Chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024) #2318

ktravis213 · 2024-06-11T18:17:35Z

Name and Institution (Required)

Name: Katherine Travis
Institution: NASA LaRC

Describe the update

This update provides new chemistry for RCOOH, monoterpenes, new PNs (PHAN, MEKPN, APAN, LIMPAN, PINPAN, AROMPN) and a new AN (RNO3).

Must be merged concurrently with: geoschem/HEMCO#285, which contains the corresponding emissions updates to GFED and FINN biomass extensions.

Expected changes

The paper describes that there will be small (+/-1 ppb changes in ozone) as a result of the new peroxynitrate (PN) species.

Reference(s)

https://egusphere.copernicus.org/preprints/2024/egusphere-2024-951/

…, PINPAN, AROMPN) and new AN (RNO3) from Travis et al., 2024 Signed-off-by: Katherine R. Travis <[email protected]>

yantosca · 2024-07-26T13:59:28Z

Thanks @ktravis and @msulprizio. I've opened a new branch off of 14.3. 0 (the parent commit) and pulled in the updates. This can go in following PR #2352.

This merge brings PR #2318 (K. Travis chemistry updates, based off version 14.3.0) up-to-date with PR #2352 (J. Brewer chemistry updates for ALK4, R4N2). Signed-off-by: Bob Yantosca <[email protected]>

yantosca · 2024-08-06T19:18:51Z

All GCHP integration tests passed:

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

GCHP      #136fa70 GEOS-Chem submod update: Merge PR #2398 (Uncomment cations for HETP)
GEOS-Chem #38b6d1801 Update HEMCO_Config.rc for CESM with Kelvin Bates emissions updates
HEMCO     #

Number of execution tests: 11

Submitted as SLURM job: 42874275
==============================================================================
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

yantosca · 2024-08-06T19:22:50Z

All GEOS-Chem Classic integration tests passed:

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

GCClassic #6f22240 GEOS-Chem submod update: Merge PR #2398 (Uncomment cations for HETP)
GEOS-Chem #38b6d1801 Update HEMCO_Config.rc for CESM with Kelvin Bates emissions updates
HEMCO     #3076296 Species ACR should use index #41 in hcox_gfed_include_gfed4.H

Using 24 OpenMP threads
Number of execution tests: 28

Submitted as SLURM job: 42874229
==============================================================================
 
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%  All execution tests passed!  %%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

yantosca · 2024-08-08T16:12:50Z

Hi @ktravis213 @kelvinhb @msulprizio: I ran a benchmark to test these changes. The plots are in our Google Drive, and here is a link that you should be able to view them at:

https://drive.google.com/drive/folders/1SlWvBitzmYPm5uoKXUX-YIdUv8c8uRTY?usp=sharing

Also note: We know there is a big slowdown in the code but that is caused by Photolysis (see #2416). @lizziel is working on a fix for that.

There is a small decrease in the mean OH. Also

###############################################################################
### OH Metrics
### Ref = 14.5.0-alpha.4 (ALK4 + R4N2 fixes from @JFBrewer)
### Dev = 14.5.0-alpha.5 (Chemistry + Emission updates from @ktravis213 and @kelvinhb)
###############################################################################

------------------------------------------------------------
Global mass-weighted OH concentration [10^5 molec cm^-3]
------------------------------------------------------------
Ref      : 13.67824118787
Dev      : 13.64446964510
Abs diff : -0.03377154277
%   diff : -0.246900

------------------------------------------------------------
CH3CCl3 (aka MCF) lifetime w/r/t tropospheric OH [years]
------------------------------------------------------------
Ref      :  4.480028
Dev      :  4.497625
Abs diff :  0.017597
%   diff :  0.392790

------------------------------------------------------------
CH4 lifetime w/r/t tropospheric OH [years]
------------------------------------------------------------
Ref      :  7.550699
Dev      :  7.581547
Abs diff :  0.030848
%   diff :  0.408541

Also, O3 at the surface shows up to 5% decrease over continents (most pronounced over N. boreal regions and the Amazon), with a corresponding increase over the N. Pacific basin.

