Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Chapter 0

                 GEOS - Chem v9 - 01 - 03 Online User's Guide
         Bob Yantosca, Michael Long, Melissa Payer, and Matthew Cooper
Atmospheric Chemistry Modeling Group
School of Engineering and Applied Sciences
Harvard University
29 Oxford Street
Cambridge, MA 02138
                            Web Posted 14 Sep 2012
                    Email<EMAIL_ADDRESS>      Also see our archive of GEOS - Chem User Guides from past releases!

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Chapter 1
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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1. Introduction

1.1 Welcome to the GEOS - Chem user community!
We (the GEOS - Chem Support Team) welcome you to the international GEOS - Chem user community. The following sections describe the expectations and responsibilities that we expect from you as a GEOS - Chem user. For additional information, please see our GEOS - Chem overview page.
1.1.1 Expectations and responsibilities
We expect you to have the required hardware and software to run GEOS - Chem. If you are not sure what hardware or software is available to you, then please check with your local IT department.
We expect that you will have at least some familiarity with the following:
   * The Fortran programming language
   * IDL (preferred), or other graphics software (e.g. Splus, Matlab)
   * The Unix environment (i.e. commands, file paths, etc.)
   * Unix scripts (not strictly required but is very helpful to know!)
   * How version control works
For more information about these topics, please follow these links:
   * GEOS - Chem wiki: GEOS - Chem programming resources
   * Presentation: GEOS - Chem User Resources, Code Development Guidelines, and Debugging Tips.
1.1.2 Register your GEOS - Chem user group
We invite you to send us a paragraph describing how you and the other members of your research group plan to use GEOS - Chem. We will add this to our GEOS - Chem People and Projects web page.
Registering your group helps us to accurately track how many research groups are using GEOS - Chem. This helps us to plan accordingly.
1.1.3 Join a working group and subscribe to the email lists
We expect you to join the Working Group that is most relevant to your area of research. The Working Groups foster communication and collaboration between GEOS - Chem users, and identify priorities for model development to the GEOS - Chem Steering Committee. Please take a moment to introduce yourself to the Working Group Chairperson via email.
Each GEOS - Chem Working Group has its own email list, so that group members can discuss various aspects of model development and validation among themselves. We have also established a general GEOS - Chem email list where we shall make announcements about new model releases, bugs and fixes, and other information pertient to the entire GEOS - Chem community. Therefore, you should subscribe to the general GEOS - Chem email list and to the email list of your Working Group.
Click HERE for more information about subscribing to the GEOS - Chem email lists.
1.1.4 Be an active member of the community
As a GEOS - Chem user, we expect you to adhere to our list of best practices. In particular, if you discover a problem (e.g. bugs, missing files, numerical issues, etc.), please alert the GEOS - Chem Support Team right away. Other GEOS - Chem users will most certainly benefit from your discovery!
Please feel free to send us your timing results from the 1-month benchmark simulation. This will allow us to keep a list of how the model is performing across several different platform/compiler combinations. We will post this information on the GEOS - Chem wiki.

1.2 The GEOS - Chem model of atmospheric chemistry and composition
1.2.1. Overview
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 Americas, 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. Since then, we have added many updates and improvements 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. Detailed aerosol microphysical simulations using GEOS - Chem may performed with the TOMAS aerosol microphysics code or the APM aerosol microphysics code.
GEOS - Chem has been parallelized using the OpenMP compiler directives, and it scales well when running across multiple CPU's on shared-memory machines. We are currently building a Grid-Independent version of GEOS-Chem in order to take advantage of distributed memory architectures and MPI parallelization.
GEOS - Chem has kept pace with changes in the meteorological data products being produced by GMAO. You can perform GEOS - Chem simulations with GMAO's GEOS - 4, GEOS - 5, MERRA, (and soon GEOS - 5.7.2!) data products on 1° x 1.25°, 2° x 2.5° or 4° x 5° global grids. GEOS - Chem has become a popular tool for regional-scale modeling. You can perform nested-grid simulations (one-way nesting) at 0.5° x 0.666° horizontal resolution for the following regions: China/SE Asia, North America, and Europe.
Those of you who are part of the GCAP project can use GEOS - Chem to perform simulations using meteorology from the GISS - II GCM (23 layers, 4° x 5° horizontal grid). You can select from several IPCC future-climate scenarios.
1.2.2. The benchmarking process
We updated our benchmarking procedure, starting with version GEOS - Chem v9 - 01 - 02. For details, GEOS - Chem benchmarking web page.

1.3 What's new in GEOS - Chem v9 - 01 - 03
The following features were introduced into GEOS - Chem public release v9 - 01 - 03:
                                    Feature
                                  Description
                                Science updates
Updated acetone chemistry
Emily Fischer has updated the acetone formulation used in GEOS - Chem. See the acetone wiki page for more information.
OVOC dry deposition updates
The reactivity factor (f0) for all OVOCs has been changed from 0 to 1, according to Karl et al. (2010). See this wiki page for more information.
Improved sea salt emission and deposition
Sea salt emissions and dry deposition have been updated according to Jaeglé et al. (2011).
Dust submicron size distribution
A more realistic partitioning for the dust mass into the submicron size bins has been applied. See this wiki page for more information.

Improved snow scavenging and washout parameterization
The following updates have been added to improve wet scavenging algorithm:
   1. Add scavenging by snow
   2. Update aerosol scavenging efficiency
PARANOX ship plume emissions
Previously, 10 molecules O3 and 1 molecule HNO3 were emitted per ship NOx molecule. Ship emissions have been updated according to Vinken et al. (2011) to account for non-linear chemistry of ship plumes. See this wiki page for more information.
Add scaling of lightning NOx for 2x2.5 MERRA simulations
Lee Murray has generated OTD/LIS local redistribution factors for use with MERRA at 2° x 2.5°. See this wiki page for more information.
Historical emission inventories of SO2, NOx, BC, and POA
Historical emission inventories of SO2, NOx, BC, and POA have been implemented according to Leibensperger et al. (2011). See this wiki page for more information.
Nested-grid updates for offline simulations
Nested-grid capability has been added to the following offline simulations:
   * Nested-grid CO2
   * Nested grid CH4 (North America)
Hg(II) gas-aerosol partitioning
This update includes the following items:
   1. Hg(II) gas-aerosol partitioning from Amos et al. (2012)
   2. Primary anthropogenic Hg(p) is emitted as Hg(II)
CH4 simulation updates
Kevin Wecht has updated the CH4 simulation to include GFED3 biomass burning emissions and linearized CH4 chemistry from GMI output. See the CH4 simulation wiki page for more information.
Daily and 3-hourly GFED3 biomass emissions
Prasad Kasibhatla updated GEOS - Chem to incorporate the capabilty to use GFED3 daily and 3-hourly fire fractions, and to regrid on the fly from the GFED3 native resolution (0.5° x 0.5°) to the model resolution. See this wiki page for more information.
Tropospheric bromine chemistry
Justin Parrella added 10 bromine tracers and their associated chemical reactions to the GEOS - Chem full chemistry simulation. See this wiki page for more information
Satellite-based NOx emission trends
Scaling factors for anthropogenic NOx emissions derived from OMI tropospheric NO2 columns (compiled by Lok Lamsal) have been implemented. See this wiki page for more information.
Stratospheric P and k (monthly climatology)
An updated linearized stratospheric chemistry scheme has been implemented into GEOS - Chem v9 - 01 - 03. See the stratospheric chemistry wiki page for more information.
                              Structural updates
Retirement of obsolete GEIA biogenic emissions
GEIA biogenic VOC emissions have been removed from GEOS - Chem v9 - 01 - 03. It is recommended that you use the MEGAN biogenic emissions in your GEOS - Chem simulations.
Structural changes to clarify science behind washout
Washout code has been split into three cases: aerosols, HNO3, and soluble gases. This was done to ensure that HNO3 is not affected by the aerosol scavenging updates and is still scavenged according to Eq. 14 from Jacob (2000).
Initial source code modification for GEOS - 5.7.2
GEOS - Chem has been modified for compatilibility with the GEOS - 5.7.2 meteorological data.
Remove support for GEOS - 3 meteorology
See this wiki page for more information.
Updates from the grid-independent GEOS - Chem model code
Modifications made for the grid-independent GEOS - Chem model include:
   1. Fixes to facilitate implementation of grid-independent code
   2. Preliminary interface to link driving GCM
MAP_A2A regridding package
Matt Cooper replaced the existing GEOS - Chem regridding routines with the MAP_A2A regridding package (developed by S.-J. Lin and refined by Bob Yantosca). The new algorithm regrids emissions from any arbitrary horizontal grid to the current model resolution.
                                   Bug fixes
Fix for GLCO3/GLPAN bug in standard chemistry mechanism
Fabien Paulot found a bug in the standard chemistry mechanism, which resulted in an artificial loss of NOx. See this wiki page for more information.
Bug fix in routine ARSL1K
The default value for the loss rate on wet aerosol (ARSL1K) has been changed from 1.0d-3 to 1.0d-30. See this wiki page for more information.
Various other bug fixes
The following updates were made to fix several bugs in GEOS - Chem v9 - 01 - 02:
   * Bug fixes for David Streets emissions for years 2005 and earlier
   * Bug fix in emep_mod.F for offline simulations
   * Bug fix in nei2005_anthro_mod.F for offline simulations
   * Bug fix to prevent crash in wetdep when encountering anomalously low PRECTOT values
   * Minor fix in Rn-Pb-Be simulation to prevent missing drydep diagnostics
   * Correct out-of-bounds error in offline aerosol simulation
   * Bug fixes in diag3.F
   * Bug fixes for nested-grid simulations
   * Bug fix for reading Hg emissions
   * Bug fix in streets anthro mod.F for offline simulations
   * Bug fixes for dicarbonyl simulations

1.4 Requirements for GEOS - Chem v9 - 01 - 03
We summarize below the hardware and software requirements that you will need in order to run GEOS - Chem. For the most up-to-date information regarding supported systems, compilers, and other hardware and software issues, please also see our wiki pages entitled Minimum System Requirements for GEOS - Chem and GEOS - Chem supported platforms and compilers.
1.4.1. Hardware requirements
To run GEOS - Chem your hardware must have:
   * Enough memory to run GEOS - Chem
         o At least 2 GB RAM
         o But more than 4 GB RAM for running at 2° x 2.5° or higher resolution
         o You may want to consider 8 GB RAM if you plan on doing any of the following:
               * Running GEOS - 4 1° x 1.25° global GEOS - Chem simulations
               * Running GEOS - 5 0.5° x 0.667° nested-grid GEOS - Chem simulations
               * Running 2° x 2.5° global GEOS - Chem simulation and saving a lot of output fields (the more output you generate the more memory GEOS - Chem will require)
   * Sufficient disk storage for met fields
1.4.2. Software requirements
GEOS - Chem requires the following software:
   1. Any Unix-style operating system, such as:
         o Linux (Red Hat, SuSE, CentOS, etc.)
         o Ubuntu
         o Fedora
         o Mac OS X (which is POSIX-compliant)
         o NOTE: GEOS - Chem cannot run on a Microsoft (XP, Vista, Windows 7) environment!
   2. A Fortran 90 compiler that supports OpenMP parallelization
         o If using the Portland Group compiler, then a C compiler (such as GNU C compiler) is also required. The gcc comes installed with most Unix builds.
   3. GNU Make (chances are your Unix system has this installed already)
   4. Git version control system (free, open-source version control software)
The Linux flavor (RedHat, SuSE, Fedora, Ubuntu, etc.) is not important. Also, 64-bit architecture is not an issue with GEOS - Chem.
GEOS - Chem v9 - 01 - 03 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, array operation syntax, and derived data types. Please view Appendix 7: GEOS - Chem Style Guide for more tips on how to write effective Fortran - 90 code.
GEOS - Chem is now managed by the version control software Git. Git allows users at remote sites to easily download GEOS - Chem over the network. Git also enables users to keep track of their changes when developing the code and enables the creation of patches that would simplify the implementation of new developements in the standard version. For all these reasons, we strongly advise you to install Git so that you can manage your local GEOS - Chem source code.

