GEOS–Chem v8–02–01 Online User's Guide
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1.1 Brief overview of GEOS–Chem
The GEOS–Chem model is a global three-dimensional model of tropospheric chemistry driven by assimilated meteorological observations from the Goddard Earth Observing System (GEOS) of the NASA Global Modeling Assimilation Office. GEOS–Chem is being developed by personnel at Harvard University and other institutions in the United States, Europe, and Asia.
GEOS–Chem began as a merging of Mian Chin's GEOS–CTM code with the emissions, dry deposition, and chemistry routines from the old Harvard–GISS 9-layer model. Over the years, several improvements have been added to GEOS–Chem. The model now uses detailed inventories for fossil fuel, biomass burning, biofuel burning, biogenic, and aerosol emissions. GEOS–Chem includes state-of-the-art transport (TPCORE) and photolysis (FAST–J) routines, as well as the SMVGEAR II chemistry solver package. GEOS–Chem has also been parallelized using the OpenMP compiler directives, and it scales well when running across multiple CPU's. We are also investigating how to port GEOS–Chem to distributed memory machines using the MPI parallelization directives.
GEOS–Chem has also kept pace with changes in the meteorological data products being produced by GMAO. GEOS–Chem can now be used with the GMAO's GEOS–3, GEOS–4, and GEOS–5 data products at either 2° x 2.5° or 4° x 5° global resolution. GEOS–Chem can also be run at 1° x 1° resolution in nested grids for both China and North America, and 0.5° x 0.667° resolution in nested grid for China.
In addition, GEOS–Chem can now be driven with meteorological data from the GISS–II GCM (23 layers, 4° x 5° horizontal grid) to perform simulations for the GCAP project.
1.2 What's new in GEOS-Chem v8-02-01
1.2.1 Updated chemistry
Chemical relations and relation rates are updated mainly from JPL06 and IUPAC06. Photolysis quantum yields are updated from FAST-JX version 6.4 data. See HERE for detailed changes compared to v8-01-04. The pressure-dependency sheme for acetone photolysis is now updated to FAST-JX version 6.4.
The format of jv_spec.dat file has slightly changed. The new format is explained in Chapter 5: GEOS-Chem run directories.
1.2.2 Updated dust scattering
1.2.3 Updated emissions
Several emission inventories are updated or newly implemented. All details concerning emissions are in Chapter 4: GEOS-Chem data directories.
1.2.4 Improved stratospheric exchangeGEOS-Chem uses now the transport routine and pressure fixer from GMI. This ensures to have a reasonable troposphere-stratosphere exchange.
1.3 What's new in GEOS–Chem v8–01–01
Here is a list of the most important improvements to GEOS–Chem since version v7–03–06 (08 Nov 2005). Please also be sure to check the GEOS–Chem wiki for a list of outstanding issues.
1.3.1 Compatibility with GEOS–5 meteorological fields
GEOS–Chem v8–01–01 is now fully compatible with the GMAO GEOS–5 operational data product (e.g. GEOS-5.0.1 and GEOS-5.1.0). You must upgrade to GEOS–Chem v8–01–01 if you wish to drive GEOS–Chem with the GEOS–5 meteorology.
Please see the GEOS–Chem wiki for a more complete account of some of the issues that were encountered during GEOS–5 implementation.
1.3.2 GEOS–1 and GEOS–STRAT meteorology is no longer supported
With the availability of several years of GMAO's GEOS–4 and GEOS–5 meteorological data products, it is no longer necessary to use the older GEOS–1 and GEOS–STRAT products. Therefore, GEOS–Chem v8–01–01 no longer supports these data sets.
NOTE: GMAO's GEOS–3 meteorological data product is still supported in GEOS–Chem v8–01–01, and will continue to be supported indefinitely.
1.3.3. Dynamic tropopause
GEOS–Chem now has the capability to perform chemistry with SMVGEAR up to the location of the actual tropopause, as diagnosed by the tropopause pressure (TROPP) meteorological field. This results in a more accurate representation of the tropopause, and causes more grid boxes in the tropics to be sent to the SMVGEAR solver. In prior versions, SMVGEAR chemistry was only done up to the location of the annual mean tropopause.
