Clean up warnings and errors.

Format consistently.
Move NHC length warning to avoid using an uninitialized value.
Add some missing exit call with errors.

Close #51.
Print output from frame 0 in MD
Minor
Invert adiabatic gamma

Invert it to make it consistent with the paper and book
Fixed the rest of the outpu formattting
Tweak Verlet list reporting
More small tweaks
One last tweak
Merge pull request #55 from TuckermanGroup/gamma

Invert adiabatic gamma
Merge pull request #56 from TuckermanGroup/output

Write output also at step 0
Merge pull request #58 from TuckermanGroup/formatted_output

Fixed the rest of the screen output writing format.
Merge branch 'master' into sim_params
Merge branch 'sim_params'

Conflicts:
	src/interface/sim_params/set_sim_params.c
Remove unused variables
Merge branch 'master' into plumed