Modify the output NetCDF subrouties to generate Thermo output

[johnmauff]

Several different output routines (outputAnalysis) exist in Samuari that write NetCDF files. These output routines are specific for each different type of coordinate system 'XYZ, RTZ' and are located in CostFunctionXYZ.cpp for the wind version of Samurai and 'thermo_reference/CostFunctionThermoXYZ.cpp' for the thermo version of Samurai. The Thermo version of outputAnalysis needs to be added to the common code base. For now, I recommend that a nearly duplicate method outputAnalysisTR is created. The elimination of duplicate code can performed on a separate PR.

[cenamiller]

See how output should be renamed: #78

[cenamiller]

John will describe how subroutines need to be changed

[cenamiller]

developed at /glade/derecho/scratch/cmille73/APAR/issue76_NC_TRoutput

Still need to do #78 and test

[cenamiller]

Kamino cloned this issue to NCAR/samurai-dev