1.5 The Git version control software
1.5.1. Why use Git?
GEOS - Chem model development is done in a distributed manner. GEOS - Chem users from many different institutions download the most recent model version and modify it according to their own particular research interests. Once a GEOS - Chem user has deemed his or her source code modifications to be mature -- usually coinciding with the submission of a paper to an academic journal -- he or she will submit his or her source code modifications to us for inclusion into the mainline "standard" model.
We used to disseminate the GEOS - Chem source code and run directories as a series of TARBALL (i.e. *.tar.gz) files (one for each version) via anonymous FTP. The advantage of this method was that each GEOS - Chem user only had to download a single file. However, as the number of GEOS - Chem users (and the submitted source code modifications) grew, this method became unwieldy. For example, if only a single file needed to be updated, the entire TARBALL file would have to be regenerated. This often led to confusion and error.
Given the large number of user code submissions, we must employ robust source code management techniques in order to ensure the integrity of the GEOS - Chem source code. Therefore, we have selected the Git version control software for GEOS - Chem source code management. Git is a relatively new version control system and offers many improvements over previous source code management software such as CVS and Subversion.
1.5.2. Advantages of using Git
   * Git avoids some of the limitations of CVS (which is by now 30-year-old software).
         * Git is a distributed source code management system. Instead of having one central GEOS - Chem repository residing on a single server, Git allows you to keep an identical copy (a.k.a. "clone") of the GEOS - Chem source code repository on your own system. Having several copies of the GEOS - Chem repository allows for redundancy in case of catastrophic server failure or other such calamity.
         * Modifications that you make to your own repository will not affect the repositories of other users. (That is, unless you consciously decide to "push" your changes to another repository).
         * When you are ready to submit your source code modifications for inclusion into the "standard" code, the GEOS - Chem Support Team can simply get them with a Git "pull" operation.
         * Git allows you to save out your source code changes to a "patch" file (a text file with a list of source code differences). This can be emailed to other users.
   * Git is in general much simpler to use than CVS.
         * With Git, you can "pull" changes from other users directly into your own local source code repository.
         * With Git, one can easily create several branches off of the "master" branch of code development. (Branching was always problematic in CVS).
               * Each branch can hold a new "feature", which may be tested independently of the rest of the code.
               * Branches can be merged back into the "master" branch when it is time to release the code.
         * The GitK tool allows you to see every single line of code that has been modified, going all the way back to the start of the project.
         * A graphic user interface (the Git Gui) lets you control Git in a more visual manner than the command-line options.
   * With Git, GEOS - Chem developers will be able to:
         * Download the most current GEOS - Chem source code online.
         * Download the most current GEOS - Chem run directories online
         * Develop and test their source code additions to GEOS - Chem in their own local repository, and
         * Submit their mature source code updates back to the GEOS - Chem Support Team for inclusion in the standard mainline code (via "Git pull" or patch files)
For more information about using Git, please see our wiki pages:
   * Chapter 8: Using Git to manage the GEOS - Chem source code
   * GEOS - Chem wiki: Version control with Git
   * GEOS - Chem wiki: Using Git with GEOS - Chem
   * The Git web page: http://www.git-scm.com

1.6 Topics covered in the GEOS - Chem User's Guide
We have arranged the GEOS - Chem User's Guide as follows:
   * Installing the GEOS - Chem source code directory, run directories,and shared data directories will be the topic of Chapter 2: Installation.
   * Compiling the GEOS - Chem source code into an executable will be covered in Chapter 3: Compilation.
   * The various shared data files (met fields, emissions inventories, oxidants, etc.), 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.
   * F90 coding practices and parallelization are the subject of Chapter 7: Coding: Practice and Style.
   * A brief summary of the most common Git commands is covered in Chapter 8: Using Git to manage the GEOS - Chem source code.
   * The Reference Section in Chapter 9 contains links to the GEOS - Chem reference guides that are generated automatically with the ProTeX too. Here you will also find a list of acknowlegments and guidelines for offering credit to GEOS - Chem developers.
   * Supplementary information GEOS - Chem, including lists of tracers by simulation, horizontal and vertical grids, meteorological data fields, diagnostic output options, chemical species, etc. are contained in the Appendices.

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Chapter 2
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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2. Installation

2.1 What you need to download before you can run GEOS - Chem
When setting up GEOS - Chem on your system, you will need to install the following components:
   1. The GEOS - Chem source code directory. This is the directory where the Fortran-90 source code files (i.e. *.F, *.F90 files) and Makefiles reside. Your Fortran compiler will create an executable from these source code files.
   2. A GEOS - Chem run directory. Here is where you will run the compiled GEOS - Chem executable. Each run directory contains:
         o Various input files that you can modify in order to select different options for your GEOS - Chem simulation
         o Files that define the GEOS - Chem's chemical and photolysis mechanisms
         o "Restart files" that hold the initial conditions for your GEOS - Chem simulation
      You may find a complete description of the run directory contents in Chapter 5.
   3. The GEOS - Chem shared data directories. This is the directory tree where the following types of data are stored:
         o Meteorological data (a.k.a. the "met fields) used to drive GEOS - Chem
         o Emissions inventories for GEOS - Chem
         o Scale factors to used to scale emissions from a base year to a given year
         o Oxidant (OH, O3) concentrations for both full-chemistry and offline simulations
         o IPCC future scenarios (for GCAP simulatons)
         o Other GEOS - Chem specific data files.
      You may find a detailed description of the GEOS - Chem shared data directories in Chapter 4.
   4. A netCDF library installation. GEOS - Chem v9 - 01 - 03 can read data files in netCDF format. Eventually, we shall replace all of GEOS - Chem's input and output files from binary punch file format to netCDF format. We are doing this as part of our Grid-Independent GEOS - Chem project, which seeks to interface GEOS - Chem with the NASA GEOS - 5 GCM.
The GEOS - Chem source code and run directories are small enough to download directly to your own disk space in your Unix account. You can download these with the Git version control software, as described in Chapter 2.2 and Chapter 2.3. You may also download our GEOS-Chem-Libraries netCDF installer via Git, as described in Chapter 2.5.
On the other hand, the GEOS - Chem shared data directories contain many large files that probably cannot all fit into your own personal disk quota. Therefore, you (or your sysadmin) should download the shared data directories to a common disk space where all GEOS - Chem users in your group can access them. The volume of data contained in the shared data directories precludes using Git; you must instead download these files via FTP, wget, or similar file transfer programs.

2.2 Downloading the GEOS - Chem Source Code
The GEOS - Chem "standard" source code is kept in a Git repository at Harvard:
git://git.as.harvard.edu/bmy/GEOS-Chem/
All official releases of the GEOS - Chem "standard" code shall originate from this repository.
You can download the directory containing the latest GEOS - Chem source code version by means of the git clone command. Type:
git clone git://git.as.harvard.edu/bmy/GEOS-Chem  Code.v9-01-03
This will create an exact copy (or "clone") of the official GEOS - Chem repository to your local disk space, in a directory named Code.v9-01-03. (You can choose a different name than Code.v9-01-03 if you wish.)
NOTE: When you clone, you will always get the most recent state of the repository. (i.e. the latest GEOS - Chem version or "bug fix" patch). If you wish to download an older version of GEOS - Chem (say v8 - 03 - 01) with Git, please follow these instructions.
Please see Chapter 3 for instructions on how to compile the GEOS - Chem source code into an executable file.

2.3 Downloading the GEOS - Chem run directories
As mentioned above, the GEOS - Chem run directory is where you will run the compiled executable file (see Chapter 3). The run directory contains several input files that you can modify in order to select the various options for your GEOS - Chem simulation.
We have compiled a collection of GEOS - Chem run directories, grouped by meteorological data type, horizontal resolution, and simulation type. These run directories are stored as individual Git repositories. This allows you to only download the particular run directories that you need.
You can use the Git clone command to download the run directories to your local disk space. The command will take the form:
git clone git://git.as.harvard.edu/bmy/GEOS-Chem-rundirs/DIR-OPTION LOCAL-DIR-NAME
LOCAL-DIR-NAME is the name you chose for your local directory to contain GEOS - Chem
DIR-OPTION may be one of the following:
                 DIR_OPTION
0.5 x 0.666 GEOS - 5 simlulations
                                  Description
0.5x0.666/NA/standard
0.5 x 0.666 GEOS - 5 offline nested grid simulation for North America

                   DIR_OPTION
2 x 2.5 GEOS - 4 simlulations
                                  Description
2x2.5/geos4/CO2_run
2 x 2.5 GEOS - 4 offline CO2 simulation
2x2.5/geos4/SOA
2 x 2.5 GEOS - 4 fullchem w/ SOA simulation
2x2.5/geos4/dicarbonyls
2 x 2.5 GEOS - 4 fullchem w/ dicarbonyls option
2x2.5/geos4/isoprene
2 x 2.5 GEOS - 4 fullchem w/ Caltech isoprene scheme
2x2.5/geos4/standard
2 x 2.5 GEOS - 4 fullchem standard (43 tracers)

                    DIR_OPTION
2 x 2.5 GEOS - 5 simulations
                                  Description
2x2.5/geos5/CO2_run
2 x 2.5 GEOS - 5 offline CO2 simulation
2x2.5/geos5/Hg
2 x 2.5 GEOS - 5 offline Hg simulation
2x2.5/geos5/SOA
2 x 2.5 GEOS - 5 fullchem w/ SOA simulation
2x2.5/geos5/dicarbonyls
2 x 2.5 GEOS - 5 fullchem w/ dicarbonyls option
2x2.5/geos5/isoprene
2 x 2.5 GEOS - 5 fullchem w/ Caltech isoprene scheme
2x2.5/geos5/standard
2 x 2.5 GEOS - 5 fullchem standard (43 tracers)

                     DIR_OPTION
4 x 5 GEOS - 4 simulations
                                  Description
4x5/geos4/SOA
4 x 5 GEOS - 4 fullchem w/ SOA simulation
4x5/geos4/dicarbonyls
4 x 5 GEOS - 4 fullchem w/ dicarbonyls option
4x5/geos4/isoprene
4 x 5 GEOS - 4 fullchem w/ Caltech isoprene scheme
4x5/geos4/standard
4 x 5 GEOS - 4 fullchem standard (43 tracers)

                     DIR_OPTION
4 x 5 GEOS - 5 simulations
                                  Description
4x5/geos5/APM
4 x 5 GEOS - 5 fullchem w/ APM aerosol microphysics option
4x5/geos5/Hg
4 x 5 GEOS - 5 offline Hg simulation
4x5/geos5/Hg_GTMM
4 x 5 GEOS - 5 offline Hg simulation with GTMM option
4x5/geos5/SOA
4 x 5 GEOS - 5 fullchem w/ SOA simulation
4x5/geos5/dicarbonyls
4 x 5 GEOS - 5 fullchem w/ dicarbonyls option
4x5/geos5/isoprene
4 x 5 GEOS - 5 fullchem w/ Caltech isoprene scheme
4x5/geos5/standard
4 x 5 GEOS - 5 fullchem standard (43 tracers)

                      DIR_OPTION
4 x 5 MERRA simulations
                                  Description
4x5/merra/Hg_GTMM
4 x 5 MERRA offline Hg simulation with GTMM option
4x5/merra/SOA
4 x 5 MERRA fullchem w/ SOA simulation
4x5/merra/dicarbonyls
4 x 5 MERRA fullchem w/ dicarbonyls option
4x5/merra/isoprene
4 x 5 MERRA fullchem w/ Caltech isoprene scheme
4x5/merra/standard
4 x 5 MERRA fullchem standard (43 tracers)

