
 J  7.10502  5.36005  8.88347 9
 J  8.88564  5.33393  7.09135 9
 H  8.01426  6.27737  9.76314 7
 H  9.90063  6.18504  8.00651 7
 J  8.91998  5.3191  10.67103 9
 J  7.12128  8.8809  5.34658 9
 J  8.91135  7.13459  5.35927 9
 H  8.04509  9.821  6.22758 7
 H  9.8264  8.00773  6.12863 7
 D  6.89427  6.95449  6.92478 3
 D  6.89031  8.96882  9.01784 3
 D  9.10989  6.98909  9.01816 3
 D  9.14867  9.0253  7.01965 3
 B  7.24567  8.13588  7.98187 1
 B  8.66696  8.04859  7.9721 1
 H  8.01295  9.80684  9.84269 7
 H  9.87065  7.99746  9.8501 7
 H  9.89039  9.85682  7.97838 7
 J  7.14591  7.06823  10.6609 9
 J  8.894  8.88631  10.63812 9
 J  8.87966  10.66296  5.30564 9
 J  7.13416  10.66282  7.10106 9
 J  8.89137  10.68602  8.92522 9
 J  7.11266  10.65395  10.68339 9
 J  10.72315  5.34338  8.91529 9
 J  10.73829  8.90913  5.2752 9
 J  10.76189  7.05762  7.11746 9
 J  10.76728  8.89394  8.91317 9
 J  10.70408  7.1336  10.73562 9
 J  10.70953  10.73769  7.09502 9


OK so download, run the command aviz and try this example!

To create a visualization, after installing AViz, one writes aviz on the command line then moves to the interactive interface. One clicks on File and selects Open, Open XYZ file and selects split.xyz. then sees dots, (more on these later). one then changes Dots to Spheres and goes for Final Quality. Some atoms are blue, some green. AViz has preprogrammed colors for different common atoms. Here there are all carbon, but different letters have been used because we want to draw them in different colors. One selects Elements, Atoms, Atoms/Molecules and then Type. Atoms labelled B,D, and J are blue by default, H is green. To zero in on the interesting region, we select that J will not be shown for now (select J atoms, remove the tick for show and then select apply.) To distinguish between B and D, select B, press set color and change the color to say red. The two central atoms change color, and you could now rotate the sample and probably find it hard to see anything. We now start to include bonds. Select bonds and let us start with the bond that connects B atoms. Make it present with say a brown color and a medium thickness. Next we do B to D, (blue and medium) and we see we connect more than nearest neighbours. If we make the Max length say 2.1 then only nearest neighbours will remain connected. Finally we draw bonds from D to H (green, medium, max length 2.1) and we can rotate (or auto rotate) zoom etc. We could press white to change the background and then snap to create the .png file that is shown below. We should go to File, Save ViewParam file to create a file called split.vpm that saves all our parameters for next time.

The .aviz/atom.particle file is saved if you click on apply while the window for creating bonds is open. See a manuscript about AViz here.

I want to try something new this year - each of you start now to draw a material that interests you. Some .xyz files on the site, or you can go to the nanotube builder site and build a nanotube yourself.

There are many other programs for different kinds of visualization. Recommended ones include

  1. Rasmol for proteins.
  2. pgplot for 2d and contour plots,matlab. mathematica are ok for general 3d applications