Please take a look at the results and let me know what you think. If this looks OK I will go ahead and merge this in.

kelvinhb · 2024-08-08T19:23:39Z

Hi team -- at first pass these changes look reasonable to me; I'd be curious if Katie has any different expectations about the direction or magnitude of OH & ozone changes, but I'd say they seem alright (and honestly smaller than expected). One question this brings up is whether we want to make changes to our lists of families / categories / lumped species for the sake of benchmarking, since now there are additional primary organics (e.g. ALK6, TMB), secondary organics (e.g. R6P, HACTA), NOy's (e.g. APAN, PHAN), RO2's, and maybe other members of these various groups. Doesn't have to happen immediately, but down the line it'd probably be good to update these with each new version number (especially since multiple simultaneous updates will probably affect this -- thinking about Jared's R4N2 update here too).

yantosca · 2024-08-08T20:09:16Z

Thanks @kelvinhb. Yes, we'd have to edit these files in GCPy to add the extra species:

yantosca · 2024-08-08T21:02:50Z

I opened a companion GCPy PR at: geoschem/gcpy#331

yantosca · 2024-08-12T14:59:04Z

@ktravis213, when you get a chance can you review the benchmark plots above? Thanks.

yantosca · 2024-08-14T18:09:05Z

@ktravis213 @kelvinhb @JFBrewer: Should ALK4P be an advected species? This is one of Jared's chemistry updates from PR #2352. It's not in the geoschem_config.yml file but is listed as advected in the species_database.yml file;

ALK4P:
  DD_F0: 1.0
  DD_Hstar: 2.94e+2
  Formula: CH3CH2CH2CH2OOH
  FullName: Peroxide from ALK4O2
  Henry_CR: 5200.0
  Henry_K0: 2.94e+2
  Is_Advected: true
  Is_DryDep: true
  Is_Gas: true
  Is_Photolysis: true
  Is_WetDep: true
  MW_g: 90.14
  WD_RetFactor: 2.0e-2

This is causing a species mismatch in the budget diagnostics. Let me know either way, thanks!!!

kelvinhb · 2024-08-14T18:12:19Z

Yes, it's a stable (non-radical) species with a long enough lifetime that it should definitely be advected!

yantosca · 2024-08-14T18:50:47Z

Thanks, I'll change that!

yantosca · 2024-08-15T14:39:55Z

@ktravis213 @kelvinhb: I re-ran the benchmark with ALK4 as an advected species and regenerated the plots with the updates that you suggested in PR geoschem/gcpy#331. Here is the link to the new plots and tables:

https://drive.google.com/drive/folders/1ncpdB70Rlpje5yYoxV0JYj7xcz2F1fp6?usp=sharing

Note: 14.5.0-alpha.5 is now going to be 14.4.3 merged up into the 14.5.0 branch. So this PR will be 14.5.0-alpha.6.

The OH metrics are now:

###############################################################################
### OH Metrics
### Ref = 14.5.0-alpha.4
### Dev = 14.5.0-alpha.6
###############################################################################

------------------------------------------------------------
Global mass-weighted OH concentration [10^5 molec cm^-3]
------------------------------------------------------------
Ref      : 13.67824118787
Dev      : 13.64393706793
Abs diff : -0.03430411994
%   diff : -0.250793

------------------------------------------------------------
CH3CCl3 (aka MCF) lifetime w/r/t tropospheric OH [years]
------------------------------------------------------------
Ref      :  4.480028
Dev      :  4.497657
Abs diff :  0.017629
%   diff :  0.393497

------------------------------------------------------------
CH4 lifetime w/r/t tropospheric OH [years]
------------------------------------------------------------
Ref      :  7.550699
Dev      :  7.581556
Abs diff :  0.030857
%   diff :  0.408663

