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GEOS-Chem v12.1.0 - Updated for GBD-MAPS project

https://zenodo.org/record/4718622

The default GEOS-Chem v12.1.0 source code (https://doi.org/10.5281/zenodo.1553349) was updated to include the following:

  1. Parameterization for N2O5 heterogneous uptake - following McDuffie et al., 2018a (impelmented in default GCv12.6.0 https://doi.org/10.5281/zenodo.3507501)
  2. Heterogeneous production of ClNO2 from sea salt aerosol - following implmentation in Shah et al., 2018 and ClNO2 yield recommendations from McDuffie et al., 2018b
  3. Reduced dry deposition rates for HNO3 at cold temperatures - following Shah et al., 2018 (implemented in default GCv12.6.0 https://doi.org/10.5281/zenodo.3507501)
  4. Updated wet deposition scheme - following Luo et al., 2019 (updated version included as an option starting in GCv12.7.0 https://doi.org/10.5281/zenodo.3634864)

Additional minor updates (bug fixes) from later versions of the default GEOS-Chem source code included here:

  1. Updated HEMCO_config.rc file to read in the uodated MEGAN/2018-05 PFT (plant functional type) file (update in 12.3.0: http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_12#12.3.0)
  2. Updated MEGAN extension to correctly calcuatle monoterpene concentraions (bug fix in v12.3.0: http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_12#12.3.0)
  3. Changed erruptive volcanic emisssions to 'R' in HEMCO_Config.rc file, maintained 'C' cycling for degassing emissions (bug fix in 12.3.0: http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_12#12.3.0)
  4. Turned on photoloysis for DHDC and turned off photolysis for DHDN (update in 12.3.2: http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_12#12.3.2)
  5. Removed CO from MEGAN HEMCO extension to avoid double counting (updated in 12.5.0)
  6. Updated volanic emissions to AeroCom (extended to 2018) (updated in 12.3.0, 12.4.0, and 12.5.0: http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_12#12.5.0)
  7. Fixed heterogeneous cloud parameters in the HetRates file (update in 12.5.0: http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_12#12.5.0)
  8. Changed stratospheric Bry $MM in HEMCO_Config to 1-12 to make sure emissions are read correctly each moth (v12.5.0: http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_12#12.5.0)
  9. Removed 27% scaling factor for POG from GFEd emissions (updated in 12.5.0, from Pai et al., 2019)
  10. Updated GFED emissions to the 4s beta version (updated in v12.8.0: http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_12#12.8.0)

References:

Luo G, Yu F, & Schwab J (2019) Revised treatment of wet scavenging processes dramatically improves GEOS-Chem 12.0.0 simulations of nitric acid, nitrate, and ammonium over the United States. Geosci. Model Dev. Discuss. 2019:1-18.

McDuffie EE, et al. (2018a) Heterogeneous N2O5 Uptake During Winter: Aircraft Measurements During the 2015 WINTER Campaign and Critical Evaluation of Current Parameterizations. J. Geophys. Res. Atmos. 123(8):4345-4372.

McDuffie EE, et al. (2018b) ClNO2 Yields From Aircraft Measurements During the 2015 WINTER Campaign and Critical Evaluation of the Current Parameterization. J. Geophys. Res. Atmos. 123(22):12,994-913,015.

Pai SJ, et al. (2019) An evaluation of global organic aerosol schemes using airborne observations. Atmos. Chem. Phys. Discuss. 2019:1-39.

Shah V, et al. (2018) Chemical feedbacks weaken the wintertime response of particulate sulfate and nitrate to emissions reductions over the eastern United States. P. Natl. Acad. Sci. 115:8110-8115.

The following is the README from the official GEOS-Chem Source code repository

README for the Official GEOS-Chem Source code repository

The Official GEOS-Chem repository (https://github.com/gcst/geos-chem) contains the source code for the GEOS-Chem model of atmospheric chemistry and composition.

