Updates for MAPL3 compatibility - #3381
Draft
lizziel wants to merge 133 commits into
Draft
Conversation
KPP/custom/custom.eqn KPP/fullchem/fullchem.eqn - Add 1 hetchem and 1 gas-phase reaction for MDL KPP/fullchem/commonIncludeVars.H - Added K_MDL as a !$OMP THREADPRIVATE variable KPP/fullchem/fullchem_SulfurChemFuncs.F90 - Added id_MDL module variable to store the ModelID of MDL - Added Cloud_CH2O_MDL function to compure CH2O -> MDL hetchem rate KPP/fullchem/gckpp*.F90 - Rebuilt with KPP 3.3.0 run/CESM/geoschem_config.yml run/GCClassic/geoschem_config.yml run/GCHP/geoschem_config.yml run/GEOS/geoschem_config.yml run/WRF/fullchem/geoschem_config.yml - Added methanediol (MDL) as a transported species run/shared/species_database.yml - Added species metadata for metheanediol CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_SulfurChemFuncs.F90 - Use "Spc(id_MDL)%Conc(I,J,L)" as the argument to MDL_g when calling Cloud_CH2O_MDL - Use "Spc(id_CH2O)%Conc(I,J,L)" as the argument to CH2O_g when calling Cloud_CH2O_MDL run/shared/species_database.yml - Fixed typo: "MDL::" -> "MDL:" Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/custom/custom.eqn
KPP/fullchem/fullchem.eqn
- Added PSO4AQ as a product to the SO2 + H2O2 rxn
- Added PSO4AQ as a product to the SO2 + O3 rxn
- Added PSO4AQ as a product to the SO2 {+O2} rxn
- Added PH2SO4 as a product to the HOCl + SO2 rxn
- Added PH2SO4 as a product to the HOBr + SO2 rxn
KPP/fullchem/gckpp_*
- Rebuilt with KPP 3.3.0
CHANGELOG.md
KPP/fullchem/CHANGELOG_fullchem.md
- Updated accordingly
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
…/10.1021/acsetair.5c00136. Includes SO2 oxidation in aerosol water by H2O2, O3, NO2, HCHO, and TMI-catalzyed O2. Addition of cloud HPLUS diagnostic since cloud pH diagnostic appears broken. Signed-off-by: Katherine R. Travis <ktravis1@discover35.prv.cube>
…/10.1021/acsetair.5c00136. Includes SO2 oxidation in aerosol water by H2O2, O3, NO2, HCHO, and TMI-catalzyed O2. Addition of cloud HPLUS diagnostic since cloud pH diagnostic appears broken. Signed-off-by: Katherine R. Travis <ktravis1@discover35.prv.cube>
…/10.1021/acsetair.5c00136. Includes SO2 oxidation in aerosol water by H2O2, O3, NO2, HCHO, and TMI-catalzyed O2. Addition of cloud HPLUS diagnostic since cloud pH diagnostic appears broken. Signed-off-by: Katherine R. Travis <ktravis1@discover35.prv.cube>
--> Change 'uptake probability' to 'sticking coefficient' for consistency --> Consolidate production trackers from 13 to 3 (PSO4MP for multiphase sulfate, and PHMSAQ and PHMSMP for HMS aqueous and multiphase production) --> Improved computational efficiency by removing ELSE blocks. --> Added _dp to constants --> Add Ionic strength diagnostic to GCHP HISTORY template Signed-off-by: Katherine R. Travis <ktravis1@discover36.prv.cube>
GeosCore/aerosol_mod.F90 GeosCore/planeflight_mod.F90 Headers/state_chm_mod.F90 KPP/fullchem/fullchem_HetStateFuncs.F90 - Renamed State_Chm%Isorrop* fields to State_Chm%Ate*, where "Ate" stands for "aerosol thermoydnamical equilibrium". ISORROPIA is no longer used so this should avoid confusion. run/GCClassic/HISTORY.rc.templates/HISTORY.rc.aerosol run/GCClassic/HISTORY.rc.templates/HISTORY.rc.fullchem run/GCHP/HISTORY.rc.templates/HISTORY.rc.fullchem - Rename diagnostic fields from "Isorrop*" to "Ate*" CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/gckpp*F90 - Rebuilt with KPP 3.3.0 KPP/fullchem/CHANGELOG_fullchem.md - Changed "[ TBD ]" to the standard "[Unreleased] - TBD" Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_HetStateFuncs.F90
- Removed id_DST{1..4} variables
- Added id_DSTbin{1..7} variables
- Updated the equation for DUST to use DSTbin{1..7} species, which
were added in GEOS-Chem 14.7.0.
