Adding in dry deposition updates to Hg0 from Feinberg22 ESPI publication + AMAP emissions #1367

arifein · 2022-09-01T21:36:37Z

This code includes the changes to the dry deposition of Hg0, based on the publication: A. Feinberg, T. Dlamini, M. Jiskra, V. Shah, N. E. Selin, 2022. Evaluating atmospheric mercury (Hg) uptake by vegetation in a chemistry-transport model. Environ. Sci. Process. Impacts. https://doi.org/10.1039/d2em00032f.

The main change is that Hg0 dry deposition reactivity (f0) is set to 3.0e-5 everywhere except for the Amazon rainforest, where it is increased to 0.2. These changes yield improved agreement with observations of Hg0 vegetation uptake, Hg0 seasonality in the Northern midlatitudes, and Hg0 levels in the Southern Hemisphere.

Note that in order to balance the dry deposition changes and maintain good agreement with levels of Hg0 in the Northern Hemisphere, the photo-reduction of Hg(II) in organic aerosol needed to be re-calibrated (HG2ORGP factor increased from 0.004 to 0.010). The altered FJX_j2j.dat file is attached here.

I also attach a benchmark file showing the resulting differences for the Hg concentrations, fluxes, and budget. This compares a run for 2015 from the patch/14.0.1 with the new version including revised Hg0 dry deposition.

FJX_j2j.dat.txt
benchmark_0208_0209.pdf

run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.Hg - As described in geoschem/geos-chem PR #1367, we now point to the CHEM_INPUTS/FAST_JX/v2022-10-Hg data folder for FAST-JX, as the FJX_j2j.dat file was modified. Signed-off-by: Bob Yantosca <[email protected]>

yantosca · 2022-10-20T16:56:50Z

Checklist of additional updates to be tacked on to this PR:

Point to the CHEM_INPUTS/FAST_JX/v2022-10-Hg/ folder in the geoschem_config.yml.Hg template file
Remove JBrO, Br_GC, and BrO_GC from HEMCO_Config.rc.Hg template file
Remove AERO_ fields from the HEMCO_Config.rc.Hg
For now, make sure all oxidant fields point to the GCClassic_Output/13.0..0 version in HEMCO_Config.rc.Hg.

yantosca · 2022-10-20T17:52:32Z

@arifein @jennyfisher @hmhorow @msulprizio @Jourdan-He: I have updated the HEMCO_Config.rc.Hg template file accordingly. Could you verify that these look OK? If so we can proceed to benchmarking.

NOTE: The AMAP emissions will come in a separate PR.

yantosca · 2022-10-20T19:43:51Z

All GCHP integration tests passed

==============================================================================
GCHP: Execution Test Results

Number of execution tests: 3
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gchp_fullchem_benchmark_merra2_c48...............Execute Simulation.....PASS
gchp_fullchem_standard_merra2_c24................Execute Simulation.....PASS
gchp_TransportTracers_geosfp_c24.................Execute Simulation.....PASS
 
Summary of execution test results:
------------------------------------------------------------------------------
Execution tests passed:        3
Execution tests failed:        0
Execution tests not completed: 0

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

arifein · 2022-10-20T20:33:24Z

@yantosca the changes look fine for me.

yantosca · 2022-10-20T21:12:50Z

Thanks @arifein. I think we still may have to get the AMAP emissions into the HEMCO_Config.rc file but that should be easy.

jennyfisher · 2022-10-21T00:25:11Z

Sorry for my github ignorance, but I am not sure where to look to see these changes in HEMCO_Config.rc? In any case, if Ari has checked I trust him!

arifein · 2022-10-21T13:11:34Z

@jennyfisher I found the list of commits here: https://github.com/geoschem/geos-chem/compare/feature/Hg0drydep+updateconfig

With the HEMCO_Config.rc.Hg file changes here: 7369c89

yantosca · 2022-10-21T13:45:44Z

Also question for you @arifein @jennyfisher @hmhorow: We have the AMAP2015 emissions, but are these to be default, or an option? We can add them in here, but we just need to know what your intent is.

yantosca · 2022-10-21T13:47:41Z

All GEOS-Chem Classic integration tests passed:

==============================================================================
GEOS-Chem Classic: Execution Test Results

Using 24 OpenMP threads
Number of execution tests: 48
==============================================================================
 
