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NOTE: Information subject to change. Please check back here often for the latest information.

v8-02-01

CHEMISTRY RELEASE date TBD

Will contain everything in v8-01-04 plus the following:

  1. Glyoxal chemistry (May Fu)
  2. Updated J(O1D) cross sections (Lin Zhang)
  3. Updated reaction rates (Jingqiu Mao, Dylan Millet, Palmer group @ U. Edinburgh)
  4. HO2 uptake (Lyatt Jaegle)
  5. Updated dust single scattering albedo (Randall Martin)

v8-01-04

EMISSIONS RELEASE date March 10, 2009

Will contain everything in v8-01-03 plus the following updates:

  1. Annual scale factors for NOx-CO-SOx from, applied to ALL inventory if needed (Aaron)
  2. Daily NOx variability from EDGAR applied to all others anthro NOx inventories
  3. Several emissions updates
    • Streets 2006, with monthly variability
    • EMEP 1990-2005 w/ ship emissions separated
    • Canadian CAC,
    • EPA fixes = CA transport + Rynda scaling,
    • VISTAS/ARP for NOx in the USA
    • MEGAN2
  4. new EPA mask (Overlap Bravo/Epa and CAC/Epa)
  5. ship NOx emitted as HNO3 + 10*O3
  6. pre-Arctas SO2 ship emissions from Streets
  7. GFED2 biomass options:
    • Monthly mean (as was in the code previously)
    • 8-day mean
    • 3-hourly mean (selected months only)
    • 3-hourly synoptic (selected months only)

Philippe Le Sager has prepared a document (PDF format) which describes the anthropogenic emissions sources in some detail.

1-year benchmarks

Run0 - v8-01-04

The 3 models compared (and their colors on the plots) were:

Color Quantity Plotted Met Field Type A.T.E. algorithm Anthro Emissions Biogenic Emissions Advection Annual Mean OH
[105 molec/cm3]
Red v8-01-01 Run0 GEOS-5 4x5 ISORROPIA GEIA/Piccot (scale year 1998)
EPA/NEI99 w/o ICARTT fix
EDGAR ship emissions 		"old" MEGAN AEF's for isoprene "old" tpcore 12.006
Green v8-01-01 Run1 GEOS-5 4x5 RPMARES GEIA/Piccot (scale year 1998)
EPA/NEI99 w/o ICARTT fix
EDGAR ship emissions 		"old" MEGAN AEF's for isoprene "old" tpcore 12.040
Blue v8-01-04-Run0 GEOS-5 4x5 RPMARES GEIA/Piccot (scale year 1998)
EPA/NEI99 w/o ICARTT fix
EDGAR ship emissions 		"new" MEGAN AEF's for isoprene "new" tpcore 10.689
Black Observations            

NOTES for Run0:

  1. This benchmark uses the same input conditions v8-01-01.
  2. All runs use the same biomass (GFED2 monthly), biofuel, biogenic (MEGAN), lightning, and aircraft emissions.

The output plots for Run0 may be downloaded from: 

ftp ftp.as.harvard.edu
cd pub/geos-chem/1yr_benchmarks/v8-01-04/geos5/2005/Run0/output

Run1 - v8-01-04

The 3 models compared (and their colors on the plots) were:

Color Quantity Plotted Met Field Type A.T.E. algorithm Anthro Emissions Biogenic Emissions Advection Annual Mean OH
[105 molec/cm3]
Red v8-01-01 Run1 GEOS-5 4x5 RPMARES GEIA/Piccot (scale year 1998)
EPA/NEI99 w/o ICARTT fix
EDGAR ship emissions 		"old" MEGAN AEF's for isoprene "old" tpcore 12.040
Green v8-01-04 Run0 GEOS-5 4x5 RPMARES GEIA/Piccot (scale year 1998)
EPA/NEI99 w/o ICARTT fix
EDGAR ship emissions 		"new" MEGAN AEF's for isoprene "new" tpcore 10.689
Blue v8-01-04 Run1 GEOS-5 4x5 RPMARES GEIA/Piccot
EDGAR emissions
EMEP European emissions
BRAVO Mexican emissions
David Streets 2006 emissions
CAC Canadian emissions
EPA/NEI99 with ICARTT fix
EDGAR ship emissions
ARCTAS ship SO2 emissions
Anthro scale year 2005 		"new" MEGAN AEF's for isoprene "new" tpcore 10.294
Black Observations            

