GEOS-Chem v11-01
Contents
Overview
History
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 |
PUBLIC RELEASE 17 Jun 2015 | TBD | 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.
v11-01a
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) |
" " |
Prevent negative tracer concentrations at poles after advection | Bug fix | Lizzie Lundgren (GEOS-Chem Support Team) | " " |
--Lizzie Lundgren (talk) 16:08, 1 July 2015 (UTC)
v11-01b
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.) |
|
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) |
|
Harmonizing Henry's Law coefficients across wet and dry deposition | Science | GEOS-Chem Support Team |
--Melissa Sulprizio (talk) 14:41, 6 July 2015 (UTC)
v11-01c
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) |
|
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) |
TBD |
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) |
TBD |
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:
|
Science | Jenny Fisher (U. Wollongong) Eloïse Marais (Harvard) Kelvin Bates (Caltech) Katie Travis (Harvard) |
TBD |
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) |
TBD |
Arctic Hg cycling | Science | Jenny Fisher (U. Wollongong) | TBD |
A snow NOx source from deep snowpack | Science | Maria Zatko (UW) Becky Alexander (UW) |
TBD |
Land cover module in GEOS-Chem | Science | Jeffrey Geddes (MIT) Michael Long (Harvard) |
TBD |
Merge standard simulation with specialty simulations for OVOC, acids, aromatics, dicarbonyls, terpenes | Science | Dylan Millet (UMN) Xin Chen (UMN) |
TBD |
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
Validation
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 |
---|---|---|
TBD | TBD |
--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:
runs/geosfp_2x25_masscons runs/geos5_2x25_masscons
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 will be validated in the 1-month benchmark simulation v11-01a. Approval date TBD.
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) !====================================================================== !$OMP PARALLEL DO & !$OMP DEFAULT( SHARED )& !$OMP PRIVATE( I, J, K ) DO K = 1, KM DO J = 1, JM DO I = 1, IM IF ( q(I,J,K,IQ) < 0.0e0_fp ) THEN q(I,J,K,IQ) = 1.0e-26_fp ENDIF ENDDO ENDDO ENDDO !$OMP END PARALLEL DO
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
These updates will be validated in the 1-month benchmark simulation v11-01b. Approval date TBD.
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 + + + + + + + + + + + + +
- to
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)
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.
- 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.