Comment out manual InvMEGAN diagnostic creation code

[eamarais]

Your name

Eloise Marais

Your affiliation

UCL, UK

What happened? What did you expect to happen?

This is only sort of a bug. It's a request to comment out unnecessary code that outputs lots of emissions estimates by default when these aren't wanted. Specifically, to comment out calls to Diagn_Create code for all "InvMEGAN_*" variables in the subroutine HCOX_Megan_Init in ./HEMCO/src/Extensions/hcox_megan_mod.F90. These aren't needed, as the user can request these be output from the HEMCO diagnostics file HEMCO_Diagn.rc.
I tested and confirmed that commenting out all these lines, recompiling and rerunning GCClassic with the diagnostics requested via HEMCO_Diagn.rc works.

What are the steps to reproduce the bug?

Intentionally left blank, as this is just a quick fix detailed above.

Please attach any relevant configuration and log files.

Attached a screenshot to show 1 of the 16 diagnostics currently set manually in the code.

What HEMCO version were you using?

3.0.0 and 3.6.0 (issue is in both)

What environment were you running HEMCO on?

Local cluster

What compiler and version were you using?

gcc 9.2.0

Will you be addressing this bug yourself?

Yes

In what configuration were you running HEMCO?

GCClassic

As what resolution were you running HEMCO?

multiple (4x5, 0.25x0.3125)

What meterology fields did you use?

GEOS-FP

Additional information

No response

[msulprizio]

Thanks for reporting this @eamarais. I've added it to our to-do list for an upcoming release (GEOS-Chem 14.4.x or 14.5.0).

[yantosca]

Hi @msulprizio and @eamarais, thanks for bringing this up. I wonder if we could figure out a way to leave the InvMEGAN diagnostics on for the fullchem_benchmark simulations (since we use them to generate inventory tables) but disable them otherwise. I can look into this.

Also note, in PR #2372 we are implementing a fix to turn off the MEGAN extension for all fullchem simulations except fullchem_benchmark. This has the added benefit of disabling the InvMEGAN diagnostic output. See this comment.

[eamarais]

Hi @yantosca, these should be output as long as these are specified in the HEMCO_Diagn.rc file.

[yantosca]

@eamarais: Maybe an easy fix is to delete those lines from the HEMCO_Diagn.rc at rundir creation for all fullchem simulations except benchmark. I can look into this.

[eamarais]

@yantosca, I don't quite follow your suggestion, as my recommendation is that it makes sense to no longer have these Diagn_Create lines in the code. These are no longer needed, as the request to output the InvMEGAN* variables can be specified by users in HEMCO_Diagn.rc and users can output these when they want, rather than having these output by default.

[yantosca]

@eamarais: Oh yes, now I see. Brain freeze.

[yantosca]

Thanks @eamarais. We can now close this issue out as PR #282 has been merged into the HEMCO "no-diff-to-benchmark" development stream. This will ship with GEOS-Chem 14.4.2 / HEMCO 3.9.2.

[zmoon]

output the InvMEGAN* variables can be specified by users in HEMCO_Diagn.rc and users can output these when they want

can be activated by adding the proper entries to the HEMCO_Diagn.rc file.

Hi there. We're having difficulty doing this in practice. I tried, for example,

InvMEGAN_AAXX    AAXX         108    -1  -1   2   kg/m2/s

but we don't get the diagnostics out.

I noticed that the block that sends data back to HcoState doesn't include these species. Could that be related? Or is my HEMCO_Diagn.rc line incorrect? Or do other HEMCO config parts need to be modified too?

[zmoon]

I tested and confirmed that commenting out all these lines, recompiling and rerunning GCClassic with the diagnostics requested via HEMCO_Diagn.rc works.

@eamarais would you be able to share what your HEMCO_Diagn.rc looked like for this?

[eamarais]

@zmoon, I don't recall changing the format of the lines in HEMCO_Diagn.rc, so it should just be the following for isoprene, for example:

InvMEGAN_ISOP ISOP 108 -1 -1 2 kg/m2/s ISOP_biogenic_emission_flux_from_MEGAN_extension

These lines are located below the commented text "MEGAN Extension" and require that extension 108 be turned on in HEMCO_Config.rc.

Hope this helps!

[drnimbusrain]

@yantosca @eamarais Following up on this discussion, can you please help clarify how to get these InvMEGAN* variable diagnostics out from latest standalone HEMCO v3.10+, e.g., AAXX, FAXX, APIN, BPIN, etc.

For example, we have some of these turned on in the HEMCO_sa_Diag.rc file as the following:

InvMEGAN_AAXX    AAXX         108    -1  -1   2   kg/m2/s
InvMEGAN_FAXX    FAXX         108    -1  -1   2   kg/m2/s
InvMEGAN_APIN    APIN         108    -1  -1   2   kg/m2/s

While we get all other diagnostics from MEGAN extension (e.g., ISOP), we do not get the AAXX, FAXX, and APIN in the output.

Thank you.

[eamarais]

@zmoon and @drnimbusrain, I feel sheepish as I realise now that my suggested modification is not suitable and that my check that it "worked" was superficial, as I output only the emissions associated with GEOS-Chem species.

@msulprizio and @yantosca, please could you revert my suggested changes to the code? Sorry about that! It does mean then that these emissions are output with every simulation. Is there a way around this, like a conditional statement in the hcox_megan_mod.F90 code?