                     DIR_OPTION
1-month benchmark results
                                 Description
benchmark_1mon/v9-01-03
Run directories used for the 4 x 5 GEOS - 5 and MERRA 1-month benchmark simulations for GEOS - Chem v9 - 01 - 03. These run directories contain the following types of files:
   1. Initial conditions (a.k.a. restart files)
   2. Input files used to select the various GEOS - Chem options
   3. Output files from the simulation
   4. IDL plotting code for creating the validation plots
   5. Validation plots in PostScript format
NOTE: We shall create a new 1-month benchmark Git repository for each new GEOS - Chem version. This will help to keep the size of the repository manageable and will facilitate downloading via Git file transfer.
benchmark_1mon/prior
Run directories used for the 4 x 5 GEOS - 5 benchmarks for GEOS - Chem versions v8 - 03 - 01, v8 - 03 - 02, v9 - 01 - 01, and v9 - 01 - 02.
Please note:
   * In each run directory, we provide a GEOS - Chem restart file that you can use to initialize your simulation. However, it is highly recommended that you not use these restart files for any of your production runs. Rather, you will probably want to generate your own restart file by spinning up the model for at least a year.
   * If you need a restart file for an offline simulation (e.g. offline aerosol, mercury, tagged CO, etc), you can use the GAMAP routine make_restart.pro to create a "fake" restart file. You can also ask the other members of the GEOS - Chem Mailing List if they have a restart file for the particular type of simulation that you are trying to do.
   * If you are using GEOS - Chem with secondary aerosol tracers, then you will also need to create a soaprod.YYYYMMDD file. This can be done with GAMAP routines regridh_restart.pro, regridv_restart.pro and rewrite_agprod.pro or directly from GEOS - Chem. Please see the GEOS - Chem wiki page for more information.
   * When you clone, you will always get the most recent state of the repository. If, you wish to download the run directories for an older version of GEOS - Chem (say v8 - 03 - 01) with Git, please follow these instructions.

2.4 Downloading the GEOS - Chem shared data directories
The GEOS - Chem shared data directories contain the various met fields, emissions, and other data that GEOS - Chem will read in during the course of a simulation. You must download the shared data directories via FTP or a similar utility (e.g. wget, FireFTP, SecureFX, etc.) The large volume of data makes it impossible to track this directory structure with Git.
If your research group consists of several GEOS - Chem users, then perhaps someone (i.e. your sysadmin or local IT guru) has already downloaded the GEOS - Chem shared directory structure to a common disk space on your servers. Nevertheless, you should still check to make sure that you have the most recent data directories and subdirectories. See Chapter 4 for complete details about the contents of the GEOS - Chem shared data directories.
2.4.1 Data archives
You may download the GEOS - Chem shared data directories from one of two archives:
   1. Harvard archive (ftp.as.harvard.edu)
   2. Dalhousie archive (rain.ucis.dal.ca)
The Dalhousie archive is not as comprehensive as the Harvard archive. However, the Dalhousie archive stores data files for the various nested grids and global 1° x 1.25° grids that are not available on the Harvard archive.
For those of you who are interested in using GEOS - Chem with the GCAP data, please contact Loretta Mickley for more information.
2.4.2 Downloading instructions
We recommend that you use the GNU wget utility to download the GEOS - Chem shared data directories. Wget allows you to download the directories and subdirectories in one fell swoop. The wget commands take the form of:
wget -r -nH "ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/DIRECTORY_NAME/"
where DIRECTORY_NAME is the name of the directory you want to download. Please see our wiki page on how to download data with wget for more information.
You can also download the shared data directories via anonymous FTP:
ftp ftp.as.harvard.edu
cd gcgrid/geos-chem/data/GEOS_0.5x0.666_CH
cd gcgrid/geos-chem/data/GEOS_0.5x0.666_NA
cd gcgrid/geos-chem/data/GEOS_1x1
cd gcgrid/geos-chem/data/GEOS_2x2.5
cd gcgrid/geos-chem/data/GEOS_4x5
cd gcgrid/geos-chem/GEOS_MEAN
cd gcgrid/geos-chem/GEOS_NATIVE
cd gcgrid/gcap/GCAP_4x5
However, for those of you who are located at Harvard, you do not need to download this data, as it is available on the Harvard internal filesystem, in directories:
/as/data/geos/GEOS_0.5x0.666_CH
/as/data/geos/GEOS_0.5x0.666_CH
/as/data/geos/GEOS_1x1
/as/data/geos/GEOS_2x2.5
/as/data/geos/GEOS_4x5
/as/data/geos/GEOS_MEAN
/as/data/geos/GEOS_NATIVE
/as/data/gcap/GCAP_4x5
If you wish to download data from the Dalhousie data archive, use this command:
wget -r -nH "ftp://rain.ucis.dal.ca/DIRECTORY_NAME/"
Please see the following links for more information:
   1. Chapter 4: GEOS - Chem data directories
   2. GEOS - Chem wiki: Downloading GEOS - Chem data directories
   3. GEOS - Chem wiki: Using wget to download data

2.5 Installing netCDF with the GEOS-Chem-Libraries package
GEOS-Chem v9-01-03 (and higher versions) require that you install netCDF on your computer system. In order to facilitate building the netCDF library, the GEOS-Chem Support Team has constructed the GEOS-Chem-Libraries installer package. With GEOS-Chem-Libraries, you can build one of the following sets of libraries:
                               Either netCDF 4.2
                               or netCDF classic
netcdf-4.2
netCDF "CLASSIC". This lacks the advanced features of netCDF - 4.2, and is more or less identical to netCDF - 3.6.
zlib-1.2.6 (netcdf-4.2 depends on this)

hdf5-1.8.8 (netcdf-4.2 depends on this)

We recommend that you try to build the netCDF-4.2 library first, since this is the most recent netCDF version. The netCDF-4.2 library is 100% backwards compatible with older netCDF-3 files. Also, many data files (e.g. GEOS-5.7.2 "raw" data) are now starting to be distributed in the newer netCDF-4 format. If you have problems building netCDF-4.2 then you can try to build the netCDF classic library, which has a simpler installation process.
Please note the following:
   1. If you are one of several GEOS-Chem users at your institution, and if you run GEOS-Chem on a common machine or cluster, then only one person (typically your IT guru) would have to install these libraries for GEOS-Chem.
   2. Any recent version of netCDF (version 3.0 or higher) may be used with GEOS-Chem. However, we recommend all GEOS-Chem users to build either netCDF-4.2 or netCDF CLASSIC with the GEOS-Chem-Libraries installer so that GEOS-Chem will be able to automatically determine the proper library linking commands.
2.5.1 Downloading the GEOS-Chem-Libraries installer package
You can use the Git source-code management software to download the GEOS-Chem-Libraries installer package onto your system. Type:
git clone git://git.as.harvard.edu/bmy/GEOS-Chem-Libraries
and then change into the GEOS-Chem-Libraries directory:
cd GEOS-Chem-Libraries
In this directory you will find the following files and subdirectories:
                               File or Directory
                                  Description
README
File describing the contents of GEOS-Chem-Libraries and how to build the netCDF libraries
GNUmakefile
Main-level makefile. This calls down to the master GNUmakefile in the src/ sub-directory.
opt/
Default directory where libraries will be installed (if you do not choose an alternate directory)
src/
Directory containing netCDF and related library distributions.
2.5.2 Installing netCDF - 4.2
Follow these instructions to install the netCDF - 4.2 library and the libraries on which it depends.
<IP_ADDRESS> Building the netCDF - 4.2 library
To build the netCDF-4.2 library (and the dependent ZLIB and HDF5 libraries) using the Intel Fortran Compiler (ifort), type one of the following commands:
make PREFIX=root_library_dir                         # If you have the Intel C compilers

make PREFIX=root_library_dir GCC=yes                 # If you don't have the Intel C compilers
To build the libraries for the PGI compiler, type one of the following commands:
make COMPILER=pgi PREFIX=root_library_dir            # If you have the PGI C compilers

make COMPILER=pgi PREFIX=root_library_dir GCC=yes    # If you don't have the PGI C compilers
Makefile options:
                                    Option
                                  Description
COMPILER
This option is used to pick the compiler that you wish to use to build netCDF-4.2 and the related libraries. At present, you may select either ifort or pgi. If you omit the COMPILER option, the default value of ifort will be selected.
PREFIX
This option is used to set root_library_dir, which is the full path name of the directory into which the netCDF-4.2 and related libraries will be installed. If you omit the PREFIX option, then root_library_dir will be automatically set to one of these default values:
GEOS-Chem-Libraries/opt/ifort/nc4/  # If COMPILER=ifort
GEOS-Chem-Libraries/opt/pgi/nc4/    # If COMPILER=pgi
If you do not have sysadmin privileges, then you can use the PREFIX option to set root_library_dir to a directory in your home space, such as /home/YOUR_USER_ID/lib (or you may install them in one of the default paths listed above). You can then ask your sysadmin to move the libraries to a common space on your machine (or cluster) where all users may access them.
GCC
If you do not have the Intel C/C++ compilers (icc, icpc) or PGI C/C++ compilers (pgcc, pgcpp) installed on your system, then you can tell the GEOS-Chem-Libraries installer to use the GNU C/C++ compilers (gcc, g++) instead. Otherwise, you can omit this option.
The libraries take approximately 20 minutes (or longer) to build. If the library installation process is successful, you will see this confirmation screen:
-------+---------+-------------------------------------
Config | Install |             Package
-------+---------+-------------------------------------
  ok   |   ok    | zlib-1.2.6
  ok   |   ok    | hdf5-1.8.8
  ok   |   ok    | netcdf-4.2
  ok   |   ok    | netcdf-fortran-4.2
-------+---------+-------------------------------------
This tells you that the netCDF-4.2 and its related libraries were installed properly.
<IP_ADDRESS> netCDF-4.2 library paths
The netCDF-4.2 (and related libraries) will be installed into the following paths. As described above, you may use the PREFIX=root_library_dir option to set the value of root_library_dir.
root_library_dir/bin           # nc-config, nf-config, ncdump, ncgen, etc.
root_library_dir/include       # Include files (*.h)
root_library_dir/lib           # Library file (libz.a)
root_library_dir/share         # Manual pages & documentation
Now that you have installed netCDF - 4.2, you may skip ahead to Chapter 2.5.4: Telling GEOS - Chem where to find the netCDF libraries.
2.5.3 Installing netCDF CLASSIC
If you have problems installing the netCDF - 4.2 libraries on your system, try installing netCDF classic instead. Follow these instructions:
<IP_ADDRESS> Building netCDF CLASSIC
To build the netCDF CLASSIC libraries (which lacks the advanced features of netCDF-4.2) using the Intel Fortran Compiler (ifort), type one of the following commands:
make CLASSIC=yes PREFIX=root_library_dir                        # If you have the Intel C compilers

make CLASSIC=yes PREFIX=root_library_dir GCC=yes                # If you don't have the Intel C compilers
To build the netCDF "CLASSIC" libraries for the PGI compiler, type:
make CLASSIC=yes COMPILER=pgi PREFIX=root_library_dir           # If you have the PGI C compilers:

make CLASSIC=yes COMPILER=pgi PREFIX=root_library_dir GCC=yes   # If you don't have the PGI C compilers
Makefile options:
                                    Option
                                  Description
COMPILER
This option is used to pick the compiler that you wish to use to build netCDF CLASSIC. At present, you may select either ifort or pgi. If you omit the COMPILER option, the default value of ifort will be selected.
PREFIX
This option is used to set root_library_dir, which is the full path name of the directory into which netCDF CLASSIC will be installed. If you omit the PREFIX option, then root_library_dir will be automatically set to one of these default values:
GEOS-Chem-Libraries/opt/ifort/nc_classic/  # If COMPILER=ifort
GEOS-Chem-Libraries/opt/pgi/nc_classic/    # If COMPILER=pgi
If you do not have sysadmin privileges, then you can use the PREFIX option to set root_library_dir to a directory in your home space, such as /home/YOUR_USER_ID/lib (or you may install them in one of the default paths listed above). You can then ask your sysadmin to move the libraries to a common space on your machine (or cluster) where all users may access them.
GCC
If you do not have the Intel C/C++ compilers (icc, icpc) or PGI C/C++ compilers (pgcc, pgcpp) installed on your system, then you can tell the GEOS-Chem-Libraries installer to use the GNU C/C++ compilers (gcc, g++) instead. Otherwise, you can omit this option.
The netCDF CLASSIC library takes several minutes to build. If the library installation process is successful, you will see this confirmation screen:
-------+---------+-------------------------------------
Config | Install |             Package
-------+---------+-------------------------------------
  --   |   --    | zlib-1.2.6
  --   |   --    | hdf5-1.8.8
  ok   |   ok    | netcdf-4.2 (netCDF classic)
  ok   |   ok    | netcdf-fortran-4.2 (netCDF classic)
-------+---------+-------------------------------------
This tells you that the netCDF CLASSIC library was installed properly. The ZLIB and HDF5 libraries are not needed for netCDF CLASSIC, and are therefore not built.
<IP_ADDRESS> netCDF CLASSIC library paths
The netCDF CLASSIC libraries will be installed into the following paths. As described above, you may use the PREFIX option to set the value of root_library_dir.
root_library_dir/bin        # nc-config, nf-config, ncdump, ncgen programs
root_library_dir/include    # Include files (*.h)
root_library_dir/lib        # Library files (*.a)
root_library_dir/share      # Manual pages & documentation
2.5.4 Telling GEOS-Chem where to find the netCDF libraries
Now that you have successfully built the netCDF (and related) libraries with the GEOS-Chem-Libraries installer, you must tell GEOS-Chem where to find the relevant library, include, and executable files. The easiest way to do this is to set environment variables in your setup files:
                                  Setup file
                                  Unix shell
.cshrc
If you use C-shell (csh) or T-shell (tcsh)
.profile
If you use Bourne shell (sh), or if you use a Macintosh
.bashrc
If you use Bourne-again shell (bash)
There are three environment variables that you need to set:
                                   Variable
                                  Description
GC_BIN
Specifies the location of the executable files (e.g. nc-config, nf-config, ncdump, etc.)
GC_INCLUDE
Specifies the location of include files (*.h, *.inc) and module files (*.mod) for the netCDF (and HDF5) libraries
GC_LIB
Specifies the location of library files (*.a)
<IP_ADDRESS> With csh or tcsh
If you use C-shell (csh) or T-shell (tcsh), then add the following lines to your .cshrc file:
setenv ROOT_LIBRARY_DIR root_library_dir
setenv GC_BIN           $(ROOT_LIBRARY_DIR)/bin
setenv GC_INCLUDE       $(ROOT_LIBRARY_DIR)/include
setenv GC_LIB           $(ROOT_LIBRARY_DIR)/lib
where root_library_dir is the directory into which you installed the libraries, as described above. Then to accept the changes, type source ~/.cshrc at the Unix prompt.
<IP_ADDRESS> With sh or bash
If you use Bourne-shell (sh), then add the following lines to your .profile file. If you use Bourne-Again shell (bash), then add these same lines to your .bashrc file.
ROOT_LIBRARY_DIR=root_library_dir
GC_BIN=$ROOT_LIBRARY_DIR/bin
GC_INCLUDE=$ROOT_LIBRARY_DIR/include
GC_LIB=$ROOT_LIBRARY_DIR/lib
export GC_BIN
export GC_INCLUDE
export GC_LIB
where root_library_dir is the directory into which you installed the libraries, as described above. Then to accept the changes, type source ~/.profile or source ~/.bashrc at the Unix prompt.
2.5.5 For more information
Please see our Installing libraries for GEOS - Chem page on the GEOS - Chem wiki for more detailed information about the GEOS-Chem-Libraries installer program. On this page we give an overview of the individual library files that are generated and the commands used to link to them. You will find this useful if you need to write other Fortran data processing software requiring netCDF file I/O.

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Chapter 3
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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3. Compilation

3.1 Overview
Once you have downloaded the GEOS - Chem source code directory, you can compile GEOS - Chem. During this process, your Fortran-90 compiler will create a binary executable file from the instructions contained in the various source code modules and files. You can then place the executable file into a GEOS - Chem run directory and start a simulation.
The compilation process involves the following steps:
   1. Selecting the proper C - preprocessor switches in the define.h file (see Chapter 3.4)
   2. Invoking the GNU Make utility with the proper options (see Chapter 3.5)
GNU Make manages the entire compilation process. A series of scripts called makefiles (see Chapter 3.3) directs GNU Make to compile the GEOS - Chem source code files in the proper order and with the proper options. These makefiles are placed throughout the GEOS - Chem source code directory.
For more information about the GEOS - Chem source code and makefiles, please see:
   * Chapter 7: Coding: Practice and Style.
   * GEOS - Chem wiki: GEOS - Chem Makefile Structure
NOTE: In general, executables cannot be easily swapped between computers (unless they are identical systems). If you want to move GEOS - Chem to a different computer, you will more than likely have to recompile it on that system.

3.2 Source code directory structure
We (the GEOS - Chem Support Team) have subdivided the GEOS - Chem source code directory into several subdirectories. This was done for the following reasons:
   1. To facilitate the installation of 3rd-party software packages such as:
         o KPP chemical solver
         o Aerosol microphysics codes (e.g. TOMAS, APM)
         o ISORROPIA II
         o Terrestrial models (e.g. CASA, Global Terrestrial Mercury Model), etc.
      into GEOS - Chem. Our guiding principle is that all 3rd-party software packages should be cleanly separatable from the mainline GEOS - Chem code. This will allow the 3rd-party software packages to be updated without having an impact on the rest of the GEOS - Chem code.
   2. To simplify the maintenace of the GEOS - Chem code files. Without subdirectories, there would have been hundreds of source code files in a single directory, and it woud have been very difficult to keep track of them all.
The current directory structure is:
                                   Directory
                                  Description
Code.v9-01-03
Main level GEOS - Chem directory .
Code.v9-01-03/GeosApm
Directory containing parallel copies of GEOS - Chem source code files (*.F) that were modified for the APM aerosol microphysics package.
Code.v9-01-03/GeosCore
Directory containing regular *.F and *.F90 source code files.
Code.v9-01-03/GeosTomas
Directory containing parallel copies of GEOS - Chem source code files (*.F, *.F90) that were modified for the TOMAS aerosol microphysics package.
Code.v9-01-03/GeosUtil
Directory containing various utility modules for GEOS - Chem:
   * bpch2_mod.F
   * charpak_mod.F
   * directory_mod.F
   * error_mod.F
   * file_mod.F
   * global_grid_mod.F90
   * grid_mod.F90
   * hdf_mod.F
   * ifort_errmsg.F
   * julday_mod.F
   * linux_err.c
   * pressure_mod.F
   * regrid_a2a_mod.F90
   * time_mod.F
   * transfer_mod.F
   * unix_cmds_mod.F
This will build these modules into a separate library, which will allow these modules to be called from code in other subdirectories.
Code.v9-01-03/GTMM
Directory containing GEOS - Chem source code files (*.F90) for the Global Terrestrial Mercury Model (GTMM) simulation.
Code.v9-01-03/ESMF
Directory containing files for the interface connecting GEOS - Chem to the NASA GEOS - 5 GCM. You can ignore these files.
Code.v9-01-03/Headers
Directory containing the define.h include file and the various GEOS - Chem Header modules, which contain many parameters and global arrays for GEOS - Chem routines.
Code.v9-01-03/ISOROPIA
Directory containing the unmodified ISORROPIA II source code files from Thanos Nenes and Havala Pye:
   * isorropiaIIcode.F
   * isrpia.inc
Code.v9-01-03/KPP
Main-level directory for the KPP solver
Code.v9-01-03/KPP/int
Directory containing KPP integrator files (i.e. rosenbrock, radau, runge-kutta, lsodes)
Code.v9-01-03/KPP/SOA
Directory containing KPP source code files for 59 tracer simulation (with secondary organic aerosols)
Code.v9-01-03/KPP/isoprene
Directory containing KPP source code files for the Caltech isoprene scheme.
NOTE: THIS NEEDS TESTING!
Code.v9-01-03/KPP/standard
Directory containing KPP source code files for 53 tracer simulation (with bromine, and without secondary organic aerosols)
Code.v9-01-03/NcdfUtil
Directory containing netCDF I/O code. This code is from Bob Yantosca's NcdfUtilities package.
Code.v9-01-03/NcdfUtil/perl
Directory containing perl scripts from the NcdfUtilities package that can be used to generate Fortran code for defining, writing, and reading a netCDF file.
Code.v9-01-03/bin
Directory where executable (geos, geostomas, geosapm) files will be sent
Code.v9-01-03/doc
Directory where automatic documentation is built
Code.v9-01-03/help
Directory containing GEOS - Chem help screen
Code.v9-01-03/lib
Directory where library (*.a) files will be created
Code.v9-01-03/mod
Directory where module (*.mod) files will be sent
Code.v9-01-03/obsolete
Directory where obsolete source code files are placed for future reference if need be
In the text below, we shall often omit the top-level Code.v9-01-03 directory and refer to files by their subdirectory only, such as:
   * Headers/define.h,
   * GeosCore/dao_mod.F
   * ISOROPIA/isoropiaII_code.F, etc.

3.3 GEOS - Chem Makefiles
The GEOS - Chem compilation process is managed by makefiles located throughout the source code directory. Makefiles direct the GNU Make utility to execute the various compilation commands in the proper sequence.
In general there are 2 types of makefiles:
   * "Router" makefiles: Makefiles that tell GNU Make to look at makefiles in other directories.
   * "Regular" makefiles: Makefiles that are used by GNU Make to compile source code programs..
The top-level source code directory (Code.v9-01-03) contains a "router" makefile, which calls down to the "regular" makefiles in the various subdirectories. In each subdirectory, the "regular" makefile tells GNU Make how to compile the source code files. When the source code in all subdirectories has been compiled, the top-level Makefile tells GNU Make to create the GEOS - Chem executable file.
Here is a list of makefiles used by GEOS - Chem:
                                   Directory
                                  Description
Code.v9-01-03/Makefile
Main-level router makefile; calls down to makefiles in other subdirectories.
Code.v9-01-03/Makefile_header.mk
Makefile fragment that defines compilation and linking commands for the IFORT, PGI, Sun/Studio, and XLF compilers. These commands are common to the makefiles in all subdirectories.
Code.v9-01-03/GeosApm/Makefile
Makefile to build the GEOS - Chem code with APM aerosol microphysics routines.
Code.v9-01-03/GeosCore/Makefile
Makefile to build the GEOS - Chem code. Also calls up to makefiles in the other subdirctories to build 3rd-party codes (e.g. KPP).
Code.v9-01-03/GeosTomas/Makefile
Makefile to build the GEOS - Chem code with TOMAS aerosol microphysics routines.
Code.v9-01-03/GeosUtil/Makefile
Makefile to build the GEOS - Chem utility modules.
Code.v9-01-03/Headers/Makefile
Makefile to build the GEOS - Chem Headers modules.
Code.v9-01-03/GTMM/Makefile
Makefile to build the GEOS - Chem code with GTMM routines.
Code.v9-01-03/ISOROPIA/Makefile
Makefile to build the GEOS - Chem code with ISORROPIA II code.
Code.v9-01-03/KPP/Makefile
Router makefile for KPP. Calls down to makefiles in subdirectories to build the KPP solver code.
Code.v9-01-03/KPP/isoprene/Makefile
Makefile that builds the KPP solver for GEOS - Chem simulations with the Caltech isoprene scheme.
Code.v9-01-03/KPP/SOA/Makefile
Makefile that builds the KPP solver for the GEOS - Chem 59 tracer simulation.
Code.v9-01-03/KPP/standard/Makefile
Makefile that builds the KPP solver for the GEOS - Chem 43 tracer simulation.
Code.v9-01-03/NcdfUtil/Makefile
Makefile to build the NcdfUtilities library routines.
Code.v9-01-03/doc/Makefile
Makefile that builds GEOS - Chem documentation files with LaTeX. Documentation files will be produced in both *.pdf and *.ps formats.
Code.v9-01-03/help/Makefile
Makefile that displays the GEOS - Chem help screen.
You will usually not have to modify any of these makefiles, unless you are adding new code into GEOS - Chem. If you need to modify makefiles, then we will be happy to assist you.
Each makefile controls several compilation options. We shall present a detailed discussion of these options in Chapter 3.5.

