1. Introduction

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 and Europe.

GEOS–CHEM began as a merging of Mian Chin's GEOS–CTM code with Harvard's emissions, dry deposition, and chemistry routines from the old GISS-II 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, and biogenic emissions. GEOS–CHEM includes state-of-the-art transport (TPCORE) and photolysis (FAST-J) routines, as well as the SMVGEAR chemistry solver package. GEOS–CHEM has also been parallelized using the OpenMP compiler directives, and it scales well when running across multiple CPU's.

GEOS–CHEM has also kept pace with changes in the meteorological data products being produced by DAO. GEOS–CHEM can now be used with the DAO's GEOS–1, GEOS–STRAT, GEOS–3, and GEOS-4 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.

1.2 What's new in GEOS–CHEM v6–02–05

Here is a list of the most important improvements to GEOS–CHEM since version v6–01–05 (08 Apr 2003):

1.2.1. Addition of extra aerosol tracers

GEOS–CHEM v6–02–05 now carries the following additional aerosol tracers for the fully-coupled NOx–Ox–Hydrocarbon–aerosol simulation and the offline aerosol simulation:

• Black carbon (both hydrophilic and hydrophobic)
• Organic Carbon (both hydrophilic and hydrophobic)
• Desert Dust (Effective radii = 0.7, 1.4, 2.4, and 4.5 microns)
• Accumulation mode sea salt (Effective radii = 0.1 – 2.5 microns)
• Coarse mode sea salt (Effective radii = 2.5 – 10 microns)

These aerosol tracers are used to compute

1.2.2. On-line mobilization of desert dust

GEOS–CHEM v6–02–05 now includes the DEAD dust mobilization package (by C. Zender et al), as well as the dust mobilization package from the GOCART model (by P. Ginoux et al). The user may select either package at runtime via a logical switch.

1.2.2. Higher degree of parallelization than in previous versions

A higher fraction of the code is parallelized In GEOS–CHEM v6–02–05 than in previous versions. The routines which compute lightning NOx emissions, stratospheric boundary conditions, and certain diagnostics have now been parallelized with OpenMP directives.

1.2.4. SO2 emissions from ship exhaust

SO2 emissions from ship exhaust are now added to the total anthropogenic SO2 emissions. This results in an extra 4.24 Tg S per year being emitted into the atmosphere.

1.2.5. Compatability with GEOS–4 meteorological fields

GEOS–CHEM v6–02–05 can be used with the GEOS–4 meteorological data fields from NASA's Global Modeling and Assimilation Office (GMAO). New transport and convection routines have been installed in order to accomodate the GEOS–4 fields. The LLNL pressure fixer has also been implemented in order to ensure that GEOS–CHEM conserves global air and tracer mass when being driven by GEOS–4 winds. For a complete list of the GEOS–4 meteorological fields that are used, please see Appendix 4.

1.2.6. Now can read compressed or uncompressed met field files

GEOS–CHEM v6–02–05 now gives users the option of reading zipped meterological data files, or to read unzipped meteorological data files directly from disk. Reading unzipped meteorological data files is more efficient, and eliminates excess clock cycles. If you have the disk space available, we recommend storing your meteorological data unzipped.

1.2.6. Now supports Intel IFC and EFC Fortran compilers

GEOS–CHEM v6–02–05 can be compiled on Linux boxes using the 32-bit IFC Intel compiler, or on SGI Itanium machines using the 64-bit Intel EFC compiler. If you have been having problems with the Portland Group F90 compiler, then we recommend switching to the IFC compiler. IFC seems to be a better compiler and it implements the parallel OpenMP directives extremely well.

1.3 Requirements for GEOS–CHEM v6–02–05

In order to run GEOS–CHEM you will need to have access to a platform which has a version of Fortran–90 that supports the OpenMP parallel processor directives. Compliant platforms and compilers include:

• SGI Origins with SGI–MIPS Fortran–90 Compiler
• SGI Itanium machines with 64-bit Intel Fortran Compiler (EFC)
• HP/Compaq Alpha machines with DEC/Compaq Fortran–90
• Linux boxes with 32-bit Intel Fortran Compiler (IFC)
• Linux boxes with Portland Group Inc. Fortran 90 Compiler (PGF90)
• Sun/Sparc machines with SUN/Forte compiler
• IBM-AIX machines

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 our GEOS–CHEM Style Guide for more tips on how to write effective Fortran–90 code.

When setting up GEOS–CHEM on your system, you will need to make sure that you have installed the following components:

1. A GEOS–CHEM source code directory
2. One or more run directories containing user-modifiable input files
3. A data directory containing files to be shared across multiple users

Installing the source code directory will be the topic of Section 2: Installation and Compilation. F90 coding practices and parallelization are the subject of Section 3: Coding: Practice and Style. The many shared data files contained in the data directory will be the focus of Section 4: Shared Data Directories. Setting up the files in your own personal run directory is discussed in Section 5: Run Directories. Running and debugging the GEOS–CHEM code is the topic of Section 6: Running GEOS–CHEM.

You may download gzipped TAR files containing the GEOS–CHEM source code, data directories, and run directories (at both 2 x 2.5 and 4 x 5 resolution) from the GEOS–CHEM Source Code and Data Files page.