GEOSChem v80101 Online User's Guide
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Appendix 8: Addenda to GEOSChem Online User's Guide
In this section we will post additions and corrections to the GEOSChem Online User's Guide.
A8.1: Addenda to v80101
After the release of v80101, 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 GEOSChem wiki pages for information about the following issues, and how to resolve them.
NOTE: These issues have now all been standardized in the GEOSChem beta v80102.
Fixes for the full-chemistry simulation:
Fixes for offline simulations:
Creating your own oxidant files for an offline aerosol simulation (cf. Section 6.1.6)
Thanks to Eric Sofen (U. Washington) for compiling this information!
NOTE: this assumes a GEOS4 30-level simulation.
The JH2O2, PH2O2, O3, and NO3 bpch files must extend only up to the tropopause. When you extract the data from the bpch file that is produced by a full chemistry simulation, these files will be either 22 or 30 vertical levels and the tropopause extends up to 17 levels. Use the routine /gamap2/regridding/trop_cut.pro to remove these upper levels.
THNO3 is a full 30 levels, and consists of HNO3+NIT.
OH needs to be 55 levels. 22 levels will come from the full-chem simulation, then this gets paired with the stratospheric data from the current OH file in the data directories (e.g. .../data/GEOS_4x5/stratOH_200203/stratOH.geos4.4x5). This is done using IDL routine gamap2/regridding/merge_o3.pro. Bob said of this IDL code, "NOTE, this file is somewhat hardwired, be prepared to dive in & tinker w/ it accordingly."
You'll also need to modify the GEOS-Chem code so that it looks for your new oxidant files (or, I suppose, overwrite the existing ones). This requires making changes in sulfate_mod.f, global_no3_mod.f, and global_hno3_mod.f. The easiest way to change where the model looks for OH is in the input.geos file.
A8.2: Addenda for beta release v80102
GEOSChem v80102 includes the following revisions over GEOSChem v80101:
All of the minor bug fixes and updates originally published in the v80101 "post-release" patches (plus a few more extra updates!) have now been standardized. See this wiki page for a complete listing.
Modifications for the GEOS5 nested-grid simulation have been added. At this point only the China simulation has been tested. Further modifications will be needed for the North America and/or Europe simulations (users will be responsible for submitting these modifications to us).
Minor modifications for the GEOS3 North America nested grid simulation. These were done to facilitate the FAA-ULS project.
You may obtain the GEOSChem v80102 source code and benchmark simulation package via anonymous FTP from:
ftp ftp.as.harvard.edu cd pub/geos-chem/beta_releases get GEOS-Chem.v8-01-02-beta.stdrun.tar.gz
If you are interested in running the GEOS-5 0.5° x 0.666° nested-grid simulation over China, you may download sample run directories for this simulation from:
ftp ftp.as.harvard.edu cd pub/geos-chem/beta_releases get GEOS5-05x066-Nested-China.rundir.tar.gz
GEOSChem v80102 adds some new C-preprocessor switches in define.h:
Switch Function GRID05x0666 Selects the GEOS5 0.5 x 0.666 grid. This option must always be used in conjunction with either NESTED_CH (nested China simulation) or NESTED_NA (nested N. America simulation). IN_CLOUD_OD
If you are using GEOS5 met fields that were reprocessed to correctly regrid the in-cloud optical depth and cloud fraction fields, then be sure to activate the IN_CLOUD_OD switch. This will cause FAST-J to interpret the optical depth correctly.
Leaving IN_CLOUD_OD deactivated commented will cause a "quick fix" (i.e. multiplying the optical depth by the cloud fracton) to be applied, which should be a good enough fix in the meantime.
NOTE: As of November 2008, the GEOS5 met fields have not yet been reprocessed. For the time being, you should leave IN_CLOUD_OD deactivated.
