GEOS-Chem 12

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Contents

Version history summary

Past releases Current release: GEOS-Chem 12.1.0 Future releases

The sections below describe each GEOS-Chem feature version and GEOS-Chem bug fix patch version belonging to the GEOS-Chem 12 series. Each feature version carries the tag 12.Y.0, which indicates that the version will be (or has been) validated with a 1-month benchmark simulation (and one or more 1-year benchmark simulations if necessary). Each patch version carries the tag 12.Y.Z, which denotes that the version preserves backwards-compatibility with the prior feature version 12.Y.0. For more information, please see our GEOS-Chem version numbering system wiki page.

Several GEOS-Chem updates have been proposed by the relevant Working Groups, but have not yet been assigned to a specific GEOS-Chem version. For a complete list of these updates, please visit our GEOS-Chem model development priorities wiki page.

Current version in development

The GEOS-Chem version listed below is currently under development.

12.2.0

The items listed below are slated to be included in GEOS-Chem 12.2.0. This is a feature release which will be benchmarked with a 1-month benchmark simulation and a 1-year Rn-Pb-Be benchmark simulation.

Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
Retire BRAVO emissions and use CEDS for Mexico instead GCST Science
  • Now in dev/12.2.0
  • This update introduces the following changes in a 1-month benchmark:
    • Δ Mean OH: 0.0019%
    • Δ MCF lifetime: -0.0040%
    • Δ CH4 lifetime: -.00036%
    • ΔNO emissions: 0.000433 Tg N
    • ΔCO emissions: -0.013199 Tg
    • ΔSO2 emissions: 0.001560 Tg S
    • ΔSO4 emissions: 0.000041 Tg S
Features NOT affecting the full-chemistry simulation:
Common set of tracers in GEOS-Chem and GEOS Transport WG
GCST
Benchmarking
  • A set of passive species will be added to the GEOS-Chem Rn-Pb-Be benchmark simulation. This will facilitate comparisons between GEOS-Chem "Classic" and/or GCHP vs. the NASA GEOS-DAS system.
ObsPack diagnostic Andy Jacobson (NOAA/ESRL) Structural
  • Delivered to GCST (May 2017)
Replace HEMCO built-in unit conversions with scale factors in config file GCST Structural
  • Differences in precision and order of operations may result in small number differences
GFAS biomass burning emissions (as an option) Mat Evans (York)
Killian Murphy (York)
Science
  • Now in dev/12.2.0 branch
Features affecting GCHP only:
New fields in GCHP output restart file GCST Bug Fix &
Structural
  • Adds additional variables to GCHP internal state for carrying across multi-segmented runs
  • Equivalent to GEOS-Chem Classic update in 12.1.0

Current bug fix patch version in development

None at this time.

Current stable version

The GEOS-Chem version listed below is considered stable and can be used to start a new research project. This version corresponds to the master branch of the GEOS-Chem source code repository on Github.

Each released version of GEOS-Chem will be assigned a unique Digital Object Identifier (DOI). This will allow you to cite each GEOS-Chem version in publications. We also have obtained a "Concept DOI", which will always point to the current stable version of GEOS-Chem: DOI 10.5281/zenodo.1343546. This can be convenient if you wish to cite GEOS-Chem without making reference to a particular version.

12.1.1

This version was released on 13 Dec 2018.

DOI: 10.5281/zenodo.2249246

GEOS-Chem 12.1.1 contains fixes and updates that do not impact the GEOS-Chem Classic full-chemistry benchmark simulation.

Feature Submitted by Type Notes
Features NOT affecting the full-chemistry (benchmark) simulation:
Bug fix for tagged CO: don't multiply emissions timestep by 60 Dylan Jones (U. Toronto) Bug fix
Skip planeflight observations outside a nested domain Lei Zhu (Harvard) Bug fix
Always enable BCPH_TPBC to allow saving out BC files in global simulations Yanxu Zhang (Nanjing) Bug fix
Fix compilation issues:
Bob Yantosca (GCST)
Haipeng Lin (PKU)
Bug fix
Features affecting GCHP only:
GCHP transport fix to prevent instant propagation from troposphere to stratosphere Seb Eastham (MIT) Bug fix

--Lizzie Lundgren (talk) 16:05, 6 December 2018 (UTC)

Previously released stable versions

We list below past releases of GEOS-Chem. But we recommend that you always download the current stable version listed above when starting a new research project.

12.1.0

This version was released on 26 Nov 2018.

DOI: 10.5281/zenodo.1553349

You can use the following Git commands to download the GEOS-Chem 12.1.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.1.0
 cd Code.12.1.0
 git checkout master
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 git checkout master

Please see the following links for complete information about the validation of GEOS-Chem 12.1.0:

  1. Approval form for 1-month benchmark simulation 12.1.0

This release contains several new features as well as fixes for issues discovered after the GEOS-Chem 12.0.3 release

Feature Submitted by Type Notes
Features affecting the full-chemistry simulation:
Budget diagnostics Lizzie Lundgren (GCST)
Chris Holmes (Florida State)
Diagnostics
  • This update introduces differences on the level of numerical noise due to unit conversions
Anthropogenic PM2.5 dust source Sajeev Philip (Dalhousie) Science
  • This update introduces the following changes:
    • DST1 emissions increased by 1.09 Tg/mon (13.1 Tg/yr)
    • Δ Mean OH: -0.000066%
    • Δ MCF lifetime: 0.0020%
    • Δ CH4 lifetime: 0.0012%
GEOS-Chem restart file updates Melissa Sulprizio (GCST) Bug Fix &
Structural
  • GEOS-Chem Classic only update
  • This update introduces the following changes:
    • Δ Mean OH: -0.016%
    • Δ MCF lifetime: 0.022%
    • Δ CH4 lifetime: 0.024%
Updates and fixes for the CEDS anthropogenic emissions inventory:
Pengfei Liu (Harvard)
Melissa Sulprizio (GCST)
Jiawei Zhuang (Harvard)
Bug fix
  • This update introduces the following changes:
    • Δ Mean OH: 0.17%
    • Δ MCF lifetime: -0.37%
    • Δ CH4 lifetime: -0.40%
HEMCO fixes:
Bob Yantosca (GCST)
Melissa Sulprizio (GCST)
Erin McDuffie (Dalhousie)
Bug fix
  • This update introduces very small changes:
    • Δ Mean OH: -0.952%
    • Δ MCF lifetime: 1.454%
    • Δ CH4 lifetime: 1.502%
Fix mass conservation in non-local PBL mixing Jintai Lin (PKU) Bug fix
  • This update introduces very small changes:
    • Δ Mean OH: 0.0057%
    • Δ MCF lifetime: -0.0061%
    • Δ CH4 lifetime: -0.0073%
Allow for SZA to 98 degrees when getting photolysis rates Eric Fleming (GMAO) Bug fix
  • This update introduces the following changes:
    • Δ Mean OH: 0.3982%
    • Δ MCF lifetime: -0.3665%
    • Δ CH4 lifetime: -0.3680%
Features NOT affecting the full-chemistry simulation:
FlexGrid Stage 1: Use HEMCO to read met fields Jiawei Zhuang (Harvard)
Jintai Lin (PKU)
Structural
Add support for continuous integration with TravisCI – automatically test each commit as soon as it is pushed to Github Jiawei Zhuang (Harvard)
Bob Yantosca (GCST)
Structural
Added netCDF diagnostics in the following areas: Bob Yantosca (GCST) Diagnostics
  • NOTE: The remaining netCDF diagnostics will be implemented into 12.2.0 and later versions, as time allows.
Convert input data for RRTMG from bpch to netCDF for input via HEMCO Bob Yantosca (GCST) Structural
Add fixes for seasonal scale factors in CH4 simulations Bram Maasakkers (SRON)
Melissa Sulprizio (GCST)
Bug fix
Move Fast-JX .dat files from the geos-chem-unittest repository to gcgrid/ExtData Chris Holmes (Florida State)
GCST
Structural
Update HEMCO configuration file for the tagged CO simulation Bob Yantosca (GCST) Bug fix
Structural updates to facilitate interfacing GEOS-Chem into WRF Haipeng Lin (Peking U)
GCST
Structural
  • This process will be ongoing throughout the GEOS-Chem 12 series of releases.
Structural updates to facilitate interfacing GEOS-Chem into GEOS-5 Christoph Keller (GMAO)
Lizzie Lundgren (GCST)
Structural
  • This process will be ongoing throughout the GEOS-Chem 12 series of releases.
Features affecting GCHP only:
Fix masking bug to correctly apply anthropogenic emissions Lizzie Lundgren (GCST) Bug fix
Remove erroneous 180 degree longitude shift in APEI regridding Lizzie Lundgren (GCST) Bug fix
Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository Lizzie Lundgren (GCST) Structural

