Fix omm

[swails]

This fixes a number of issues with the OpenMM integration:

• Makes sure unit cell vectors are set correctly for non-orthogonal cells
• Resolves a bunch of compiler warnings associated with structs that had no external linkage (fixed by making them static)
• Resolves more compiler warnings about assigning to char* via = (you can do this with std::string, but not char*)
• Adds the functionality to write out a system.xml file that can be used with OpenMM in standalone mode if you request 0 steps with dynamic_omm.

[swails]

@jayponder -- I submitted this PR to go directly into your master branch. It only touches the OpenMM stuff, though, and fixes things so it works correctly with triclinic cells. I can resubmit the PR to go to a different branch if you want me to, but I can't see a reason why this shouldn't go into master, personally. (I just don't want to screw up anything you might be working on).

Let me know if I'm good to merge this to master.

Thanks!

[swails]

I'm going to go ahead and merge this.