Fixed broken examples by adding NULL after stess/atom commands

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11786 f3b2605a-c512-4ea7-a41b-209d697bcdaa
Fixed broken basal example

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11787 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11788 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11789 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11790 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11791 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11792 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11793 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11794 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11795 f3b2605a-c512-4ea7-a41b-209d697bcdaa
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11796 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11797 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11798 f3b2605a-c512-4ea7-a41b-209d697bcdaa
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11799 f3b2605a-c512-4ea7-a41b-209d697bcdaa
import write_dump support for cfg style dumps
Merge remote-tracking branch 'lammps-ro/master' into lammps-icms

Resolved Conflicts:
	src/MC/fix_bond_break.cpp
more cleanups
ifdef out currently unused code
some more cleanups based on warnings from newer gcc