Changed local variable to class member (in ddMd/StructureFactor)
Changes to calculation of maximum structure factor.
Merge remote branch 'origin/upstream-devel' into upstream-devel
Changes to allow DdMd::Integrator::run to be invoked repeatedly.
Also added set and get functions to DdMd potential energies.
Fixed DdMd::timer to allow start/stop, added OUTPUT_DIAGNOSTICS ddSim command.
Merge branch 'devel' of git://github.com/dmorse/simpatico into upstream-devel

Conflicts:
	src/ddMd/diagnostics/StructureFactor.cpp
	src/ddMd/diagnostics/StructureFactorGrid.cpp
Editing documentation about commands, adding some notes.
Adapted ddMd/StructureFactorGrid to recent changes related to clear() method.
Modified serialization notes, superficial clean-up of util/param classes.
Fixing bug in DdMd::Simulation.cpp, when compiled with dihedrals.
Added INTER_ prefix to header guard macros in Inter namespace.
Added "setClassName" to some interactions in which it was missing.
Adding interactionClassName() accessors for DdMd potentials.
Updated comments.
Merge remote branch 'medapuram/upstream-devel' into devel
Editing TODO and README files only.
Bugfix: Added className to ParamComposite copy constructor.
Fixed a small mistake in mcMd/configIos/DdMdConfigIo
Merge branch 'upstream-devel' of github.com:medapuram/simpatico into upstream-devel
Merge branch 'devel' of git://github.com/dmorse/simpatico into upstream-devel
Merge branch 'my-copy' into HEAD in order to test upstream/devel branch by comparing results from old simulations.

Conflicts:
	src/ddMd/diagnostics/StructureFactorGrid.cpp
Merge branch 'merge-upstream-mycopy' of ssh://github.com/medapuram/simpatico into merge-upstream-mycopy