GEOS-Chem v11-01

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Revision as of 18:59, 9 September 2015 by Lizzie Lundgren (Talk | contribs) (Outstanding issues not yet resolved in GEOS-Chem v11-01)

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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) Approved 07 Jul 2015
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)
" "
Prevent negative tracer concentrations at poles after advection Bug fix Lizzie Lundgren (GEOS-Chem Support Team) " "

--Bob Y. (talk) 15:23, 7 July 2015 (UTC)


Please see the the following links for complete information about the validation of GEOS-Chem v11-01b:

  1. Approval form for 1-month benchmark simulation v11-01b
  2. Results for 1-year benchmark simulation v11-01b-Run0
  3. Results for 1-year benchmark simulation v11-01b-RnPbBe
Feature Type Submitted by Status
Update DMS climatology to Lana Science Tom Breider (Harvard) 1-month benchmark:
Approved on 04 Aug 2015

1-year benchmark:
Approved on 19 Aug 2015

Impaction scavenging for hydrophobic BC Science Qiaoqiao Wang (Max Planck Institute) " "
Homogeneous IN removal Science Qiaoqiao Wang (Max Planck Institute) " "
Density of OA update Science Melanie Hammer (Dalhousie)
Eloïse Marais (Harvard)
" "
Improved dust size distribution scheme Science Li Zhang (Colorado U.)
Daven Henze (Colorado U.)
" "
Addition of BrC UV absorption to address impacts on OH
  • This feature is optional (default off)
Science Melanie Hammer (Dalhousie) " "
Acid uptake on dust aerosols
  • This feature is optional (default off)
Science T. Duncan Fairlie (NASA/LARC) " "
Now treat DST2-DST4 as coarse mode in wet scavenging Bug fix T. Duncan Fairlie (NASA/LARC) " "
Online emission of marine primary organic aerosol (POA)
  • This feature is optional (default off)
Science Brett Gantt (NCSU)
Matthew Johnson (NASA Ames)
" "
Update of PMN + O3 reaction products in globchem.dat file Bug fix Dylan Millet (UMN) " "
Bug fix in RRTMG array sizes Bug fix Sebastian Eastham (MIT) " "
Bug fixes in rrtmg_rad_transfer_mod.F Bug fix Sebastian Eastham (MIT)
David Ridley (MIT)
" "
Bug fix for black carbon in ucx_mod.F Bug fix Sebastian Eastham (MIT) " "
Bug fix for archiving P(Ox)/L(Ox) from full-chemistry simulations via the ND20 diagnostic Bug fix GEOS-Chem Support Team " "
Bug fix for linking files when compiling with PGI Bug fix GEOS-Chem Support Team " "

--Melissa Sulprizio (talk) 13:46, 3 August 2015 (UTC)


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

Feature Type Submitted by Status
Updates to PAH code Science Carey Friedman (MIT) 1-month benchmark in progress
Hg Ocean MLD bug fixes Bug fix Amanda Giang (MIT) " "
Hg Ocean rate coefficients (as an option, not default) Science Shaojie Song (MIT) " "
Hg Arctic process updates Science Jenny Fisher (Wollongong) " "
Hg emission updates (NEI2011, NPRI2011, UNEP2010 with adjustments for in-plume reduction and emission controls) Science Yanxu Zhang (Harvard)
Amanda Giang (MIT)
" "
Bug fix for sea salt alkalinity in sulfate_mod.F Bug fix Johan Schmidt (Harvard) " "
Correct problem in OTD-LIS local redistribution files for GEOS-5 Bug fix Christoph Keller (Harvard)
Lu Hu (Harvard)
" "
Bug fixes for the ND21 diagnostic Bug fix Sebastian Eastham (MIT) " "
Bug fix for custom nested grid in tpcore_bc_mod.F Bug fix Shannon Koplitz (Harvard), GCST " "
Bug fix for monoterpenes in ND46 diagnostic Bug fix Jared Brewer (CSU) " "
GEOS-Chem timers Structural Matt Yannetti (GCST) " "
Initial modifications for running GEOS-chem with the GMAO MERRA2 reanalysis met field product Structural Bob Yantosca (GCST)
  • The following unit tests passed:
    • merra2_4x5_RnPbBe
    • merra2_4x5_CH4
    • merra2_4x5_tagO3
    • merra2_4x5_POPs
  • Full integration of MERRA2 in GEOS-Chem (i.e. making "full-chemistry" simulations compatible with MERRA2) will take longer.
    • Scale factors for lightning, dust, and other emissions will need to be recomputed based on 1-year (or longer) simulations.

