Add CEDS 0.1 x 0.1 degree emissions #2171

yantosca · 2024-02-29T22:47:40Z

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Name: Bob Yantosca
Institution: Harvard + GCST

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Describe the update

This is the companion PR to #1745.

Expected changes

As described in #1745

Related Github Issue(s)

Closes Adding CEDS at 0.1 degree as a global emission inventory #1745

Tagging @msulprizio

run/GCHP/ExtData.rc.templates/ExtData.rc.TransportTracers

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem

yantosca · 2024-03-20T21:02:00Z

@1Dandan @Ruijun-Dang: Just wanted to tag #1745 (comment) on this PR. Will await your feedback before proceeding.

- use AerMass in OCPISOA to avoid unnecessary recalculation - removed unnecessary OCPI reference when SVPOA is activated

- replace verbose representation of SOA and OCPI with OCPISOA

…nSVPOA - also includes some rewrites for better readability

1Dandan · 2024-06-21T16:24:26Z

Hi @yantosca @msulprizio, the seasonality problem as mentioned in #1745 should be fixed in the new version of v2024-06. File names remain the same as those in v2023-04, and thus all v2023-04 can be replaced by v2024-06 for HEMCO_Config.rc and ExtData.rc templates. Let me know if you want other inputs from me.

R4N2 was a common product of alkane, isoprene, and monoterpene oxidation and produced organonitrate SOA but we don’t want ALK4 to produce organonitrate SOA as discusses in #1625. A fix from Jared Brewer is included here. NOTE: The KPP fullchem mechanism has not been rebuilt with these fixes to facilitate merging these updates up to the latest GEOS-Chem release. These updates will also need to be added to the custom.eqn file. Signed-off-by: Melissa Sulprizio <[email protected]>

run/shared/species_database.yml run/shared/species_database_hg.yml - Allow for KPP_AbsTol and KPP_RelTol tags. - Set KPP_AbsTol to 1.0e25 for all dummy species, in order to prevent these from being considered when computing the error norm. Headers/species_mod.F90 - Add KPP_AbsTol and KPP_RelTol to the Species derived type Headers/species_database_mod.F90 - Add "KPP_AbsTol" and "KPP_RelTol" to the tags array - Add code to parse KPP_AbsTol and KPP_RelTol tags - Remove the "places" keyword and just pass the number of decimal places, for a consistent appearance - Trimmed trailing whitespace - Updated comments Headers/state_chem_mod.F90 - Add KPP_AbsTol and KPP_RelTol 1-D arrays. These are initialized at the same time as the Map_KppVar mapping array. This will allow us to replace missing values at initialization, and just copy the values to ATOL and RTOL each timestep. This is more efficient. GeosCore/fullchem_mod.F90 GeosCore/mercury_mod.F90 - Replace missing values in State_Chm%KPP_AbsTol and State_Chm%KPP_RelTol with default values. This preserves the absolute and relative tolerances for species that were specified in species_database.yml. - Copy State_Chm%KPP_AbsTol to the KPP ATOL array - Copy State_Chm%KPP_RelTol to the KPP RTOL array Signed-off-by: Bob Yantosca <[email protected]>

CHANGELOG.md - Added notes describing how we can now define KPP absolute and relative tolerances for species in species_database.yml Signed-off-by: Bob Yantosca <[email protected]>

Headers/roundoff_mod.F90 - Bug fix: First cast to dble or flex. Then round off if the places argument is > 0. This allows us to just cast w/o rounding off if needed. run/shared/species_database_mod.F90 - Changed 1.0e+25_8 to 1.0e+25 in for KPP_AbsTol (LBRO2H) CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>

GeosCore/fullchem_mod.F90 - Removed extraneous "<" character Signed-off-by: Bob Yantosca <[email protected]>

@yantosca

This merge brings PR #2359 (Allow per-species definition of KPP absolute and relative solver tolerances; Set absolute tolerances of dummy species to large value, by @yantosca) into the GEOS-Chem 14.5.0 development stream. This PR adds structural updates to allow per-species setting of the KPP absolute & relative tolerances. This now allows us to assign a large absolute tolerance (1e25) to KPP dummy species, which excludes them from the error norm computations. This results in a faster simulation at the cost of numerical noise. Signed-off-by: Bob Yantosca <[email protected]>

