Difference between revisions of "Bugs and fixes"

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Please also be sure to visit our [[Common GEOS-Chem error messages]] wiki page for more general information about some frequently encountered errors.  Also visit our [[Currently unresolved issues in GEOS-Chem]] and [[Known issues caused by compiler bugs]] wiki pages for more information about unresolved issues.
 
Please also be sure to visit our [[Common GEOS-Chem error messages]] wiki page for more general information about some frequently encountered errors.  Also visit our [[Currently unresolved issues in GEOS-Chem]] and [[Known issues caused by compiler bugs]] wiki pages for more information about unresolved issues.
  
== Bugs and fixes lists are being migrated to Github ==
+
== Bugs and fixes lists have now been migrated to Github ==
  
 
We have been migrating bug reports to our GEOS-Chem issue tracker, which is located on our Github repository: https://github.com/geoschem/geos-chem/issues/.  We recommend that you also look through both the open and closed issues on this page, as your issue might be listed there.
 
We have been migrating bug reports to our GEOS-Chem issue tracker, which is located on our Github repository: https://github.com/geoschem/geos-chem/issues/.  We recommend that you also look through both the open and closed issues on this page, as your issue might be listed there.
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{| border=1 cellspacing=0 cellpadding=5  
 
{| border=1 cellspacing=0 cellpadding=5  
 
|-bgcolor="#CCCCCC"
 
|-bgcolor="#CCCCCC"
!width="100px"|Version
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!Version
!width="500px"|List of bugs and issues (now at the Github issue tracker)
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!Released
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!colspan="2"|List of bugs and issues (now posted on the listed Github repository)
  
 
|-valign="top"
 
|-valign="top"
|[[GEOS-Chem 12#12.7.0|12.7.0]]
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|13.0.0
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|TBD
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
 
|
 
|
*[https://github.com/geoschem/geos-chem/milestone/4 '''Milestone 12.7.0 (open issues)''']
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*[https://github.com/geoschem/geos-chem/milestone/8 '''Milestone 13.0.0''' (open issues)]
*[https://github.com/geoschem/geos-chem/milestone/4?closed=1 '''Milestone 12.7.0 (closed issues)''']
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*[https://github.com/geoschem/geos-chem/milestone/8?closed=1 '''Milestone 13.0.0''' (closed issues)]
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|-valign="top"
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|[[GEOS-Chem 12#12.9.3|12.9.3]]
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|06 Aug 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/16?closed=1 '''Milestone 12.9.3''']
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|-valign="top"
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|[[GEOS-Chem 12#12.9.2|12.9.2]]
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|24 Jul 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/15?closed=1 '''Milestone 12.9.2''']
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|-valign="top"
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|[[GEOS-Chem 12#12.9.1|12.9.1]]
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|17 Jul 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/14?closed=1 '''Milestone 12.9.1''']
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 +
|-valign="top"
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|[[GEOS-Chem 12#12.9.0|12.9.0]]
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|17 Jul 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/10?closed=1 '''Milestone 12.9.0''']
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|-valign="top"
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|[[GEOS-Chem 12#12.8.2|12.8.2]]
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|27 May 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/13?closed=1 '''Milestone 12.8.2''']
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|-valign="top"
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|[[GEOS-Chem 12#12.8.1|12.8.1]]
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|21 May 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/12?closed=1 '''Milestone 12.8.1''']
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|-valign="top"
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|[[GEOS-Chem 12#12.8.0|12.8.0]]
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|04 Mar 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/7?closed=1 '''Milestone 12.8.0''']
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|-valign="top"
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|[[GEOS-Chem 12#12.7.2|12.7.2]]
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|09 Mar 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/11?closed=1 '''Milestone 12.7.2''']
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|-valign="top"
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|[[GEOS-Chem 12#12.7.1|12.7.1]]
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|19 Feb 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/9?closed=1 '''Milestone 12.7.1''']
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|-valign="top"
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|[[GEOS-Chem 12#12.7.0|12.7.0]]
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|03 Feb 2020
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/4?closed=1 '''Milestone 12.7.0''']
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|-valign="top"
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|[[GEOS-Chem 12#12.6.3|12.6.3]]
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|25 Nov 2019
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|[https://github.com/geoschem/gchp geoschem/gchp]
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|[https://github.com/geoschem/gchp/milestone/2?closed=1 '''Milestone 12.6.3''']
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|-valign="top"
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|[[GEOS-Chem 12#12.6.2|12.6.2]]
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|15 Nov 2019
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/6?closed=1 '''Milestone 12.6.2''']
  
 
|-valign="top"
 
|-valign="top"
 
|[[GEOS-Chem 12#12.6.1|12.6.1]]
 