NOTES for Run1:

  1. This benchmark uses the same input conditions v8-01-04 Run0.
  2. NOTE: v8-01-04 Run1 uses the "approximate random cloud overlap" option in FAST-J, whereas v8-01-04 Run0 used the "linear overlap option". Please see the cloud overlap options in FAST-J page for more information.
  3. All runs use the same biomass (GFED2 monthly), biofuel, biogenic (MEGAN), lightning, and aircraft emissions.

The output plots for Run1 may be downloaded from: 

ftp ftp.as.harvard.edu
cd pub/geos-chem/1yr_benchmarks/v8-01-04/geos5/2005/Run1/output

Post-release patches

A couple of issues were reported after the release of v8-01-04:

Fabien Paulot (fabienpaulot@gmail.com) wrote:

The tracer id is hardcoded in the sulfate module (sulfate_mod.f which causes error when calling the ship emission module (GET_EMEP_ANTHRO) if the user wants to modify the tracer list. I just replaced 26 by IDTSO2 and 30 by IDTNH3 to fix the problem. See line 6594.

This issue was due to a typo in sulfate_mod.f. The error only occurred during aerosol-only offline simulations.


Prasad Kasibhatla (psk9@duke.edu) wrote:

I also noticed in the standard distribution, that the CPU time for the one month full chem simulation at Harvard went from 56 minutes for v8-01-02 to 75 minutes for v8-01-03 to 121 minutes for v8-01-04, an increase of a factor of 2.2. I was wondering if you have looked at this slowdown?

This issue was traced to the way the !$OMP PARALLEL DO loops were implemented in the TPCORE advection module tpcore_fvdas_mod.f. Claire Carouge has fixed this by changing the order of some of the parallel loops in the code. The updated TPCORE now runs much faster than before!


Hongyu Liu (hyl@nianet.org) reported:

The following references need to be deleted from the OBJS section in the Makefile:
   arctas_ship_emiss_mod.o       \
   cac_anthro_mod.o              \
   scale_anthro_mod.o            \
   tpcore_fvdas_mod.o            \
   vistas_anthro_mod.o           \
since these are already listed in the MODS section. Having these listed twice will cause a link-time error.


Colette Heald (heald@atmos.colostate.edu) wrote:

I wanted to let you know that to get v8-01-04 to compile [with the SunStudio compiler], I needed to modify the code in Makefile.sparc on L354 (i.e. under the line for gamap_mod.o) from:
   f90 -fpp -stackvar -O0 -xfilebyteorder=big16:%all
to the following:
   f90 -fpp -O0 -stackvar -xfilebyteorder=big16:%all $(FARCH) -c $*.f
otherwise it fails in input_mod.f compilation with messages that it did not recognize gamap_mod.f.
I also wanted to point out that there is a syntax error on L1040 of rpmares_mod.f (a comma after the write(6,*) but before the statement), which can cause compile to fail depending on the compiler options.


Fabien Paulot (fabienpaulot@gmail.com) also reported...

..an overestimate in the North-South mass flux computed in the new TPCORE. A geometric scale factor was applied twice when computing the flux. The updated TPCORE now correctly computes the NS mass flux.


All users of GEOS-Chem v8-01-04 should replace the existing versions of sulfate_mod.f and tpcore_fvdas_mod.f with the fixed files. If you are using the PGI compiler, then also get the new Makefile.pgi file. If you are using the SunStudio compiler, then get the new Makefile.sparc file.

