GEOS-Chem 12

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GEOS-Chem v11-02-final will also carry the designation GEOS-Chem 12.0.0. We are migrating to a purely numeric versioning system in order to adhere more closely to software development best practices. For a complete description of the new versioning system, please see our GEOS-Chem version numbering system wiki page.




Version history summary

Previous major release Current stable version Version in development
GEOS-Chem v11-01-public GEOS-Chem 12.0.0
(DOI 10.5281/zenodo.1343547)
GEOS-Chem 12.1.0
Released01 Feb 2017 Released 10 Aug 2018 Release TBD
GC v11-01 online manual GC 12 online manual GC 12 benchmark history

The sections below describe each GEOS-Chem feature version and GEOS-Chem 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.

12.1.0

The items listed below are slated to be included in GEOS-Chem 12.1.0. This is a feature release which will be validated with a 1-month benchmark simulation.

Feature Submitted by Type Status
Features affecting the full-chemistry simulation:
FlexGrid: Use HEMCO to read met fields and enable nested simulations over any custom domains Jiawei Zhuang (Harvard)
Jintai Lin (PKU)
Structural
  • NOTE: FlexGrid might result in slight differences in met fields w/r/t the current regridding method. This could have an impact on the full-chemistry simulations.
Anthropogenic PM2.5 dust source Sajeev Philip (Dalhousie) Science
  • Update 29 Jun 2018: Fixed an initialization issue that caused much more dust to be emitted than the expected 13.1 Tg/yr.
  • Code updates have been added to GC git repository, but are commented out until we officially release this feature in 12.1.0.
NetCDF Output Phase 3b: Updates to eliminate differences between single and multi-segmented GEOS-Chem runs GCST
Christoph Keller
Bug Fix &
Structural
Add missing RCO sector to CEDS emissions entries Pengfei Liu (Harvard) Bug fix Implemented 15 Aug 2018
Features NOT affecting the full-chemistry simulation:
Updated flux diagnostics Chris Holmes (Florida State)
GCST
Structural/
Benchmarking
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.

Current stable version

The GEOS-Chem version listed below is considered stable and can be used to start a new research project.

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 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

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 Status
Features affecting the full-chemistry (benchmark) simulation:
Turn off TRASH emissions by default to avoid double counting GCST
Eloise Marais (U. Birmingham)
Bug fix Implemented 27 Jul 2018
  • 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 Implemented 27 Jul 2018
  • 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 Implemented 19 Jul 2018
  • 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 Implemented 19 Jul 2018
  • 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 Implemented 18 Jul 2018
  • NOTE: 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 Implemented 16 Jul 2018.
  • Results approved by Eloise Marais.
  • NOTE: 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 Implemented 11 Jul 2018, pending validation
  • NOTE: 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 Implemented 03 Jul 2018
  • NOTE: 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 Implemented 27 Jun 2018
  • NOTE: 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
  • NOTE: 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 Implemented 09 Aug 2018
Limit flash rate density in hcox_lightnox_mod.F90 Lee Murray (Rochester) Bug fix Implemented 09 Aug 2018
Initial structural modifications for interfacing GEOS-Chem into WRF Haipeng Lin (Peking U.) Structural This process is ongoing
Minor fixes for mercury chemistry updates implemented in v11-02f Colin Thackray (Harvard) Bug fix Implemented 02 Aug 2018
Restore default timestep for MERRA-2 nested grid simulations to 10/20 Ke Li (Harvard) Bug fix Implemented 30 Jul 2018
Remove duplicate C3HI spectrum in FJX_spec.dat and FJX_j2j.dat Tomas Sherwen (York) Bug fix Implemented 27 Jul 2018
  • 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 Implemented 24 Jul 2018
Bring two-way nested-grid code option up-to-date Yingying Yan (PKU)
Jintai Lin (PKU)
Structural Implemented 24 Jul 2018
  • 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 Implemented 23 Jul 2018
Add PH2O2 to the default list of prod/loss families in the KPP mechanisms GCST Structural Implemented 19 Jul 2018
  • 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 v2.1.007, which includes minor updates:
  1. Fixed error in HEMCO "exact" cycling option
  2. Stop with error if multiple containers have the same name
  3. Bug fix for distributing emissions in the vertical dimension
  4. Add extra error checks in HEMCO standalone module
  5. Remove null string character from netCDF unit string
  6. Bug fix for HEMCO soil NOx error with ifort 17
GCST
Christoph Keller
Jenny Fisher
Structural &
Bug fix
Update history:
  1. Implemented 09 Aug 2018
  2. Implemented 20 Jul 2018
  3. Implemented 19 Jul 2018
  4. Implemented 18 Jul 2018
  5. Implemented 17 Jul 2018
  6. Implemented 26 Jun 2018
Bug fix for reference time in netCDF diagnostic files GCST Bug fix Implemented 12 Jul 2018
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 Update history:
  1. Implemented 19 Jul 2018
  2. Implemented 11 Jul 2018
Fix issues in complexSOA and complexSOA_SVPOA restart files Eloise Marais (U. Birmingham) Bug fix Implemented 05 Jul 2018
Avoid double counting CEDS and GEIA NH3 biofuel emissions Christoph Keller (NASA/GMAO)
GCST
Bug fix Implemented 29 Jun 2018
  • NOTE: 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 Implemented 26 Jun 2018
  • NOTE: 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 Implemented 26 Jun 2018
  • NOTE: Full-chemistry difference-tests yielded identical results w/r/t v11-02-rc.

--Bob Yantosca (talk) 14:01, 10 August 2018 (UTC)

Previously released stable versions

TBD

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? When added? Directory
QFED biomass burning OPTIONAL New data files for QFED v2.5r1 12.0.0 HEMCO/QFED/v2018-07
GFED4 biomass inventory 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

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 v11-03. Click on the links below to see the results from each set of unit tests:

Unit test Date
TBD

Previous issues now resolved in GEOS-Chem 12

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

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

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)