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
We have rebuilt the KPP solver files with KPP 3.3.0. The previous commit had used a development version of KPP which was unreleased. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_SulfurChemFuncs.F90 - We have removed the scavenging factor of 0.7 from the expression for the DUST variable in routine SET_SO2, based on a suggestion by Katie Travis (@ktravis213). - Cosmetic changes (indentation, etc. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #3072 (Add PSO4AQ and PH2SO4 as products to certain reactions, by @yantosca and @fsolmon) into the GEOS-Chem 14.8.0 development stream. PR #3072 does the following - Adds PSO4AQ as a product to the SO2 + H2O2 rxn - Adds PSO4AQ as a product to the SO2 + O3 rxn - Adds PSO4AQ as a product to the SO2 {+O2} rxn - Adds PH2SO4 as a product to the HOCl + SO2 rxn - Adds PH2SO4 as a product to the HOBr + SO2 rxn Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/custom/custom.eqn KPP/fullchem/fullchem.eqn - Updated the version number to 14.8.0 - Added citation Travis et al 2025 to HMS + OH + SO2 rxn CHANGELOG.md - Removed leftover line from merge conflict Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/shared/species_database.yml - Removed several leftover dummy species Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_HetStateFuncs.F90 - Removed extraneous comma at end of line after id_DSTbin3 - Removed the 0.7 wet scavenging factor as per @ktravis213
KPP/custom/custom.eqn KPP/fullchem/fullchem.eqn - Added comments denoting additional multiphase sulfate rxns as coming from the Travis2025 paper Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
This merge brings PR #3132 (Add methanediol chemistry into the fullchem mechanism (cf. Yang et al 2025), by @laura-hyesung-yang and @yantosca) into the GEOS-Chem 14.8.0 development stream. In PR #3132 we have done the following: 1. Implemented methanediol chemistry as per Laura Yang et al, GRL, 2025. 2. Rebuilt the fullchem mechanism with KPP 3.3.0. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
…TOMAS and new particle formation by organics and updated ternary scheme. Also KPP modified to fix bug for missing PSO4AQ and PH2SO4 terms in equations needed by TOMAS.
KPP/fullchem/fullchem_HetStateFuncs.F90
- Added the following species ID flags as arguments to routine
fullchem_SetState_Het, calling Ind_ from within the subroutine
(which is computationally inefficient):
- id_DSTbin{1..7}, id_pFe, id_SO2, id_SO4
- Removed Ind_ from the USE State_Chm_Mod statement in the
fullchem_SetStateHet routine
GeosCore/fullchem_mod.F90
- Added local variables id_DSTbin{1..7}, id_pFe, id_SO2, id_SO4,
which are set in Init_FullChem adn passed as arguments to
fullchem_SetStateHet
Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
run/shared/species_database.yml - Added metadata for PHMSAQ and PHMSMP dummy species Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Headers/state_chm_mod.F90 - Bug fix: Rename the metadata for all former ISORROP* diagnostics to ATE*. This indicates that ISORROPIA is no longer used, but we now use the term ATE (for aerosol thermodynamical equilibrium) instead. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_RateLawFuncs.F90 - Removed k_ex1 variable, we only need k - Renamed gammaKT to gamma - Separated local varaiables from arguments - Added comments - Cosmetic changes (whitespace, indentation) Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_SetStateHet - Add calls to SafeDiv to prevent div-by-zero conditions - Do not call ReactoDiff_Corr when l_r is zero, as this will get placed into the denominator, which will cause an div-by-zero - Removed the xradi variable, now use State_Chem%AeroRadi directly - Removed e+0 from numerical constants - Cosmetic changes (indentation, comments, line breaks, aesthetics) Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_RateLawFuncs.F90 - Renamed "CRITRH" parameter to "RH_35_PERCENT" for clarity - Renamed "CRITRH2" parameter to "RH_50_PERDCENT" for clarity CHANGELOG.md - Updated accordingy Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
KPP/fullchem/fullchem_HetStateFuncs.F90 - Changed "hydroxide*3" to "hydroxide**3" in the expression for Fe_d_a. This was a typo. Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…ctmEnv Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…cover Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
The code in this file is still written for MAPL2 Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…_mod Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…anch) Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
…ates Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
Signed-off-by: Lizzie Lundgren <elundgren@seas.harvard.edu>
yantosca
added
category: Feature Request
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Coming soon....
Name and Institution (Required)
Name:
Institution:
Describe the update
Please provide a clear and concise overview of the update.
Expected changes
Please provide details on how this update will impact model output and include plots or tables as needed.
Reference(s)
If this is a science update, please provide a literature citation.
Related Github Issue
Please link to the corresponding Github issue(s) here. If fixing a bug, there should be an issue describing it with steps to reproduce.