|[[GEOS-Chem 12#12.6.1|12.6.1]]
|
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|28 Oct 2019
*[https://github.com/geoschem/geos-chem/milestone/5?closed=1 '''Milestone 12.6.1''']
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|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|[https://github.com/geoschem/geos-chem/milestone/5?closed=1 '''Milestone 12.6.1''']
  
 
|-valign="top"
 
|-valign="top"
|[[GEOS-Chem 12#12.6.0|12.6.0]]
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|width="80px"|[[GEOS-Chem 12#12.6.0|12.6.0]]
|
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|width="100px"|18 Oct 2019
*[https://github.com/geoschem/geos-chem/milestone/2?closed=1 '''Milestone 12.6.0''']
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|width="200px"|[https://github.com/geoschem/geos-chem geoschem/geos-chem]
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|width="400px"|[https://github.com/geoschem/geos-chem/milestone/2?closed=1 '''Milestone 12.6.0''']
  
 
|}
 
|}

Latest revision as of 14:25, 6 August 2020

On this page we list the GEOS-Chem specific bugs and issues that users have recently encountered, and how to fix them.

Please also be sure to visit our Common GEOS-Chem error messages wiki page for more general information about some frequently encountered errors. Also visit our Currently unresolved issues in GEOS-Chem and Known issues caused by compiler bugs wiki pages for more information about unresolved issues.

Bugs and fixes lists have now been migrated to Github

We have been migrating bug reports to our GEOS-Chem issue tracker, which is located on our Github repository: https://github.com/geoschem/geos-chem/issues/. We recommend that you also look through both the open and closed issues on this page, as your issue might be listed there.

Version Released List of bugs and issues (now posted on the listed Github repository)
13.0.0 TBD geoschem/geos-chem
12.9.3 06 Aug 2020 geoschem/geos-chem Milestone 12.9.3
12.9.2 24 Jul 2020 geoschem/geos-chem Milestone 12.9.2
12.9.1 17 Jul 2020 geoschem/geos-chem Milestone 12.9.1
12.9.0 17 Jul 2020 geoschem/geos-chem Milestone 12.9.0
12.8.2 27 May 2020 geoschem/geos-chem Milestone 12.8.2
12.8.1 21 May 2020 geoschem/geos-chem Milestone 12.8.1
12.8.0 04 Mar 2020 geoschem/geos-chem Milestone 12.8.0
12.7.2 09 Mar 2020 geoschem/geos-chem Milestone 12.7.2
12.7.1 19 Feb 2020 geoschem/geos-chem Milestone 12.7.1
12.7.0 03 Feb 2020 geoschem/geos-chem Milestone 12.7.0
12.6.3 25 Nov 2019 geoschem/gchp Milestone 12.6.3
12.6.2 15 Nov 2019 geoschem/geos-chem Milestone 12.6.2
12.6.1 28 Oct 2019 geoschem/geos-chem Milestone 12.6.1
12.6.0 18 Oct 2019 geoschem/geos-chem Milestone 12.6.0

Issues resolved in GEOS-Chem 12.5.0

The bugs and technical issues listed below will be resolved GEOS-Chem 12.5.0, release date TBD.

Module or area Issue that was resolved Git commit ID
Chemistry
  1. Bug fix: Make sure stratospheric BrY concentrations are properly read each month
  2. Add photolysis menu to input.geos for specifying FAST-JX directory
  3. Correction for CFCs in the chemistry mechanism
  4. Fix typo in CLD_PARAMS routine in gckpp_HetRates.F90
  1. 0588a269
  2. 03e94fed
  3. 1b9f69f0
  4. 95d124e0
Diagnostics
  1. Enable GEOS-Chem "Classic" netCDF (History) diagnostics to be subsetted vertically and horizontally
  2. Enable accurate cloud pH diagnostic calculation via post-processing
  1. 6acd4ce3
  2. 1c15e54a
Structural updates
  1. Add optional capability to compile GEOS-Chem Classic and GCHP using CMake
  1. pull/27
Emissions
  1. Fixes for GFED4 biomass burning emissions, including:
    • Change the HEMCO cycling flag so that the model crashes if it doesn't find the right GFED year
    • Remove the 27% scaling of POG to POA and emit 1:1 instead
  1. 381386fb
Fixes affecting GCHP only:
Structural updates
  1. Update GCHP to use MAPL v1.0.0 and ESMF v8.0.0 beta snapshot 28
    • Will introuduce faster parallel I/O
    • Will enable full use of gfortran compiler

--Bob Yantosca (talk) 17:03, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.4.0

The bugs and technical issues listed below will be resolved GEOS-Chem 12.4.0, release date TBD.

