Documented variable icenter.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4874 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed array accessing mismatch between Fortran and C++.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4875 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed memory access issue with particle names.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4876 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed invalid memory access.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4877 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed memory access issue with exclusion lists.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4878 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed memory access issue when assigning values to sparse matrix.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4879 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fixed unintended assignment (instead of comparison) in conditional clause.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4880 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Made debugging flags more useful and disabled outputting binaries to the exe directory.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4881 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Fix for another memory access violation.

git-svn-id: https://svn.ices.utexas.edu/repos/clsb/trunk/moil@4882 90e2fc84-bd37-0410-82f1-ae2f889bfac2
Removed binary object files from repository.
Merge branch 'master' of github.com:jmbr/moil
Reenabled output of energy of bonded interactions.