Control flow sandbox

[johnmauff]

This PR brings in a number of changes to the control follow for the Samurai-THERMO code that is necessary for execution. It should be noted that the Samurai-THERMO mode is not yet generating correct answers but rather runs without encountering an SEGV.

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 48.30247% with 335 lines in your changes missing coverage. Please review.

Project coverage is 32.55%. Comparing base (7b6252b) to head (076b229). Report is 13 commits behind head on thermo_asap.

Files with missing lines	Patch %	Lines
src/VarDriver3D.cpp	12.97%	208 Missing :warning:
src/CostFunction3D.cpp	64.44%	64 Missing :warning:
src/NetCDF_XYZ.cpp	0.00%	47 Missing :warning:
src/VarDriver.cpp	0.00%	8 Missing :warning:
src/CostFunctionRTZ.cpp	0.00%	4 Missing :warning:
src/CostFunctionXYZ.cpp	33.33%	2 Missing :warning:
src/CostFunctionCOAMPS.cpp	0.00%	1 Missing :warning:
src/CostFunctionXYP.cpp	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## thermo_asap #109 +/- ## =============================================== + Coverage 32.42% 32.55% +0.13% =============================================== Files 53 53 Lines 17524 17847 +323 =============================================== + Hits 5682 5810 +128 - Misses 11842 12037 +195 ```

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[johnmauff]

@cenamiller Would you be able to review this PR?

[cenamiller]

Hi @johnmauff, can you point me to your setup/scripts? I'm running on derecho (/glade/derecho/scratch/cmille73/APAR/PR109_control_flow_sandbox/samurai/) and the beltrami and beltramiTR runs can't find dunion_mt.snd

[cenamiller]

Ran beltrami and beltramiTR cases here: /glade/derecho/scratch/cmille73/APAR/PR109_control_flow_sandbox/

beltramiTR run converges but still errors (issue #111 ) in output stage:

            CG iteration    1852:  r_norm =          42.24328300     rel_resid =   0.0000988566
            MT LS: Number of function evals = 1
            MT LS: step = 1.0000000000
    Newton Iteration: 14    J = 1185.6727801145     Residual = 42.2432829949
    Minimum J: 1185.6727801145
    Found minimum in 14 outer Newton iterations.
    (and a total of 53865 inner CG iterations.)
    FINAL  ||g(X)||/||g(X0)|| = 0.0000988566
             (Linesearch iterations = 14 )

runTime: Cost3D minimize: 349.7246610000 Outputting increment... NetCDF: Numeric conversion not representable Error writing netcdf file ./samurai_XYZ_thermo_increment.nc Outputting analysis... NetCDF: Numeric conversion not representable Error writing netcdf file ./samurai_XYZ_thermo_analysis.nc runTime: Cost3d update: 3.8585730000 Analysis successful!