--Melissa Sulprizio (talk) 15:21, 26 November 2018 (UTC)

12.0.3

This version was released on 16 Oct 2018.

DOI: 10.5281/zenodo.1464210

You can use the following Git commands to download the GEOS-Chem 12.0.3 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.0.3
 cd Code.12.0.3
 git checkout master
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 git checkout master
Feature Submitted by Type Notes
Features affecting GCHP only:
Fix incorrect run configuration for offline sea salt emissions in GCHP Sebastian Eastham (MIT) Bug fix
Fix bug in application of CFC surface mixing ratios in GCHP Sebastian Eastham (MIT) Bug fix

--Lizzie Lundgren (talk) 18:21, 16 October 2018 (UTC)

12.0.2

This version was released on 10 Oct 2018.

DOI: 10.5281/zenodo.1455215

You can use the following Git commands to download the GEOS-Chem 12.0.2 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.0.2
 cd Code.12.0.2
 git checkout master
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 git checkout master

This version contains fixes for specialty simulations that were identified after the release of GEOS-Chem 12.0.1.

Feature Submitted by Type Notes
Features NOT affecting the full-chemistry (benchmark) simulation:
Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics Bo Zheng (NIA) Bug fix Implemented 04 Oct 2018
Fixes to correct missing BC/OC biomass emissions and incorrect aerosol drydep in TOMAS simulations Pengfei Liu (Harvard) Bug fix Implemented 25 Sep 2018
Avoid double-counting of emissions in the CO2 simulation Beata Bukosa (U. Wollongong)
Christoph Keller (GMAO)
Bug fix Implemented 24 Sep 2018.

--Lizzie Lundgren (talk) 18:21, 16 October 2018 (UTC)

12.0.1

This version was released on 24 Aug 2018.

DOI: 10.5281/zenodo.1403144

You can use the following Git commands to download the GEOS-Chem 12.0.1 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.0.1
 cd Code.12.0.1
 git checkout master
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 git checkout master

GEOS-Chem 12.0.1 contains fixes for minor issues discovered after the GEOS-Chem 12.0.0 release.

Feature Submitted by Type Notes
Features NOT affecting the full-chemistry (benchmark) simulation:
Fix typo when registering the State_Chm%SSAlk field Shuting Zhai (U. Washington)
GCST
Bug fix
Add fixes for several compilation issues:
  1. Nullify rather than deallocate 3D met arrays for compatibility with gfortran 6+ when using GCHP
  2. Add a more robust test for netCDF-Fortran in Makefile_header.mk
  3. Fix compilation issues encountered with GNU Fortran 8.2.0
  4. Fix compilation issues encountered with Intel Fortran 18
GCST Bug fix
Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions Colin Thackray (Harvard) Bug fix
Fix mis-indexing in the ND05 diagnostic GCST Bug fix
Minor updates to facilitate interfacing GEOS-Chem into GEOS-5 Lizzie Lundgren (GCST) Structural

--Bob Yantosca (talk) 14:31, 10 October 2018 (UTC)

12.0.0

This version was released on 10 Aug 2018

DOI 10.5281/zenodo.1343547

You can use the following Git commands to download the GEOS-Chem 12.0.0 source code and GEOS-Chem Unit Tester package.

 # Download the GEOS-Chem source code
 git clone https://github.com/geoschem/geos-chem Code.12.0.0
 cd Code.12.0.0
 git checkout -b 12.0.0
 cd .. 

 # Download the GEOS-Chem Unit Tester, from which run directories can be generated
 git clone https://github.com/geoschem/geos-chem-unittest UT
 cd UT
 git checkout -b 12.0.0

For more information about getting set up with GEOS-Chem, please see the GEOS-Chem Online User's Guide.

The table below shows the updates that were added to GEOS-Chem 12.0.0. Most of these fix issues that were reported by users during the GEOS-Chem v11-02 release candidate testing period (June 22 thru August 10 2018).

Please see the following links for complete information about the validation of GEOS-Chem 12.0.0:

  1. Approval form for 1-month benchmark simulation 12.0.0
  2. Results for 1-year benchmark simulation 12.0.0-Run0
Feature Submitted by Type Notes
Features affecting the full-chemistry (benchmark) simulation:
Turn off TRASH emissions by default to avoid double counting GCST
Eloise Marais (U. Birmingham)
Bug fix
  • This update introduces relatively small changes:
    • Mean OH decreased by 0.12%
    • MCF lifetime increased by 0.23%
    • CH4 lifetime increased by 0.24%
    • O3 STE flux increased by 0.042%
Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory GCST Bug fix
  • This update introduces relatively small changes:
    • Mean OH decreased by 0.15%
    • MCF lifetime increased by 0.28%
    • CH4 lifetime increased by 0.29%
    • O3 STE flux increased by 0.043%
Bug fix for liquid water content in gckpp_HetRates.F90 Jiayue Huang (U. Washington)
Quanjie Chen (U. Washington)
Bug fix
  • This update introduces relatively small changes:
    • Mean OH increased by 1.91%
    • MCF lifetime decreased by 2.41%
    • CH4 lifetime decreased by 2.41%
    • O3 STE flux decreased by 0.18%
Bug fix for CH4 boundary conditions Lee Murray (Rochester) Bug fix
  • Results approved by Lee Murray
  • This update introduces small changes:
    • Mean OH decreased by 0.48%
    • MCF lifetime increased by 0.82%
    • O3 STE decreased by: 0.022%
Fixed typo in call to GAMMA_HOBr_AER Xuan Wang
GCST
Bug fix
  • This update produced only very small differences w/r/t internal run v11-02-rc-DICEnewrc
    • Mean OH decreased by -0.058%
    • MCF lifetime increased by 0.082%
    • CH4 lifetime increased by 0.084%
    • O3 STE flux decreased by 0.005%
Correct issues when specifying DICE-Africa emissions: Eloise Marais (U. Birmingham)
GCST
Bug Fix
  • Results approved by Eloise Marais.
  • This update produced only very small differences w/r/t internal run v11-02-rc-arctasship:
    • Mean OH increased by 0.07%
    • MCF lifetime decreased by 0.12%
    • CH4 lifetime decreased by 0.13%
    • O3 STE flux decreased by -0.0023%
Add missing Criegee intermediate reaction Xin Chen (UMN) Bug fix
  • This update produced only very small differences w/r/t internal run v11-02-rc-arctasship:
    • Mean OH decreased by 0.00002%
    • MCF lifetime was unchanged
    • CH4 lifetime increased by 0.001%
    • O3 STE flux increased by 0.0001%
Bug fix for ARCTAS_SHIP in HEMCO_Config.rc files Barron Henderson (EPA) Bug Fix
  • This update only produced very small differences w/r/t internal run v11-02-rc-gfed2016:
    • Mean OH decreased by 0.0004%
    • O3 STE flux decreased by 0.0007%
    • MCF and CH4 lifetimes were unchanged
Bug fix in FlexChem: do not zero out ACTA, EOH, HCOOH concentrations Katie Travis (MIT) Bug Fix
  • This update only produced very small differences w/r/t v11-02-rc:
    • Mean OH decreased by 0.083%
    • MCF lifefime increased by 0.112%
    • CH4 lifetime increased by 0.112%
    • O3 STE flux decreased by 0.011%
Add GFED4.1 data for 2015 and 2016; Use GFED4.1 2016 in benchmarks Kate O'Dell (CSU)
GCST
Science
  • Data files downloaded 27 Jun 2018
  • This update only produced small differences:
    • Mean OH increased by 0.60%
    • MCF lifefime decreased by 0.65%
    • CH4 lifetime decreased by 0.64%
    • O3 STE flux decreased by 0.0093%
Features NOT affecting the full-chemistry simulation:
Bug fixes for stratospheric chemistry: GCST Bug fix
Limit flash rate density in hcox_lightnox_mod.F90 Lee Murray (Rochester) Bug fix
Initial structural modifications for interfacing GEOS-Chem into WRF Haipeng Lin (Peking U.) Structural
  • This process is ongoing in GEOS-Chem 12
Minor fixes for mercury chemistry updates implemented in v11-02f Colin Thackray (Harvard) Bug fix
Restore default timestep for MERRA-2 nested grid simulations to 10/20 Ke Li (Harvard) Bug fix
Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat Tomas Sherwen (York) Bug fix
  • A difference test w/r/t the previous commit yielded identical results
Fixed typo that prevented PM2.5 from being archived to netCDF output Jonathan Moch (Harvard)
GCST
Bug fix
Bring two-way nested-grid code option up-to-date Yingying Yan (PKU)
Jintai Lin (PKU)
Structural
  • This option is invoked by compiling with EXCHANGE=y
  • A difference test w/r/t the previous commit yielded identical results.
Do not force L=1 by default in planeflight_mod.F Katie Travis (MIT)
GCST
Bug fix
Add PH2O2 to the default list of prod/loss families in the KPP mechanisms GCST Structural
  • This update facilitates saving out oxidant fields from a full-chemistry simulation that can be used to drive an aerosol-only simulation.
Update to HEMCO v2.1.008, which includes minor updates:
  1. Fixed error in HEMCO "exact" cycling option
    • NOTE: This update introduced an unforeseen side-effect which will be fixed in GEOS-Chem 12.1.0.

Update to HEMCO v2.1.007, which includes minor updates:

  1. Stop with error if multiple containers have the same name
  2. Bug fix for distributing emissions in the vertical dimension
  3. Add extra error checks in HEMCO standalone module
  4. Remove null string character from netCDF unit string
  5. Bug fix for HEMCO soil NOx error with ifort 17
GCST
Christoph Keller
Jenny Fisher
Structural &
Bug fix
Bug fix for reference time in netCDF diagnostic files GCST Bug fix
Updates for QFED biomass burning emissions:
  1. Update to QFED v2.5r1
  2. Fix QFED v2.4r6 files for 2016/10/13
Christoph Keller (NASA GMAO) Bug fix
Fix issues in complexSOA and complexSOA_SVPOA restart files Eloise Marais (U. Birmingham) Bug fix
Avoid double counting CEDS and GEIA NH3 biofuel emissions Christoph Keller (NASA/GMAO)
GCST
Bug fix
  • The default HEMCO behavior is to prioritize CEDS over GEIA NH3 anthro and biofuel emissions. But to avoid confusion, we will explicitly request this behavior in the HEMCO_Config.rc files that ship with the GEOS-Chem Unit Tester.
Bug fixes for v11-02 simulations using the RRTMG radiative transfer model Chris Holmes (U. Florida) Bug Fix
  • This only affects the RRTMG simulations. Full-chemistry difference-tests yielded identical results w/r/t v11-02-rc.
Now always declare the netCDF time variable with an unlimited dimension Chris Holmes (U. Florida) Structural
  • Full-chemistry difference-tests yielded identical results w/r/t v11-02-rc.

New data directories

The following HEMCO data directories have been added or updated for GEOS-Chem 12. You will have to download the directories relevant to your simulation.

Inventory Type What was added? Version added Directory
RRTMG input data OPTIONAL netCDF input data files for the RRTMG specialty simulation (converted from the old "binary punch" format files) 12.1.0 HEMCO/RRTMG/v2018-11/
CEDS anthropogenic emissions DEFAULT Reduce file size for CEDS inventory 12.1.0 HEMCO/CEDS/v2018-08/YYYY
QFED biomass burning emissions OPTIONAL New data files for QFED v2.5r1 12.0.0 HEMCO/QFED/v2018-07
GFED4 biomass burning emissions DEFAULT GFED4.1 data files for 2015 and 2016 have been added 12.0.0 HEMCO/GFED4/v2015-10/2015
HEMCO/GFED4/v2015-10/2016
MEGAN DEFAULT Global 0.25x0.3125 CLM4 PFT and emission factor input files for MEGAN v11-02f HEMCO/MEGAN/v2017-07/
MODIS LAI DEFAULT Updated 0.25 x 0.25 MODIS LAI files (2005-2011) v11-02f CHEM_INPUTS/MODIS_LAI_201707/
Lightning NOx DEFAULT GEOS-FP OTD-LIS redistribution factors for Apr 2012 - Jul 2017 and MERRA-2 OTD-LIS redistribution factors for any date v11-02f HEMCO/LIGHTNOX/v2017-09/
Volcanic SO2 emissions DEFAULT OMI-based volcanic emissions for 2005-2012 v11-02f HEMCO/VOLCANO/v2018-03/
APEI DEFAULT Historical Canadian emissions v11-02f HEMCO/APEI/v2016-11/
EDGAR v4.3 OPTIONAL Annual global anthropogenic emissions for 1970-2010 at 0.1x0.1 resolution v11-02f HEMCO/EDGARv43/v2016-11/
C2H6_2010 DEFAULT Global fossil fuel and biofuel emissions of C2H6 for 2010 v11-02f HEMCO/C2H6_2010/v2017-05/
DICE-Africa DEFAULT Biofuel and diffuse anthropogenic emissions for Africa v11-02f HEMCO/DICE_Africa/v2016-10/
Trash burning emissions OPTIONAL Global trash burning emissions from Wiedinmyer et al. (2014) v11-02f HEMCO/TrashEmis/v2015-03/
SEABIRD NH3 DEFAULT NH3 emissions from arctic sea birds v11-02f HEMCO/NH3/v2018-04
OMOC OPTIONAL Spatially varying OM/OC ratio v11-02e HEMCO/OMOC/v2018-01
NOAA GMD CH4 DEFAULT Monthly mean surface methane distributions v11-02e HEMCO/NOAA_GMD/v2018-01
UCX Tropchem only Input files for applying linearized stratospheric chemistry production and loss rates saved out from a UCX simulation using GEOS-Chem v11-02d v11-02e HEMCO/UCX/v2018-02/
IODINE DEFAULT Monthly emission fluxes of organic iodine compounds (CH3I, CH2I2, CH2ICl, CH2IBr) from Carlos Ordonez. v11-02d HEMCO/IODINE/v2017-03/
GMI DEFAULT New symbolic links:
  • gmi.clim.RIPA.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25
  • gmi.clim.RIPB.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25
  • gmi.clim.RIPD.geos5.2x25.nc -> gmi.clim.RIP.geos5.2x25
  • gmi.clim.IPMN.geos5.2x25.nc -> gmi.clim.PMN.geos5.2x25
  • gmi.clim.NPMN.geos5.2x25.nc -> gmi.clim.PMN.geos5.2x25
v11-02c HEMCO/GMI/v2015-02/
NEI2011 North American emissions DEFAULT (global)
OPTIONAL (nested NA)
Monthly mean data files (created from the existing hourly data in HEMCO/NEI2011/v2015-03) v11-02a HEMCO/NEI2011/v2017-02-MM/
ALD2 DEFAULT Fields for ALD2 emissions, including:
  • Seawater concentration of acetaldehyde
  • Heterotrophic respiration rates, used to compute biogenic emissions of ALD2 and EOH