1.3.4. Updated lightning with OTD/LIS local redistribution
The lightning NOx emissions algorithm in GEOS–Chem v8–01–01 has been substantially rewritten to try to better match the observational distribution of lightning flashes. The location of lightning flashes now follows the patterns observed by the OTD/LIS satellite instruments.
1.3.5 Updated global and regional anthropogenic emissions
In GEOS–Chem v8–01–01, the default GEIA/Piccot anthropogenic emissions can now be overwritten with a combination of global and regional anthropogenic emissions inventories, including:
Click HERE to view a table with more detailed information about each of these inventories.
NOTE: In a future version of GEOS–Chem, we will be introducing an improved algorithm to scale fossil fuel emissions from the baseline year of 2000 to the present year (cf. Aaron van Donkelaar).
1.3.6 GFED2 biomass burning emissions
In GEOS–Chem v8–01–01, you may select either the default Duncan et al (2001) biomass burning emissions, or the GFED2 biomass burning emissions.
NOTE: At present only the GFED2 monthly mean emissions have been implemented. The 8-day-averaged GFED2 emissions will be introduced into a future version of GEOS–Chem (cf. Ray Nassar).
1.3.7 Safer floating-point operations
GEOS–Chem v8–01–01 includes some extra floating point error traps (e.g. safe division, avoiding division by zero, etc.) in order to prevent NaN and infinity values from propagating throughout the code. Also, a bug fix was implemented into SMVGEAR in order to better screen out negative values.
1.3.8 Aerosol Thermodynamic Equilibrium with RPMARES
It was recently discovered that the version of ISORROPIA that ships with GEOS–Chem can give bad values when computing the aerosol thermodynamical equilibrium for grid boxes where relative humidity is below 30%. Therefore, until further notice we have reverted back to the RPMARES code for computing aerosol thermodynamical equilibrium until further notice.
1.3.9 Compatibility with SunStudio 11/12 and Intel Fortran Compiler 10
GEOS–Chem v8–01–01 now ships with Makefiles for compiling with the newest Sun or Intel Fortran compilers. Options for using the TotalView Debugger are also now included in the makefiles.
1.4 What's new in GEOS–Chem v7–03–06
NOTE: This section described the new features in v7–03–06, which was the last public release of GEOS–Chem. We shall keep this section here for your reference.
1.4.1. Compatibility with Intel Fortran Compiler version 9.0
GEOS–Chem v7–03–06 is now compatible with the Intel Fortran Compiler version 9.0. This compiler (named "ifort") optimizes much better than previous compiler versions and is much more stable. When GEOS–Chem is compiled with Intel Fortran Compiler v9, a 1-month, 4x5, full-chemistry simulation now finishes 1/2 hour faster than if the code were compiled with previous Intel Fortran compiler versions.
1.4.2. EMEP anthropogenic emissions over Europe
GEOS–Chem v7–03–06 now allows you to "overwrite" the existing anthropogenic emissions over Europe with the EMEP anthropogenic emissions for the following tracers: NOx, CO, ALK4, MEK, ALD2, PRPE, and C2H6. For more information about the EMEP emissions, click HERE.
1.4.3. MEGAN biogenic emissions
GEOS–Chem v7–03–06 now allows you to select MEGAN biogenic emissions or for the following species: Isoprene, Acetone, PRPE (>= C3 Alkenes), Monoterpenes, and Methyl Butenol. You may also select the default GEIA biogenic emissions. However, GEIA biogenic emissions are now considered "deprecated" and will be removed from GEOS–Chem at a future date. For the time being, you may select either MEGAN or GEIA biogenic emissions.
1.4.4. Ability to regrid emissions data from 1x1 grid on the fly
GEOS–Chem v7–03–06 now contains code to regrid emissions (or other) data which is on the GMAO 1° x 1° grid (360 longitudes x 181 latitudes) to the current model resolution on-the-fly. This will eliminate the need for offline regridding of emissions data with IDL code. At present, the MEGAN emissions, the EMEP emisisions, and AVHRR LAI data (for MEGAN) are stored on the GEOS 1° x 1° grid. Other types of 1° x 1° emissions data will be added in the near future as time allows.
