This is the first draft of the changes to modify ddMd to include
a signature of molecules.
Reading indivitual members of the AtomContext is now available through
Context only.
Trivial
Last changes pointed out by dave has been included
The coding is done! All necessary changes have been done to make molecules
home! The code compiles on its own and it doesn't have the modifications of
External Potential!
The new chainmaker add in order to include the context for ddMd!
A new example is added as a test for context feature of the ddMd!
The example is working and producing meaningful results!
Merge pull request #23 from TaherGhasimakbari/molecule

Molecule
Merge branch 'devel' into molecule
Merge branch 'master' into molecule
Merge branch 'molecule' of github.com:/dmorse/simpatico into molecule
Superficial edits of Atom context additions.
Editing Taher's DDMD_MOLECULE branch.
Adding documentation ot AtomContext struct.
Edited ChainMaker to output species, molecule, atom ids in that order.
Associate suffix _z with MOLECULES option.
Add hasMolecules flag to DdMd[Ordered]ConfigIo classes.
Fixing bug in ConfigIoFactory.cpp
Modified molecule example, fixed bug in ConfigIoFatory.cpp_r