(added with the PAN updates)

v11-02a HEMCO/ALD2/v2017-03/
POET DEFAULT Anthropogenic emissions of ethanol from the POET inventory
(added with the PAN updates)
v11-02a HEMCO/POET/v2017-03/
Soil NOx DEFAULT New file: DepReservoirDefault.nc
Read default DEP_RESERVOIR fields from file when not found in HEMCO restart file
v11-02a HEMCO/SOILNOX/v2014-07/

NOTES:

  1. DEFAULT denotes that the inventory is part of the default HEMCO emissions configuration that you get when you run GEOS-Chem "out-of-the-box".
  2. OPTIONAL denotes optional inventories that you may use (or not) according to your research needs.

--Bob Yantosca (talk) 20:02, 29 June 2018 (UTC)

Validation

In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v11-03.

1-month and 1-year benchmarks

For complete information about the benchmark simulations used to validate GEOS-Chem v11-03, please see our GEOS-Chem 12 benchmark history wiki page.

Unit tests for GEOS-Chem 12

We perform a full set of unit tests on GEOS-Chem on an almost daily basis. These tests ensure that each new feature being added does not break any existing functionality.

Here are the unit tests that we ran before submitting 1-month benchmark simulation for GEOS-Chem 12.0.0. Click on the links below to see the results from each set of unit tests:

Unit test Date
TBD

Performance

Please see the following resources below for more information about the performance of GEOS-Chem 12.0.0.

GEOS-Chem "Classic" performance

We have performed several timing tests with GEOS-Chem "Classic" 12.0.0 and have posted our results on the wiki:

We invite you to add your own time test results to the wiki.

--Bob Yantosca (talk) 18:06, 17 August 2018 (UTC)

GCHP performance

Help us pool performance information across systems by contributing your GCHP run information on our GCHP Timing Tests page.

--Bob Yantosca (talk) 18:06, 17 August 2018 (UTC)

Previous issues now resolved in GEOS-Chem 12

The following bugs and/or technical issues have been resolved in GEOS-Chem 12.

GCHP transport fix to prevent instant propagation from troposphere to stratosphere

This fix was included in 12.1.1, which was released on 13 Dec 2018 .

Sebastian Eastham describes this bug fix as follows:

GCHP uses a simple mass conservation kludge which rescales global tracer concentrations between transport steps. This is equivalent to the pressure fixer in GC-Classic, used to account for inconsistency between the surface pressure field (which sets the vertical grid spacing up to the upper troposphere) and the averaged wind speeds. Although the scaling factor is usually small, this can cause nonphysical redistribution of mass. This is especially problematic because mass can be transferred to, or from, the stratosphere, which should be impossible given that the stratosphere operates on fixed pressure levels. In a future update, this problem will be resolved by direct application of mass fluxes archived from GEOS in place of winds, but while that update is in development we have produced an interim fix

This patch forces mass redistribution to be constrained to the variable pressure levels in the troposphere. Although this slightly increases spurious mixing in the troposphere, it prevents changes in the troposphere from being instantly propagated to the stratosphere. This can have significant effects when inspecting (e.g.) the response to changes in surface emissions of NOx.

--Lizzie Lundgren (talk) 16:03, 6 December 2018 (UTC)
--Bob Yantosca (talk) 15:50, 13 December 2018 (UTC)

Always enable BCPH_TPBC to allow saving out BC files in global simulations

This fix was included in 12.1.1, which was released on 13 Dec 2018 .

Yanxu Zhang reported an issue in GEOS-Chem 12.1.0 where BC files would not save out, even when turned on in the Nested Grid Menu of input.geos. To resolve this issue, we will always add USER_DEFS += -DBPCH_TPBC in Makefile_header.mk. The switch to turn on saving out boundary condition files is still controlled by the options in input.geos, but this fix ensures the tpcore_bc_mod.F code is always compiled.

--Melissa Sulprizio (talk) 15:40, 30 November 2018 (UTC)
--Bob Yantosca (talk) 15:49, 13 December 2018 (UTC)

Skip planeflight observations outside a nested domain

This fix was included in 12.1.1, which was released on 13 Dec 2018 .

Lei Zhu provided a fix for planeflight_mod.F to skip flight observations outside the nested domains. With the fix, the code works for all 0.5 and 0.25 nested domains. For more information please see the pull request on Github.

--Melissa Sulprizio (talk) 13:29, 27 November 2018 (UTC)
--Bob Yantosca (talk) 15:48, 13 December 2018 (UTC)

Allow for SZA to 98 degrees when getting photolysis rates

This update was included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.

Eric Palmer (GMAO) wrote:

I see that the code that calls the photolysis rates (in flexchem_mod.F90), is only called when the solar zenith angle is < 90 degrees (COS(SZA) > 0.). However, Fast-Jx allows for SZA down to 98 degrees, which is important in the stratosphere-mesosphere where sunlight still illuminates at high altitudes if the sun is below the horizon at the surface. To allow for SZA down to 98 deg, I made the following one line change:
      IF ( State_Met%SUNCOSmid(I,J) > 0.e+0_fp ) THEN
to:
      IF ( State_Met%SUNCOSmid(I,J) > -0.13917e+0_fp ) THEN
where -0.13917e+0_fp = COS(98 degrees) This looks like it has the desired effect, as species with sharp gradients across the terminator (eg: Br, BrO), are now more "rounded" and look much more like GMI (which also allows SZA down to 98 degrees). This also eliminates the problem with the non-conservation of bromine family species in the mesosphere due to transport across the terminator (ie, the sharp edges of a square wave).

--Lizzie Lundgren (talk) 14:59, 16 October 2018 (UTC)
--Bob Yantosca (talk) 16:09, 26 November 2018 (UTC)

Fix bug in application of CFC surface mixing ratios in GCHP

This update was included in GEOS-Chem 12.0.3, which was released on 16 Oct 2018.

This fix is urgent, as any current users of the last several versions of GCHP will be see bad results for relevant species. We recommend that all GCHP users implement this update if not updating to the latest version.

