A colleague showed me GAUSSIAN 09 which comes with GaussView 5 for drawing structures. What impressed me was the snappiness of the Clean function.
What algorithm is used for the Clean function?
The GaussView 5 Reference can be downloaded from the publisher’s web site. It doesn’t seem to contain the information that I’m looking for.
Background: As part of a project called SAN – Self Aware Network, I have a similar problem, though with additional constraints. To find the distribution of points in space, I implemented a genetic algorithm. Unfortunately, with large structures, this algorithm tends to get stuck in local minima. I documented the algorithm in the report SAN: Location Optimizer. A mathematician friend implemented a solution using gradient descend. Yesterday, he showed me some nice results, but it’s nowhere as snappy as GaussView.
I also contacted Gaussian technical support. Their response: “Unfortunately, no. We do not have additional documentation about this function, other than what is already present in the GV5 manual. This function just uses a very simple MM expression with crude parameters just to provide a simple way to "clean" a structure drawn "by hand" in GaussView. It is certainly not intended to give accurate geometries (it is expected that one is going to use some other model in Gaussian to run a geometry optimization and get a good geometry). The purpose is simply as another aid as part of building a structure in GaussView, so one may "clean" a structure faster (not always) than otherwise using "modify bond", "modify angle", "modify dihedral" tools.”