We have migrated from Bitbucket to Github!

As of June 2018, we have migrated the GEOS-Chem source code repository to back Github. Going forward, please make sure to clone or pull code updates ONLY from this repository.

GEOS-Chem Development

Branches

This repository contains several branches. Each branch contains code updates belonging to a particular line of development.

  • The master branch always contains the current stable version. You should never add new code directly into this branch. Instead, open a new branch off of master and add your code there.

  • The dev/X.Y.Z branches always contains in-development code for upcoming version X.Y.Z. Code in dev/X.Y.Z is very much "work in progress" and should not be relied upon until it has been fully debugged, validated, and merged back into the master branch.

  • The GEOS branch contains updates that are specific to the interface between GEOS-Chem and the NASA GEOS-DAS Earth System Model. Most GEOS-Chem users can simply ignore this branch.

  • From time to time, you will see other branches pertaining to new lines of development being created. These branches usually will start with feature/ or bugfix/. Once the code in these branches has been sufficiently validated, these branches will be merged back into the master branch. You should not use code in these branches.

Versions

GEOS-Chem versions are now denoted by 3 digits (X.Y.Z):

  • The X digit is the major version number. A change in X denotes that the current version contains a significant update that breaks backwards-compatibility with the prior series of GEOS-Chem versions. Major structural updates typically will require an update to X. In the past we have changed the X digit when replacing SMVGEAR with FlexChem (version 10 to version 11) and replacing legacy emissions with HEMCO (version 9 to version 10).

  • The Y digit is the feature version number. A change in Y denotes that a 1-month benchmark has been performed to validate a new feature or set of features. Some (but not all) Y versions will have 1-year benchmarks performed as well. In general, the Y digit changes whenever a new feature breaks backwards compatibility with one or more run directories from the prior version.

  • The Z digit is the bug fix (or patch) version number. A change in Z denotes that a bug fix was made that does not break backwards compatibility with run directories from the prior verison. Z will also be updated when bug fixes or minor updates are made to one or more of the GEOS-Chem "Specialty" simulations. Updating specialty simulations should not affect the output of the GEOS-Chem 1-month or 1-year benchmark simulations.

For more information, please see this wiki page: http://wiki.geos-chem.org/GEOS-Chem_version_numbering_system

All benchmarked GEOS-Chem versions are tagged in the Git history. Use git tag in your terminal to see a list of available tags. Tags will also be highlighted in the gitk browser window.

Citing GEOS-Chem versions with DOI's

You can now cite GEOS-Chem in publications with a Digital Object Identifier (DOI). Each GEOS-Chem release will be assigned its own individual DOI. DOI's for each GEOS-Chem version will be posted on the GEOS-Chem website and GEOS-Chem wiki.

We have also generated a concept DOI, which will always point to the current stable version of GEOS-Chem (i.e. corresponding to the master branch): DOI

Documentation

Web site

The GEOS-Chem web site is a good place to get started. It will point you to many important GEOS-Chem resources.

Online user's manual

You can find the The GEOS-Chem User's Guide online here:

Wiki

The most up-to-date information about GEOS-Chem is posted on the GEOS-Chem wiki. Here you will find information about technical issues, bug fixes, and other pertinent topics.

GEOS-Chem run directories

To generate GEOS-Chem run directories, please clone the geos-chem-unittest repository and follow the instructions as listed on this GEOS-Chem wiki page: http://wiki.seas.harvard.edu/geos-chem/index.php/Creating_GEOS-Chem_run_directories

Support

We encourage GEOS-Chem users to use the Github issue tracker attached to this repository to report bugs or technical issues with the GEOS-Chem code.

You are also invited to direct GEOS-Chem support requests to the GEOS-Chem Support Team at geos-chem-support@as.harvard.edu.

14 Nov 2018 GEOS-Chem Support Team geos-chem-support@as.harvard.edu