1.4.5. Met field updates
GEOS–Chem v7–03–06 now contains the following updates for meteorological met fields
1.4.6. New simulations
In GEOS–Chem v7–03–06, the following offline simulations have been added:
1.4.7. Improved land / water / ice diagnosis and lightning NOx rescaling
In GEOS–Chem v7–03–06, the diagnosis of which grid boxes are over land, water, and ice, respectively, has been improved in order to ensure better consistency among the different types of met fields.
Lightning NOx emissions have been rescaled accordingly so that the totals match that of the previous model versions. However while the annual total of lightning NOx emissions may be the same as previous versions, the distribution of the lightning NOx emissions will be different and will reflect the new diagnosis of land, water, and ice boxes.
Also, lightning NOx emissions have been turned off in the polar regions, since very little (if any) lightning occurs there.
1.4.8. Improved sea-air exchange for ocean emissions
In GEOS–Chem v7–03–06, we now use the formulation for sea-air exchange as given by Nightingale et al [2000b], Geophys. Res. Lett., 27, 2117-2120. This formulation is used for the emissions of DMS, CH3I, acetone, and sea-salt.
1.4.9. Updated treatment of aerosols
In GEOS–Chem v7–03–06, we have introduced the following improvements for the treatment of aerosols.
1.4.10. Diagnostic updates
In GEOS–Chem v7–03–06, we have incorporated the following improvements to the diagnostics:
The plane flight diagnostic (ND40) now archives both tropospheric column aerosol optical depth, as well as column aerosol optical depth from the surface to the location of the aircraft. These diagnostics will facilitate comparision of GEOS–Chem modeled data with observations from both satellites and aircraft.
The plane flight diagnostic (ND40) also now scales aerosol optical depths to 400 nm.
Minor fixes have been made to the ND49 timeseries diagnostic. Also, all timeseries diagnostics can now archive grid box height.
1.4.11. Technical updates
In GEOS–Chem v7–03–06, we have incorporated the following technical improvements:
We have removed obsolete code for SLOW–J and CO–OH parameterization. These are not used anymore. Furthermore, these codes make frequent use of old F77-style common blocks, which will make it difficult for us to convert GEOS–Chem to the Earth System Model Framework.
We have removed lots of other obsolete variables, particularly those in old common blocks.
GEOS–Chem v7–03–06 is now able to create diaginfo.dat and tracerinfo.dat files for GAMAP which are customized to the particular simulation that is being done. You will not have to manually edit these files anymore.
1.5 Requirements for GEOS–Chem v8–02–01
GEOS–Chem v8–02–01 is written in the Fortran–90 language. Fortran–90 is an extension of Fortran–77, which for many years has been the standard programming language for scientific computing. GEOS–Chem takes advantage of several powerful features of Fortran–90, including dynamic memory allocation, modular program design, and array operation syntax. Please view Appendix 7: GEOS–Chem Style Guide for more tips on how to write effective Fortran–90 code.
Please see the section on our wiki entitled Minimum System Requirements for GEOS–Chem and GEOS–Chem supported platforms and compilers for the most up-to-date information regarding supported systems, compilers, and other hardware and software issues.
When setting up GEOS–Chem on your system, you will need to make sure that you have installed the following components:
Installing the source code directory will be the topic of Chapter 2: Installation and of Chapter 3: Compilation. F90 coding practices and parallelization are the subject of Chapter 7: Coding: Practice and Style. The many shared data files contained in the data directory will be the focus of Chapter 4: Data Directories. Setting up the files in your own personal run directory is discussed in Chapter 5: Run Directories. Running and debugging the GEOS–Chem code is the topic of Chapter 6: Running GEOS–Chem.
You may download gzipped TAR files containing the GEOS–Chem source code, data directories, and run directories (at 2° x 2.5°, 4° x 5°, and higher resolutions) from the GEOS–Chem Source Code and Data Files page.
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