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Actually, monte carlo codes like Geant4 (or MCNP, or whatever else you might use) are not aware of molecules at all. As far as Geant4 is concerned, each material is just a collection of independent atoms at different densities. If you are concerned with the chemistry side of things, you will have to work out how to couple Geant4 results with a computational chemistry or molecular dynamics code.
In general, ignoring chemical bonds has very little impact on monte carlo results (bonds are usually < 1eV, whereas most applications of monte carlo run orders of magnitude higher). Since neutrons do not interact with charged particles, bonds don't make a difference at any energy. If you are using extremely low energy charged particles, and are interested in the energy deposition on a very, very fine scale, then you might be concerned.
On Fri, 14 Jun 2013 16:45:05 GMT, Zack Snyder wrote:
> Hello Joel, > > Thank you for your reply. From what I can tell, the same things appear > to be occurring in both water and ice, which leads me to believe that > everything is now working fine. I was misunderstanding the output > slightly, so I am partially to blame. One of my concerns is about the > molecular structure of ice versus water. Ice has a crystal structure and > I do not know if this is taken into account by Geant4 when building ice > via the code I quoted in a previous message or if Geant4 must be told to > do so in some fashion. In addition, I do not know whether this will have > a noticeable effect on neutron interaction or not.
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