3.4 Setting the C - preprocessor switches
Before compiling GEOS - Chem, you must set the proper C - preprocessor switches to inform the Fortran-90 compiler which scientific options you would like compiled into the GEOS - Chem executable.
3.4.1 What is the C - preprocessor?
The C - preprocesor (or CPP for short) is a feature of the C and C++ programming languages that allows you to compile blocks of code only if certain conditions are met. For example, let's say you have two blocks of code, Block A and Block B. If you set a certain switch in the code, then Block A will get compiled into the executable but Block B will not. When you run the executable, it will behave as if Block B had never existed. If you set a different switch, then Block B will be compiled but Block A will not, and the executable will behave as if Block A had never existed.
All modern Fortran compilers have inherited the C - preprocessor feature. Some Fortran compilers even call it the "Fortran preprocessor" (FPP). Therefore, even though GEOS - Chem is written in Fortran-90, we can still incorporate C - preprocesor commands into the source code.
With the C - preprocessor, you can design software to handle many different conditions, such as multiple compiler/platform combinations, different file formats, and the like. At compilation time, you can direct the C - preprocessor to only choose the options relevant to the particular computer system you are running on. Options that are not relevant to your system will be ignored. This is a standard programming technique.
The C - preprocessor statments take the form of #define and #if - #endif statements. A simple example from GEOS - Chem is:
#if   defined( GEOS_4 )
      WRITE( 6, '(a)' ) 'Using GMAO GEOS-4 met fields'
#elif defined( GEOS_5 )
      WRITE( 6, '(a)' ) 'Using GMAO GEOS-5 met fields'
#elif defined( GEOS_57 )
      WRITE( 6, '(a)' ) 'Using GMAO GEOS-5.7.x met fields'
#elif defined( MERRA )
      WRITE( 6, '(a)' ) 'Using GMAO MERRA met fields'
#elif defined( GCAP  )
      WRITE( 6, '(a)' ) 'Using GCAP/GISS met fields'
#endif
Here the #elif tag stands for "else if". An #else tag is also allowed.
If we have #defined the GEOS_5 C - preprocessor switch (see Chapter 3.4.2), then GEOS - Chem will be compiled for use with the GEOS - 5 met fields. The block of code that prints out the message "Using GMAO GEOS-5 met fields" will be built into the exectuable, and all other print statements will be ignored.
C - preprocessor statements must be placed into the first column of a Fortran source code file, or else you may encounter a syntax error.
3.4.2 Selecting the proper C - preprocessor switches for your simulation
GEOS - Chem uses C - preprocessor switches to select various options, including:
   1. The meteorological fields that GEOS - Chem will use
   2. The horizontal and vertical grids for the GEOS - Chem simulation
   3. The type of compiler you will use to create the GEOS - Chem executable
   4. Options for special simulations (e.g. mercury)
These switches are located in header file Headers/define.h, and are as follows:
Met Fields

GCAP
Use GISS met fields for GCAP simulation (23 layer, 4° x 5°)
GEOS_4
Use GEOS - 4 met fields (55 layer, hybrid, 1985 - 2006)
GEOS_5
Use GEOS - 5 met fields (72 layer, hybrid, 2005 - present)
GEOS_57
Use GEOS - 5.7.2 met fields (72 layer, hybrid, 2011 - present )
MERRA
Use MERRA met fields (72 layer, hybrid, 1979-2010)
Grids

NESTED_CH
Use China/SE Asia nested grid (GEOS - 5 only)
NESTED_NA
Use N. American nested-grid (GEOS - 5 only)
NESTED_EU
Use European nested grid (GEOS - 5 only)
SEAC4RS
Use SEAC4RS nested grid (GEOS - 5.7.2 only).
Note: This grid was developed for the SEAC[4]RS campaign.
GRID025x03125
Use 0.25° x 0.3125 ° nested grid (SEAC4RS only)
GRID05x0666
Use 0.5 ° x 0.667 ° nested grids
GRID1x1
Use 1° x 1° grid
GRID1x125
Use 1° x 1.25° grid (GEOS - 4 only)
GRID2x25
Use 2° x 2.5° grid
GRID4x5
Use 4° x 5° grid
GRIDREDUCED
Reduce the number of vertical levels on the fly:
   * Use the 30-level GEOS - 4 grid
   * Use the 47-level GEOS - 5 grid
   * Use the 47-level GEOS - 5.7.2 grid
   * Use the 47-level MERRA grid
Compilers

LINUX_PGI
Compile for Linux with PGI compiler
LINUX_IFORT
Compile for Linux with Intel Fortran Compiler (IFORT 9.x or 10.x)
Other options

GTMM_Hg
Compile for a mercury simulation using the online Global Terrestrial Mercury Model (a.k.a. GTMM). GTMM is turned off by default in order to save compilation time. For more information about using GTMM in a GEOS - Chem mercury simulation, please see this PDF.

The C - preprocessor switches in Headers/define.h take the form of:
!#define GEOS_5 'GEOS_5'
etc. (The quotes are necessary to facilitate compilation on the Linux platforms). In order to activate a particular switch, simply remove the comment character (exclamation mark) from the first column of the line. To de-activate a switch, simply place a comment character (exclamation mark) in the first column of the line.
Please take note of the following:
   1. When you change any of the C - preprocessor switches, you should issue a make realclean command (see Chapter 3.5.1). This will remove all previously-created compiler output files (e.g. *.o, *.mod) and executables. After doing make realclean, you can compile GEOS - Chem with whichever options you choose.
   2. You may only select one particular met field type (GCAP, GEOS_4, GEOS_5, GEOS_57), one particular grid type (GRID025x03125, GRID05x0666, GRID1x125, GRID2x25, GRID4x5), and one particular compiler.
   3. If you have selected GRID05x0666, then you must also select NESTED_CH, NESTED_NA, or NESTED_EU. This will select the proper 0.5° x 0.666° nested grid region (China/SE Asia, North America, or Europe).
   4. If you have selected GRID025x03125, then you must also select SEAC4RS.

3.5 Compiling the GEOS - Chem source code
Once you have properly set the C - preprocessor switches in the Headers/define.h header file for the type of simulation that you want to perform, you can compile the GEOS - Chem code.
To compile the code, you need to be in the Code.v9-01-03 top-level directory. There are a large choice of compilation options available. The list of options can be printed to the screen by typing:
make help
3.5.1 Makefile options
Here is a description of all available make options for GEOS - Chem:
                                    Targets
Target name
Description
all
Default target (synonym for "lib exe")
lib
Builds all GEOS - Chem source code (synonym for "libkpp libutil libcore")
libcore
Only builds GEOS - Chem objects & libraries in GeosCore subdir
libiso
Only builds GEOS - Chem objects & libraries in ISOROPIA subdir
libkpp
Only builds GEOS - Chem objects & libraries in KPP subdir
libnc
Only builds GEOS - Chem objects & libraries in NcdfUtil subdir
ncdfcheck
Checks that your netCDF library has been installed properly
libutil
Only builds GEOS - Chem objects & libraries in GeosUtil subdir
libheaders
Only builds GEOS - Chem objects & libraries in Headers subdir
exe
Build GEOS - Chem executable
clean
Removes *.o, *.mod, geos* files in source code subdirs only
realclean
Removes all *.o, *.mod, geos*, lib*.a, *.tex, *.ps, *.pdf files everywhere
doc
Builds GEOS - Chem documentation (*.ps, *.pdf) with ProTeX in doc subdir
docclean
Removes *.tex, *.ps, *.pdf from the doc subdir
help
Displays the help screen
                Special targets for TOMAS aerosol microphysics
tomas
Build GEOS - Chem + TOMAS code (synonym for "libtomas exetomas")
libtomas
Only builds GEOS - Chem + TOMAS objects & libraries
exetomas
Only builds GEOS - Chem + TOMAS executable
cleantomas
Removes *.o *.mod files in GeosTomas directory only
                 Special targets for APM aerosol microphysics
apm
Build GEOS - Chem + APM code (synonym for "libapm exeapm")
libapm
Builds GEOS - Chem + APM objects & libraries in GeosApm directory
exeapm
Builds GEOS - Chem + APM executable in GeosApm directory
cleanapm
Removes *.o *.mod files in GeosApm directory only
                    Special targets for Mercury simulation
allhg
Build GEOS - Chem + GTMM code
                                Optional flags
                                   Flag name
                                  Description
COMPILER=___
Choice of the compiler. Options: ifort pgi sun xlf (default is ifort)
HDF5=yes
Enables writing diagnostic timeseries output to HDF5 files (default is no)
DEBUG=yes
Compiles GEOS - Chem for use w/ a debugger (default is no)
BOUNDS=yes
Turns on subscript-array checking (for debugging purposes) (default is no)
OMP=[yes|no]
Turns OpenMP parallelization on/off (default is yes)
IPO=yes
Turns on optmization options -ipo -static (default is no) (ifort only)
TRACEBACK=yes
Turns on -traceback option (default is no) (ifort only)
NONUMA=yes
Turns on -mp=nonuma option (pgi only)
CHEM=___
Specifies which simulation is done. Options: standard, SOA, isoprene (default is standard).
KPPSOLVER=___
Specifies the integrator used w/ KPP:
         Options: lsodes radau5 rosenbrock runge_kutta (default is rosenbrock)
                                  Make option
                                  Option name
Description
-jN
-j enables you to compile GEOSChem using N processors simultaneously. This will shorten the total compilation time. (RECOMMENDED!)
When starting with a new version of GEOS - Chem, you should always issue this command:
make realclean
This will clear out any precompiled files and executables (if any have been left in the source code directory inadvertently).
The default target is all. This option, which will cause GNU Make to compile the GEOS - Chem source code and create the executable file, will be selected if you type either
make
or
make all
3.5.2 Optional flags and defaults
To build GEOS - Chem, you need to specify one of the makefile targets listed above (see Chapter 3.5.1), plus optional flags.
Several of the optional flags have default settings:
   1. The default compiler is the Intel Fortran Compiler (ifort)
   2. The default NOx-Ox-HC-aerosol chemistry (aka "full-chemistry) simulation is "standard" (53 advected tracers, no secondary organic aerosols)
   3. The KPP chemical solver will will use the Rosenbrock integrator by default
   4. HDF5 diagnostic files (for ND50, ND51, ND51b timeseries) will be turned off by default. (NOTE: This feature may be superseded by GEOS - Chem's netCDF I/O capabilities.)
   5. OpenMP parallelization is turned on
Finally, any of the optional flags can be specified in one of two ways:
   1. As a command-line argument to the GNU Make utility:
For example, if we want to use the PGI compiler instead of the Intel Fortran Compiler, we could type:
            make COMPILER=pgi ...
   2. As an Unix environment variable:
If you want to use the PGI compiler, but do not wish to keep typing COMPILER=pgi every time you call GNU Make, you could type this instead:
   3.             setenv COMPILER pgi
            make ...
For clarity, we shall use command-line arguments in the examples below.
3.5.3 Examples
To build the GEOS - Chem executable with all defaults (Intel Fortran Compiler, 53-tracer full-chemistry mechanism, OpenMP parallelization turned on) one can simply type:
make -j4
Here we have used the -j4 option to split the compilation among 4 processors (assuming you have this many processors available to you). This reduces the total compilation time drastically!
If you wanted to select a different compiler (e.g. PGI), but keep all of the other defaults, type:
make -j4 COMPILER=pgi
Depending on your PGI compiler setup, you may also have to add the PGI option NONUMA=yes.
If you wish to turn off the parallelization (e.g. for debugging purposes), you can type:
make -j4 OMP=no
To invoke the Intel Fortran Compiler's -traceback debugging option (which prints the list of routines that were being called at the point when the run died), type:
make -j4 TRACEBACK=yes
If you want to test for array-out-of-bounds errors, then type:
make -j4 BOUNDS=yes
If you wish to use a debugger (like Totalview) to debug a multi-processor GEOS - Chem simulation, type:
make -j4 DEBUG=yes
If you wish to use a debugger (like Totalview) to debug a single-processor GEOS - Chem simulation, type:
make -j4 DEBUG=yes OMP=no
If you wish to compile the code and build the executable in two separate steps, you may type:
make lib
make exe
To automatically generate the GEOS - Chem Reference Guide documentation in PostScript and PDF formats, type:
make doc
To remove all compiler-produced files (i.e. *.o, *.mod) and executable files from the source code directories (but not from the mod, lib, bin directories), type:
make clean
And to remove everything and start over from scratch, type:
make realclean
Please note:
   1. On some systems, the GNU Make command will be called gmake instead of make.
   2. We recommend updating your compiler to Intel Fortran Compiler (IFORT) Version 11.1.058 or higher versions. Version 11 produces similar results to Version 10.
   3. We also recommend that PGI compiler users migrate to Intel Fortran Compiler (IFORT) Version 11.1.058 or higher.
   4. If you wish to compile GEOS - Chem with the TOMAS aerosol microphysics option, you must be in the GeosTomas directory before invoking the make command. For more information on how to compile GEOS - Chem with the TOMAS microphysics option, see the Building GEOS - Chem with TOMAS wiki page.
   5. For more information about debugging array-out-of-bounds errors, please see Chapter 7.2, GEOS - Chem debugging tips.

