Initial arma commit. This *will not* compile yet, and the transition to using 
armadillo is incomplete. Lots of work is left.
No global arma namespace; more conversion.
Down to only 2 compile time errors.
Compilation errors elimnated from ionmd.cpp/hpp for now. New ones now from
minimize.cpp/hpp.
Added new dot inline functions for vec/double * dot products
Updated .gitignore to ignore some more data files.
Everything compiles, but segaults when running.
Attempting use of an arma matrix for pre-calculating Coulomb interaction.
Conversion to force functions returning values instead of storing them.

This still doesn't actually work yet in that minimize.cpp needs to be
updated to reflect these changes. As with most commits in this branch,
this is mostly a checkpoint.
Compiles with matrix changes, but need to hunt bugs.
Simulations now run with armadillo.
Merge branch 'arma'