You may obtain the data directories for the GEOS5 0.5 x 0.666 nested grid China simulation (i.e. emissions files and met field files) from
ftp ftp.as.harvard.edu cd pub/geos-chem/data/GEOS_0.5x0.666_CH
Met fields for year YYYY and month MM are stored in the subdirectories: GEOS_5/YYYY/MM
Emissions and other data are stored in the following subdirectories:
C3H8_C2H6_200109/ MEGAN_200510/ Streets_200607/ TOMS_200701/ acetone_200108/ aircraft_NOx_200202/ ann_mean_trop_200202/ biofuel_200202/ biogenic_200203/ biomass_200110/ carbon_200411/ drydep_200203/ dust_200605/ fastj_200203/ fossil_200104/ leaf_area_index_200202/ leaf_area_index_200412/ lightning_NOx_200203/ lightning_NOx_200709/ pco_lco_200203/ pnoy_200106/ scalefoss_200202/ soil_NOx_200203/ stratOH_200203/ stratjv_200203/ sulfate_sim_200210/ sulfate_sim_200508/ tagged_CO_200106/
Chapter 4 contains a full description of the data contained in these directories. Also, in each of these subdirectories you will find a README file which describes how the data was regridded to the GEOS5 0.5 x 0.666 China nested grid.
Here are sample input.geos files for the GEOSChem 0.5 x 0.666 nested-grid China simuation:
input.geos.china_05x066_BC4x5: Use this file to run GEOS-Chem at 4 x 5 resolution to save out the boundary conditions for the nested grid trasnport routine.
input.geos.china_05x0666: Use this file to run a nested grid China simulation at 0.5 x 0.666 resolution.
The following switches should be set in the input.geos.china_05x0666_BC4x5 file:
%%% NESTED GRID MENU %%%: Save TPCORE 4x5 BC's : T TPCORE 4x5 BC directory : ./BC_4x5 4x5 BC timestep [min] : 180 LL box of 4x5 BC region : 51 21 UR box of 4x5 BC region : 67 37 1x1 offsets I0_W, J0_W : 3 3
This will tell GEOSChem to save out the 4x5 boundary conditions with the proper settings.
Also note that the following switches should be set in the input.geos.china_05x0666 file:
%%% EMISSIONS MENU %%% ... => Use EMEP emissions? : F => Use BRAVO emissions?: F ... => Use lightning NOx : T => Scale glb flrate?: T => OTD reg redist? : F => OTD loc redist? : T => Use CTH param? : T ... %%% NESTED GRID MENU %%%: Save TPCORE 4x5 BC's : F TPCORE 4x5 BC directory : ./BC_4x5/ 4x5 BC timestep [min] : 180 LL box of 4x5 BC region : 51 21 UR box of 4x5 BC region : 67 37 1x1 offsets I0_W, J0_W : 3 3
Because the nested grid domain lies over China, we don't need to use the EMEP (European) or BRAVO (Mexican) emission datasets, so the switches that toggle these options may be set to F. Also, OTDLIS redistribution factors for the lightning (CTH option) have now been computed by Lee Murray, so we can select that option in the Lightning NOx menu.
You may obtain a TAR file with run directories for the GEOS5 0.5 x 0.666 nested grid simulation from:
ftp ftp.as.harvard.edu cd pub/geos-chem/beta_releases/ GEOS5-05x066-Nested-China.rundir.tar.gz
The GEOS5 0.5 x 0.666 China nested grid has longitude centers at:
70.000 70.667 71.333 72.000 72.667 73.333 74.000 74.667 75.333 76.000 76.667 77.333 78.000 78.667 79.333 80.000 80.667 81.333 82.000 82.667 83.333 84.000 84.667 85.333 86.000 86.667 87.333 88.000 88.667 89.333 90.000 90.667 91.333 92.000 92.667 93.333 94.000 94.667 95.333 96.000 96.667 97.333 98.000 98.667 99.333 100.000 100.667 101.333 102.000 102.667 103.333 104.000 104.667 105.333 106.000 106.667 107.333 108.000 108.667 109.333 110.000 110.667 111.333 112.000 112.667 113.333 114.000 114.667 115.333 116.000 116.667 117.333 118.000 118.667 119.333 120.000 120.667 121.333 122.000 122.667 123.333 124.000 124.667 125.333 126.000 126.667 127.333 128.000 128.667 129.333 130.000 130.667 131.333 132.000 132.667 133.333 134.000 134.667 135.333 136.000 136.667 137.333 138.000 138.667 139.333 140.000 140.667 141.333 142.000 142.667 143.333 144.000 144.667 145.333 146.000 146.667 147.333 148.000 148.667 149.333
and latitude centers at:
-11.000 -10.500 -10.000 -9.500 -9.000 -8.500 -8.000 -7.500 -7.000 -6.500 -6.000 -5.500 -5.000 -4.500 -4.000 -3.500 -3.000 -2.500 -2.000 -1.500 -1.000 -0.500 0.000 0.500 1.000 1.500 2.000 2.500 3.000 3.500 4.000 4.500 5.000 5.500 6.000 6.500 7.000 7.500 8.000 8.500 9.000 9.500 10.000 10.500 11.000 11.500 12.000 12.500 13.000 13.500 14.000 14.500 15.000 15.500 16.000 16.500 17.000 17.500 18.000 18.500 19.000 19.500 20.000 20.500 21.000 21.500 22.000 22.500 23.000 23.500 24.000 24.500 25.000 25.500 26.000 26.500 27.000 27.500 28.000 28.500 29.000 29.500 30.000 30.500 31.000 31.500 32.000 32.500 33.000 33.500 34.000 34.500 35.000 35.500 36.000 36.500 37.000 37.500 38.000 38.500 39.000 39.500 40.000 40.500 41.000 41.500 42.000 42.500 43.000 43.500 44.000 44.500 45.000 45.500 46.000 46.500 47.000 47.500 48.000 48.500 49.000 49.500 50.000 50.500 51.000 51.500 52.000 52.500 53.000 53.500 54.000 54.500 55.000
A8.3: Addenda for beta release v80103
GEOSChem v80103 includes the following revisions over GEOSChem v80102:
The existing version of TPCORE in GEOSChem has been replaced with a version based on the GMI model. This was done in order to rectify the "polar overshoot" problem in the stratosphere. (Click here for more info)
Various fixes for the diagnostics were implemented, including:
Fix to ensure consistency between the ND51 satellite diagnostic and the ctm.bpch file. (Click here for more info)
Fixes in diag3.f in the ND22 (J-values) and ND34 (biofuel emissions) diagnostics. (Click here for more info)
CAVEAT: The repositioning of the calls to diagnostic routines described above may affect the concentrations for certain tracers, especially dust and sea salt aerosols. If you are comparing results from GEOSChem v8-01-03 to older versions then you may need to keep this in mind. Please see this wiki post for more information.
You may obtain the GEOSChem v80103 source code and benchmark simulation package via anonymous FTP from:
ftp ftp.as.harvard.edu cd pub/geos-chem/beta_releases get GEOS-Chem.v8-01-03-beta.stdrun.tar.gz
GEOSChem v80103 now contains a new feature: the ability to generate automatic documentation (with Protex) directly from the documentation headers in certain source code files. At present, the only files that contain Protex-ready documentation are tpcore_fvdas_mod.f90 and pjc_pfix_mod.f. However, as time allows, this will be expanded to other GEOSChem source code files.
Before you can generate the automatic documentation, you must first make sure that you have the LaTeX utilities (e.g. latex, dvips, dvipdf) installed on your system. These usually come standard with most versions of Linux nowadays. A copy of the Protex script is included in the Code.v8-01-03/doc subdirectory for your convienience.
To build the documentation file, simply type:
cd Code.v8-01-03 make doc
This will cause the *.tex, *.ps, and *.pdf files to be created in the Code.v8-01-03/doc subdirectory.
If you wish to remove the *.tex, *.ps, and *.pdf files from the Code.v8-01-03/doc subdirectly, simply type:
cd Code.v8-01-03 make docclean
Claire Carouge and Bob Yantosca have implemented a fix into diag3.f for the ND22 (J-value) diagnostic such that there is now a test for the name of each tracer. As a side-effect of this fix, you may no longer type all into the input.geos file. You must explicitly list each tracer number. For example, you may type:
ND22: J-Values : 47 1 7 8 20 99 => JV time range : 11 13
Likewise as a result of the fix that was made for the ND34 diagnostic, you must explicitly declare the tracer numbers for which you wish to archive biofuel emissions. For example, use this line in input.geos:
ND34: Biofuel emissions : 1 1 4 5 9 10 11 18 19 20 21
A8.4: Addenda for beta release v80104
GEOSChem v80104 is our “Emissions” release. This version standardizes several new emissions features that users have submitted to us over the past several months. Also incorporated are the anthropogenic scale factors for years 1985-2005 from Aaron van Donkelaar.
