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geoschem / geos-chem

GEOS-Chem "Science Codebase" repository. Contains GEOS-Chem science routines, run directory generation scripts, and interface code. This repository is used as a submodule within the GCClassic and GCHP wrappers, as well as in other modeling contexts (external ESMs).
http://geos-chem.org
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[QUESTION] customized chemical mechanism #1306

Closed jinlx closed 1 year ago

jinlx commented 2 years ago

Hi there, I am looking for docs to customize mechanism in GEOS-Chem but it seems that the previous doc has been deleted. Everything related to KPP is merged to https://kpp.readthedocs.io/en/latest/index.html but I am not able to find the previous doc on how to customize mechanism. I was wondering if it's easy to put previous manual in the new web or another place so that people can still easily follow the manual to change chemistry in GEOS-Chem .

Cheers, Lixu

yantosca commented 2 years ago

Thanks for writing @jinlx. We have moved the information about using KPP with GEOS-Chem to this link: geos-chem-shared-docs/supplemental-guides/using-kpp-with-gc.html.

KPP is now being developed as a general open-source software package, and as such, we have updated the documentation at https://kpp.readthedocs.io/ accordingly.

yantosca commented 2 years ago

Oops the link should be: https://geos-chem.readthedocs.io/en/latest/geos-chem-shared-docs/supplemental-guides/using-kpp-with-gc.html.

jinlx commented 2 years ago

Thanks for the quick reply Bob! I will close the issue for now!

yantosca commented 2 years ago

Thanks @jinlx. Let me know if anything in the doc needs updating. We are trying to update all the docs (KPP, GEOS-Chem, HEMCO, etc.) before 14.0.0 gets released.

Also note: 14.0.0 will have code generated by KPP 2.5.0, so you will need to update your KPP version if you plan on modifying mechanisms in 14.0.0 or higher versions. We are currently in the benchmarking process for 14.0.0, so maybe a mid-Aug release.

jinlx commented 1 year ago

HI @yantosca ! This is a follow-up question for adding new compound in the GEOS-Chem. I recently checked customized GEOS-Chem simulation with newly added compounds. The model runs smoothly and I can get those compounds information in GEOSChem.SpeciesConc.yyyymmdd_0000z.nc4. However, species concentration are all 0 for newly added comounds (emission information added). Also those newly added compounds are not saved in HEMCO_diagnostics.yyyymmddhhmm.nc even though I have set up in the HEMCO_Diagn.rc.

In order to get those new speices saved, I was wondering if we need to make any edition in input.geos (i.e., ADVECTED SPECIES MENU) and species_database.yml.

Thanks, Lixu

stale[bot] commented 1 year ago

This issue has been automatically marked as stale because it has not had recent activity. If there are no updates within 7 days it will be closed. You can add the "never stale" tag to prevent the Stale bot from closing this issue.

yantosca commented 1 year ago

We can close out this issue.