Sebastian Eastham describes this bug as follows:

Basically, we specify a target year for CFC emissions to be read in in input.geos, so (eg) we can specify “2050” and all surface VMRs for CFCs will be set according to the expected value for 2050. Usually, though, we use a value of 0 – meaning “use the current year”. In GCC, the value Input_Opt%CFCYEAR is set to Get_Year () during initialization, and the offset is calculated in UCX_mod, meaning the right year gets used. However, in GCHP this isn’t possible because Get_Year doesn’t return the right value until after initialization. There was a workaround in UCX_mod already where we had a local variable “CFCYEAR” which was a copy of Input_Opt%CFCYEAR, and which got set to Get_Year() at runtime if it was still zero; however, this wasn’t being propagated in the case of an ESMF environment (where UCXNETCDF is .False.) because we only passed Input_Opt rather than the updated local variable. As a result, the CFC “emissions” were always for 1950 rather than for the true target year.

--Lizzie Lundgren (talk) 21:18, 15 October 2018 (UTC)
--Bob Yantosca (talk) 16:10, 26 November 2018 (UTC)

Fix incorrect run configuration for offline sea salt emissions in GCHP

This update was included in GEOS-Chem 12.0.3, which was released on 16 Oct 2018.

The offline sea salt emissions applied in GCHP starting in 12.0.0 contained a bug due to incorrect settings in HEMCO_Config.rc. SALA and SALC sea salt values read from file should be scaled and applied to BrSALA and BrSALC respectably. However, the HEMCO_Config.rc settings resulted in applying the scaled values to SALA and SALC instead. This bug was identified by Seb Eastham (MIT) and is corrected by updating the species column in HEMCO_Config.rc. No source code updates are necessary but you must create a new run directory or apply the fix in your existing run directories.

--Lizzie Lundgren (talk) 21:13, 15 October 2018 (UTC)
--Bob Yantosca (talk) 16:10, 26 November 2018 (UTC)

Update HEMCO configuration file for tagged CO simulation

This update was included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.

The tagged CO simulation was still using NEI2005 emissions over the US by default, while all other simulations had retired the NEI2005 option and were using NEI2011 instead. For consistency, we will use NEI2011 with the tagged CO simulation and remove NEI2005.

In addition, the CEDS and DICE_Africa inventories were omitted from tagged CO HEMCO configuration file. To maintain consistency with the full-chemistry simulations, these inventories are now added for tagged CO and are turned on by default.

--Melissa Sulprizio (talk) 17:37, 21 September 2018 (UTC)
--Bob Yantosca (talk) 16:10, 26 November 2018 (UTC)

Fix regional tile file used for APEI inventory in GCHP

This bug fix only requires downloading updated files from gcgrid/ExtData/GCHP/TileFiles

The regional tile file used by GCHP for regrigding the APEI inventory from native resolution to cubed sphere was incorrect at the time of the 12.0.0 release. The tile file erroneously caused the APEI inventory to be regridded at a 180 degree longitude offset. Corrected tile files now replace the erroneous ones at gcgrid/ExtData/GCHP/TileFiles. No changes are necessary to the model source code or the GCHP run directory.

--Lizzie Lundgren (talk) 17:30, 19 September 2018 (UTC)

Fix masked anthropogenic emissions bug in GCHP

This update was included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.

Integration of the DICE-Africa inventory in GCHP resulted in erroneously masking out total global anthropogenic emissions outside of Africa. Updating the Africa mask file from containing regional bounds to global bounds corrects the problem. GCHP users who are using the DICE-inventory prior to 12.1.0 can fix the issue by updating their Africa mask file to MASKS/v2014-07/AF_LANDMASK.geos.05x0666.global.nc which is now available on gcgrid.

--Lizzie Lundgren (talk) 16:50, 14 September 2018 (UTC)
--Bob Yantosca (talk) 16:11, 26 November 2018 (UTC)

Add support for continuous integration with TravisCI

This update was included in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.

We have now linked the GEOS-Chem Github repository to the continuous integration tool TravisCI. Each time a commit is pushed to the repository, TravisCI will perform a test to ensure that the commit will not "break" GEOS_Chem. Right now, TravisCI only compiles GEOS-Chem, but we will eventually implement compile-and-run tests in the near future.

You can see the TravisCI status page for GEOS-Chem here: https://travis-ci.com/geoschem/geos-chem/builds

Also, if you navigate to the "commits" page of the GEOS-Chem Github repository, you will see a green checkmark next to each commit that was checked by TravisCI:

Travis ci.png

NOTE: As of this writing, only the dev/12.1.0 branch is being checked by TravisCI. When we merge this into the master branch, then all future branches will be checked.

--Bob Yantosca (talk) 16:11, 26 November 2018 (UTC)

Replace HEMCO built-in unit conversions with scale factors in config file

This update will be included in GEOS-Chem 12.2.0 or later.

HEMCO checks the unit string in HEMCO_Config.rc for each emission and converts to HEMCO standard units (kg/m2/s) upon file read if the input units are different. For VOCS, it further converts to kgC/m2/s. The code for the unit conversions is in HEMCO/Core/hco_unit_mod.F90.

Since the automatic unit conversion is performed during HEMCO file read it does not get executed in GCHP which uses MAPL/ESMF for I/O. GCHP users must instead manually include the conversion information as scale factors in HEMCO_Config.rc. To increase clarity and to make GCHP and GCC better match we plan on removing the HEMCO built-in unit conversions and replacing them with scale factors in HEMCO_Config.rc. This change may result in small number differences due to order of operations and precision of scale factors.

--Lizzie Lundgren (talk) 19:57, 23 August 2018 (UTC)
--Bob Yantosca (talk) 16:11, 26 November 2018 (UTC)

Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics

This update was included in GEOS-Chem 12.0.2, which was released on 10 Oct 2018.

Bo Zhang wrote:

We encountered a potential issue in the satellite diagnostic ND51b in GEOS-Chem v11-01. We find some kind of discontinuity in total column AOD (a sum of all aerosol species) along the west-east direction. It feels like data are missing/reduced occasionally in every other pixels alone the W-E direction. We are running v11-01 with full chemistry + UCX driven by MERRA2. The same problem remains after switching to MERRA. We checked AOD maps in monthly output which looks normal.

Bob Yantosca replied:

In recent versions of GEOS-Chem, the number of advected species increased (to accommodate additional halogen and SOA species). So we had to increase the non-species tracer numbers to 500:
     !  ND51 tracer numbers:
     !  ============================================================================
     !  1 - nAdvect   : GEOS-CHEM advected species               [v/v        ]
     !  501           : OH concentration                         [molec/cm3  ]
     !  502           : NOy concentration                        [v/v        ]
     !  503           : Relative Humidity                        [%          ]
     !  ... etc ...
Complicating matters further, some ND51/ND51b quantities, including the AOD’s, were only updated on every chemistry timestep (20 mins) instead of on every dynamic timestep (10 mins). There was a CASE statement in routine WRITE_DIAG51 to divide by the proper counting array to create the average quantity:
        SELECT CASE( Input_Opt%ND51_TRACERS(W) )

           CASE( 91, 92, 76, 77 )                
           ... etc ...

           CASE( 84:89, 115:121 )                
           ... etc ...

           CASE( 105:114 )                
           ... etc ...
 
           CASE DEFAULT
           ... etc ...

        END SELECT
But we just realized that this CASE statement had the old ND51/ND51b tracer numbers ( < 500) and not the new ones.

