GEOS-Chem v11-01

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Revision as of 16:37, 26 June 2015 by Lizzie Lundgren (Talk | contribs) (v11-01b)

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The table below shows the previous, current, and successive versions of GEOS-Chem:

Previous version This version Next version
GEOS-Chem v10-01 GEOS-Chem v11-01 TBD
View v10-01 benchmark history View v11-01 benchmark history TBD

--Bob Y. (talk) 20:29, 17 June 2015 (UTC)

What's new in this version

NOTE: v11-01a, v11-02b, etc. denote 1-month benchmark simulations, which are designed to evaluate GEOS-Chem's performance at intermediate stages of development.


Please see the Benchmark approval form for GEOS-Chem v11-01a for complete information about the validation of GEOS-Chem v10-01a.

Feature Type Submitted by Status
Incorporate moisture into air quantities, tracer units, and tracer unit conversions Science &
Bug fix
Lizzie Lundgren (GEOS-Chem Support Team) TBD
Correct bug in below cloud average mixing ratio calculation in DO_MERRA_CONVECTION to improve mass balance Bug fix Lizzie Lundgren (GEOS-Chem Support Team) " "
Added the capability to print out tracer masses every few hours, in order to check for mass conservation Structural Lizzie Lundgren (GEOS-Chem Support Team) " "
Fix bug in RRTMG that prevents storage of O3 and CH4 RFs Bug fix David Ridley (MIT)
Sebastian Eastham (MIT)
" "

--Melissa Sulprizio (talk) 20:32, 25 June 2015 (UTC)


NOTE: This version will require a 1-month benchmark simulation and 1-year benchmark simulation.

Feature Type Submitted by Status
Update DMS climatology to Lana Science Tom Breider (Harvard) TBD
Impaction scavenging for hydrophobic BC Science Qiaoqiao Wang (Max Planck Institute)
Homogeneous IN removal Science Qiaoqiao Wang (Max Planck Institute)
Online emission of marine primary organic aerosol (POA) Science Brett Gantt (NCSU)
Matthew Johnson (NASA Ames)
Density of OA update Science Melanie Hammer (Dalhousie)
Eloïse Marais (Harvard)
Addition of BrC UV absorption to address impacts on OH Science Melanie Hammer (Dalhousie)
Acid uptake on dust aerosols Science T. Duncan Fairlie (NASA/LARC)
Improved dust size distribution scheme Science Li Zhang (Colorado U.)
Daven Henze (Colorado U.)
Metal catalyzed oxidation of SO2 (as a switch) Science Becky Alexander (UW)
Update of PMN + O3 reaction products in globchem.dat file Bug fix Dylan Millet (UMN)
Harmonizing Henry's Law coefficients across wet and dry deposition Science GEOS-Chem Support Team

--Lizzie Lundgren (talk) 16:37, 26 June 2015 (UTC)


NOTE: This version will require a 1-month benchmark simulation only.

Feature Type Submitted by Status
Updates to PAH code Science Carey Friedman (MIT) TBD
Remove in-plume reduction of Hg Science Yanxu Zhang (Harvard) " "

--Melissa Sulprizio (talk) 18:23, 16 June 2015 (UTC)

In the pipeline

The following features are slated for inclusion in GEOS-Chem v11-01:

Feature Type Submitted by Status
CO2 direct effect on isoprene emissions Science Amos Tai (CUHK)
Criegee intermediates Science Dylan Millet (U. Minnesota)
Eloïse Marais (Harvard)

