Updates from GMAO for GEOS #2062

lizziel · 2023-12-06T17:26:57Z

Name and Institution (Required)

Name: Lizzie Lundgren
Institution: Harvard University

Describe the update

Updates include the following:

Updates impacting the standard offline model:
- Two new optional diagnostics to track number of negative concentrations after KPP integration
  - State_Diag%KPPNegatives is number of grid cells with negative concentration after KPP integration
  - State_Diag%KPPNegatives0 is number of grid cells with negative concentration after first KPP integration attempt
GEOS-only updates:
- Add run-time option to check for negatives after KPP integration (Input_Opt%KppCheckNegatives)
- Add run-time parameter for KPP tolerance inflation factor for second KPP integration attempt (Input_Opt%KppTolScale)
- Turn off 3 heterogeneous reactions in stratosphere by default (previously default was not to do this)
- Add parameter to define RATS phase
- Move GEOS diagnostic exports to geos_interface.F90
- Always prescribe H2O in both the stratosphere and troposphere in GEOS
- Updates for GEOS H2O tendency and Ox diagnostics
- Add logic to determine whether to apply H2O tendency to Q
- Add subroutine to set H2O from specific humidity (GEOS_SetH2O)
- Use absolute data paths in GEOS-Chem ExtData yaml file used in GEOS
- Set species friendly to moist by default
- Add inventory for GEOS 3-hourly methane within PBL
- Turn off GEOS-Chem convection by default
- Update Fast-JX input directory

Expected changes

This is a zero diff update for offline GEOS-Chem.

Reference(s)

None

Related Github Issue(s)

None

…me regression

…s via the Input_Opt%TurnOffHetRates toggle. This is the preferred solution for GEOS runs. The 5 heterogenous reactions are: ClNO3 + HBr --> BrCl + HNO3 ClNO3 + BrSALA --> BrCl + HNO3 ClNO3 + BrSALC --> BrCl + HNO3 BrNO3 + HCl --> BrCl + HNO3 HOCl + HBr --> BrCl + H2O This toggle was added to a previous version of GEOS-Chem (v12) but its functionality did not get transferred to the updated heterogeneous chemistry reaction rate code. This is a zero-diff change unless one enables the Input_Opt%TurnOffHetRates toggle.

…in the previous commit

…ly, this update now sets H2O at the beginning of the GEOS-Chem run, at the same time when all other species are updated from the internal state. This is important to make sure that the H2O tendency gets properly calculated.

… can cause mass balance violations. This update adds the option to repeat the integration with HSTART reset to zero and increased error tolerances. Both of these factors reduce the risk of negative concentrations. This update only applies to GEOS

…dly to chemistry

# Conflicts: # Headers/input_opt_mod.F90 # Interfaces/GCHP/Chem_GridCompMod.F90

…P integration

…ng analysis increment

yantosca

These changes look OK to merge. I've noted some comments for efficiency.

GeosCore/fullchem_mod.F90

christophkeller · 2023-12-06T21:21:04Z

Good points @yantosca! The suggested changes look good to me, thanks for pointing them out!

lizziel · 2023-12-06T21:43:24Z

@christophkeller, I added another commit on top of this with some minor changes. State_Diag%KPPnegatives0 is now set outside of the MODEL_GEOS loop so it is available for all configurations of the model. The check for negatives now includes condition IERR >= 0. This is to avoid double-counting when incrementing diagnostic State_Daig%KppError which was already incremented if IERR < 0.

You probably noticed I excluded all KPP directory updates. The updates from Eric Fleming have conflicts with JPL updates from Kelvin Bates that have gone into dev/14.3.0. Would it be possible for Eric to make new KPP updates as needed on top of 14.3.0?

lizziel · 2023-12-06T21:44:13Z

@yantosca, thanks for the recommendations! I pushed updates to address all of your comments.

christophkeller · 2023-12-07T01:36:31Z

@christophkeller, I added another commit on top of this with some minor changes. State_Diag%KPPnegatives0 is now set outside of the MODEL_GEOS loop so it is available for all configurations of the model. The check for negatives now includes condition IERR >= 0. This is to avoid double-counting when incrementing diagnostic State_Daig%KppError which was already incremented if IERR < 0.

You probably noticed I excluded all KPP directory updates. The updates from Eric Fleming have conflicts with JPL updates from Kelvin Bates that have gone into dev/14.3.0. Would it be possible for Eric to make new KPP updates as needed on top of 14.3.0?

This is fine, I suspected that this might happen. Once released, we can go through 14.3.0 to make sure that all of Eric's updates are being integrated.

yantosca

Good to merge! Thanks @lizziel.

…mmitted in the previous commit" This reverts commit be4b499.

This reverts commit 2d6db44.

…to feature/updates_for_geos # Conflicts: # GeosCore/fullchem_mod.F90 # Headers/state_diag_mod.F90 # Interfaces/GCHP/Chem_GridCompMod.F90 # run/GEOS/GEOSCHEMchem_ExtData.yaml # run/GEOS/geoschem_config.yml Signed-off-by: Lizzie Lundgren <[email protected]>

Signed-off-by: Lizzie Lundgren <[email protected]>

…units Signed-off-by: Lizzie Lundgren <[email protected]>

Signed-off-by: Lizzie Lundgren <[email protected]>

lizziel · 2023-12-18T17:16:44Z

I updated the branch to be off of dev/no-diff-to-benchmark rather than dev/14.3.0. @yantosca, could you take a look again? Should be good to merge once you give the go-ahead.

yantosca

Thanks @lizziel. Good to merge!