3.6 Advanced compilation techniques
Here we describe a couple of methods by which you may partially automate the compilation process.
3.6.1 Compiling GEOS - Chem with from Unix shell scripts
It is possible to write a shell script to compile the GEOS - Chem code, such as the following:
#!/bin/tcsh -f    # Script definition line
cd Code.v9-01-03  # your code dir
rm -f log         # clear log file
make -j4 > log    # build the code
exit(0)           # exit normally
You can then run this script interactively, or submit it to the queueing system on your computer cluster.
3.6.2 Compiling GEOS - Chem with a run-directory Makefile
The GNU Make utility is a powerful and flexible software development tool. With a little effort, you can design a Makefile that can be placed into your GEOS - Chem run directory that will create a GEOS - Chem executable and start a simulation. Here is an example:
# This makefile is a "router" makefile.  It calls the Makefile
# in the GEOS-Che code directory (with various user-supplied options)
# to build and run the GEOS-Chem model.

# Define variables
SHELL   = /bin/sh

# Make the development version "Code" the default directory
ifndef GEOSDIR
GEOSDIR = /home/bmy/Code.v9-01-03
endif

# Date string DDDHHMM a la "trun"
DATE = `date +%j%H%M`

#=============================================================================
# Makefile targets: type "make help" for a complete list!
#=============================================================================

.PHONY: all geos clean realclean doc docclean help logclean

geos:
	@$(MAKE) -C $(GEOSDIR)
	cp -f $(GEOSDIR)/bin/geos .
	rm -f log.$(DATE)
	./geos > log.$(DATE) &
	tail -f log.$(DATE)

clean:
	@$(MAKE) -C $(GEOSDIR) clean
	rm -f log*

realclean:
	@$(MAKE) -C $(GEOSDIR) realclean
	rm -f log*

doc:
	@$(MAKE) -C $(GEOSDIR) doc

docclean:
	@$(MAKE) -C $(GEOSDIR) docclean

help:
	@$(MAKE) -C $(GEOSDIR) help
At the heart of this Makefile are two important blocks of code, the first being:
# Make the development version "Code" the default directory
ifndef GEOSDIR
GEOSDIR = /home/bmy/Code.v9-01-03
endif

# Date string DDDHHMM a la "trun"
DATE = `date +%j%H%M`
This block defines the location of the GEOS - Chem source code directory, which is saved in a variable called GEOSDIR. If a value for GEOSDIR is not passed as a command-line argument, then GEOSDIR will be set to /home/bmy/Code.v9-01-03 (you can edit this location for your own setup). Also, a default date/time string is saved in the variable DATE. This date/time string will be appended to the GEOS - Chem log file output.
The second block of code is used to compile and run the GEOS - Chem code:
geos:
	@$(MAKE) -C $(GEOSDIR)
	cp -f $(GEOSDIR)/bin/geos .
	rm -f log.$(DATE)
	./geos > log.$(DATE) &
	tail -f log.$(DATE)
The lines:
	@$(MAKE) -C $(GEOSDIR)
	cp -f $(GEOSDIR)/bin/geos .
tell GNU Make to call down to the "router" makefile in the GEOS - Chem source code directory /home/bmy/Code.v9-01-03. GNU Make will compile GEOS - Chem and create the executable file /home/bmy/Code.v9-01-03/bin/geos. This file is then copied to the run directory.
The next 3 lines:
	rm -f log.$(DATE)
	./geos > log.$(DATE) &
	tail -f log.$(DATE)
removes the log file (if it already exists), runs the GEOS - Chem executable (thus starting the simulation), and follows the log file output wit the Unix tail -f command.
For more information, please see:
   * GNU Make manual
   * Chapter 6: Running GEOS - Chem

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4. GEOS - Chem Shared Data Directories

4.1 Overview
The GEOS - Chem shared data directories contain the various met fields, emissions, and other data that GEOS - Chem will read in during the course of a simulation. You must download the shared data directories via FTP or a similar utility (e.g. wget, FireFTP, SecureFX, etc.).
Please see the following sections for more information about the servers from where you may download the GEOS - Chem shared data directories:
   1. Chapter 2.4.1: Data Archives
   2. Chapter 2.4.2: Downloading instructions
Here follows a description of each of the subdirectories of the 1° x 1°, 2° x 2.5°, and 4° x 5° data directories, and the files contained within them.

4.2 The GEOS_1x1 directories
GEOS - Chem v9 - 01 - 03 can regrid emissions data stored at its native resolution (typically on the GMAO 1° x 1° horizontal grid or generic 1° x 1° grid) to coarser resolution. The subdirectories of GEOS_1x1 (listed below) contain emissions and other input data at this native resolution.
Assume that all files are in GEOS - Chem binary punch format unless otherwise specified. We have started the process of migrating from binary punch format to COARDS-compliant netCDF. At present, only a small fraction of data files have been migrated to netCDF.
Please note:
   * For GEOS - Chem nested grid simulations, these files have been specially regridded to the various 0.5° x 0.666° nested-grid regions (China/SE Asia, North America, Europe). For more information, please see the GEOS - Chem nested grid simulations wiki page.
   * The new GEOS_NATIVE mirrors the subdirectories contained in GEOS_1x1. Eventually, only the GEOS_NATIVE directory will be used as GEOS - Chem moves toward reading data on their native resolution -- which in many cases will be at finer resolution than 1° x 1°.