@yuanjianz

This merge brings PR #2315 (ix bugs in PDER, OCPISOA and TotalOC in complexSOA, by @yuanjianz) into the GEOS-Chem 14.5.0 development stream. This PR fixes several minor bugs in the complex SOA scheme as described in issues #2314 and #2321. Signed-off-by: Bob Yantosca <[email protected]>

Previously these values were zero due to an issue in ISORROPIA. With the update to HETP we can now enable these cations. Signed-off-by: Lizzie Lundgren <[email protected]>

This merge brings the GEOS-Chem 14.4.2 release into the GEOS-Chem 14.5.0 development stream. 14.4.2 is a zero-diff update. The CHANGELOG.md has been updated accordingly. Signed-off-by: Bob Yantosca <[email protected]>

@lizziel

This merge brings PR #2398 (Pass non-zero Ca2, Mg, and K cations to HETP, by @lizziel) into the GEOS-Chem 14.5.0 development stream. This PR uncomments setting Ca2+, K+, and Mg+ cation values passed to HETP. Previously these values were zero due to an issue in ISORROPIA. With the update to HETP we can enable these cations. Signed-off-by: Bob Yantosca <[email protected]>

Resolved conflicts in: CHANGELOG.md KPP/fullchem/fullchem.eqn KPP/fullchem/fullchem.kpp run/shared/species_database.yml Signed-off-by: Melissa Sulprizio <[email protected]>

@msulprizio

This merge brings PR #2352 (Add fixes for ALK4 and R4N2 chemistry from Brewer et al. (2023, JGR), by @msulprizio) into the GEOS-Chem 14.5.0 development stream. R4N2 was a common product of alkane, isoprene, and monoterpene oxidation and produced organonitrate SOA but we don’t want ALK4 to produce organonitrate SOA as discusses in #1625. A fix from Jared Brewer is included here. Signed-off-by: Bob Yantosca <[email protected]>

Due to an oversight, we had forgotten to rebuild the KPP solver files for PR #2352. This has now been done. We will re-tag this PR with 14.5.0-alpha.4 to re-trigger 1-month benchmarks. Signed-off-by: Bob Yantosca <[email protected]>

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem - Added entries for CEDS 0.1 x 0.1 degree emissions. NOTE: ExtData.rc.fullchem will be updated later. CHANGELOG.md - Updated accordingly Signed-off-by: Bob Yantosca <[email protected]>

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem - CEDS01 comment update "1750-2019" -> "1980-2019" - Also updated header comments run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.TransportTracers run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.TransportTracers run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCHP/ExtData.rc.templates/ExtData.rc.carbon run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem run/GCHP/ExtData.rc.templates/ExtData.rc.TransportTracers - Added entries for CEDS_01x01 as the default - Now make CEDSv2 an option Signed-off-by: Bob Yantosca <[email protected]>

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCHP/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem - For container "CEDS01_TOLU_WST", added scale factor=26, cat=1, hier=5. This had been omitted due to a cut-n-paste error. Signed-off-by: Bob Yantosca <[email protected]>

run/GCHP/ExtData.rc.TransportTracers - Fixed typo: "shoul'd" -> "should Signed-off-by: Bob Yantosca <[email protected]>

This rebase merge brings PR #2171 (CEDS 0.1 x 0.1 emissions) atop PR #2352 (ALK4 & R4N2 chemistry updates) Signed-off-by: Bob Yantosca <[email protected]>

1Dandan · 2024-08-12T20:22:08Z

Hi @yantosca, I noticed that the CEDS 0.1 version is still v2023-04, which needs to be changed to v2024-06.
Also, I deleted all files at CEDS/v2023-04 at http://geoschemdata.wustl.edu/ExtData/HEMCO/CEDS/ to avoid any confusion as v2024-06 should be used instead.

yantosca · 2024-08-12T20:32:29Z

Thanks @1Dandan, yes I just rebased the existing code atop of dev/14.5.0. I'll push another commit to update the directory paths.

