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) | 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)
v11-01b
NOTE: This version will require a 1-month benchmark simulation and 1-year benchmark simulation.
Please see the the following links for complete information about the validation of GEOS-Chem v11-01b:
- Approval form for 1-month benchmark simulation v11-01b
- Approval form for 1-year benchmark simulation v11-01b-Run0
- Approval form for 1-year benchmark simulation v11-01b-Run1
- Budgets and plots for 1-year benchmark simulation v11-01b-RnPbBe
Feature | Type | Submitted by | Status |
---|---|---|---|
Update DMS climatology to Lana | Science | Tom Breider (Harvard) | Awaiting benchmark approval |
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
|
Science | Melanie Hammer (Dalhousie) | " " |
Acid uptake on dust aerosols
|
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)
|
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)
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) |
|
Remove in-plume reduction of Hg | Science | Yanxu Zhang (Harvard) | TBD |
Harmonizing Henry's Law coefficients across wet and dry deposition | Science | GEOS-Chem Support Team |
|
--Melissa Sulprizio (talk) 17:13, 20 July 2015 (UTC)
v11-01d
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:
|
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) |
--Melissa Sulprizio (talk) 13:33, 3 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 |
Flexchem | Science | Mike Long (Harvard) | TBD |
Uniformity of units | Science | Lizzie Lundgren (GEOS-Chem Support Team) |
|
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 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:
|
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 |
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) 13:33, 3 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
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 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:
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 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) !====================================================================== !$OMP PARALLEL DO & !$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)
Bug fixes for ND21 diagnostic
These fixes will be validated in the 1-month benchmark simulation v11-01c. Approval date TBD.
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)
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 unit conversion between [v/v] and [kg] (Air Quantity Updates for v11-01a). We have since found that the dry mixing ratio has a moisture signature. We expect moist mixing ratio to show a moisture signature but not dry mixing ratio. This issue is currently under investigation.
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.