Module or area Issue that was resolved Git commit ID
Photolysis
  1. Bug fix: Rebuild chemical mechanisms for FAST-JX fix added in 12.3.2
  2. Add photolysis menu to input.geos for specifying FAST-JX directory
  1. fcd0cfba
  2. d34a9cd2

--Bob Yantosca (talk) 17:04, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.2

The bugs and technical issues listed below will be resolved GEOS-Chem 12.3.2.

Module or area Issue that was resolved Git commit ID
Chemistry
  1. Fix inconsistency for species H2402 between GCHP and GEOS-Chem "Classic"
  1. rel/12.3.2
Photolysis
  1. Remove duplicate entry for species ClNO2 in the FJX_j2j.dat file
  2. Species DHDC was not listed as photolyzing in the GEOS-Chem species database
  1. rel/12.3.2
  2. d7c48d14
Fixes affecting GCHP only:
Emissions
  1. Disable Br2 offline seasalt emissions to match GEOS-Chem Classic default
  2. Fix HEMCO diagnostics settings for lightning NO and seasalt emissions
  1. f6ac477a
  2. cda5044e

--Bob Yantosca (talk) 16:37, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.1

The bugs and technical issues listed below were resolved GEOS-Chem 12.3.1 (release 08 Apr 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Planeflight diagnostic now writes out data for the last timestep of the day
  2. Fix the netCDF diagnostic for noontime J-values
  1. 04da94cd
  2. f4d43b7a
Structural
  1. Do not allocate memory to array MINIT in strat_chem_mod.F90
  2. Declare State_Met%Area_M2 as 2-dimensional, not 3-dimensional
  1. 729fd2a7
  2. e4af25f3b

--Bob Yantosca (talk) 20:06, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.3.0

The bugs and technical issues listed below were resolved GEOS-Chem 12.3.0 (release date TBD).

Module or area Issue that was resolved Git commit ID
Diagnostics / Restart files
  1. Further bug fix for netCDF diagnostics spanning leap years
  1. fb093d61
Emissions
  1. Bug fixes for the HEMCO interpolation algorithm
  2. Updates from the NASA GEOS development branch
  3. Add option to always use simulation year for specified fields
  4. Prevent zero emissions for MEGAN_Mono extension species
  5. Updates to the volcanic emissions extension
  1. e947fc80
  2. 7df3fc8e
  3. 23189032
  4. af86c4dd
  5. 07c10319

--Bob Yantosca (talk) 15:53, 21 March 2019 (UTC)

Issues resolved in GEOS-Chem 12.2.1

The bugs and technical issues listed below were resolved GEOS-Chem 12.2.1 (release date 28 Feb 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics / Restart files
  1. Bug fix: netCDF diagnostic collections with frequency "End" now properly span leap year days
  1. ca68f508
CO2 simulation
  1. Fix for CO2 simulation chemical source
  1. N/A
TOMAS simulations
  1. Restore DST1, DST2, DST3, and DST4 in TOMAS simulations
  1. 5ed3e9cf
Fixes affecting GCHP only:
Emissions etc.
  1. Use online sea flux emissions by default in GCHP
  2. Update MODIS LAI source directory to match GEOS-Chem Classic
  1. 9759d26b
  2. N/A
Met fields
  1. Missing scaling factors for MERRA-2 simulations with GCHP
  1. ?

--Bob Yantosca (talk) 17:03, 15 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.2.0

The bugs and technical issues listed below were resolved GEOS-Chem 12.2.0 (release date 19 Feb 2019).

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fix bug in stratospheric aerosol surface area in netCDF diagnostics
  1. e4fecf01
Fixes affecting GCHP only:
Restart files
  1. GCHP bug fix: Use checkpoint output as the subsequent restart file

--Bob Yantosca (talk) 20:02, 14 March 2019 (UTC)

Issues resolved in GEOS-Chem 12.1.1

The bugs and technical issues listed below were resolved in GEOS-Chem 12.1.1, which was released on 13 Dec 2018.

Module or area Issue that was resolved Git commit ID
Compilation issues
  1. Always enable BPCH_TPBC to allow saving out BC files in global simulations
  2. Add hco_interface_mod.o to list of dependencies for get_met_mod.o and only compile get_met_mod.F90 and flexgrid_mod.F90 for GEOS-Chem "Classic"
  3. Add flexgrid_read_mod.o to list of dependencies for hcoi_gc_main_mod.o
  1. 072ec9d6
  2. 096ad29d
  3. f9b2f195
Diagnostics
  1. Skip planeflight observations outside a nested domain
  1. f6f90fd4
Tagged CO simulation
  1. Bug fix for tagged CO: don't multiply emissions timestep by 60
  1. 8a1b078e
Fixes affecting GCHP only:
Transport (FvDycore)
  1. GCHP transport fix to prevent instant propagation from troposphere to stratosphere

--Bob Yantosca (talk) 14:12, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.1.0

The bugs and technical issues listed below were resolved in GEOS-Chem 12.1.0, which was released on 26 Nov 2018.