--Melissa Sulprizio (talk) 18:46, 9 September 2015 (UTC)


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

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)
Update biomass burning emissions to GFED4.1, includes:
  • Daily and diurnal factors
Science Prasad Kasibhatla (Duke)
Christoph Keller (Harvard)
Metal catalyzed oxidation of SO2 (as a switch) Science Becky Alexander (UW)
Monthly mean surface methane distributions Science Lee Murray (NASA GISS/LDEO)
Ocean ammonia emission inventory Science Fabien Paulot (NOAA/GFDL)

--Melissa Sulprizio (talk) 17:42, 4 August 2015 (UTC)

In the pipeline

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

Feature Type Submitted by Status
NetCDF output: Flexible diagnostic package and tracer restart file Science GEOS-Chem Support Team TBD
Harmonizing Henry's Law coefficients across wet and dry deposition Science GEOS-Chem Support Team
  • In progress
  • This update will require its own benchmark
Flexchem Science Mike Long (Harvard) TBD
Uniformity of units Science Lizzie Lundgren (GEOS-Chem Support Team)
  • To be implemented after Flexchem
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 code updates (emissions, chemistry, ocean, land) Science Hg and POPs WG 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)
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
Updated halogen chemistry Science Tomás Sherwen (York)
Johan Schmidt (Harvard)
Oxidants and Chemistry WG
Update SO2 scavenging in convective updrafts for consistency Science Duncan Fairlie (NASA/LARC) TBD
Sedimentation of stratospheric aerosols Science Sebastian Eastham (MIT) TBD

--Melissa Sulprizio (talk) 16:38, 20 August 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 were validated in the 1-month benchmark simulation v11-01a, which was approved on 07 Jul 2015.

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)

Prevent negative tracer concentrations after advection

These updates were validated in the 1-month benchmark simulation v11-01a, which was approved on 07 Jul 2015.

In GEOS-Chem v11-01a, we have included a fix for negative tracer concentrations following advection. Tracer concentrations may become negative within routine TPCORE_FVDAS at the poles with values on the order of -1e-10 v/v or smaller in v10-01. Negative values can cause GEOS-Chem to stop downstream if TOMAS is enabled due to a negative NK check within routine MNFIX in tomas_mod.F.

To fix this issue, we set all negative tracer concentration values to 1.0e-26 at the end of advection. The fix, inserted in routine TPCORE_FVDAS within tpcore_fvdas_mod.F90, is shown below. This code is not inserted in nested region advection routines because none of the nested regions overlap the poles.

      ! MODIFICATION by Harvard Atmospheric Chemistry Modeling Group
      ! Set tracer concentration to a small positive number if concentration 
      ! is negative. Negative concentrations may occur at the poles.
      ! (ewl, 6/30/15) 
!$OMP PARALLEL DO        &
      DO K = 1, KM
      DO J = 1, JM
      DO I = 1, IM
         IF ( q(I,J,K,IQ) < 0.0e0_fp ) THEN
            q(I,J,K,IQ) = 1.0e-26_fp

Note that the reasons for negative values at the poles is not currently understood and is listed in the Outstanding issues not yet resolved in GEOS-Chem v11-01 section of this wiki page.

--Lizzie Lundgren (talk) 16:37, 1 July 2015 (UTC)

Update of PMN + O3 reaction products in globchem.dat file

This update was validated with 1-month benchmark simulation v11-01b and 1-year benchmark simulation v11-01b-Run0. This version was approved on 19 Aug 2015.

