LCM: Changes to hierarchy of fracture criterion classes to reflect
base class modification. Changed cohesive connectivity to use
entity ids instead of entity pointers.
LCM: Hooked up surface elements but get segfault when destroying
mesh to create a new one in adaption. Trying to find out cause.
Added source term evaluator for Aeras shallow water equations, for Oksana to fill in
for TC4.  Unlike the earlier source evaluator (removed from the repository at some point),
the new one has a vector layout, so that a source for each of the variables can be set (h, u, v).
By default, the source is set to "None".  To see an example for how to call the source term
from the input file, please see ShallowWater/TC2/input.xml .
LCM: Replaced declare_element with declare_entity in creation of
interface element. Fixed computation of highest id to assign to new
surface element.
Fix off by 1 index.
Add periodic BC.
LCM: Surface elements are handled as 3D even at the STK level.
Need to make changes to account for that.
Wrote Aeras response that calculates the L2 error in a solution w.r.t. a hard-coded (analytical)
reference solution.  Right now, the exact solution to TC2 is hard-coded in the response -- need to clean
this up to make the exact solution name a parameter read in from the input file.  For TC2, results appear reasonable:
error is 0 for when Final Time = 0 (final solution = initial solution, as it should be).

Need to make this a relative error instead of absolute error, in addition to above clean up.
Merge branch 'master' of software.sandia.gov:/space/git/Albany
LCM: Prepare subgraph to introduce ability to ignore surface elements
to deal with the issue of those being stored as 3D cells in STK.
LCM: Star creation ignores cells that belong to interface part.
Completed implementation of L2 error response (which computed the absolute and relative L2 error
in the computed solution w.r.t. an analytic exact solution) for Aeras Shallow Water problems.
For an example of how to call this response, please see:

examples/Aeras/ShallowWater/TC2/input.xml

The response will actually produce 3 responses (a response of length 3, reported as 3
separate responses in the output).  They are:

1.) The absolute error in the solution w.r.t. the exact solution.
2.) The norm of the exact solution.
3.) The relative error in the solution w.r.t. the exact solution (1.) divided by 2.)).

Right now, only the exact solution for TC2 is coded in the response; other analytical
solutions can be added if desired to the class Aeras::ShallowWaterResponseL2Error.

Note that when the exact solution is 0, 3.) will evaluate to nan or inf b/c of a division by 0
in calculating the relative error.  A warning is printed to the screen in this case.
Made it so error is called if "Zero" or "TC2" is not selected as reference solution for
Aeras::ShallowWaterResponseL2Error.

Also added logic to CMakeLists.txt so that ShallowWaterResponseL2Error class does not
try to be compiled when Aeras is not enabled in the cmake configure script.
LCM: Some integer type cleanup.
Discovered an error in the L2 error response for Aeras for parallel runs.  Fixed it.
L2 error calculation now works correctly in serial as well as parallel.
Changed it so final_time is passed to evaluateResponse in ModelEvaluator instead of
time 0.  This makes more sense for responses, which are calculated at the final time.

Some clean ups of ShallowWaterResponseL2Error class for Aeras.
Changed evaluateResponse call to take in curr_time, which is now set correctly
to the final time of the solution in Piro_RythmosSolver_Def.hpp in Trilinos (there was a bug
before).
Commnted out Andy's hack to not observe solution at first time step (this _was_
being activated, b/c of a return statement after the print statement).
This is because it is of interest to write the 1st time step solution to the
exodus file for Aeras problems.
Added flag to toggle cloud physics from input file.
<Parameter name="Compute Cloud Physics" type="bool" value="false"/>
- default is false.
- if true, cloud "src terms" will be added to tracer and temperature residual.
Merge branch 'master' of software.sandia.gov:/space/git/Albany