Module or area Issue that was resolved Git commit ID
CH4 simulation
  1. Add fixes for seasonal scale factors in CH4 simulations
  1. 6f48d045
Chemistry and Photolysis
  1. Allow for SZA to 98 degrees when getting photolysis rates
  2. Move Fast-JX .dat files from the geos-chem-unittest repository to gcgrid/ExtData
  1. d06ae04a
  2. 03e94fed
Emissions
  1. Add missing RCO sector to CEDS emissions entries
  2. Include CEDS ship emissions as default global ship emissions inventory
  3. Reduce file size for CEDS inventory
  4. HEMCO bug fix: prevent excessive attempts to read the HEMCO restart file when using GEOS-Chem "Classic"
  5. Add fix for collapsing model levels to reduced grid
  6. Fix unit conversion in HCO_UNIT_GetAreaScal
  1. 642dd0af
  2. e71d0d67
  3. 20451cb4
  4. 3f62e749
  5. 820b8d7d
  6. 7dfd99da
PBL Mixing
  1. Fix mass conservation in non-local PBL mixing
  1. 57c75178
Tagged CO simulation
  1. Update HEMCO configuration file for the tagged CO simulation
  1. 02aaad73
Fixes affecting GCHP only:
Emissions (GCHP)
  1. Fix masking bug to correctly apply anthropogenic emissions
  2. Remove erroneous 180 degree longitude shift in APEI regridding
Structural (GCHP)
  • Move GCHP run directory creation from GEOS-Chem Unit Tester to GCHP repository

--Bob Yantosca (talk) 15:12, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.3

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.3, which was released on 16 Oct 2018.

Module or area Issue that was resolved Git commit ID
Fixes affecting GCHP only:
Emissions (GCHP)
  1. Fix incorrect run configuration for offline sea salt emissions in GCHP
  2. Fix bug in application of CFC surface mixing ratios in GCHP

--Bob Yantosca (talk) 22:01, 21 December 2018 (UTC)

Issues resolved in GEOS-Chem 12.0.2

The bugs and technical issues listed below were be resolved in GEOS-Chem 12.0.2, which was released on 10 Oct 2018.

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fixed local-time averaging in ND51 and ND51b satellite timeseries diagnostics
  1. 14b29d3d
Specialty simulations
  1. Correct missing BC/OC biomass emissions and aerosol drydep in TOMAS simulations
  2. Avoid double-counting of emissions in the CO2 simulation
  1. 6a944b92
  2. 8320e73d

--Bob Yantosca (talk) 19:16, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.1

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.1, which was released on 24 Aug 2018.

Module or area Issue that was resolved Git commit ID
Diagnostics
  1. Fix typo when registering the State_Chm%SSAlk field
  2. Fix mis-indexing in the ND05 diagnostic
  1. 55d16873
  2. 8e118c0e
Mercury
  1. Fixes for the Hg specialty simualtion: Restore biomass emissions and do not double-count anthropogenic emissions
  1. e1e6668b
Structural updates
  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
  1. ff7b0c3c
  2. a4d55055
  3. e0959563
  4. 9833fff4

--Bob Yantosca (talk) 19:20, 16 July 2019 (UTC)

Issues resolved in GEOS-Chem 12.0.0

The bugs and technical issues listed below were resolved in GEOS-Chem 12.0.0, which was released on 10 Aug 2018.

Module or area Issue that was resolved
Aerosols
Chemistry
Diagnostics
Emissions
Specialty simulations
Structural updates
  • Initial structural updates to interface GEOS-Chem into WRF
  • Now always declare the netCDF time variable with an unlimited dimension

Issues resolved in GEOS-Chem v11-01

The bugs and technical issues listed below were resolved in GEOS-Chem v11-01. Also be sure to visit our Known issues caused by compiler bugs wiki page for a list of compiler-related issues and workarounds.

Module or area Issue that was resolved
Aerosol-only simulation
CH4 simulation
Chemistry
CO2 simulation
Cloud convection
Compiler / Fortran issues Compiler issues:

Fortran language issues:

Diagnostics
Emissions (via HEMCO)
Mercury and POPs simulations
Met fields and derived quantities
netCDF I/O
Photolysis
Regridding
RRTMG radiative transfer model
Marine POA simulations
Radon-Lead-Beryllium simulation
Species database and definitions of physical constants
Tagged CO simulation
Tagged O3 simulation
TOMAS aerosol microphysics
Various structural updates
Wet deposition

--Bob Yantosca (talk) 19:57, 23 January 2017 (UTC)

Bugs and fixes in older GEOS-Chem versions

For a complete list of bugs and fixes in older GEOS-Chem versions, please see:

--Bob Yantosca (talk) 20:47, 2 January 2019 (UTC)