Dylan Millet wrote:

I'd like to submit the following change for the globchem.dat file. The PMN + O3 reaction does not give the appropriate products. We should change:
   A  505 8.20E-18  0.0E+00      0 0     0.00     0.     0.         
         PMN           +     O3                                              
   =1.000NO2           +0.600CH2O          +1.000HO2           +             
   +                   +                   +                   +             
   +                   +                   +                   +             
   +                   +                   +                   +
   A  505 8.20E-18  0.0E+00      0 0     0.00     0.     0.         
         PMN           +     O3                                              
   =1.000CH2O          +1.000MCO3          +1.000NO3           +             
   +                   +                   +                   +             
   +                   +                   +                   +             
   +                   +                   +                   +
It won't have a major impact, but it is currently is wrong, and my sense (Mat as well) is that this falls under 'bug fix' rather than science update.

--Bob Y. (talk) 17:55, 26 June 2015 (UTC)

Modifications to ND20 to archive afternoon P(O3) and L(O3)

This update was validated with 1-month benchmark simulation v11-01b and 1-year benchmark simulation v11-01b-Run0. This version was approved on 19 Aug 2015.

Bob Yantosca wrote:

I was able to make a couple of modifications that will let you just archive afternoon P(O3) and L(O3), since that may let you avoid the too-low-values at night. If you look in diag_pl_mod.F, in routine DIAG20, you will see these new lines:
! !DEFINED PARAMETERS:                                                                    
     ! Local time limits (optional)                                                      
     REAL(fp), PARAMETER :: LT_START = 12.0e+0_fp
     REAL(fp), PARAMETER :: LT_END   = 16.0e+0_fp
!$OMP+DEFAULT( SHARED )                                                                   
!$OMP+PRIVATE( I, J, L, P_Ox, L_Ox, JLOOP, LT )                                           
!$OMP+SCHEDULE( DYNAMIC )                                                                 
     DO L = 1, LD65
     DO J = 1, JJPAR
     DO I = 1, IIPAR

        ! Zero P(Ox), L(Ox) variables for safety's sake                                  
        P_Ox  = 0e+0_fp
        L_Ox  = 0e+0_fp

        ! JLOOP is the 1-D grid box index for SMVGEAR arrays                             
        JLOOP = JLOP(I,J,L)

        ! If this is a grid box where we have done chemistry, then ...                   
        IF ( JLOOP > 0 ) THEN

           !%%% NOTE: If you want to restrict output to a given local                    
           !%%% time range, then uncomment these lines of code.                          
           !%%% (bmy, 7/9/15)                                                            
           ! Get the local time at box (I,J,L)                                           
           !LT = GET_LOCALTIME( I, J, L )                                                
           ! Skip processing if we are outside of the desired                            
           ! local time range (bmy, 7/9/15)                                              
           !IF ( LT < LT_START .or. LT > LT_END ) CYCLE                                  

           ! Increment counter of valid grid boxes                                       
           COUNT(I,J,L) = COUNT(I,J,L) + 1

(I also defined the LT variable and put in a USE statement for the GET_LOCALTIME function, not shown.)
So if you want to restrict archiving of P(O3) and L(O3) to a given window, you can modify the LT_START and LT_END to the starting and ending hour of the local time window. Values must be in the range 0.0 to 23.99 hours. Then also uncomment the lines after the IF ( JLOOP > 0 ) block.
In addition, I fixed a few minor issues in the DIAG20 and WRITE20 routines. For example, the bpch file was being saved with the wrong JFIRST value, so I corrected that. Also, I made the code more efficient by not trying to compute P(O3) and L(O3) where JLOOP == 0 (i.e. where chemistry wasn't done).

--Melissa Sulprizio (talk) 17:22, 3 August 2015 (UTC)

Bug fixes for the ND21 diagnostic

These fixes will be validated with the 1-month benchmark simulation v11-01c.

Sebastian Eastham wrote:

I was looking at some output for a recent run with v10-01 and realized that diagnostic 21 (OD_MAP) no longer produces the expected data. I only know for certain that this happens when the UCX is enabled, as I do not run with the trop-only version of the code. It basically comes down to index mismatching between aerosol_mod, diag3_mod and gamap_mod.
Once implemented, it should restore output of diagnostic 21 when UCX is active. Prior to this patch, selecting diagnostic 21 with “all” output seemed to result in the incorrect number of tracers and misassignments.