Updated the following configuration files to read CEDS 0.1 x 0.1 degree emissions data from the HEMCO/CEDS/v2024-06 folder: run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.aerosol run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.carbon run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.tagCO run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.TransportTracers run/GCHP/ExtData.rc.templates/ExtData.rc.carbon run/GCHP/ExtData.rc.templates/ExtData.rc.fullchem run/GCHP/ExtData.rc.templates/ExtData.rc.TransportTracers Also updated the CHANGELOG.md accordingly. Signed-off-by: Bob Yantosca <[email protected]>

CHANGELOG.md - Edited previous comment to note that the CEDS data are in v2024-06 Signed-off-by: Bob Yantosca <[email protected]>

yantosca · 2024-08-12T21:38:16Z

@1Dandan: DIrectory paths updated in commit 91acc1a. Will start integration testing and fix any further issues that arise.

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem - Fixed mismatching brackets for CEDS_01x01_SHIP for NO emissions Signed-off-by: Bob Yantosca <[email protected]>

yantosca · 2024-08-13T14:20:50Z

All GEOS-Chem integration tests passed:

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

GCClassic #0c22a3a GEOS-Chem submod update: PR #2352 post-merge fix (rebuild KPP files)
GEOS-Chem #769698837 Fix mismatching brackets in HEMCO_Config.rc template
HEMCO     #e68ebae HEMCO 3.9.2 release

Using 24 OpenMP threads
Number of execution tests: 28

Submitted as SLURM job: 43586737
==============================================================================

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

run/GCHP/ExtData.rc.templates/ExtData.rc.carbon - Change climatology data entries from e.g "2009 Y" to "Y Y F2009-..." - Remove slug left over from Git merge Signed-off-by: Bob Yantosca <[email protected]>

viral211 · 2024-09-25T23:14:11Z

Hi @yantosca and @1Dandan, CEDS also identifies their versions with the release date (https://github.com/JGCRI/CEDS/releases) and users can confuse that with the folder names in our CEDS data directory. For example, CEDS had a new version called v_2024_04_01, but I think our folder v2024-06 has CEDS version v_2021_4_21 data. Could we display the CEDS version prominently to avoid any confusion? Thanks.

1Dandan · 2024-09-26T15:35:15Z

Thanks @viral211 for the suggestion. I agree that it is confusing as our processed version may conflict with the releasing date of the original version. I add a line in the README of This is a seasonality fixed version based on the original released version of v2021_4_21_Release (https://data.pnnl.gov/group/nodes/dataset/13488). Would you @viral211 @yantosca have further suggestions to make it clear?

yantosca self-assigned this Feb 29, 2024

yantosca changed the title ~~Edit HEMCO_Config.rc.fullchem for CEDS 0.1 degree emisisons~~ Add CEDS 0.1 x 0.1 degree emissions Feb 29, 2024

yantosca added category: Feature Request New feature or request topic: Input Data Related to input data topic: Configuration Files Related to GEOS-Chem configuration files labels Feb 29, 2024

yantosca added this to the 14.4.0 milestone Feb 29, 2024

yantosca mentioned this pull request Mar 1, 2024

"Too many nested brackets" error in HEMCO 3.8.0 geoschem/HEMCO#261

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msulprizio reviewed Mar 4, 2024

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yantosca mentioned this pull request Mar 12, 2024

Allow up to 10 nested brackets in the HEMCO_Config.rc file geoschem/HEMCO#262

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yantosca added deferred Issues/PRs that we cannot work on right away help needed: Request Input From Community We need GC community to provide a fix/update and removed deferred Issues/PRs that we cannot work on right away labels Mar 20, 2024

yantosca linked an issue Mar 20, 2024 that may be closed by this pull request

Adding CEDS at 0.1 degree as a global emission inventory #1745

Open

yantosca removed this from the 14.4.0 milestone Mar 20, 2024

yantosca added the deferred Issues/PRs that we cannot work on right away label Mar 22, 2024

yantosca deleted the branch main May 30, 2024 18:55

yantosca closed this May 30, 2024

msulprizio reopened this May 30, 2024

msulprizio changed the base branch from dev/14.4.0 to main May 30, 2024 19:16

yuanjianz added 3 commits June 8, 2024 02:02

Simplified and removed unnecessary codes

81912e0

- use AerMass in OCPISOA to avoid unnecessary recalculation - removed unnecessary OCPI reference when SVPOA is activated