4.2.1 The anth_scale_factors_201111 subdirectory
NOTES:
   1. This is an update of the anth_scale_factors_200911 subdirectory.
   2. The anth_scale_factors_200811 subdirectory is now obsolete.
   3. This is an update of the now obsolete anth_scale_factors_200905 subdirectory. Scale factors are updated to include 2006. It follows same sources as previous updates. Each species was combined into a single file for ease of creation/use.
REFERENCES:
   1. GEOS-Chem wiki: Scale factors for anthropogenic emissions
   2. Van Donkelaar, A., R. V. Martin, W. R. Leaitch, A. M. Macdonald, T. W. Walker, D. G. Streets, Q. Zhang, E. J. Dunlea, J. L. Jimenez, J. E. Dibb, L. G. Huey, R. Weber, and M. O. Andreae, Analysis of aircraft and satellite measurements from the Intercontinental Chemical Transport Experiment (INTEX-B) to quantify long-range transport of East Asian sulfur to Canada, , Atmos. Chem. Phys, 8, 2999-3014, 2008.
Files
Description
CO-AnnualScalar.201105-Fix.geos.1x1
Scale factor files for CO for years 1985 to 2006 on the GMAO 1° x 1° grid.
For years before 1985, these will scale emissions to 1985.
For years  after   2006, these will scale emissions from 2006 to later years.
This file corrects a bug in the scale factors over S. Africa and should be used with GEOS - Chem v9 - 01 - 02 and higher.
CO-AnnualScalar.geos.1x1
Scale factor files for CO for years 1985 to 2006 on the GMAO 1° x 1° grid.
NOTE: This file contains a bug in the scale factors over S. America and is only preserved for backwards compatibility with older model versions.
NOx-AnnualScalar.geos.1x1
Scale factor files for NOx for years 1985 to 2010 on the GMAO 1° x 1° grid. Scale factors for years 2000 - 2010 were updated for the anthropogenic scaling factors from OMI (compiled by Lok Lamsal).
For years before 1985, these will scale emissions to 1985.
For years  after   2010, these will scale emissions from 2010 to later years.
SOx-AnnualScalar.geos.1x1
Scale factor files for SOx for years 1985 to 2006 on the GMAO 1° x 1° grid.
For years before 1985, these will scale emissions to 1985.
For years  after   2006, these will scale emissions from 2006 to later years.
4.2.2 The APM_201011 subdirectory
NOTES:
   1. This dataset is only used if the GEOS-Chem code is compiled for APM
REFERENCES:
   1. GEOS-Chem wiki: APM aerosol microphysics
   2. Yu, F., and G. Luo, Simulation of particle size distribution with a global aerosol model: Contribution of nucleation to aerosol and CCN number concentrations, Atmos. Chem. Phys., 9, 7691-7710, 2009.
   3. Yu, F., G. Luo, T. Bates, B. Anderson, A. Clarke, V. Kapustin, R. Yantosca, Y. Wang, S. Wu, Spatial distributions of particle number concentrations in the global troposphere: Simulations, observations, and implications for nucleation mechanisms, J. Geophys. Res., 115, D17205, doi:10.1029/2009JD013473, 2010.
   4. Yu, F., Ion-mediated nucleation in the atmosphere: Key controlling parameters, implications, and look-up table, J. Geophy. Res., 115, D03206, doi:10.1029/2009JD012630, 2010.
Files
Description
DACTS.txt
Text file containing the CCN activation dry diameter (m) lookup table.
Values are baded on k-Kohler Theory (Petters Kreidenweis, 2009) and generated by Fangqun Yu (SUNY Albany), 2010.
FERR.dat
Text file containing error function values.
IMN_LT/Yu_IMN_1H2S04.txt
IMN_LT/Yu_IMN_2RH.txt
IMN_LT/Yu_IMN_3T.txt
IMN_LT/Yu_IMN_4Q.txt
IMN_LT/Yu_IMN_5S.txt
IMN_LT/Yu_IMN_J5D.txt
IMN_LT/Yu_IMN_Rstar3D.txt
Text files containing ion-mediated nucleation rate (cm[-3]s[-1]) lookup tables.
YCK_LT/Yu_CK_1R1.txt
YCK_LT/Yu_CK_2D1.txt
YCK_LT/Yu_CK_3R2.txt
YCK_LT/Yu_CK_4D2.txt
YCK_LT/Yu_CK_5T.txt
YCK_LT/Yu_CK_6P.txt
YCK_LT/Yu_CK_7CK.txt
Text files containing coagulation kernel (cm[3]s[-1]) lookup tables.
YIONRATE.txt
Text file containing the ionization rate (ion-pairs cm[-3]s[-1]) lookup table by magnetic latitude.
4.2.3 The ARCTAS_SHIP_2008 subdirectory
NOTES:
   1. This dataset is only implemented in ARCTAS-NRT version of GEOS-Chem
REFERENCES:
   1. GEOS-Chem wiki: ARCTAS ship emissions
   2. Zhang, Q., D. G. Streets, G. Carmichael, K. He, H. Huo, A. Kannari, Z. Klimont, I. Park, S. Reddy, D. Chen, L. Duan, Y. Lei, L. Wang and Z. Yao, Asian emissions in 2006 for the NASA INTEX-B mission, Atmos. Chem. Phys., 9, 5131-5135, 2009.
   3. Chin, Streets, et al., NASA/GSFC, based on EDGAR 2000
   4. EDGAR 3.2 FT2000 global inventory
Files
Description
Arctas_CO2_ship_2008.generic.1x1
Ship emissions of CO2 [kg/yr] on the generic 1° x 1° grid.
Arctas_CO_ship_2008.generic.1x1
Ship emissions of CO [kg/yr] on the generic 1° x 1° grid.
Arctas_SO2_ship_2008.generic.1x1
Ship emissions of SO2 [kg/yr] on the generic 1° x 1° grid.
4.2.4 The BRAVO_200607 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: BRAVO regional inventory
   2. Kuhns, H., M. Green, and V. Etyemezian, Big Bend Regional Aerosol and Visibility Observational (BRAVO) Study Emissions Inventory, 2003. [PDF]
Files
Description
BRAVO.CO.generic.1x1
File containing BRAVO Mexican emissions of CO [molec/cm2/s] on the generic 1° x 1° grid.
BRAVO.NOx.generic.1x1
File containing BRAVO Mexican emissions of NOx [molec/cm2/s] on the generic 1° x 1° grid.
BRAVO.SO2.generic.1x1
File containing BRAVO Mexican emissions of SO2 [molec/cm2/s] on the generic 1° x 1° grid.
BRAVO.MexicoMask.generic.1x1
File containing the mask for the BRAVO Mexican emissions on the generic 1° x 1° grid. Grid boxes where BRAVO emissions exist have a value of 1; other boxes have a value of 0.
4.2.5 The bromine_201205 subdirectory
NOTES:
   1. In the updated linearized stratospheric chemistry scheme introduced in GEOS - Chem v9 - 01 - 03, the bromine species are hardwired to be ignored for now. Stratospheric Bry concentrations from Liang et al. (2010) are read in strat_chem_mod.F90, following the original implementation by Justin Parrella.
   2. Emissions of CHBr3 and CH2Br2 are read in bromocarb_mod.F from 2° x 2.5° data files and regridded to the model resolution.
REFERENCES:
   1. GEOS-Chem wiki: Bromine chemistry mechanism
   2. Liang, Q., Stolarski, R. S., Kawa, S. R., Nielsen, J. E., Douglass, A. R., Rodriguez, J. M., Blake, D. R., Atlas, E. L., and Ott, L. E., Finding the missing stratospheric Bry: a global modeling study of CHBr3 and CH2Br2, Atmos. Chem. Phys., 10, 2269-2286, 2010.
   3. Parrella, J.P., D.J. Jacob, Q. Liang, Y. Zhang, L.J. Mickley, B. Miller, M.J. Evans, X. Yang, J.A. Pyle, N. Theys, and M. Van Roozendael, Tropospheric bromine chemistry: implications for present and pre-industrial ozone and mercury, submitted to Atmos. Chem. Phys., 2012. [pdf]
Files in CCM_stratosphere_Bry/
Description
Bry_Stratosphere_day.bpch.geos4.2x25
Bry_Stratosphere_night.bpch.geos4.2x25
Monthly mean daytime and nighttime stratospheric Bry concentrations on the GEOS - 4 vertical grid (55 layers), for the 2° x 2.5° horizontal grid.
Bry_Stratosphere_day.bpch.geos5.2x25
Bry_Stratosphere_night.bpch.geos5.2x25
Monthly mean daytime and nighttime stratospheric Bry concentrations on the GEOS - 5 vertical grid (72 layers), for the 2° x 2.5° horizontal grid.
Bry_Stratosphere_day.bpch.merra.2x25
Bry_Stratosphere_night.bpch.merra.2x25
Symbolic links to the *.geos5.2x25 files described above.
Files in VSL_emissions/
Description
SLBromine_Emission.2x25.nc
NetCDF file containing emissions of short-lived bromine tracers CHBr3 (440 Gg/yr) and CH2Br2 (62 Gg yr) on the 2° x 2.5° horizontal grid. Emissions data were supplied by Qing Liang.
4.2.6 The CAC_200801 subdirectory
REFERENCE:
   1. GEOS-Chem wiki: CAC regional inventory
   2. Data: http://www.ec.gc.ca/pdb/cac/cac_home_e.cfm
Files
Description
CAC2002-CO.geos.1x1
CAC2005-CO.geos.1x1
Anthro CO  emissions [kg/yr], base year 2002 and 2005 on the GMAO 1° x 1° grid.
CAC2002-NH3.geos.1x1
CAC2005-NH3.geos.1x1
Anthro NH3  emissions [kg/yr], base year 2002 and 2005 on the GMAO 1° x 1° grid.
CAC2002-NOx.geos.1x1
CAC2005-NOx.geos.1x1
Anthro NOx  emissions [kg/yr], base year 2002 and 2005 on the GMAO 1° x 1° grid.
CAC2002-SOx.geos.1x1
CAC2005-SOx.geos.1x1
Anthro SOx  emissions [kg/yr], base year 2002 and 2005 on the GMAO 1° x 1° grid.
CanadaMask.geos.1x1
Mask to define Canadian region for the CAC emissions on the GMAO 1° x 1° grid. Grid boxes where CAC emissions exist have a value of 1; other boxes have a value of 0.
CAC2007-CO.geos.1x1
CAC2007-NH3.geos.1x1
CAC2007-NOx.geos.1x1
CAC2007-SOx.geos.1x1
CAC2008-CO.geos.1x1
CAC2008-NH3-01.geos.1x1
CAC2008-NH3-02.geos.1x1
CAC2008-NH3-03.geos.1x1
CAC2008-NH3-04.geos.1x1
CAC2008-NH3-05.geos.1x1
CAC2008-NH3-06.geos.1x1
CAC2008-NH3-07.geos.1x1
CAC2008-NH3-08.geos.1x1
CAC2008-NH3-09.geos.1x1
CAC2008-NH3-10.geos.1x1
CAC2008-NH3-11.geos.1x1
CAC2008-NH3-12.geos.1x1
CAC2008-NH3.geos.1x1
CAC2008-NOx.geos.1x1
CAC2008-SOx.geos.1x1
GEOS - Chem does not yet use these files. We have added these here in anticipation of an update that will be applied post-v9 - 01 - 03.
4.2.7 The CO2_201003 subdirectory
NOTES:
   1. These data files are also available on the GMAO 2° x 2.5° and 4° x 5° grids. They are stored in the GEOS_2x2.5/CO2_201003 and GEOS_4x5/CO2_201003 directories, respectively.
   2. At present, the GEOS-Chem CO2 simulation reads data from directly from the GEOS_2x2.5/CO2_201003 and GEOS_4x5/CO2_201003 directories. The data stored in GEOS_1x1/CO2_201003 is mainly kept for future reference.
REFERENCES:
   1. GEOS-Chem wiki: CO2 simulation
   2. Andres, R.J, G. Marland, I. Fung, and E. Matthews, A 1°x1° distribution of carbon dioxide emissions from fossil fuel consumption and cement manufacture, Glob. Biogeochem. Cycles, 10, 419-429, 1996.
   3. Andres, R. J., Gregg, J. S., Losey, L., Marland, G., and Boden, T. A.: Monthly, global emissions 10 of carbon dioxide from fossil fuel consumption, Tellus B, accepted, 2011.
   4. Baker, D. F., et al., TransCom 3 inversion intercomparison: Impact of transport model errors on the interannual variability of regional CO2 fluxes, 1988-2003, Global Biogeochem. Cycles, 20, GB1002, doi:10.1029/2004GB002439, 2006.
   5. Corbett & Koehler, Updated emissions from ocean shipping, J. Geophys. Res., 108, D20, 4650, 2003.
   6. Corbett, J. J., and H. W. Koehler, Considering alternative input parameters in an activity-based ship fuel consumption and emissions model: Reply to comment by Øyvind Endresen et al. on Updated emissions from ocean shipping, J. Geophys. Res., 109, 2004.
   7. Endresen, O, et al., A historical reconstruction of ships fuel consumption and emissions, J. Geophys. Res, 112, D12301, 2007.
   8. Nassar, R., Jones, D. B. A., Suntharalingam, P., Chen, J. M., Andres, R. J., Wecht, K. J., Yantosca, R. M., Kulawik, S. S., Bowman, K. W., Worden, J. R., Machida, T., and Matsueda, H.: Modeling global atmospheric CO2 with improved emission inventories and CO2 production from the oxidation of other carbon species, Geosci. Model Dev., 3, 689-716, doi:10.5194/gmd-3-689-2010, 2010.
   9. Takahashi, T, et al. (2009), Climatological mean and decadal change in surface ocean pCO2, and net sea-air CO2 flux over the global oceans, Deep-Sea Research II, 2009.
   10. Wofsy, S.C., et al., HIAPER Pole-to-Pole Observations (HIPPO): Fine grained, global scale measurements of climatically important atmospheric gases and aerosols, Philosophical Transactions of the Royal Society A, 369, 2073-2086, doi: 10.1098/rsta.2010.0313, 2011.
   11. Yevich, R. and J.A. Logan, An assessment of biofuel use and burning of agricultural waste in the developing world, Global Biogeochemical Cycles, 17(4), 1095, doi:10.1029/2002GB00152, 2003.
Files
Description
Aviation_Regions.generic.1x1
File that defines the aircraft regions for the generic 1° x 1° grid.
Aviation_Regions.geos.05x0666
File that defines the aircraft regions for the GMAO 0.5° x 0.666° grid.
Aviation_Regions.geos.1x1
File that defines the aircraft regions for the GMAO 1° x 1° grid.
Aviation_Regions.geos.1x125
File that defines the aircraft regions for the GMAO 1° x 1.25° grid.
Net_terrestrial_exch_5.29Pg.geos.1x1
Net terrestrial exchange data from TRANSCOM 3 climatology (cf. Baker et al 2006). Data is on the GMAO 1° x 1° grid.
biofuel/biofuel_CO2.1x1-1985
CO2 biofuel emissions (base year 1985) from Yevich & Logan 2003, on the generic 1° x 1° grid.
biofuel/biofuel_CO2.1x1-1995
CO2 biofuel emissions from Yevich & Logan 2003, on the generic 1° x 1° grid grid. The 1985 values were scaled to 1995 for 3 separate regions based on Table 16. of Yevich & Logan:
   1. 180-30W Latin America
   2. 30W-60E Africa (including Middle East)
   3. 60-180E Asia
biofuel/biofuel_CO2.geos.05x0667-1985
CO2 biofuel emissions (base year 1985) from Yevich & Logan 2003, on the GMAO 0.5° x 0.666° grid.
biofuel/biofuel_CO2.geos.05x0667-1995
CO2 biofuel emissions from Yevich & Logan 2003, on the GMAO 0.5° x 0.666° grid. The 1985 values were scaled to 1995 for 3 separate regions based on Table 16. of Yevich & Logan:
   1. 180-30W Latin America
   2. 30W-60E Africa (including Middle East)
   3. 60-180E Asia
biofuel/biofuel_CO2.geos.1x1-1985
CO2 biofuel emissions (base year 1985) from Yevich & Logan 2003, on the GMAO 1° x 1° grid.
biofuel/biofuel_CO2.geos.1x1-1995
CO2 biofuel emissions from Yevich & Logan 2003, on the GMAO 1° x 1° grid grid. The 1985 values were scaled to 1995 for 3 separate regions based on Table 16. of Yevich & Logan:
   1. 180-30W Latin America
   2. 30W-60E Africa (including Middle East)
   3. 60-180E Asia
fossilfuel_andres/annual/ff.YYYY.generic.1x1
Annual CO2 fossil fuel emissions from Robert J. Andres, for years YYYY = 1985 to 2006. Data is on the generic 1° x 1° grid.
NOTE: This data is now obsolete and is superseded by the data contained in annual_v2010.
fossilfuel_andres/annual_v2010/ff.YYYY.geos.1x1
Updated annual CO2 fossil fuel emissions from the CDIAC inventory (version 2010, by Robert J. Andres), for years YYYY = 1979 to 2009. Data is on the GMAO 1° x 1° grid.
NOTE: The CDIAC inventory goes back to 1950, but we only provide files starting in 1979, since that is the earliest date at which you can run a GEOS - Chem simulation. Contact Ray Nassar for more information.
ALSO NOTE: To obtain these 1° x 1° data, please contact the GEOS - Chem Support Team.
fossilfuel_andres/monthly_v2010/ff.YYYYMM.geos.1x1
Updated monthly CO2 fossil fuel emissions from the CDIAC inventory (version 2010, by Robert J. Andres), for years YYYY = 1979 to 2009 and MM = 1 .. 12. Data is on the GMAO 1° x 1° grid.
NOTE: The CDIAC inventory goes back to 1950, but we only provide files starting in 1979, since that is the earliest date at which you can run a GEOS - Chem simulation. Contact Ray Nassar for more information.
ALSO NOTE: To obtain these 1° x 1° data, please contact the GEOS - Chem Support Team.
ship_ICOADS/co2_MM.geos.1x1
ship_ICOADS/co2_MM_hp.geos.1x1
Monthly mean CO2 emissions from the ICOADS ship inventory (Corbett et al) on the GEOS 1° x 1° grid, for months MM = 01 .. 12.
4.2.8 The carbon_200909 subdirectory
NOTES:
   1. The data in this directory is not used in GEOS-Chem, but is left here for reference. GEOS-Chem uses the data directly regridded on GMAO 2° x 2.5° or GMAO 4° x 5° grids.
4.2.9 The EDGAR_200607 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: EDGAR anthropogenic and ship emissions
Files
Description
CO/EDGAR.f1000co.generic.1x1
CO/EDGAR.f2000co.generic.1x1
CO/EDGAR.f3000co.generic.1x1
CO/EDGAR.f4000co.generic.1x1
CO/EDGAR.f5100co.generic.1x1
CO/EDGAR.f5400co.generic.1x1
CO/EDGAR.f5700co.generic.1x1
CO/EDGAR.f5800co.generic.1x1
CO/EDGAR.f8000co.generic.1x1
CO/EDGAR.i1000co.generic.1x1
CO/EDGAR.i2000co.generic.1x1
CO/EDGAR.i5000co.generic.1x1
CO/EDGAR.w4095co.generic.1x1
Files on the generic 1° x 1° grid containing EDGAR CO emissions (baseline year 2000) for the following sectors:
   * F10 Industrial
   * F20 Power Generation (fossil fuel)
   * F30 Conversion (fossil fuel)
   * F40 Res + Comm + Other (fossil fuel)
   * F51 Road Transport (fossil fuel)
   * F54 Land (Non-Road) Transport
   * F57 Air Transport (fossil fuel)
   * F58 Shipping (fossil fuel)
F80 Oil Production (fossil fuel)
   * I10 Iron and Steel Production
   * I20 Non-Ferrous Production
   * I50 Pulp and Paper Production
   * W40 Waste Incineration (NOTE: 1995 emissions!)
CO/EDGAR.COScalar-1985-2000.geos.1x1
CO/EDGAR.COScalar-1986-2000.geos.1x1
CO/EDGAR.COScalar-1987-2000.geos.1x1
CO/EDGAR.COScalar-1988-2000.geos.1x1
CO/EDGAR.COScalar-1989-2000.geos.1x1
CO/EDGAR.COScalar-1990-2000.geos.1x1
CO/EDGAR.COScalar-1991-2000.geos.1x1
CO/EDGAR.COScalar-1992-2000.geos.1x1
CO/EDGAR.COScalar-1993-2000.geos.1x1
CO/EDGAR.COScalar-1994-2000.geos.1x1
CO/EDGAR.COScalar-1995-2000.geos.1x1
Files on the on the GMAO 1° x 1° grid containing scale factors for EDGAR CO emissions for years 1985-1995.
These scale factors scale the emissions up to the year 2000.