PAN updates Science Emily Fischer (CSU)
NetCDF output: Flexible diagnostic package and tracer restart file Science GEOS-Chem Support Team TBD
Flexchem Science Mike Long (Harvard) TBD
Uniformity of units Science Lizzie Lundgren (GEOS-Chem Support Team)
  • To be implemented after Flexchem
Monthly mean surface methane distributions Science Lee Murray (NASA GISS/LDEO) TBD
Fix to direct/diffuse radiation Science &
Bug fix
Katie Travis TBD
Fix for NO3 + ISOP product Science Katie Travis TBD
Update MODIS LAI fields through 2015 Science Barron Henderson (UF) TBD
Updated organic deposition Science Katie Travis (Harvard)
Jenny Fisher (U. Wollongong)
Hg emission update: NEI, EDGAR, NPRI, UNEP Science Hg and POPs WG TBD
Optimized ocean rate coefficients for Hg simulation Science Shaojie Song (MIT) TBD
Update offline oxidant fields for Hg simulation Science Viral Shah (UW)
Johan Schmidt (Harvard)
Dry deposition updates for Hg simulation Science Bess Corbitt (Harvard) TBD
New atmospheric Hg redox mechanism Science Hannah Horowitz (Harvard) TBD
GTMM revision Science Bess Corbitt (Harvard) TBD
EPA-derived BC/OA emissions over US (1990-2012) Science David Ridley (MIT) TBD
Update density of BC to 1.8 and add absorption enhancement factor in input.geos Science Xuan Wang (MIT) TBD
Updates to isoprene chemistry, includes:
  • Fast photolysis of carbonyl nitrates
  • Aerosol uptake of organic nitrates
Science Jenny Fisher (U. Wollongong)
Eloïse Marais (Harvard)
Kelvin Bates (Caltech)
Katie Travis (Harvard)
Nighttime isoprene chemistry updates Science Rebecca Schwantes (Caltech) TBD
Remove dependence of species drydep on HNO3 drydep Science Katie Travis (Harvard)
Jenny Fisher (U. Wollongong)
Arctic Hg cycling Science Jenny Fisher (U. Wollongong) TBD
A snow NOx source from deep snowpack Science Maria Zatko (UW)
Becky Alexander (UW)
Land cover module in GEOS-Chem Science Jeffrey Geddes (MIT)
Michael Long (Harvard)
Merge standard simulation with specialty simulations for OVOC, acids, aromatics, dicarbonyls, terpenes Science Dylan Millet (UMN)
Xin Chen (UMN)
Automate redistribution of NOx in HEMCO Science Lee Murray (NASA GISS/LDEO) TBD
Injection height for fire emissions Science Emily Fischer (CSU) TBD
Improved lightning emission scheme Science Lee Murray (NASA GISS/LDEO) TBD

--Melissa Sulprizio (talk) 19:03, 22 June 2015 (UTC)

New data directories

The following new data directories have been added for GEOS-Chem v11-01. You will have to download the directories relevant to your simulation.

  • TBD


In this section we provide information about the benchmarks and tests that we have done to validate GEOS-Chem v11-01.

1-month and 1-year benchmarks

For complete information about the benchmark simulations used to validate GEOS-Chem v11-01, please see our GEOS-Chem v11-01 benchmark history wiki page.

--Melissa Sulprizio 10:30, 5 May 2015 (EDT)

Unit tests for GEOS-Chem v11-01

We performed a full set of unit tests on GEOS-Chem before submitting each 1-month benchmark. Click on the links below to see the results from each set of unit tests:

Unit test Date Notes

--Melissa Sulprizio 10:30, 5 May 2015 (EDT)

Previous issues now resolved in GEOS-Chem v11-01

The following bugs and/or technical issues have now been resolved in GEOS-Chem v11-01.

Added a test for mass conservation

These updates will be validated in the 1-month benchmark simulation v11-01a. Approval date TBD.

In GEOS-Chem v11-01a, we have added a mass conservation check capability. This will let you see at a glance if GEOS-Chem is conserving mass.

In the GEOS-Chem Unit Tester, we have created two new run directories:


which are instances of the 2° x 2.5° CO2 simulation, but with zero emissions and with a constant (e.g. 370 ppm) initial condition field.

You can make a fresh copy of one (or both) of these directories with the gcCopyRunDirs script to a convenient location in your account. Once you have done that, then follow these steps:

1. Let's say you want to run the geos5_2x5_masscons test. First cd into the copied geos5_2x25_masscons directory.
2. Make sure you specify your desired start & end dates in your input.geos file. Also make sure to put a 3 on the last day of the simulation in the OUTPUT MENU section.
3. Then type this command:
   make -j4 TRACEBACK=y NO_ISO=y mp
this will start compiling and running the GEOS-5 mass conservation test. The Makefile in this run directory will automatically set a new Makefile option, MASSCONS=y, which disables output to the bpch, timeseries, and restart files. Instead, the mass of the total CO2 tracer will be printed out to a file named tracer_mass_kg.dat (you can rename this in the ND49 MENU section of input.geos). The output will look similar to this:
 2.887072562747136E+015  : 2012/07/01 06:00
 2.887072562747084E+015  : 2012/07/01 12:00
 2.887072562747109E+015  : 2012/07/01 18:00
 2.887072562747105E+015  : 2012/07/02 00:00
 2.887072562747306E+015  : 2012/07/02 06:00
 2.887072562747272E+015  : 2012/07/02 12:00
 2.887072562747154E+015  : 2012/07/02 18:00
 2.887072562746720E+015  : 2012/07/03 00:00
The output shows the sum of CO2 tracer (in kg) over all longitudes, latitudes and levels, with a corresponding time stamp. As you can see from this example, mass is conserved to about the 11th decimal place, which indicates good mass conservation.

--Bob Y. (talk) 21:53, 24 June 2015 (UTC)

Outstanding issues not yet resolved in GEOS-Chem v11-01

The following issues have not yet been resolved in GEOS-Chem v11-01. Some of these issues represent questions of open research rather than bugs in the source code.

  • None yet