Also, the new species are now in the plots, e.g.:

yantosca · 2024-08-15T14:54:55Z

@ktravis213 @kelvinhb: Should MACR be now ACR in HEMCO_Diagn.rc? I noticed ACR wasn't there:

270:#####  MACR emissions                                                     #####
272:EmisMACR_Total     MACR   -1     -1  -1   3   kg/m2/s  MACR_emission_flux_from_all_sectors
273:EmisMACR_Aircraft  MACR   0      20  -1   3   kg/m2/s  MACR_emission_flux_from_anthropogenic
618:InvAEIC_MACR         MACR   0    20  1   3   kg/m2/s  MACR_emission_flux_from_AEIC_inventory

as well as the other emissions STYR, TMB, etc. I can add those in.

Also MGLY has to be added to the benchmark_categories.yml. Is that a primary organic? (Sorry, my chemistry is very lacking.)

Warning: species MGLY has emissions diagnostics but is not in benchmark_categories.yml

ktravis213 · 2024-08-15T16:43:29Z

Hi Bob, We don't want to replace MACR, but add ACR yes!

…

On Thu, Aug 15, 2024 at 10:55 AM Bob Yantosca ***@***.***> wrote: @ktravis213 <https://github.com/ktravis213> @kelvinhb <https://github.com/kelvinhb>: Should MACR be now ACR in HEMCO_Diagn.rc? I noticed ACR wasn't there: 270:##### MACR emissions #####272:EmisMACR_Total MACR -1 -1 -1 3 kg/m2/s MACR_emission_flux_from_all_sectors273:EmisMACR_Aircraft MACR 0 20 -1 3 kg/m2/s MACR_emission_flux_from_anthropogenic618:InvAEIC_MACR MACR 0 20 1 3 kg/m2/s MACR_emission_flux_from_AEIC_inventory — Reply to this email directly, view it on GitHub <#2318 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABEUK64KYM67UZFPLLDMJ5LZRS6NLAVCNFSM6AAAAABJE3J3HWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOJRGQ2TINJWGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

run/CESM/HEMCO_Config.rc - Trim trailing whitespace run/CESM/geoschem_config.yml run/GEOS/geoschem_config.yml run/WRF/fullchem/geoschem_config.yml - Add ACR, ALK4P, ALK7, APAN, APINP, APINN, AROMPN, BPINO, BPINN, BPINP, BPINOOH, BPINON, BUTN, C96O2H, C96N, C4H6, EBZ, LIMAL, LIMKB, LIMKET, LIMN, LIMNB, LIMO2H, MEKPN, MYRCO, PHAN, PIN, PINAL, PINONIC, PINO3H, PINPAN, R7N2, R7P, RCOOH, RNO3, STYR, TMB as advected species run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml - Restore ALK4P as an advected species run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.fullchem - Add Emis*Total and Emis*Bioburn entries for ACR, C4H6, HCOOH, STYR - Add InvGFED* entries for ACR, C4H6, HCOOH, MVK, STYR run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.fullchem run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.fullchem - Restore ALK4P as an advected species run/GCHP/HISTORY.rc.templates/HISTORY.rc - Add Emis*BioBurn entries for ACR, C4H6, HCOOH, STYR, - Add Inv*BioBurn entries for ACR, C4H6, HCOOH, STYR run/GEOS/HEMCO_Config.rc - Add new GFED species run/WRF/fullchem/HEMCO_Config.rc - Change Verbose from "0" to "false" - Add "VerboseOnCores: root" - Add new biomass burning species (from FURA onwards) - Add CEDS entries for EBZ and TMB species - Change emitted species "MACR" to "ACR" in EPA16 entries - Update CEDS scale factors as they are in GCClassic/GCHP - Remove .and. in ((( and ))) brackets and list them individually - Change "$GCAPVERTRESL" to "$GCAPVERTRES" as in GCClassic/GCHP - Add GT_Chlorine entries - Update GFED data dir to v2023-03 - Write HEMCO_Restart file in the ./Restarts folder - Now use Vohra timezones - Use v2023-10 folder for NOAA_GMD_CH4 - Add scale factors as for GCClassic and GCHP run/shared/setupConfigFiles.sh - Now insert ASOA* and ASOG* entries after species AROMPN (formerly after AROMP5) Signed-off-by: Bob Yantosca <[email protected]>

