Initial refactoring. Complete OpenMP port. Wrap existing MPI and CUDA makefiles.

.gitignore

puremd_rc_1003/AUTHORS

puremd_rc_1003/COPYING

puremd_rc_1003/ChangeLog

puremd_rc_1003/INSTALL

puremd_rc_1003/Makefile

puremd_rc_1003/Makefile.am

puremd_rc_1003/NEWS

puremd_rc_1003/PG-PuReMD/aclocal.m4

puremd_rc_1003/PG-PuReMD/center_mass.cu.noshuffle

puremd_rc_1003/PG-PuReMD/center_mass.h.noshuffle

puremd_rc_1003/PG-PuReMD/configure.ac

puremd_rc_1003/PG-PuReMD/cuda_copy.objdump

puremd_rc_1003/PG-PuReMD/cuda_hydrogen_bonds.cu.noshuffle

puremd_rc_1003/PG-PuReMD/dev_system_props.cu.noshuffle

puremd_rc_1003/PG-PuReMD/doc/NOTES.txt

puremd_rc_1003/PG-PuReMD/dual_matvec.cu.noshuffle

puremd_rc_1003/PG-PuReMD/matvec.cu.noshuffle

puremd_rc_1003/PG-PuReMD/reduction.cu.noshuffle

puremd_rc_1003/PG-PuReMD/src/Makefile.in