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Add CEDS 0.1 x 0.1 degree emissions #2171

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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)

Tagging @msulprizio

@yantosca yantosca self-assigned this Feb 29, 2024
@yantosca 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 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 yantosca added this to the 14.4.0 milestone Feb 29, 2024
@yantosca 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 yantosca linked an issue Mar 20, 2024 that may be closed by this pull request
@yantosca
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@1Dandan @Ruijun-Dang: Just wanted to tag #1745 (comment) on this PR. Will await your feedback before proceeding.

@yantosca yantosca removed this from the 14.4.0 milestone Mar 20, 2024
@yantosca yantosca added the deferred Issues/PRs that we cannot work on right away label Mar 22, 2024
@yantosca yantosca deleted the branch main May 30, 2024 18:55
@yantosca yantosca closed this May 30, 2024
@msulprizio msulprizio reopened this May 30, 2024
@msulprizio 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
- 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
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1Dandan commented Jun 21, 2024

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.

msulprizio and others added 6 commits June 26, 2024 08:48
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 <mpayer@seas.harvard.edu>
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 <yantosca@seas.harvard.edu>
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 <yantosca@seas.harvard.edu>
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 <yantosca@seas.harvard.edu>
GeosCore/fullchem_mod.F90
- Removed extraneous "<" character

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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 <yantosca@seas.harvard.edu>
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 <yantosca@seas.harvard.edu>
run/GCHP/ExtData.rc.TransportTracers
- Fixed typo: "shoul'd" -> "should

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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 <yantosca@seas.harvard.edu>
@yantosca yantosca force-pushed the feature/ceds-0.1-degree branch from 5b9946e to 34f8f67 Compare August 12, 2024 20:07
@yantosca yantosca changed the base branch from main to dev/14.5.0 August 12, 2024 20:08
@1Dandan
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1Dandan commented Aug 12, 2024

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.

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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.

@yantosca 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
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 <yantosca@seas.harvard.edu>
CHANGELOG.md
- Edited previous comment to note that the CEDS data are in v2024-06

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
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@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 <yantosca@seas.harvard.edu>
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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 <yantosca@seas.harvard.edu>
@viral211
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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.

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1Dandan commented Sep 26, 2024

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 yantosca changed the base branch from dev/14.5.0 to main November 8, 2024 17:26
@yantosca yantosca linked an issue Nov 20, 2024 that may be closed by this pull request
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yantosca commented Dec 2, 2024

Also see issue #2581. There seems to be a newer version of CEDS available. Should we skip this CEDS version and proceed to the newest version?

Tagging @1Dandan @Mashiat25 @eamarais @jaegle

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eamarais commented Dec 3, 2024

@yantosca, I'd suggest skipping this CEDS version. @1Dandan is probably more familiar with the different versions, so could comment based on their experience.

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yantosca commented Dec 3, 2024

Thanks @eamarais. We can wait for @1Dandan's assessment.

@yantosca yantosca added the deferred Issues/PRs that we cannot work on right away label Dec 3, 2024
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1Dandan commented Dec 4, 2024

Sure I think it is great to include the new version of CEDS (v2024_07_08) as long as they release the gridded dataset.
I had some light email conversations with Steven Smith at PNNL about the CEDS emission development (CEDS-SatEM), which includes some explicit point sources for SO2 (https://zenodo.org/records/7958231). Possibly the new version of CEDS (v2024_07_08) is a step beyond the CEDS-SatEM with point sources of SO2 (?), as said in the releasing note. The time-series comparisons they released against the prior CEDS version (v_2021_04_20 - I guess it is typo and should be the same as v_2021_04_21; Also the one currently implemented in GEOS-Chem) show quite similar trend. I think we need to wait for the gridded dataset to compare the differences for the spatial distribution of emissions especially for SO2 point sources. Or maybe @Mashiat25 you already get the gridded dataset? Hopefully the effects on other aerosol precursors across CEDS versions of v_2021_04_21 and v2024_07_08 are very small.

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randallvmartin commented Dec 4, 2024 via email

@msulprizio
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Based on discussion with the GCST and @randallvmartin and @djxjacob we think the best way forward is to:

  1. Proceed with merging this PR for version 14.6.0 (now in development). This will replace the default CEDSv2 option with CEDS_01x01.
  2. When CEDS v2024_07_08 is ready for implementation into GEOS-Chem/HEMCO we can proceed with either:
    a. Replacing CEDS_01x01 with the updated version CEDS_v2024_07_08. For this scenario, we would ideally we would the updated version at 0.1x0.1 resolution but this is not currently availably yet. As mentioned above, @1Dandan is in communication with the CEDS team.
    b. Including CEDS_v2024_07_08 as an option in addition to CEDS_01x01. In that case, users interested in using emissions for more recent years could choose to use CEDS_v2024_07_08, while users interested in high-resolution simulations still have the option to utilize the higher resolution CEDS_01x01 option.

With that said, @yantosca @1Dandan are we ready to change this pull request from a draft PR and mark it as ready for review?

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eamarais commented Dec 6, 2024

@msulprizio sounds like a reasonable strategy. I wasn't aware when I suggested skipping to the most recent version that the dataset isn't actually ready to implement.

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yantosca commented Dec 6, 2024

@msulprizio: We would have to merge the current 14.5.0 into this version and retest. There have been several emissions updates from the @kelvinhb that went into 14.5.0 that are not reflected yet in this PR.

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category: Feature Request New feature or request deferred Issues/PRs that we cannot work on right away topic: Configuration Files Related to GEOS-Chem configuration files topic: Emissions Related to emissions inventories used in GEOS-Chem topic: Input Data Related to input data
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