This merge brings PR # ( , by @) into Signed-off-by: Bob Yantosca <[email protected]>

run/CESM/HEMCO_Config.rc - Trim trailing whitespace run/CESM/geoschem_config.yml run/GEOS/geoschem_config.yml run/WRF/fullchem/geoschem_config.yml - Add ACR, ALK4P, ALK7, APAN, APINP, APINN, AROMPN, BPINO, BPINN, BPINP, BPINOOH, BPINON, BUTN, C96O2H, C96N, C4H6, EBZ, LIMAL, LIMKB, LIMKET, LIMN, LIMNB, LIMO2H, MEKPN, MYRCO, PHAN, PIN, PINAL, PINONIC, PINO3H, PINPAN, R7N2, R7P, RCOOH, RNO3, STYR, TMB as advected species run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml - Restore ALK4P as an advected species run/GCHP/HEMCO_Diagn.rc.templates/HEMCO_Diagn.rc.fullchem - Add Emis*Total and Emis*Bioburn entries for ACR, C4H6, HCOOH, STYR - Add InvGFED* entries for ACR, C4H6, HCOOH, MVK, STYR run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml.fullchem run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.fullchem - Restore ALK4P as an advected species run/GCHP/HISTORY.rc.templates/HISTORY.rc - Add Emis*BioBurn entries for ACR, C4H6, HCOOH, STYR, - Add Inv*BioBurn entries for ACR, C4H6, HCOOH, STYR run/GEOS/HEMCO_Config.rc - Add new GFED species run/WRF/fullchem/HEMCO_Config.rc - Change Verbose from "0" to "false" - Add "VerboseOnCores: root" - Add new biomass burning species (from FURA onwards) - Add CEDS entries for EBZ and TMB species - Change emitted species "MACR" to "ACR" in EPA16 entries - Update CEDS scale factors as they are in GCClassic/GCHP - Remove .and. in ((( and ))) brackets and list them individually - Change "$GCAPVERTRESL" to "$GCAPVERTRES" as in GCClassic/GCHP - Add GT_Chlorine entries - Update GFED data dir to v2023-03 - Write HEMCO_Restart file in the ./Restarts folder - Now use Vohra timezones - Use v2023-10 folder for NOAA_GMD_CH4 - Add scale factors as for GCClassic and GCHP run/shared/setupConfigFiles.sh - Now insert ASOA* and ASOG* entries after species AROMPN (formerly after AROMP5) Signed-off-by: Bob Yantosca <[email protected]>

yantosca · 2024-08-19T14:34:31Z

@ktravis213 @kelvinhb: I re-ran the benchmark again to make sure that we saved out the new species to HEMCO diagnostics. Please see:

gcc-14.5.0-alpha.6-1mo benchmark results

We do now get the new species in the biomass burning output:

BioBurn_Emissions.pdf

OH metrics are as before:

###############################################################################
### OH Metrics
### Ref = 14.5.0-alpha.4
### Dev = 14.5.0-alpha.6
###############################################################################

------------------------------------------------------------
Global mass-weighted OH concentration [10^5 molec cm^-3]
------------------------------------------------------------
Ref      : 13.67824118787
Dev      : 13.64393706793
Abs diff : -0.03430411994
%   diff : -0.250793

------------------------------------------------------------
CH3CCl3 (aka MCF) lifetime w/r/t tropospheric OH [years]
------------------------------------------------------------
Ref      :  4.480028
Dev      :  4.497657
Abs diff :  0.017629
%   diff :  0.393497

------------------------------------------------------------
CH4 lifetime w/r/t tropospheric OH [years]
------------------------------------------------------------
Ref      :  7.550699
Dev      :  7.581556
Abs diff :  0.030857
%   diff :  0.408663

I will merge this PR (and geoschem/HEMCO#285) pending successful integration tests merged up to dev/14.5.0 and dev/3.10.0.