Therefore, we have made the following fixes, which should eliminate any striping or discontinuities

  1. Archive most ND51/ND51b tracers (except for NOy, which has special handling) on every dynamic timestep. Remove the GOOD_CHEM, GOOD_CT_CHEM, GOOD_EMIS, GOOD_CT_EMIS arrays.
  2. Update the CASE statement shown above so that all tracers (except NOy) are divided by the number of dynamic timesteps when each grid box was within the proper local time range.
Also note: the ND51/ND51b diagnostics were developed in an ad-hoc fashion and were were never really thought out holistically. It is possible that there may be some issues with some of the other quantities in ND51/ND51b, but the GCST is not planning on investigating further. The bpch diagnostics will be eventually removed from GEOS-Chem once we have a satisfactory equivalent local-time averaging netCDF diagnostic.

--Bob Yantosca (talk) 15:12, 10 October 2018 (UTC)

Fix typo when registering the State_Chm%SSAlk field

This update was included in GEOS-Chem 12.0.1, which was released on 24 Aug 2018.

Shuting Zhai wrote:

I found a typo in state_chm_mod.F90 where we register the State_Chm%SSAlk field. I believe this line:
     CALL Register_ChmField( ... State_Chm%pHCloud,  ...  )
Should be:
     CALL Register_ChmField( ... State_Chm%SSAlk, ... )

Upon fixing this issue, the GCST discovered that the State_Chm%SSAlk array cannot be registered as a single array because it is dimensioned as (IIPAR,JJPAR,LLPAR,2). When registering quantities, the 4th dimension is always interpreted as the number of chemical species. Therefore, registering State_Chm%SSAlk in this way caused an error.

The solution is to register the two dimensions of State_Chm%SSAlk separately:

  1. SSAlkAccum points to State_Chm%SSAlk(:,:,:,1)
  2. SSAlkCoarse points to State_Chm%SSAlk(:,:,:,2)

This update will require you to list Chem_SSAlkAccum and Chem_SSAlkCoarse as requested diagnostics instead of the single field Chem_SSAlk in the HISTORY.rc file ( which specifies input options for netCDF diagnostics).

--Bob Yantosca (talk) 15:33, 23 August 2018 (UTC)

Fixes for compilation issues

We have added several fixes for issues encountered during GEOS-Chem compilation:

  1. Add a more robust test for netCDF-Fortran in Makefile_header.mk
  2. Fixes for compilation issues encountered with GNU Fortran 8.2.0
  3. Fixes for compilation issues encountered with Intel Fortran 18

--Bob Yantosca (talk) 14:26, 22 August 2018 (UTC)

Fix mis-indexing in the ND05 diagnostic

This update was included in GEOS-Chem 12.0.1, which was released on 24 Aug 2018.

For a complete description of this issue, please see this post on our Sulfate aerosols wiki page.

--Bob Yantosca (talk) 14:18, 22 August 2018 (UTC)

Bug fix for HEMCO soil NOx error with ifort 17

This fix was included in GEOS-Chem 12.0.0.

For complete information about this issue and how it was resolved, please see this post on our Implementation of HEMCO in GEOS-Chem wiki page..

--Bob Yantosca (talk) 13:54, 27 June 2018 (UTC)

FlexChem bug fix: do not zero ACTA, EOH, HCOOH

This fix was included in GEOS-Chem 12.0.0.

For complete information about this bug and how it was fixed, please see this post on our FlexChem wiki page.

--Bob Yantosca (talk) 14:42, 27 June 2018 (UTC)

Avoid double counting CEDS and GEIA NH3 biofuel emissions

This fix was included in GEOS-Chem 12.0.0.

Eloise Marais wrote:

If CEDS includes NH3 emissions, then this will be double counting. I recommend using CEDS, as GEIA is very out of date (1998 according to the HEMCO configuration file I have).

Daniel Jacob replied:

We should use the GEIA NH3 natural emission inventory (1° x 1° file from Eleanor Morris) but not the GEIA NH3 biofuel inventory.

UPDATE 29 Jun 2018:

We discovered that HEMCO's default behavior is to ignore the GEIA NH3 anthro and biofuel emissions if CEDS is turned on. This is shown in the HEMCO.log file when VERBOSE = 3:

 Register_Base: Checking GEIA_NH3_ANTH
HEMCO: Entering Get_targetID (hco_config_mod.F90) ( 4)
 Skip container GEIA_NH3_ANTH because of CEDS_NH3_WST
. . .
 Register_Base: Checking GEIA_NH3_BIOF
HEMCO: Entering Get_targetID (hco_config_mod.F90) ( 4)
 Skip container GEIA_NH3_BIOF because of CEDS_NH3_WST_Cat00002

But for the sake of clarity, we will modify the HEMCO_Config.rc files to explicitly request this behavior:

(((.not.CEDS.or.EDGARv43

# GEIA NH3 anthro (skip if CEDS or EDGARv43 is on)
0 GEIA_NH3_ANTH $ROOT/NH3/v2014-07/NH3_geos.4x5.nc         NH3_ANTH     1990/1-12/1/0 C xy  kg/m2/s NH3 - 1 1 

# GEIA NH3 biofuel (skip if CEDS or EDGARv43 is on)
(((BIOFUEL
0 GEIA_NH3_BIOF $ROOT/NH3/v2014-07/NH3_biofuel.geos.1x1.nc NH3_BIOFUEL  1998/1-12/1/0 C xy  kg/m2/s NH3 - 2 1
)))BIOFUEL

))).not.CEDS.or.EDGARv43

--Bob Yantosca (talk) 21:02, 29 June 2018 (UTC)

Fix bug in ARCTAS_SHIP_SO2 scale factors

This fix was included in GEOS-Chem 12.0.0.

For a complete description of this issue and how it was resolved, please see this post on our Ship Emissions wiki page.

--Bob Yantosca (talk) 15:54, 3 July 2018 (UTC)

Fix issues in complexSOA and complexSOA_SVPOA restart files

This fix was included in GEOS-Chem 12.0.0.

Eloise Marais wrote:

I just wanted to draw your attention to a few issues with the restart files provided on the ftp site (http://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/). The complexSOA and complexSOA_SVPOA restart files (4° x 5° and 2° x 2.5°) both have a species entry for IEPOX and also IEPOXD, IEPOXB, and IEPOXA, but should only have the latter 3. This is the same for RIP. The number of species in the 4° x 5° and 2° x 2.5° files for complexSOA is also different.

To fix these issues, we have generated new restart files for the complexSOA and complexSOA_SVPOA simulations. You can download these to your SPC_RESTARTS folder with the following commands:

 wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.2x25_complexSOA.nc"
 wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.2x25_complexSOA_SVPOA.nc"
 wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.4x5_complexSOA.nc"
 wget "ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/SPC_RESTARTS/initial_GEOSChem_rst.4x5_complexSOA_SVPOA.nc"

--Bob Yantosca (talk) 18:01, 5 July 2018 (UTC)

Bug fix for reference time in netCDF diagnostic files

This fix was included in GEOS-Chem 12.0.0.

