Changed 2.5 cps to be minSlices

Changed the hardcoded criteria of 2.5 cps to be passed as minSlices for
the MCNPXModel
Changed the XSDRN ranking to MCNPX

Using the mcnpx rankings for the MCNPX pertubations, as I observed a
large that the top values are not very repeatble between the two models
Extended the RPM model so print takes a geo

Add an optional argument to print geo to print a user provided geometry.
The default is still (no object passed) is to print the geometry of the
self object.
Removed Light Guide

Removed the light guide material from the MCNPX model. This was for
simplicity, as it made the pertubations more difficult.
Switched to just doubleing the genome

Pertubations implemeted as doubling the genome length and just flipping
bits.  This was much easier to implement.  Working model (for create)
with prints, supporting code not updated yet.
Removed prints and  cleanedup

Removed the print statements and cleaned up the code to remove the
references to pertubations based on thickness and not on doubling the
geometry.
Sanity check on doubling genome
Fixed minor errors
Changed Light Guide material to HDPE

Changed the light guide material to HDPE, as the differnet thickness in
the light guide caused slightly lower interaction rates when the
geometry was doubled (see pg. 29 for more information).
Changed GARunSript

Changed the GARunScript