Difference between revisions of "GEOS-Chem versions"
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cd pub/geos-chem/patches/v8-01-04 | cd pub/geos-chem/patches/v8-01-04 | ||
get sulfate_mod.f | get sulfate_mod.f | ||
− | get tpcore_fvdas_mod. | + | get tpcore_fvdas_mod.f90 |
get Makefile.sparc | get Makefile.sparc | ||
get Makefile.pgi | get Makefile.pgi |
Revision as of 16:04, 2 April 2009
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:
- Glyoxal chemistry (May Fu)
- Updated J(O1D) cross sections (Lin Zhang)
- Updated reaction rates (Jingqiu Mao, Dylan Millet, Palmer group @ U. Edinburgh)
- HO2 uptake (Lyatt Jaegle)
- 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:
- Annual scale factors for NOx-CO-SOx from, applied to ALL inventory if needed (Aaron)
- Daily NOx variability from EDGAR applied to all others anthro NOx inventories
- 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
- new EPA mask (Overlap Bravo/Epa and CAC/Epa)
- ship NOx emitted as HNO3 + 10*O3
- pre-Arctas SO2 ship emissions from Streets
- 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 | 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" 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" 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" tpcore | 10.689 |
Black | Observations |
NOTES for Run0:
- This benchmark uses the same input conditions v8-01-01.
- 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 | 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" 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" 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" tpcore | 10.294 |
Black | Observations |
NOTES for Run1:
- This benchmark uses the same input conditions v8-01-04 Run0.
- 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.
- 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) wrote:
- This line in Makefile.pgi
tpcore_fvdas_mod.o : tpcore_fvdas_mod.f90 CMN_GCTM $(F90) -c -Mextend -r8 $*.f90
- has to be changed to:
tpcore_fvdas_mod.o : tpcore_fvdas_mod.f90 CMN_GCTM
- i.e. the second line can be deleted.
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:
- Installation of new version of TPCORE (based on GMI model) to fix polar overshoot in stratosphere
- Minor bug fix for ND51 diagnostic
- Minor bug fixes in diag3.f
- Minor diagnostic fixes in main.f
v8-01-02
BETA RELEASE November 2008
Contains everything in v8-01-01, with the following additions:
- GEOS-5 0.5 x 0.666 degree nested-grid simulation for China/SE Asia
- Improvements to the GEOS-3 1x1 nested-grid simulation for N. America
- Modifications for using reprocessed GEOS-5 met fields (i.e. w/ corrected optical depths)
- Several bug fixes and improvements for robustness, scientific algorithms, and diagnostics
v8-01-01
PUBLIC RELEASE May 2008
Contains everything in v7-04-13, with the following additions:
- Compatibility for GEOS-5 met fields.
- Now uses RPMARES instead of ISORROPIA
- 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:
- 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.
- Use Run0 if you need to make a clean comparison between the GEOS-4 and GEOS-5 met fields.
- 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:
- 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.
- 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
- "Too many levels" error in the photolysis routine OPMIE.f
- Confusing comments corrected in routine SOA_PARA in carbon_mod.f
- Numerical noise error in upbdflx_mod.f
- Problem w/ ND65 diagnostic and the dynamic tropopause
- Negative tracer found in WETDEP
- Negative relative humidity from met fields causing negative tracer
- Run dies in RPMARES unexpectedly
- Error in sulfate_mod.f caused by switching from ISORROPIA to RPMARES
Fixes for offline simulations
- Array-out-of-bounds error in tagged_co_mod.f
- Wrong MERGE.O3 filename specified (this is an issue for offline Hg chemistry)
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:
- Offline H2/HD simulation (cf. Lyatt Jaegle et al)
- 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.
- Bug fix -- replace GEMISNOX w/ module arrays to avoid common block errors in lightning & aircraft NOx emissions
- Bug fix -- cap variable tropopause at 200hPa for polar regions (90S-60S and 60N-90N)
- Lee Murray's local lightning redistribution of lightning flashes
- 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:
- Results from v7-04-13-Run can be downloaded from FTP directory
- pub/geos/1yr_benchmarks/v7-04-13/geos4/2005/Run/output/pdf
- Output plots from v7-04-13-Run can be viewed on the web HERE.
- 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
- Variable tropopause has bug fix from v7-04-11 but not 200 hPa cap at polar latitudes
- 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