--Melissa Sulprizio (talk) 16:32, 3 August 2015 (UTC)

Bug fix for custom grid in tpcore_bc_mod.F

This fix will be validated with the 1-month benchmark simulation v11-01c.

Shannon Koplitz wrote:

I think there may be a redundant call to allocate the custom nested grid array BC at line 2045 in tpcore_bc_mod.F.
It looks like the call to allocate that array is given earlier in the code at line 1977, and the double call appears to result in an allocation error when attempting to save out BCs for a custom nested grid.

Melissa Sulprizio responded:

I found a few other places where the array BC is used. From what I see, it appears that BC is used in SAVE_GLOBAL_TPCORE_BC specifically for the custom grid, but in READ_WINDOW_TPCORE_BC, GET_4x5_BC, and GET_2x25_BC it's used in a more general sense (for all nested grids). So I think the issue here is that BC is unintentionally used for two different purposes. I think if we remove the second allocation and only allocate BC when LWINDO_CU is true, we'd get errors in the last three routines that I mentioned.
I suggest we change BC for the custom nested grid to BC_CU. In SAVE_GLOBAL_TPCORE_BC, we would modify the following code (in green text):
        IF ((IC .eq. 1) .and. LWINDO_CU )THEN

           ! IC == 1 : Save BC's to file (custom window)

           ! Open file for writing, if necessary
           CALL OPEN_BC_FILE( am_I_Root, Input_Opt, RC,
    &                         WINDOW=IC, FOR_WRITE=.TRUE. )

           ! Loop over each tracer
           DO N = 1, N_TOT_TRC

              ! Save concentrations in WINDOW REGION to disk
              DO L = 1, LLPAR
    &               STT(I1_BC:I2_BC,J1_BC:J2_BC,L,N)

              ! Write boundary conditions to binary punch file
    &               HALFPOLAR, CENTER180, CATEGORY, N,
    &               UNIT,      TAU,       TAU,      RESERVED,
    &               IM_BC,     JM_BC,     LLPAR,    I1_BC,
    &               J1_BC,     1,   BC_CU(1:IM_BC, 1:JM_BC, 1:LLPAR, N))


     ! Boundary condition array for CUSTOM NESTED REGION
        IF ( AS /= 0 ) CALL ALLOC_ERR( 'BC_CU' )
        BC_CU = 0e+0_fp

We would also have to declare BC_CU at the top of the module and deallocate it in CLEANUP_TPCORE_BC.

--Melissa Sulprizio (talk) 16:56, 3 August 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.

Moisture signature in dry mixing ratio

In v11-01a we separated mixing ratio into dry and moist mixing ratios in order to correct the legacy unit conversion between [v/v] and [kg] where dry air molecular weight was used with total air pressure (Air Quantity Updates for v11-01a). The output concentrations of GEOS-Chem are now dry mixing ratio [v/v] and show an artefact of the moisture, with slightly elevated values towards the equator near the surface. While we expect that dry mixing ratio would show a moisture signature given the behavior of legacy GEOS-Chem, there is debate about whether this result is consistent with the expected science. This issue is currently under investigation by the Carbon and Transport Working Groups.

Cause of negative tracer concentrations at the poles is unknown

Tracer concentrations at the poles may become negative within advection. A fix is included in v11-01 that resets negative values to positive at the end of TPCORE_FVDAS but the underlying cause of the negative values is not addressed. All negative values are small enough to not significantly impact advection mass balance.

Mercury simulation inconsistently passing optimization unit tests in v11-01c

There are inconsistent differences in the diagnostics and ocean restart files when running unit tests on GEOS-5 4x5 and 2x2.5 mercury simulations in v11-01c. When running a test of ten GEOS-5 4x5 Hg unit tests, the trac_avg file failed with differences seven times and the ocean restart file failed with differences eight times. We have isolated the issue to a single call to depo_mercury_mod.F routine ADD_HG2_SNOWPACK that occurs in convection_mod.F routine NFCLDMX. Commenting out the call and conducting ten GEOS-5 4x5 Hg unit tests results in all tests passing. The issue appears to be an optimization problem but is currently unresolved.

--Lizzie Lundgren (talk) 18:59, 9 September 2015 (UTC)