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Scientific Visualization - Taming the masses

© Adam Hughes

As has been discussed here earlier, scientific computing is a rapidly growing field, and computer simulation in particular is now solving many of the most difficult science problems around. But as computers grow ever more efficient, they are creating new problems to be tackled. One of the most pressing is, "How do we analyze all of this data??" While there are many answers to this question, more and more researchers are relying on the sophistication of modern scientific visualization for their data analysis needs.

To stick with a familiar subject, let's consider some of the options available to the computational chemist when he needs to see what's going on in his system. Of course, systems can vary greatly in terms of total number of atoms, interaction types, etc., and there are plenty of tools available to suit any need. If a scientist is looking at small systems and just wants to see where the atoms are in space, almost any visualization package will do. Generally, atoms are rendered as some sort of spheres, while the bonds that connect them are represented as sticks. An example of a software package that can produce this kind of rendering is Rasmol. Information about this software package can be found at http://www.umass.edu/microbio/rasmol.

If a researcher is conducting {\em ab initio} calculations and wants to gain insight into his problem, he may need to take a different approach. As you may recall, {\em ab initio}, or quantum, calculations include an explicit treatment of the electrons in a system. Because of this, information about electron density and complex interaction patterns can be gleaned from the results of such calculations. This allows the scientist to produce elaborate and impressive electron density plots which give a much better graphical representation of reality than the old ball and stick models. One currently poplular program, Molden, allows the researcher to take advantage of this capability. The Molden homepage contains more information about the package and can be accessed at http://www.caos.kun.nl/~schaft/molden/mo...

Finally, there are those problems whose data are not suited to being displayed through the use of any of the commercially-available, functionally pre-defined software. In these cases, the researcher must devise a way to accomplish his visualization goals. While some scientist may actually go ahead and write a small software package to address specific needs, it generally behooves them to seek a more general approach that can be applied time and again to their various research problems. Luckily, a very powerful tool is available to scientists at this time : AVS. AVS stands for Advanced Visualization systems, and it is a completely generalized visualization package that allows the scientist to customize every aspect of his graphic display. With a little work, he can read data of any format, and produce truly stunning visuals, or he can simply use pre-developed applications to get

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