NOTE: Boldfaced items are new to v80104!
Emissions Inventories turned on in the v80104 1-month benchmark runs:
Scalings & Mechanisms updates in v8-01-04, used in 1-month benchmarkruns:
Other emissions options not used in 1-month benchmark runs, but which are new to GEOS-Chem v8-01-04:
We are in the process of preparing a detailed document describing the emissions. In the meantime, for more information, please see:
You may obtain the GEOSChem v80104 source code and benchmark simulation package via anonymous FTP from:
ftp ftp.as.harvard.edu cd pub/geos-chem/beta_releases get GEOS-Chem.v8-01-04-beta.stdrun.tar.gz
If you are interested in running the GEOS5 0.5° x 0.666° nested-grid simulation over China, you may download sample run directories for this simulation from:
ftp ftp.as.harvard.edu cd pub/geos-chem/beta_releases get GEOS5-05x066-Nested-China.rundir.tar.gz
You must obtain the new emissions data files from the following directories. (NOTE: some of these directories have subdirectories, please make sure to download everything. We recommend using 3rd-party FTP software such as Mozilla's FireFTP.)
ftp ftp.as.harvard.edu cd pub/geos-chem/data/GEOS_1x1
anth_scale_factors_200811/ ARCTAS_SHIP_2008/ CAC_200801/ EMEP_200806/ EPA_NEI_200806/
GFED2_200601/ (New data: years 2006, 2007)
In input.geos, you now need to turn on O3 and HNO3 as active chemical species. This is done by bracketing them with parentheses in the TRACER MENU section. This is necessary to implement some of the new ship emissions.
Tracer #2 : 2 Ox 48.0 (O3) NO2 2NO3 ... Tracer #7 : 7 HNO3 63.0 (HNO3)
The globchem.dat chemical mechanism file must also be modified accordingly. We need to add EMISSION reactions for O3 and HNO3 so that SMVGEAR will recognize these as emission species. This is done as follows:
A 0 0.00E+00 0.0E+00 0 0 0.00 0. 0. EMISSION + =1.000O3 + + + + + + + + + + + + + + + A 0 0.00E+00 0.0E+00 0 0 0.00 0. 0. EMISSION + =1.000HNO3 + + + + + + + + + + + + + + +
If you are using the versions of input.geos and globchem.dat that shipped with the standard run TAR file then you will be OK. You can make sure you have the correct globchem.dat file by checking the header to see if it there is a sentence which says:
(1) Now includes emissions rxn for HNO3 and O3
There is one further modification in input.geos. The new EMISSIONS MENU is listed below. Many of the options are the same as before, but this also reflects the new emissions options that were added in v80104.
%%% EMISSIONS MENU %%% : Turn on emissions? : T Emiss timestep (min) : 60 Include anthro emiss? : T => Scale to (1985-2005): -1 => Use EMEP emissions? : T => Use BRAVO emissions?: T => Use EDGAR emissions?: T => Use STREETS emiss? : T => Use CAC emissions? : T Use EPA/NEI99 (anth+bf)?: T w/ ICARTT modif.? : T w/ VISTAS NOx emis? : F Include biofuel emiss? : T Include biogenic emiss? : T => Use MEGAN inventory?: T Include biomass emiss? : T => Seasonal biomass? : F => Scaled to TOMSAI? : F => Use GFED2 biomass? : --- => monthly GFED2? : T => 8-day GFED2? : F => 3-hr GFED2? : F => synoptic GFED2? : F Individual NOx sources :--- => Use aircraft NOx? : T => Use lightning NOx : T => Scale glb flrate?: T => OTD reg redist? : F => OTD loc redist? : T => Use CTH param? : T => Use MFLUX param? : F => Use PRECON param?: F => Use soil NOx : T Use SHIP emissions :--- => global EDGAR ? : T => EMEP over EUROPE ? : T => ship SO2 Colbert ? : F => ship SO2 Arctas ? : T Use AVHRR-derived LAI? : F
For more information about which options these switches toggle, please see this document on the GEOSChem wiki.
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