Modified Makefiles in cuda-sem-dpd so one can specify CUDA path (since it is different on every mashine).
Fix typo in cuda-sem.cu
Integrated changes from vanilla-microfluidics to the vanilla-walls.
debugging and refactoring
minor perf on cell lists
Merge branch 'master' of https://github.com/rossinelli/CTC into diego

Conflicts:
	cuda-dpd-sem/Makefile
	cuda-dpd-sem/dpd/Makefile
	vanilla-walls/Makefile
	vanilla-walls/main.cpp
	vanilla-walls/particles.cpp
Moved particles, tomatosandwich and all these things back to main.cpp
Added two new things - equalibrate code (with dumps, equlibrate, filling in particles
arrays, etc) and funnel-bouncer which marks, bounce and computeForces
The code is checked using bouncer-check.cpp. This code is still require additional checks