The updated files are available for download from: 

ftp ftp.as.harvard.edu
cd pub/geos-chem/patches/v8-01-04
get sulfate_mod.f
get tpcore_fvdas_mod.f90
get Makefile.sparc
get Makefile.pgi

Note

All users of GEOS-Chem v8-01-04 should turn on the mass flux diagnostics (ND24/ND25/ND26) in input.geos to be safe. See this bug report.

--Bob Y. 10:31, 2 April 2009 (EDT)

v8-01-03

BETA RELEASE December 2008

Contains everything in v8-01-02 plus the following updates:

v8-01-02

BETA RELEASE November 2008

Contains everything in v8-01-01, with the following additions:

v8-01-01

PUBLIC RELEASE May 2008

Contains everything in v7-04-13, with the following additions:

  1. Compatibility for GEOS-5 met fields.
  2. Now uses RPMARES instead of ISORROPIA
  3. Implements floating point error traps (e.g. to prevent division by zero) in a few critical places

Also note that we have implemented the fix for the Last year of GFED2 biomass emissions, (which is now 2006) into v8-01-01.

1-Year Benchmarks

We have done two 1-year benchmarks for GEOS-Chem v8-01-01:

Run0

The 3 models compared (and their colors on the plots) were:

Color Quantity Plotted Met Field Type Lightning algorithm A.T.E. algorithm Annual Mean OH
[105 molec/cm3]
Red v7-04-12 Run2 GEOS-4 4x5 near-land w/ OTD-LIS regional scaling ISORROPIA 12.816
Green v7-04-13 GEOS-4 4x5 updated non-near-land w/ OTD-LIS local scaling ISORROPIA 12.147
Blue v8-01-01 Run0 GEOS-5 4x5 updated non-near-land w/ OTD-LIS local scaling ISORROPIA 12.006
Black Observations        

NOTES for Run0:

  1. This benchmark uses the same input conditions and emissions as v7-04-13.
    • The only difference is that this benchmark was done w/ GEOS-5 met and v7-04-13 was done w/ GEOS-4 met.
  2. Use Run0 if you need to make a clean comparison between the GEOS-4 and GEOS-5 met fields.
  3. Results from Run0 may be viewed on the web HERE.

Run1

The 3 models compared (and their colors on the plots) were:

Color Quantity Plotted Met Field Type Lightning algorithm A.T.E. algorithm Annual Mean OH
[105 molec/cm3]
Red v7-04-13 GEOS-4 4x5 updated non-near-land w/ OTD-LIS local scaling ISORROPIA 12.147
Green v8-01-01 Run0 GEOS-5 4x5 updated non-near-land w/ OTD-LIS local scaling ISORROPIA 12.006
Blue v8-01-01 Run1 GEOS-5 4x5 updated non-near-land w/ OTD-LIS local scaling RPMARES 12.040
Black Observations        

NOTES for Run1:

  1. The only difference between Run0 and Run1 is that Run0 uses ISORROPIA and Run1 uses RPMARES to compute the aerosol thermodynamical equilibrium. We recently learned that ISORROPIA can return incorrect values at low RH.
    • Use Run0 if you need to make a clean comparison between ISORROPIA and RPMARES.
  2. Results from Run0 may be viewed on the web HERE.

Post-release patches

After the release of v8–01–01, some minor bugs and issues were discovered. Most of these involve numerical errors (i.e. computations that result in NaN's or underflow conditions). Other minor bugs are only relevant to a particular type of offline simulation. In any case, most of these issues have simple fixes.

Please see the following GEOS–Chem wiki pages for information about the following issues, and how to resolve them.

NOTE: As of November 2008, these post-release patches are now part of the standard GEOS-Chem v8-01-02 source code.

Fixes for the full-chemistry simulation

Fixes for offline simulations

Lines of code

For those of you who are curious as to how many lines of code are in this version of GEOS-Chem, here is a counting of code lines, comment lines, and blank lines. NOTE: These totals also accounts for the v8-01-01 post-release patches, while excluding many lines of obsolete code that had been commented out and slated for deletion. 