@msulprizio: The ModelE2.1 integration test failed with:

HEMCO ERROR: Cannot find file for current simulation time: /n/holyscratch01/external_repos/GEOS-CHEM/gc
grid/data/ExtData/HEMCO/GCAP2/GMI/v2015-02/40L/gmi.clim.RCOOH.geos5.2x25.nc - Cannot get field GMI_LOSS
_RCOOH. Please check file name and time (incl. time range flag) in the config. file
 
HEMCO ERROR: Error encountered in routine HCOIO_Read!
 
HEMCO ERROR: Error in HCOIO_DATAREAD called from HEMCO ReadList_Fill: GMI_LOSS_RCOOH
 --> LOCATION: ReadList_Fill (HCO_ReadList_Mod.F90)
 
HEMCO ERROR: Error in ReadList_Fill (3) called from HEMCO ReadList_Read
 --> LOCATION: ReadList_Read (HCO_ReadList_Mod.F90)
 Error in ReadList_Read called from hco_run

looks like an issue in the HEMCO_Config.rc file. I am investigating.

run/GCHP/geoschem_config.yml.templates/geoschem_config.yml.fullchem - Added the species introduced by PR #2318 to the transported species list. Somehow this was either not added or lost in a merge. Signed-off-by: Bob Yantosca <[email protected]>

yantosca · 2024-08-19T18:54:56Z

Update: The ModelE2.1 integration test is failing due to a missing file. See #2427 for details.

Also, the "alldiags" integration test was failing on the budget diagnostics. This was caused by additional species that were not listed as transported species in geoschem_config.yml. This is now fixed in commit d7e1248.

yantosca · 2024-08-19T21:21:18Z

After merging up to 14.5.0 (locally), all integration tests passed except ModelE2.1:

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

CodeDir   : 8da455b GEOS-Chem submod update: PR #2425 post-merge fix (CHANGELOG.md update_
GEOS-Chem : 368d8bb4b PR #2318 post-merge fix: Add missing species to geoschem_config.yml
HEMCO     : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
Cloud-J   : d20050f Update version to 7.7.3
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 30

Submitted as SLURM job: 44252377
==============================================================================

gc_2x25_ModelE2.1_fullchem..........................Execute Simulation....FAIL

Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 29
Execution tests failed: 1
Execution tests not yet completed: 0

The ModelE2.1 test failed due to a missing file as described in #2427.

yantosca · 2024-08-19T21:55:02Z

All GCHP integration tests passed:

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

CodeDir       : 8588f5e GEOS-Chem submod update: PR #2425 post-merge fix (CHANGELOG.md update_
MAPL          : 231d53c Merge pull request #36 from geoschem/feature/improve_hflux_regridding
GMAO_Shared   : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake    : ad5deba Added ecbuild as a submodule of ESMA_cmake
gFTL-shared   : 4b82492 Merge branch 'upstream_v1.5.0' into feature/v1.5.0
FMS           : 259759d Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : af42462 Merge PR #8 (Add PLEadv diagnostic for offline advection in GCHP)
geos-chem     : 20566e803 Bug fix: Add ALK4P to geoschem_config.yml templates
HEMCO         : 41605bd HEMCO 3.9.3 release
yaFyaml       : 19afe50 Merge branch 'upstream_v1.0.4' into feature/v1.0.4
pFlogger      : 2c4b724 Merge branch 'upstream_v1.9.1' into feature/v1.9.1
Cloud-J       : d20050f Update version to 7.7.3
HETP          : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Number of execution tests: 12

Submitted as SLURM job: 44256832
==============================================================================

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

yantosca · 2024-08-19T22:02:55Z

The GCHP "benchmark" and "alldiags" tests are now failing with this error:

Fortran runtime error: Index '201' of dimension 3 of array 'state_diag%drydepchm' above upper bound of 175

