Missing output variables

Questions, issues, or suggestions related to post-processing of model output.
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zmenzo
Posts: 37
Joined: Tue Feb 18, 2020 11:14 pm

Missing output variables

Post by zmenzo » Tue May 04, 2021 11:30 pm

Hello,

In the users guide there are output variables that I cannot locate in the diag or history output. For example spechum (real) (nVertLevels, nCells, Time). Does this have to do with the " Allocated by: jedi_da" or the "Accessed in code as ‘spechum’ from the ‘diag’ pool"). I am aware that I can get spechum from the mixing ratio. But is there not a direct spechum output?

Thanks as always

mgduda
Posts: 466
Joined: Mon Feb 26, 2018 7:35 pm

Re: Missing output variables

Post by mgduda » Wed May 05, 2021 5:38 pm

The "Allocated by: jedi_da" note in the User's Guide for the spechum field does indicate that this field will only be allocated and accessible in MPAS-Atmosphere if the "jedi_da" package is active, which only happens when the namelist option config_jedi_da is true. Interestingly, a grep through the atmosphere core code for "spechum" only turns up one match, which happens to be the definition of the field in the Registry.xml file. So, it looks as though this field is neither computed nor used in the model. In short, then, you'll need to compute specific humidity from mixing ratio (qv).
NCAR/MMM

zmenzo
Posts: 37
Joined: Tue Feb 18, 2020 11:14 pm

Re: Missing output variables

Post by zmenzo » Wed May 05, 2021 9:48 pm

Thank you so much for all the information. I've found in the manual how to config the jedi_da. Since it is hidden by default, I'm assuming I just add it into my namelist in the correct section and true it to true. However, since you said it still will not compute spechum, does that mean it will not calculate temperature as well? Just for my better edification, why would the default be NOT to calculate spechum and temperature?

Also, why are some variables relegated to the history and others to the diagnostics? I guess I am still having a difficult time understanding the difference beyond the "Files contain mostly 2d diagnostic fields & mostly 3d prognostic and diagnostic files from the model." description. And when it comes to removing variables from the stream_files, are there any that need to stay in there in order for the model to run or to use additional options like convert_mpas afterward (i.e., zEdge, indexToEdgeID, latVertex, etc.)?

I apologize for the wave of questions but really appreciate all of your assistance.

mcurry
Posts: 78
Joined: Mon Oct 29, 2018 5:33 pm
Location: Boulder, Co

Re: Missing output variables

Post by mcurry » Thu May 06, 2021 12:38 am

Hi Zemero,
However, since you said it still will not compute spechum, does that mean it will not calculate temperature as well?
Instead of giving you the answer for whether temperature is computed or not, I recommend adding the temperature field to an output stream, running a short simulation on a coarse grid and producing a single output file from the stream you added to the temperature field to. You could simply add the temperature field to the history stream, run a simulation on the 240 km mesh for 2 hours, and have the history stream output one file on the hour. Once the simulation is finish, you can check the history file and see if the temperature has realistic atmospheric values (in Kelvin). If the temperature field is all 0.0's (the default value) you'll know that its not being calculated and that you'll have to diagnose it and then output it to the stream you added temperature.

I think this will give you a good exercise of removing/adding variables to a stream list and output a variable to a stream in the code.
Just for my better edification, why would the default be NOT to calculate spechum and temperature?
I'll let someone else answer this question.
Also, why are some variables relegated to the history and others to the diagnostics?
From my understanding the history file contains the state variables of the atmosphere, temperature, pressure, and water vapor, from which other fields can be computed from and I believe most diagnostic fields can be computed from those variables. However, I think someone with more experience in NWP could expand on my answer.
And when it comes to removing variables from the stream_files, are there any that need to stay in there in order for the model to run or to use additional options like convert_mpas afterward (i.e., zEdge, indexToEdgeID, latVertex, etc.)?
For this question, I'll point you to one of the introductory paragraphs in Chapter 5 of the user guide:
Two classes of streams exist in MPAS: immutable streams and mutable streams. Immutable streams are those for which the set of fields that belong to the stream may not be modified at model run-time; however, it is possible to modify the interval at which the stream is read or written, the filename template describing the files containing the stream on disk, and several other parameters of the stream. In contrast, all aspects of mutable streams, including the set of fields that belong to the stream, may be modified at run-time. The motivation for the creation of two stream classes is the idea that an MPAS core may not function correctly if certain fields are not read in upon model start-up or written to restart files, and it is therefore not reasonable for users to modify this set of required fields at run-time.
Thus, the output and diagnostic streams are mutable streams, and you can alter their stream_lists as you see fit (or remove the stream all together).
NCAR|MMM

zmenzo
Posts: 37
Joined: Tue Feb 18, 2020 11:14 pm

Re: Missing output variables

Post by zmenzo » Thu May 06, 2021 9:02 pm

Thank you both very much for your explanations.
I am still relatively new to coding and using climate models, so these conversations are incredibly insightful.

Zach

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