updating docstrings to reflect all classes are using structure_io.atoms Atom and Atoms classes
adding new Atom and Atoms classes.

Adding new StructureAtom and StructureAtoms classes for use by all
StructureGenerator clases. Replaces the chemistry sub-package
Atom and Atoms classes.
Updating code to use new Atom/Atoms classes
fixing bug in argparser argument format
bug fix
using the van der Waals constant from tools.refdata