Error termination. Backtrace:
#0  0x7639c2 in grav_settling
	at /n/holyscratch01/jacob_lab/ryantosca/tests/14.5.0/gc2318/GCHP_it/CodeDir/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/GeosCore/sulfate_mod.F90:1827
#1  0x764e1a in __sulfate_mod_MOD_chemsulfate
	at /n/holyscratch01/jacob_lab/ryantosca/tests/14.5.0/gc2318/GCHP_it/CodeDir/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/GeosCore/sulfate_mod.F90:436
#2  0x4d7948 in __chemistry_mod_MOD_do_chemistry
	at /n/holyscratch01/jacob_lab/ryantosca/tests/14.5.0/gc2318/GCHP_it/CodeDir/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/GeosCore/chemistry_mod.F90:556
#3  0x4b3cbf in __gchp_chunk_mod_MOD_gchp_chunk_run
	at /n/holyscratch01/jacob_lab/ryantosca/tests/14.5.0/gc2318/GCHP_it/CodeDir/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/Interfaces/GCHP/gchp_chunk_mod.F90:1357
#4  0x49752f in run_
	at /n/holyscratch01/jacob_lab/ryantosca/tests/14.5.0/gc2318/GCHP_it/CodeDir/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/Interfaces/GCHP/Chem_GridCompMod.F90:2880
#5  0x4a2204 in run2
	at /n/holyscratch01/jacob_lab/ryantosca/tests/14.5.0/gc2318/GCHP_it/CodeDir/src/GCHP_GridComp/GEOSChem_GridComp/geos-chem/Interfaces/GCHP/Chem_GridCompMod.F90:2052

It could be that more species need to be listed as advected. I am investigating.

yantosca · 2024-08-20T15:37:50Z

After merging up to 14.5.0 (locally), and fixing several post-merge issues (mostly missing or duplicate entries in configuration files), all GCHP integration tests now pass:

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

CodeDir       : 8588f5e GEOS-Chem submod update: PR #2425 post-merge fix (CHANGELOG.md update_
MAPL          : 231d53c Merge pull request #36 from geoschem/feature/improve_hflux_regridding
GMAO_Shared   : 4ddb3ec Merge pull request #2 from geoschem/feature/mapl-upgrade
ESMA_cmake    : ad5deba Added ecbuild as a submodule of ESMA_cmake
gFTL-shared   : 4b82492 Merge branch 'upstream_v1.5.0' into feature/v1.5.0
FMS           : 259759d Merge pull request #3 from geoschem/feature/update_gmao_libs
FVdycoreCubed : af42462 Merge PR #8 (Add PLEadv diagnostic for offline advection in GCHP)
geos-chem     : 586260f10 PR #2318 post-merge fix: Use less drydep fields for the alldiags test
HEMCO         : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
yaFyaml       : 19afe50 Merge branch 'upstream_v1.0.4' into feature/v1.0.4
pFlogger      : 2c4b724 Merge branch 'upstream_v1.9.1' into feature/v1.9.1
Cloud-J       : d20050f Update version to 7.7.3
HETP          : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Number of execution tests: 12

Submitted as SLURM job: 44324820
==============================================================================

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

yantosca · 2024-08-20T15:43:03Z

All GCClassic execution tests (except ModelE2.1) passed:

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

CodeDir   : 8da455b GEOS-Chem submod update: PR #2425 post-merge fix (CHANGELOG.md update_
GEOS-Chem : 368d8bb4b PR #2318 post-merge fix: Add missing species to geoschem_config.yml
HEMCO     : d0d5fca PR #285 post-merge fix: Update CHANGELOG.md
Cloud-J   : d20050f Update version to 7.7.3
HETP      : 2a99b24 Merge pull request #2 from geoschem/bugfix/initialize_local_variables

Using 24 OpenMP threads
Number of execution tests: 30

Submitted as SLURM job: 44252377
==============================================================================

gc_2x25_ModelE2.1_fullchem..........................Execute Simulation....FAIL

See issue #2427 for details.