Total number of files    :          217
Number of files searched :          217
Number of files skipped  :            0

Number of lines searched :       174177
Number of comment lines  :        77788
Number of blank lines    :        25981
Number of code lines     :        70408

Ratio: Comments/Code     :        1.1048176

Results were generated with IDL program linecount.pro by Bob Yantosca,

--Bob Y. 14:27, 8 August 2008 (EDT)

v7-04-13

BETA RELEASE November 2007

Contains everything in v7-04-12, with the following additions:

  1. Offline H2/HD simulation (cf. Lyatt Jaegle et al)
  2. Bug fix in "smvgear.f" -- due to a design flaw, you could have a situation where you could have negative or zero tracer in a box even if the global & local error criteria were satisfied. If this condition is encountered, we now revert to the concentrations at the end of the previous internal timestep, and then reduce the internal timestep and try again until we get convergence.
  3. Bug fix -- replace GEMISNOX w/ module arrays to avoid common block errors in lightning & aircraft NOx emissions
  4. Bug fix -- cap variable tropopause at 200hPa for polar regions (90S-60S and 60N-90N)
  5. Lee Murray's local lightning redistribution of lightning flashes
  6. Minor bug fixes for GCAP and diagnostics

Also note that the Last year of GFED2 biomass emissions is still 2005 in this version. If you want to use the 2006 emissions you will have to edit the source code module "gfed2_biomass_mod.f".

1-Year Benchmarks

Run

The 3 models compared (and their colors on the plots) were:

Color Quantity Plotted Met Type Lightning algorithm
Red v7-04-12 Run1 GEOS-4 4x5 ancient
Green v7-04-12 Run2 GEOS-4 4x5 near-land w/ OTD-LIS regional scaling
Blue v7-04-13 GEOS-4 4x5 updated non-near-land w/ OTD-LIS local scaling
Black Observations    

NOTES:

  1. Results from v7-04-13-Run can be downloaded from FTP directory
    • pub/geos/1yr_benchmarks/v7-04-13/geos4/2005/Run/output/pdf
  2. Output plots from v7-04-13-Run can be viewed on the web HERE.
  3. v7-04-13-Run uses the same input conditions and emissions as v7-04-12-Run2, except for the updated lightning emissions as described above.

v7-04-12

BETA RELEASE October 2007

  1. Variable tropopause has bug fix from v7-04-11 but not 200 hPa cap at polar latitudes
  2. NOTE: There is a bug in this version when lightning emissions are turned off. The bug will be fixed in v7-04-13. For the time being, if you must turn lighting emissions off in v7-04-12, please do this by setting FLASHRATE = 0 in the lightning_nox_nl_mod.f.

1-Year Benchmarks

We have already done the following 1-year benchmark simulations:

Run1

In FTP directory: /as2/pub/ftp/pub/geos-chem/1yr_benchmarks/v7-04-12/geos4/2005/Run1

View output plots via the web HERE.

  • Run w/ 4x5 GEOS-4 for met field year 2005 (spun up thru 2003 & 2004)
  • with G-C "old" fossil fuel (GEIA + EPA/NEI99)
  • with G-C "default" climatological biomass burning
  • with old lightning parameterization
  • with MEGAN biogenic emissions
  • with SMVGEAR chemistry up to dynamic tropopause
  • with new dust emissions (w/ GOCART source function)
  • with new TOMS/SBUV ozone columns for FAST-J photolysis
  • with variable tropopause on

Run2

In FTP directory: /pub/geos-chem/1yr_benchmarks/v7-04-12/geos4/2005/Run2

View output plots via the web HERE.

  • Run w/ GEOS-4 for met field year 2005 (spun up thru 2003 & 2004)
  • with G-C "old" fossil fuel (GEIA + EPA/NEI99)
  • with G-C "default" climatological biomass burning
  • with new lightning parameterization (with OTD/LIS v2 regional redistribution of flashes)
  • with MEGAN biogenic emissions
  • with SMVGEAR chemistry up to dynamic tropopause
  • with new dust emissions (w/ GOCART source function)
  • with new TOMS/SBUV ozone columns for FAST-J photolysis
  • with variable tropopause on
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