yantosca · 2024-01-05T16:39:22Z

@msulprizio @lizziel: Integration tests now running

yantosca · 2024-01-05T19:11:47Z

All GEOS-Chem Classic integration tests passed (except TOMAS):

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

GCClassic #457a610 GEOS-Chem submod update: Merge PR #2095 (Increase time in GCHP int tests)
GEOS-Chem #aad13ea0a Merge PR #2062 (Updates from GMAO for GEOS)
HEMCO     #a5d5169 HEMCO 3.7.2 release

Using 24 OpenMP threads
Number of execution tests: 27

Submitted as SLURM job: 14497727
==============================================================================
 
Summary of test results:
------------------------------------------------------------------------------
Execution tests passed: 25
Execution tests failed: 2
Execution tests not yet completed: 0

All GEOS-Chem Classic integration tests were zero-diff w/r/t PR #2095 except for:

TOMAS (failed)
APM (parallel error)
RRTMG (numerical noise in RRTMG collection output)

yantosca · 2024-01-05T19:13:33Z

All GCHP integration tests passed:

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

GCHP      #5692f34 GEOS-Chem submod update: Merge PR #2084 (Fix exe name in int tests)
GEOS-Chem #aad13ea0a Merge PR #2062 (Updates from GMAO for GEOS)
HEMCO     #a5d5169 HEMCO 3.7.2 release

Number of execution tests: 5

Submitted as SLURM job: 14497816
==============================================================================
 

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

Also, all GCHP integration tests were zero-diff w/r/t PR #2095.

Signed-off-by: Lizzie Lundgren <[email protected]>

@lizziel

This merge brings the dev/no-diff-to-benchmark branch into the branch for PR #1992 (Fix issues in the carbon simulation, branch feature/carbon-sim-fixes). The latest update in the dev/no-diff-to benchmark was the merge of PR #2062 (Updates from GMAO for GEOS, by @lizziel.) Signed-off-by: Bob Yantosca <[email protected]>

Christoph Keller added 14 commits May 26, 2023 10:26

Bug fix: get GEOS_CH4 through HEMCO

0eb3b7c

Update ExtData update templates to make sure that the model passes ti…

1706b3e

…me regression

add reaction rate updates as suggested by Eric Fleming

2d6db44

revert changes in build_mechanism.sh that got accidentally committed …

be4b499

…in the previous commit

make online washout default for GEOS runs

b3863d1

Update photolysis to include updates by Eric Fleming

3f60625

Update Q directly within GEOS-Chem. This is possible since Q is frien…

35f173f

…dly to chemistry

Merge branch 'feature/cakelle2/fix_kpp_negatives' into geoscf/CFv2/rc1

15aeaf7

# Conflicts: # Headers/input_opt_mod.F90 # Interfaces/GCHP/Chem_GridCompMod.F90

Bug fix to properly count number of negatives concentrations after KP…

31f73d5

…P integration

Merge branch 'feature/cakelle2/fix_kpp_negatives' into geoscf/CFv2/rc1

0b59550

add option to stop printing # of negative concentrations after applyi…

6644f25

…ng analysis increment

yantosca requested changes Dec 6, 2023

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lizziel marked this pull request as ready for review December 8, 2023 16:31

lizziel changed the base branch from dev/14.3.0 to dev/no-diff-to-benchmark December 8, 2023 16:31

lizziel changed the base branch from dev/no-diff-to-benchmark to dev/14.3.0 December 8, 2023 16:32

lizziel changed the title ~~Updates from GMAO for GEOS excluding KPP~~ Updates from GMAO for GEOS Dec 11, 2023

yantosca approved these changes Dec 14, 2023

View reviewed changes

Revert "revert changes in build_mechanism.sh that got accidentally co…

bb3ddc8

…mmitted in the previous commit" This reverts commit be4b499.

lizziel added 6 commits December 18, 2023 11:14

Revert "add reaction rate updates as suggested by Eric Fleming"

14c090a

This reverts commit 2d6db44.

Add new KPP diagnostics to HISTORY.rc templates

99e092e

Signed-off-by: Lizzie Lundgren <[email protected]>

Update GEOS-only unit conversions to new method of specifying target …

23c9926

…units Signed-off-by: Lizzie Lundgren <[email protected]>

Make new KPP negative diagnostics off by default

e5be79b

Signed-off-by: Lizzie Lundgren <[email protected]>

Remove duplicate KPP diagnostic when setting archive logical

0c89ca1

Signed-off-by: Lizzie Lundgren <[email protected]>

lizziel force-pushed the feature/updates_from_gmao branch from 5b4b385 to 0c89ca1 Compare December 18, 2023 17:04

lizziel changed the base branch from dev/14.3.0 to dev/no-diff-to-benchmark December 18, 2023 17:08

lizziel requested a review from yantosca December 18, 2023 17:16

yantosca approved these changes Dec 18, 2023

View reviewed changes

yantosca merged commit aad13ea into dev/no-diff-to-benchmark Jan 5, 2024

yantosca deleted the feature/updates_from_gmao branch January 5, 2024 19:14

yantosca mentioned this pull request Jan 5, 2024

Merge no-diff-to-benchmark updates into the 14.3.0 development stream #2106

Merged

1 task

lizziel added a commit that referenced this pull request Jan 5, 2024

Update changelog for PR #2058 and #2062

2ba0a60

Signed-off-by: Lizzie Lundgren <[email protected]>

yantosca added this to the 14.3.0 milestone Jan 8, 2024

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Updates from GMAO for GEOS #2062

Updates from GMAO for GEOS #2062

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Updates from GMAO for GEOS #2062

Updates from GMAO for GEOS #2062

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lizziel commented Dec 6, 2023 • edited Loading

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