@ktravis213

This merge brings PR #2318 (Chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024), by @ktravis213) into the GEOS-Chem 14.5.0 development stream. This PR introduces several new chemistry reactions following the Travis et al 2024 article. Signed-off-by: Bob Yantosca <[email protected]>

run/CESM/geoschem_config.yml run/GCClassic/geoschem_config.yml.templates/geoschem_config.yml run/GCHP/geoschem_config.yml.templates/geoschem_config.yml run/GEOS/geoschem_config.yml run/WRF/fullchem/geoschem_config.yml - Add transported species: ALK4N2, AROMCHO, HACTA, TLFUONE. These are listed as transported in species_database.yml and need to be also listed here in geoschem_config.yml. Otherwise this will cause a species mismatch in the budget diagnostics. run/shared/species_database.yml - Fix typo: "<KF2" -> "KF2" Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Removed a duplicate entry for EmisHCOOH_Total from the Emissions collection. This was probably left over from the merge up to the dev/14.5.0 branch. Also consolidated all HCOOH emissions diagnostics together in the same block. Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Only keep the fields that are necessary for fullchem benchmarks in the DryDep collection. This is similar to what is being done in PR #2144 (which will be merged later). Signed-off-by: Bob Yantosca <[email protected]>

yantosca · 2024-08-20T16:02:53Z

This PR has now been merged into the GEOS-Chem 14.5.0 development stream, and will be tagged as 14.5.0-alpha.6. We can now close this out.

@yantosca

This merge brings PR # (Update GFED4_Climatology entries for period 2010-2023 with new species, by @yantosca) into the GEOS-Chem 14.5.0 development stream. This is the companion PR to issue #2415. We have re-generated the GFED4 climatology and GFED4 monthly mean data files by running the HEMCO standalone simulation for the period 2010-2023. We have also included the new species that were introduced in PR #2318 and HEMCO PR https://github.com/geoschem//HEMCO#285. Signed-off-by: Bob Yantosca <[email protected]>

ktravis213 · 2024-09-04T19:42:42Z

Photolysis species:
This is the update for FJX_J2j.dat

167 APINP     PHOTON    PINAL OH HO2                      1.000 /CH3OOH/
168 PINAL     PHOTON    CO HO2 C96O2                      1.000 /ActAld/
169 PINO3H    PHOTON    CO HO2 C96O2                      1.000 /CH3OOH/
170 PINONIC   PHOTON    CO HO2 C96O2                      1.000 /MGlyxl/
171 C96O2H    PHOTON    OH AROMRO2 ACET CH2O RCO3 MEK     1.000 /CH3OOH/
172 BPINP     PHOTON    OH CH2O HO2 BPINO                 1.000 /CH3OOH/
173 BPINOOH   PHOTON    OH HO2 LIMO3 ACET RCHO R4O2       1.000 /CH3OOH/
174 LIMO3H    PHOTON    OH CO2 MCO3 RCHO CH2O R4O2        1.000 /CH3OOH/
175 LIMO2H    PHOTON    OH CO2 MCO3 RCHO CH2O R4O2        1.000 /MGlyxl/
176 LIMAL     PHOTON    CO HO2 LIMO3                      1.000 /ActAld/

@yantosca

This merge brings PR # (Bug fix: Reorder photo rxns for PNs and ANs (from PR #2318), by @yantosca) into the GEOS-Chem 14.5.0 development stream. This PR reorders the photo rxns that were added in PR #2318 so that they now follow PPN as listed in Cloud-J config file FJX_j2j.dat. Signed-off-by: Bob Yantosca <[email protected]>

