MERGE OpenMD trunk changes 1803:1811 into development branch
fixing the build system
Creating busticated version of OpenMD
Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
Fixed Makefile problems with the samples and added several missing makefiles.
Added md file for half of a icosahedron.
new ideal structures
Added a bunch of bond order parameter test cases.