[Clustersim] Merging

[John Michael Schneiderman]

I have added the Monte Carlo simulation to the the new branch. The 
documentation for all the classes will be done by tomorrow night. So, FYI if 
you're working on the CVS right now, I would wait it will be less 
frustrating. The documentation will also be posted on our website.
        Also, I have changed the way the atom class works. I created a 
co-ordinate 
class for the positions, velocities and accelerations. All of the other 
classes use this class as well when dealing with anything that has an x, y, 
and z. Later on we can make them inline methods so that there isn't a speed 
hit while using it. Using this class has simplified many of the complex 
operations that were being done in the simulations, as we can now modify all 
three values with one line instead of multiple lines. So, where the classes 
use to have to written as:
        object.x = object.x + 5;
        object.y = object.y + 5;
        object.z = object.z + 5;
can now be written as:
        object = object + 5;
I have implemented all of the usual methods for easy operational use.
        Also there is a new sample file on the CVS for providing a user with a 
template for creating their own files for running multiple runs in series. 
It's also based on the the confParser class, since one way to look at a 
providing a file as another way of saying you are providing a series of 
defaults for runs. 

        If there are any questions, please post them to clustersim mailing 
list, and 
not just to me, never know when someone else might have the same question.

John

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