With the updated monoterpene/PN/AN chemistry and emissions added in 14.5.0-alpha.6 (updates on top of PR #2318), emissions for >=C6 alkanes from CEDS were added to HEMCO_Config.rc. These were incorrectly assigned to species ALK6 (not defined) when they should be assigned to ALK7. Other fixes here include: - Update HEMCO_Diagn.rc (and HISTORY.rc for GCHP) to save out ALK7 emissions - Fix category for CEDS ship emissions of HCOOH and ALK7 in HEMCO_Config.rc (should be 10, not 1) - Make fullchem HEMCO_Diagn.rc for WRF consistent with GCClassic version Closes #2459 Signed-off-by: Melissa Sulprizio <[email protected]>

@msulprizio

This merge brings PR #2462 (Bug fix: ALK6 in HEMCO_Config.rc should be ALK7, by @msulprizio) into the GEOS-Chem 14.5.0 development stream. This PR fixes a bug introduced in PR #2318, where the ALK7 species was erroneously named ALK6 in HEMCO configuration files. Signed-off-by: Bob Yantosca <[email protected]>

Chemistry for RCOOH, monoterpenes, new PNs (PHAN, MEKPN, APAN, LIMPAN…

6bf23a9

…, PINPAN, AROMPN) and new AN (RNO3) from Travis et al., 2024 Signed-off-by: Katherine R. Travis <[email protected]>

yantosca added category: Feature Request New feature or request topic: Chemical Mechanisms Related to KPP and/or GEOS-Chem chemistry mechanisms labels Jul 10, 2024

yantosca changed the base branch from main to dev/14.5.0 July 16, 2024 16:43

msulprizio changed the title ~~Chemistry for RCOOH, monoterpenes, new PNs (PHAN, MEKPN, APAN, LIMPAN…~~ Chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024) Jul 18, 2024

msulprizio mentioned this pull request Jul 18, 2024

Emissions of new species (ALK6, C4H6, EBZ, STYR, TMB) from fires and anthropogenic emission #2390

Closed

yantosca self-assigned this Aug 1, 2024

yantosca mentioned this pull request Aug 1, 2024

Add emission factors for ALK6, C4H6, EBZ, STYR, TMB emissions in GFED and FINN biomass burning geoschem/HEMCO#285

Merged

yantosca added the topic: Emissions Related to emissions inventories used in GEOS-Chem label Aug 5, 2024

yantosca added this to the 14.5.0 milestone Aug 5, 2024

yantosca mentioned this pull request Aug 8, 2024

Update benchmark YAML files with new species for GEOS-Chem 14.5.0 geoschem/gcpy#331

Merged

yantosca mentioned this pull request Aug 14, 2024

Merge GEOS-Chem 14.4.3 into the 14.5.0 development branch #2425

Merged

yantosca pushed a commit that referenced this pull request Aug 15, 2024

Rebase PR #2318 (Chemistry of RCHO, HCOOH ...) to commit 8f0a167

99802a3

This merge brings PR # ( , by @) into Signed-off-by: Bob Yantosca <[email protected]>

yantosca mentioned this pull request Aug 19, 2024

Missing GMI prod/loss files for GCAP2 40L grid #2427

Closed

yantosca self-requested a review August 20, 2024 16:01

yantosca approved these changes Aug 20, 2024

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yantosca closed this Aug 20, 2024

yantosca mentioned this pull request Sep 10, 2024

Inconsistencies between photolysis species listed in species_database.yml and FJX_j2j.dat for fullchem mechanism #2456

Closed

msulprizio mentioned this pull request Sep 11, 2024

Inconsistency in species defined in GEOS-Chem and HEMCO config following pull request #2318 #2459

Closed

msulprizio mentioned this pull request Sep 13, 2024

Bug fix: ALK6 in HEMCO_Config.rc should be ALK7 #2462

Merged

msulprizio mentioned this pull request Oct 1, 2024

Use ALK6 species name for >= C6 alkanes instead of ALK7 #2493

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yantosca mentioned this pull request Nov 12, 2024

Fix incorrect species classification in benchmark_categories.yml geoschem/gcpy#345

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Chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024) #2318

Chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024) #2318

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Chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024) #2318

Chemistry for RCOOH, monoterpenes, new PNs and ANs from Travis et al. (2024) #2318

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