Maria Zatko wrote:

For the sake of run time, we would like to run GEOS-Chem with the old (15/30 minute timesteps) instead of the recommended timesteps (10/20 minutes). I noticed that the output netcdf files have different timestamps depending on the timestep (e.g., 10/20 minutes, 15/30 minutes) used. For example, when 10/20 minute timesteps are used, the time units in the following netcdf output files range from 0 to 23 UTC:
     GEOSChem3hrInst.SpeciesConcWithMet.20150701_0000z.nc4 (file size: 4.6 GB)
     GEOSChem3hrInst.SpeciesConcWithMet.20150702_0000z.nc4 (file size: 5.3 GB)
     time:units = "minutes since 2015-07-01 00:00:00 UTC"
When 15/30 minute timesteps are used, the time units in the following output files include hour 24:
     GEOSChem3hrInst.SpeciesConcWithMet.20150701_0000z.nc4 (file size: 4.6 GB)
     GEOSChem3hrInst.SpeciesConcWithMet.20150701_2400z.nc4 (file size: 5.3 GB)
     GEOSChem3hrInst.SpeciesConcWithMet.20150702_2400z.nc4 (file size: 5.3 GB)
     time:units = "minutes since 2015-07-01 24:00:00 UTC"

I wanted to check in to see if others have run into this issue as well.

Bob Yantosca replied:

This issue is caused by floating-point roundoff error in converting from the Julian date to the calendar date. I have created a more robust fix for this issue, which now computes the correct netCDF file reference time independent of the model "heartbeat" timestep.

To apply the fix:

  1. Copy the patch file ftp://ftp.as.harvard.edu/pub/exchange/bmy/nc_ref_time_fix.txt to your computational server.
  2. Change to your GEOS-Chem v11-02 release candidate code directory and check out the "master" branch.
  3. Type: git am < nc_ref_time_fix.txt
The fix will be standardized in the GEOS-Chem 12.0.0 release.

--Bob Yantosca (talk) 15:10, 12 July 2018 (UTC)

Bug fix for CH4 boundary conditions

This fix was included in GEOS-Chem 12.0.0.

Lee Murray wrote:

I’ve been testing the release candidate, and believe that we need to change the default input.geos options for the Standard and Benchmark simulations in the unit tester to :
    %%% EMISSIONS MENU %%%  : 
    Turn on emissions?      : T  
    HEMCO Input file        : HEMCO_Config.rc
     => 1ppt MBL BRO Sim.?  : F
    Switches for UCX        :---
     => Use CH4 emissions?  : F
     => Turn on surface BCs :---
        => CH4?             : F
        => OCS?             : T
        => CFCs?            : T
        => Cl species?      : T
        => Br species?      : F
        => N2O?             : T
     => Set initial glob MRs:---
        => strat. H2O?      : T
     => CFC emission year   : 0
By default in the unit tester, => CH4 is still enabled. This appears to set up conflict between the older UCX surface layer and the newer HEMCO methane PBL boundary conditions, causing air to be a mix of preindustrial and present-day values (see below for Jul 1, 2013 surface methane in a benchmark run). Setting it to F and/or removing LCH4SBC causes the methane to behave as expected, i.e., being set by HEMCO in all simulations, with the expected spatial pattern. Also, we can slate Online CH4 chemistry?  : T in the Chemistry Menu and Input_Opt%LCH4CHEM for future removal, as it no longer does anything.

--Melissa Sulprizio (talk) 18:16, 16 July 2018 (UTC)

Fixed typo in call to GAMMA_HOBr_AER

This fix was included in GEOS-Chem 12.0.0.

Xuan Wang wrote:

When looking back at the standard GC codes of v11-02d, I found a bug in the function HETHOBr_SS_JS (in module KPP/Standard/gckpp_HetRates.F90). When calling the gamma calculation, in v11-02d, around line 3514, we have:
      CALL Gamma_HOBr_AER(rAer, denAir, 2, TK, clConc, brConc, &
                          hConc, GAM_HOBr, r_gp)
This will cause both HOBr+Cl- (X=1) and HOBr+Br- (X=2) on sea salt use the gamma of HOBr + Br- (X=2). It should be:
      CALL Gamma_HOBr_AER(rAer, denAir, X, TK, clConc, brConc, &
                          hConc, GAM_HOBr, r_gp)
It looks like a typo which could lead to quite different result for halogen chemistry.

--Bob Yantosca (talk) 20:26, 17 July 2018 (UTC)

Bug fix for liquid water content in gckpp_HetRates.F90

This fix was included in GEOS-Chem 12.0.0.

Jiayue Huang wrote:

Qianjie Chen and I think that there is potential a bug in KPP/Standard/gckpp_HetRates.F90 for halogen chemistry in the model v11-02d/e/f.

In the original code, we were using the grid-box average liquid water content, which likely underestimates the in-cloud Br- and Cl- concentration. So we think that we should change it to in-cloud liquid water content by dividing the cloud fraction. This results in increases the S(IV)+Br reaction in cloud, and thus reduces the BrO abundance, mainly in the 30-90N region.

This bug fix is to use cloud fraction when calculating liquid water content [cm3 H2O/cm3 air] in routine GET_HALIDE_CLDConc, which is used to calculate the in-cloud concentrations of Br- and Cl-.

--Bob Yantosca (talk) 15:48, 20 July 2018 (UTC)

Add PH2O2 to the default list of prod/loss families in the KPP mechanisms

This fix was included in GEOS-Chem 12.0.0.

The P(H2O2) field is required as input in the aerosol-only simulations. To simplify saving out new oxidant fields, we now include P(H2O2) by default in the prod/loss families so that it is saved out when users turn on the prod/loss diagnostic in either bpch or netCDF format.

--Bob Yantosca (talk) 16:16, 20 July 2018 (UTC)

Fixed typo that prevented PM2.5 from being archived to netCDF output

This fix was included in GEOS-Chem 12.0.0.

In routine Set_AerMass_Diagnostic of module GeosCore/diagnostics_mod.F90, there was a typo in the IF block where the PM2.5 diagnostic values get copied into State_Diag%PM25. The code in RED below:

       IF ( Archive_BetaNO ) THEN
          State_Diag%PM25(I,J,L)            = ...etc...

needs to be replaced by the code in GREEN:

       IF ( Archive_PM25 ) THEN
          State_Diag%PM25(I,J,L)            = ...etc...

--Bob Yantosca (talk) 20:33, 24 July 2018 (UTC)

Add entries to HEMCO_Config.rc for SOAP and pFe in CEDS inventory

This fix was included in GEOS-Chem 12.0.0.

The CEDS emissions entries in HEMCO_Config.rc were missing for species SOAP and pFe. To fix this, add the following lines in GREEN:

0 CEDS_CO_AGR     $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_agr            1950-2014/1-12/1/0 C xy kg/m2/s CO    26     1/2/12 5
0 CEDS_SOAP_AGR   -                                                                      -                 -                  - -  -       SOAP  26/280 1/2/12 5
0 CEDS_CO_ENE     $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_ene            1950-2014/1-12/1/0 C xy kg/m2/s CO    26     1/2/12 5
0 CEDS_SOAP_ENE   -                                                                      -                 -                  - -  -       SOAP  26/280 1/2/12 5
0 CEDS_CO_IND     $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_ind            1950-2014/1-12/1/0 C xy kg/m2/s CO    26     1/2/12 5
0 CEDS_SOAP_IND   -                                                                      -                 -                  - -  -       SOAP  26/280 1/2/12 5
0 CEDS_CO_TRA     $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_tra            1950-2014/1-12/1/0 C xy kg/m2/s CO    26     1/2/12 5
0 CEDS_SOAP_TRA   -                                                                      -                 -                  - -  -       SOAP  26/280 1/2/12 5
0 CEDS_CO_SLV     $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_slv            1950-2014/1-12/1/0 C xy kg/m2/s CO    26     1/2/12 5
0 CEDS_SOAP_SLV   -                                                                      -                 -                  - -  -       SOAP  26/280 1/2/12 5
0 CEDS_CO_WST     $ROOT/CEDS/v2018-04/CO-em-anthro_CMIP_CEDS_195001-201412.nc            CO_wst            1950-2014/1-12/1/0 C xy kg/m2/s CO    26     1/2/12 5
0 CEDS_SOAP_WST   -                                                                      -                 -                  - -  -       SOAP  26/280 1/2/12 5
0 CEDS_SO2_AGR    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc           SO2_agr           1950-2014/1-12/1/0 C xy kg/m2/s SO2   -      1/2/12 5
0 CEDS_SO4_AGR    -                                                                      -                 -                  - -  -       SO4   63     1/2/12 5
0 CEDS_pFe_AGR    -                                                                      -                 -                  - -  -       pFe   66     1/2/12 5
0 CEDS_SO2_ENE    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc           SO2_ene           1950-2014/1-12/1/0 C xy kg/m2/s SO2   -      1/2/12 5
0 CEDS_SO4_ENE    -                                                                      -                 -                  - -  -       SO4   63     1/2/12 5
0 CEDS_pFe_ENE    -                                                                      -                 -                  - -  -       pFe   66     1/2/12 5
0 CEDS_SO2_IND    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc           SO2_ind           1950-2014/1-12/1/0 C xy kg/m2/s SO2   -      1/2/12 5
0 CEDS_SO4_IND    -                                                                      -                 -                  - -  -       SO4   63     1/2/12 5
0 CEDS_pFe_IND    -                                                                      -                 -                  - -  -       pFe   66     1/2/12 5
0 CEDS_SO2_TRA    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc           SO2_tra           1950-2014/1-12/1/0 C xy kg/m2/s SO2   -      1/2/12 5
0 CEDS_SO4_TRA    -                                                                      -                 -                  - -  -       SO4   63     1/2/12 5
0 CEDS_pFe_TRA    -                                                                      -                 -                  - -  -       pFe   66     1/2/12 5
0 CEDS_SO2_SLV    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc           SO2_slv           1950-2014/1-12/1/0 C xy kg/m2/s SO2   -      1/2/12 5
0 CEDS_SO4_SLV    -                                                                      -                 -                  - -  -       SO4   63     1/2/12 5
0 CEDS_pFe_SLV    -                                                                      -                 -                  - -  -       pFe   66     1/2/12 5
0 CEDS_SO2_WST    $ROOT/CEDS/v2018-04/SO2-em-anthro_CMIP_CEDS_195001-201412.nc           SO2_wst           1950-2014/1-12/1/0 C xy kg/m2/s SO2   -      1/2/12 5
0 CEDS_SO4_WST    -                                                                      -                 -                  - -  -       SO4   63     1/2/12 5
0 CEDS_pFe_WST    -                                                                      -                 -                  - -  -       pFe   66     1/2/12 5

--Melissa Sulprizio (talk) 16:07, 27 July 2018 (UTC)

Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat

This fix was included in GEOS-Chem 12.0.0.

Tomas Sherwen wrote:

I've just found that both FJX_spec.dat the redundant CH3I spectrum and the new spectrum are both present in FJX_spec.dat and FJX_j2j.dat (in v12.0.0). This will have been due to the spectrum in my branch being under the species alias of "CH3IT" to preserve (and ignore) the use of "CH3I" in the namespace of the code for the existing methyl iodide simulation when the iodine simulation was developed. The "CH3IT" variables were replaced "CH3I" in the v11-1-Patches branches with halogen chemistry provided to GCST, but the existing methyl iodide simulation variable was not removed. There are no double ups in the KPP mechanism itself.
Please remove lines 276-281 in FJX_spec.dat (copied below).
    "
    CH3I 243 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10
             3.958E-20 4.769E-20 8.257E-19 2.154E-19 7.349E-20 3.351E-20
             1.034E-20 4.435E-21 2.272E-21 4.393E-22 4.052E-24 0.000E+00
    CH3I 300 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 0.000E+00 J10
             3.958E-20 4.769E-20 8.376E-19 2.438E-19 9.355E-20 4.680E-20
             1.529E-20 6.532E-21 3.328E-21 6.783E-22 1.038E-23 0.000E+00
    "
Please also remove the line 124 in FJX_j2j.dat (copied below).
    "
     123 CH3I PHOTON I PRODUCTS 1.000 /CH3I /
    "

--Melissa Sulprizio (talk) 17:44, 27 July 2018 (UTC)

Outstanding issues not yet resolved in GEOS-Chem 12

Inconsistency in H2402 concentrations in GCHP vs GEOS-Chem Classic

We have discovered an inconsistency with the concentrations of the halogen species H2402 (chemical formula: C2Br2F4) between GEOS-Chem "Classic" and GCHP. This inconsistency appears as the large fractional difference above ~50 km in the lower-right frame of the plot below.

H2402 issue.png

We have traced this issue to the fact that surface boundary conditions for H2402 used by GCHP differ from those used by GEOS-Chem "Classic", and also that the boundary conditions in GEOS-Chem "Classic" are read in improperly. A fix will be made in an upcoming GEOS-Chem version.

--Bob Yantosca (talk) 20:10, 7 December 2018 (UTC)

RRTMG does not compile with GNU Fortran

For a complete description of this issue, please see this post on our Coupling GEOS-Chem with RRTMG wiki page.

--Bob Yantosca (talk) 18:55, 3 August 2018 (UTC)

TOMAS40 simulations exit with a floating-point exception

We were unit testing the TOMAS40 code in the GEOS-Chem v11-02-release-candidate (soon to be finalized as 12.0.0) with the debugging flags:

make –j8 DEBUG=y BOUNDS=y FPEX=y NO_ISO=y ut &

which revealed a a NaN error. This was thrown at line 903 of GeosCore/tomas_mod.F:

           ERR_VAR = 'Gcout'
           ERR_MSG = 'After COND_NUC'
            ! check for NaN and Inf (win, 10/4/08)
            do jc = 1, icomp-1
               ERR_IND(1) = I
               ERR_IND(2) = J
               ERR_IND(3) = L
               ERR_IND(4) = 0
               call check_value( Gcout(jc), ERR_IND, ERR_VAR, ERR_MSG )

!               if( IT_IS_FINITE(Gcout(jc))) then
!                  print *,'xxxxxxxxx Found Inf in Gcout xxxxxxxxxxxxxx'
!                  print *,'Location ',I,J,L, 'comp',jc
!                  call debugprint( Nkout, Mkout, i,j,l,'After COND_NUC')
!                  stop
!               endif
            enddo

This error might be caused by the several chemistry and emissions updates that have been added to GEOS-Chem. The GEOS-Chem Support Team has referred the error to the TOMAS development team, who will be investigating further.

--Bob Yantosca (talk) 16:56, 6 August 2018 (UTC)

TOMAS simulations cannot use netCDF diagnostics

The TOMAS simulations depend on many of the "binary punch" (aka "bpch") diagnostics. As of this time, we have not yet been able to convert these to the new netCDF diagnostics. Therefore, as of GEOS-Chem 12.0.0, all TOMAS simulations must use the binary punch diagnostic option (which is turned ON by default at compile time). If you try to compile a TOMAS simulation with netCDF diagnostics (i.e. with makefile option NC_DIAG=y), then a compile-time error will be generated.

--Bob Yantosca (talk) 15:28, 9 August 2018 (UTC)