Model-Diagnostics.md

 Amongst the most critical choices to make when configuring a CEFI simulation are which diagnostics - or model outputs - to generate.  These determine the analyses that can be conducted to understand the model dynamics and the model applications that are possible.  They also determine these size of the model output files and the storage space required.  Care must thus be taken to ensure that the most critical output is generated without overburdening storage limits.
 
-MOM6 and COBALT each include hundreds of possible diagnostics. A reference of MOM6 diagnostics module can be found [here](https://mom6.readthedocs.io/en/main/api/generated/modules/mom_diagnostics.html?highlight=diag#detamom-diagnostics).  A full list of available COBALT diagnostics can be found in COBALT's diagnostic registration routine ([cobalt_reg_diag.F90](https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/ocean_BGC/blob/dev/cefi/generic_tracers/cobalt_reg_diag.F90)).  A tutorial for adding new diagnostics in COBALT is provided here (*add link*).
+MOM6 and COBALT each include hundreds of possible diagnostics. A reference of MOM6 diagnostics module can be found [here](https://mom6.readthedocs.io/en/main/api/generated/modules/mom_diagnostics.html?highlight=diag#detamom-diagnostics).  A full list of available COBALT diagnostics can be found in COBALT's diagnostic registration routine ([cobalt_reg_diag.F90](https://github.com/NOAA-CEFI-Regional-Ocean-Modeling/ocean_BGC/blob/dev/cefi/generic_tracers/cobalt_reg_diag.F90)). You can use the following command to capture diagnostic variable names in the registration routine:
+```
+git clone git@github.com:NOAA-CEFI-Regional-Ocean-Modeling/ocean_BGC.git --recursive
+cd ocean_BGC/generic_tracers/
+grep -oP 'vardesc\("\K[^"]+' cobalt_reg_diag.F90
+```
+A tutorial for adding new diagnostics in COBALT is provided here (*add link*).
 
 The "diagnostic table" controls which diagnostics are generated.  The default ocean and sea ice diagnostics for CEFI's regional MOM6 simulations can be found *here*, while the default ocean biogeochemical diagnostics can be found [here](https://github.com/NOAA-GFDL/CEFI-regional-MOM6/blob/feature/diag_table_cleanup/xmls/NWA12/diag_tables/diag_table_CEFI_COBALT_default). The file begins by defining broad output categories across which the diagnostics will be organized (check the output file section [here](https://cefi-regional-mom6.readthedocs.io/en/latest/InputsOutputs.html#file-section) for more details).