Supported SVPOA in SNAOM parameterized effective radius

f79c946

- replace verbose representation of SOA and OCPI with OCPISOA

Fixed bug only including Isoprene SOA OC for TotalOC in complexSOA_no…

2592c6d

…nSVPOA - also includes some rewrites for better readability

msulprizio and others added 6 commits June 26, 2024 08:48

Update CHANGELOG for KPP_AbsTol and KPP_RelTol updates

9f22811

CHANGELOG.md - Added notes describing how we can now define KPP absolute and relative tolerances for species in species_database.yml Signed-off-by: Bob Yantosca <[email protected]>

Fixed typo in fullchem_mod.F90

813ea43

GeosCore/fullchem_mod.F90 - Removed extraneous "<" character Signed-off-by: Bob Yantosca <[email protected]>

yantosca and others added 12 commits July 16, 2024 12:29

Uncomment setting Ca2, K, and Mg cation values passed to HETP

0276c54

Previously these values were zero due to an issue in ISORROPIA. With the update to HETP we can now enable these cations. Signed-off-by: Lizzie Lundgren <[email protected]>

Merge GEOS-Chem 14.4.2 back into the 14.5.0 development stream

0a17228

This merge brings the GEOS-Chem 14.4.2 release into the GEOS-Chem 14.5.0 development stream. 14.4.2 is a zero-diff update. The CHANGELOG.md has been updated accordingly. Signed-off-by: Bob Yantosca <[email protected]>

Merge 'origin/dev/14.5.0' into bugfix/alk4-chem-brewer2023

6548a8b

Resolved conflicts in: CHANGELOG.md KPP/fullchem/fullchem.eqn KPP/fullchem/fullchem.kpp run/shared/species_database.yml Signed-off-by: Melissa Sulprizio <[email protected]>

Fixed typo in ExtData.rc.TransportTracers

012639a

run/GCHP/ExtData.rc.TransportTracers - Fixed typo: "shoul'd" -> "should Signed-off-by: Bob Yantosca <[email protected]>

Rebased PR #2171 (CEDS 0.1 degree) atop of PR #2352

34f8f67

This rebase merge brings PR #2171 (CEDS 0.1 x 0.1 emissions) atop PR #2352 (ALK4 & R4N2 chemistry updates) Signed-off-by: Bob Yantosca <[email protected]>

yantosca force-pushed the feature/ceds-0.1-degree branch from 5b9946e to 34f8f67 Compare August 12, 2024 20:07

yantosca changed the base branch from main to dev/14.5.0 August 12, 2024 20:08

yantosca added topic: Emissions Related to emissions inventories used in GEOS-Chem and removed help needed: Request Input From Community We need GC community to provide a fix/update deferred Issues/PRs that we cannot work on right away labels Aug 12, 2024

yantosca added 2 commits August 12, 2024 17:29

Updated CHANGELOG.md to denote CEDS/v2024-06 folder

aa379cc

CHANGELOG.md - Edited previous comment to note that the CEDS data are in v2024-06 Signed-off-by: Bob Yantosca <[email protected]>

Fix mismatching brackets in HEMCO_Config.rc template

7696988

run/GCClassic/HEMCO_Config.rc.templates/HEMCO_Config.rc.fullchem - Fixed mismatching brackets for CEDS_01x01_SHIP for NO emissions Signed-off-by: Bob Yantosca <[email protected]>

Fix minor issues in the ExtData.rc.carbon template

acf8ff8

run/GCHP/ExtData.rc.templates/ExtData.rc.carbon - Change climatology data entries from e.g "2009 Y" to "Y Y F2009-..." - Remove slug left over from Git merge Signed-off-by: Bob Yantosca <[email protected]>

yantosca changed the base branch from dev/14.5.0 to main November 8, 2024 17:26

yantosca linked an issue Nov 20, 2024 that may be closed by this pull request

Implementation of latest version of CEDS (v_2024_07_08) #2581

Open

yantosca mentioned this pull request Nov 20, 2024

Implementation of latest version of CEDS (v_2024_07_08) #2581

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Add CEDS 0.1 x 0.1 degree emissions #2171

Add CEDS 0.1 x 0.1 degree emissions #2171

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Add CEDS 0.1 x 0.1 degree emissions #2171

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yantosca commented Feb 29, 2024

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