Execution tests:
------------------------------------------------------------------------------
gc_025x03125_CH4_geosfp_47L_na...................Execute Simulation.....PASS
gc_025x03125_fullchem_geosfp_47L_na..............Execute Simulation.....PASS
gc_05x0625_CH4_merra2_47L_na.....................Execute Simulation.....PASS
gc_05x0625_fullchem_merra2_47L_na................Execute Simulation.....PASS
gc_2x25_aerosol_merra2...........................Execute Simulation.....PASS
gc_2x25_CH4_merra2...............................Execute Simulation.....PASS
gc_2x25_CO2_merra2...............................Execute Simulation.....PASS
gc_2x25_fullchem_merra2..........................Execute Simulation.....PASS
gc_2x25_Hg_merra2................................Execute Simulation.....PASS
gc_2x25_metals_merra2............................Execute Simulation.....PASS
gc_2x25_POPs_BaP_merra2..........................Execute Simulation.....PASS
gc_2x25_tagCH4_merra2............................Execute Simulation.....PASS
gc_2x25_tagCO_merra2.............................Execute Simulation.....PASS
gc_2x25_tagO3_merra2.............................Execute Simulation.....PASS
gc_2x25_TransportTracers_merra2..................Execute Simulation.....PASS
gc_2x25_TransportTracers_merra2_LuoWd............Execute Simulation.....PASS
gc_4x5_aerosol_geosfp............................Execute Simulation.....PASS
gc_4x5_aerosol_merra2............................Execute Simulation.....PASS
gc_4x5_CH4_geosfp................................Execute Simulation.....PASS
gc_4x5_CH4_merra2................................Execute Simulation.....PASS
gc_4x5_fullchem_aciduptake_merra2................Execute Simulation.....PASS
gc_4x5_fullchem_APM_merra2.......................Execute Simulation.....PASS
gc_4x5_fullchem_benchmark_merra2.................Execute Simulation.....PASS
gc_4x5_fullchem_complexSOA_merra2................Execute Simulation.....PASS
gc_4x5_fullchem_complexSOA_SVPOA_merra2..........Execute Simulation.....PASS
gc_4x5_fullchem_geosfp...........................Execute Simulation.....PASS
gc_4x5_fullchem_marinePOA_merra2.................Execute Simulation.....PASS
gc_4x5_fullchem_merra2...........................Execute Simulation.....PASS
gc_4x5_fullchem_merra2_47L.......................Execute Simulation.....PASS
gc_4x5_fullchem_merra2_LuoWd.....................Execute Simulation.....PASS
gc_4x5_fullchem_RRTMG_merra2.....................Execute Simulation.....PASS
gc_4x5_fullchem_TOMAS15_merra2_47L...............Execute Simulation.....PASS
gc_4x5_fullchem_TOMAS40_merra2_47L...............Execute Simulation.....PASS
gc_4x5_Hg_geosfp.................................Execute Simulation.....PASS
gc_4x5_Hg_merra2.................................Execute Simulation.....PASS
gc_4x5_metals_merra2.............................Execute Simulation.....PASS
gc_4x5_POPs_BaP_geosfp...........................Execute Simulation.....PASS
gc_4x5_POPs_BaP_merra2...........................Execute Simulation.....PASS
gc_4x5_tagCH4_geosfp.............................Execute Simulation.....PASS
gc_4x5_tagCH4_merra2.............................Execute Simulation.....PASS
gc_4x5_tagCO_geosfp..............................Execute Simulation.....PASS
gc_4x5_tagCO_merra2..............................Execute Simulation.....PASS
gc_4x5_tagO3_geosfp..............................Execute Simulation.....PASS
gc_4x5_tagO3_merra2..............................Execute Simulation.....PASS
gc_4x5_TransportTracers_geosfp...................Execute Simulation.....PASS
gc_4x5_TransportTracers_geosfp_LuoWd.............Execute Simulation.....PASS
gc_4x5_TransportTracers_merra2...................Execute Simulation.....PASS
gc_4x5_TransportTracers_merra2_LuoWd.............Execute Simulation.....PASS
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 48
Execution tests failed: 0
Execution tests not yet completed: 0

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

yantosca · 2022-10-21T18:21:10Z

Added entries for the AMAP/UNEP Global Mercury Assessment emissions to the HEMCO_Config.rc.Hg template file in commit: c7f17d5. These emissions are stored in the ExtData/HEMCO/MERCURY/v2022-10 data path.

NOTE: This PR will go into branch dev/14.1.0 and not main.

jennyfisher · 2022-10-23T22:37:11Z

Thanks @yantosca!

@arifein - just following up on Bob's Q about whether to make the AMAP emissions default... what did you use for your benchmarking? My preference would be to make AMAP default, but I'm not sure if that would mess with the tuning you have done already...

Also @yantosca can you please let me know when this has gone into dev/14.1.0 so we can pull it down here? Thanks!

yantosca · 2022-10-24T13:30:33Z

The HEMCO_Config.rc file from Helene Angot has AMAP as the default emissions. I added that to the PR. If that's OK we can keep it .

arifein · 2022-10-24T13:31:23Z

Hi @jennyfisher @yantosca, I used the AMAP emissions for my study as well as benchmarking v12-v14 Hg GEOS-Chem versions, so I would also lean to having it as a default.

yantosca · 2022-10-24T14:07:36Z

@jennyfisher @arifein: Excellent! That is all ready in this PR. We think this will be one of the first alpha benchmarks for 14.1.0.

jennyfisher · 2022-10-24T22:28:25Z

Fantastic!

Just to confirm - this isn't yet in the dev/14.1.0 branch, right? We're currently running (testing) using the dev branch (for the other Hg fixes), so as soon as these updates are in dev/14.1.0 we will pull them in, too.

