LCM: Refactor topology. Remove stale and repeated code. More
clean up changes (WIP).
LCM: remove the obsolete HDiff problem, cleanup other stuff

The hydrogen transport capability now resides in the Mechanics Problem
LCM: fix missing comma
LCM: comment out a few headers in the Mechanics Problem
LCM: first steps in adding the damage equation to the Mechanics Problem

Also, changed the Transport Residual to accept the scalar_dot instead of
computing it. The damage equation will use the Transport Residual as well.
LCM: work on adding damage field to Mechanics Problem

Hopefully this will allow us to test out the adaptive topology modification
algorithms until we have a nice projection capability.
Added cast of double to ScalarT to get new code to compile with SG.

For ScalarT = Sacado::PCE::OrthogPoly<>

The following did not compile:

	ScalarT a,b;
	double c;
	a = std::max(c, b);
but this does ..
	a = std::max((ScalarT) c, b);
LCM: Add Explicit version of Cap Model for Qiushi

Also continue working towards implementing the damage equation
fix a bug in Kinematics evaluator, a factor of 0.5 was missing when computing strain
Re-baselined 3 tests due to minor changes in Rythmos time integrator.

Temporarily disabled NSRayleighBernard2DwithNeut test - negative temperatures
develop during the test.
use "Strain Flag" material.xml to signal small_strain case
move CapImplicitModel to Constitutive Model Interface, verified against benchmark solutions
Merge branch 'master' of software.sandia.gov:/space/git/Albany
Added new AERAS problem XZ Scalar Adection.

Pair programmed with Bill Spotz.

Added new scalar advection problem, including data from
the Schar paper. This includes new functions for the
Transfrom Mesh and Initial Condition methods.
Changed "AERAS" to "Aeras"

Since "Aeras" is a word and not an acronym, I decided to change most
spellings to the lowercase but capitalized form.  This includes
directories, filenames, the namespace, and input file strings.  This
excludes -D definitions and maxros, such as header file protection.
Additional changes from "AERAS" to "Aeras"
Apparently, changing the directory and file names from AERAS to Aeras
should have been done separately from changing the file contents.
Hopefully this gets things to be correct.
Found a couple AERAS stragglers
Spherical Exodus grids for testing.
Updates to QCAD's Poisson-Schrodinger iteration capabilities:
 - more flexible damping capabilities, including ability of PoissonSource to "mix" a given quantum density with the one computed from the eigenvectors.
 - consolidated P-S iteration code in QCAD Solver so P-S and P-S-CI use same functions.
 - added ability to fix the quantum occupancy (i.e. charge) in the PoissonSource evaluator

The maximum number of responses is increased to 500 (previous maximum allowed was 100), as this was limiting the number of single particle wave functions QCAD's P-S-CI mode could use.