Cheers,
Jenny

yantosca · 2022-10-25T13:37:30Z

@jennyfisher, it is not yet in the dev/14.1.0 branch but is currently in feature/Hg0drydep+updateconfig in the geoschem/geos-chem repo. That has been merged up to 14.1.0.

We will be bringing the 14.1.0 updates in probably starting this week.

jennyfisher · 2022-10-25T23:34:16Z

Great, thanks! Just to clarify, does that mean if we pull feature/Hg0drydep+updateconfig it will have these updates and the previous updates to the Hg simulation (that were in the dev branch before)?

yantosca · 2022-10-28T19:59:05Z

Great, thanks! Just to clarify, does that mean if we pull feature/Hg0drydep+updateconfig it will have these updates and the previous updates to the Hg simulation (that were in the dev branch before)?

@jennyfisher: Yes, if you pull the feature/Hg0drydep+updateconfig branch, it will have all of the 13.4.1 Hg chemistry plus the drydep update and AMAP emissions.

jennyfisher · 2023-01-09T00:01:12Z

Hi @yantosca - I've just cloned dev/14.1.0 and am starting to test. I noticed a couple of switches that still exist in HEMCO_Config.rc, even though we removed the sections for these as they were no longer used:

AERO_HG2_PARTITION
LRED_JNO2

I think that these lines can be deleted now. @arifein @viral211 - can you confirm this is correct?

arifein · 2023-01-09T13:24:43Z

Hi @jennyfisher, I agree that they are no longer used. However, I still see legacy lines of code referring to LRED_JNO2 in ocean_mercury_mod.F90 and mercury_mod.F90 that may also have to be deleted for it to be removed in HEMCO_Config.rc as well:

GeosCore/mercury_mod.F90:  USE Ocean_Mercury_Mod, ONLY : LRED_JNO2
GeosCore/mercury_mod.F90:    LRED_JNO2=.TRUE. ! Make propto JNO2 otherwise [OH]
GeosCore/mercury_mod.F90:    CALL GetExtOpt( HcoState%Config, -999, 'LRED_JNO2', &
GeosCore/mercury_mod.F90:                    OptValBool=LRED_JNO2, FOUND=FOUND, RC=RC )
GeosCore/mercury_mod.F90:       errMsg = 'LRED_JNO2 not found in HEMCO_Config.rc file!'
GeosCore/mercury_mod.F90:       LRED_JNO2 = .FALSE.
GeosCore/mercury_mod.F90:    WRITE( 6, 110   ) LRED_JNO2
GeosCore/mercury_mod.F90:110 FORMAT( 'LRED_JNO2  is set to ', L1                          )
GeosCore/ocean_mercury_mod.F90:  PUBLIC :: LRED_JNO2,   LGEOSLWC
GeosCore/ocean_mercury_mod.F90:  LOGICAL   :: LRED_JNO2,   LGEOSLWC

yantosca · 2023-01-09T14:10:46Z

Hi @jennyfisher, thanks for bringing this up. I can create a PR for fixing this.

arifein added 3 commits August 30, 2022 15:34

Corrected unit error in HEMCO_Diagn.rc

3e7fe21

Added in dry deposition updates to Hg0 from Feinberg22 ESPI publication

44ba80f

Added relevant citation for code

7c81396

msulprizio deleted the branch geoschem:dev/14.1.0 September 19, 2022 15:53

msulprizio closed this Sep 19, 2022

msulprizio added this to the 14.1.0 milestone Sep 19, 2022

msulprizio reopened this Sep 19, 2022

msulprizio changed the base branch from patch/14.0.1 to dev September 19, 2022 15:56

msulprizio changed the base branch from dev to main October 18, 2022 16:51

yantosca added category: Feature Request New feature or request specialty simulations labels Oct 18, 2022

yantosca requested a review from msulprizio October 20, 2022 17:51

yantosca self-assigned this Oct 20, 2022

yantosca changed the title ~~Adding in dry deposition updates to Hg0 from Feinberg22 ESPI publication~~ Adding in dry deposition updates to Hg0 from Feinberg22 ESPI publication + AMAP emissions Oct 21, 2022

yantosca mentioned this pull request Oct 21, 2022

Bug fixes for Prod/Loss diagnostics for Hg simulation -- Closes #1284, #1285 #1356

Merged

msulprizio changed the base branch from main to dev/14.1.0 November 2, 2022 16:27

msulprizio approved these changes Nov 2, 2022

View reviewed changes

msulprizio merged commit 630bf8b into geoschem:dev/14.1.0 Nov 2, 2022

msulprizio added the topic: Hg or POPs simulations Related to the GEOS-Chem Mercury Simulation label Oct 1, 2024

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Adding in dry deposition updates to Hg0 from Feinberg22 ESPI publication + AMAP emissions #1367

Adding in dry deposition updates to Hg0 from Feinberg22 ESPI publication + AMAP emissions #1367

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Adding in dry deposition updates to Hg0 from Feinberg22 ESPI publication + AMAP emissions #1367

Adding in dry deposition updates to Hg0 from Feinberg22 ESPI publication + AMAP emissions #1367

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