CO/EDGAR.COScalar-2002-2000.geos.1x1
CO/EDGAR.COScalar-2001-2000.geos.1x1
CO/EDGAR.COScalar-1999-2000.geos.1x1
CO/EDGAR.COScalar-1998-2000.geos.1x1
CO/EDGAR.COScalar-1997-2000.geos.1x1
CO/EDGAR.COScalar-1996-2000.geos.1x1
Files on the on the GMAO 1° x 1° grid containing scale factors for EDGAR CO emissions for years 1985-1995.
These scale factors scale the emissions from 2000 to the given year.
NOx/EDGAR.b1000nox.generic.1x1
NOx/EDGAR.b2000nox.generic.1x1
NOx/EDGAR.b3000nox.generic.1x1
NOx/EDGAR.b4000nox.generic.1x1
NOx/EDGAR.b5100nox.generic.1x1
NOx/EDGAR.f1000nox.generic.1x1
NOx/EDGAR.f2000nox.generic.1x1
NOx/EDGAR.f3000nox.generic.1x1
NOx/EDGAR.f4000nox.generic.1x1
NOx/EDGAR.f5100nox.generic.1x1
NOx/EDGAR.f5400nox.generic.1x1
NOx/EDGAR.f5700nox.generic.1x1
NOx/EDGAR.f5800nox(IEA).generic.1x1
NOx/EDGAR.f8000nox.generic.1x1
NOx/EDGAR.i1000nox.generic.1x1
NOx/EDGAR.i3000nox.generic.1x1
NOx/EDGAR.i4000nox.generic.1x1
NOx/EDGAR.i5000nox.generic.1x1
NOx/EDGAR.w4000nox.generic.1x1
Files on the generic 1° x 1° grid containing EDGAR NOx emissions (baseline year 2000) for the following sectors:
   * B10 Bio-industry (not used)
   * B20 Power generation (not used)
   * B30 Charcoal production (not used)
   * B40 RCO (not used)
   * B51 Road transport (Eth.) (not used)
   * F10 Industrial
   * F20 Power Generation (fossil fuel)
   * F30 Conversion (fossil fuel)
   * F40 Res + Comm + Other (fossil fuel)
   * F51 Road Transport (fossil fuel)
   * F54 Land (Non-Road) Transport
   * F57 Air Transport (fossil fuel)
   * F58 Ship exhaust (fossil fuel)
   * F80 Oil Production (fuel combustion)
   * I10 Iron and Steel Production
   * I30 Chemical Production
   * I40 Cement Production
   * I50 Pulp & Paper Production
   * W40 Waste incineration
NOx/EDGAR.NOxScalar-1985-2000.geos.1x1
NOx/EDGAR.NOxScalar-1986-2000.geos.1x1
NOx/EDGAR.NOxScalar-1987-2000.geos.1x1
NOx/EDGAR.NOxScalar-1988-2000.geos.1x1
NOx/EDGAR.NOxScalar-1989-2000.geos.1x1
NOx/EDGAR.NOxScalar-1990-2000.geos.1x1
NOx/EDGAR.NOxScalar-1991-2000.geos.1x1
NOx/EDGAR.NOxScalar-1992-2000.geos.1x1
NOx/EDGAR.NOxScalar-1993-2000.geos.1x1
NOx/EDGAR.NOxScalar-1994-2000.geos.1x1
NOx/EDGAR.NOxScalar-1995-2000.geos.1x1
NOx/EDGAR.NOxScalar-1996-2000.geos.1x1
NOx/EDGAR.NOxScalar-1997-2000.geos.1x1
Files on the on the GMAO 1° x 1° grid containing scale factors for EDGAR NOx emissions for years 1985-1995.
These scale factors scale the emissions up to the year 2000.

NOx/EDGAR.NOxScalar-2002-2000.geos.1x1
NOx/EDGAR.NOxScalar-2001-2000.geos.1x1
NOx/EDGAR.NOxScalar-1999-2000.geos.1x1
NOx/EDGAR.NOxScalar-1998-2000.geos.1x1
NOx/EDGAR.NOxScalar-1997-2000.geos.1x1
NOx/EDGAR.NOxScalar-1996-2000.geos.1x1
Files on the on the GMAO 1° x 1° grid containing scale factors for EDGAR NOx emissions for years 1985-1995.
These scale factors scale the emissions from 2000 to the given year.
NOx/anth_NOx_scale.DJF.generic.1x1
NOx/anth_NOx_scale.MAM.generic.1x1
NOx/anth_NOx_scale.JJA.generic.1x1
NOx/anth_NOx_scale.SON.generic.1x1
Files on the generic 1° x 1° grid contaning SEASONAL SCALE FACTORS which are computed as ( GEIA nox per season ) / ( GEIA NOx per year )
   * WINTER seasonal ratios (DJF)
   * SPRING seasonal ratios (MAM)
   * SUMMER seasonal ratios (JJA)
   * AUTUMN seasonal ratios (SON)
SOx/EDGAR.f1000so2.generic.1x1
SOx/EDGAR.f2000so2.generic.1x1
SOx/EDGAR.f3000so2.generic.1x1
SOx/EDGAR.f4000so2.generic.1x1
SOx/EDGAR.f5100so2.generic.1x1
SOx/EDGAR.f5400so2.generic.1x1
SOx/EDGAR.f5700so2.generic.1x1
SOx/EDGAR.f5800so2(IEA).generic.1x1
SOx/EDGAR.f8000so2.generic.1x1
SOx/EDGAR.i1000so2.generic.1x1
SOx/EDGAR.i2000so2.generic.1x1
SOx/EDGAR.i3000so2.generic.1x1
SOx/EDGAR.i4000so2.generic.1x1
SOx/EDGAR.i5000so2.generic.1x1
SOx/EDGAR.w4000so2.generic.1x1
Files on the generic 1° x 1° grid containing EDGAR SOx emissions (baseline year 2000) for the following sectors:
   * F10 Industrial
   * F20 Power Generation (fossil fuel)
   * F30 Conversion (fossil fuel)
   * F40 Res + Comm + Other (fossil fuel)
   * F51 Road Transport (fossil fuel)
   * F54 Land (Non-Road) Transport
   * F57 Air Transport (fossil fuel)
   * F58 Ship exhaust (fossil fuel)
   * F80 Oil Production (fuel combustion)
   * I10 Iron and Steel Production
   * I20 Non-Ferrous Production
   * I30 Chemical Production
   * I40 Cement Production
   * I50 Pulp & Paper Production
   * W40 Waste incineration
SOx/EDGAR.SOxScalar-2002-2000.geos.1x1 SOx/EDGAR.SOxScalar-2001-2000.geos.1x1 SOx/EDGAR.SOxScalar-1999-2000.geos.1x1 SOx/EDGAR.SOxScalar-1998-2000.geos.1x1
Files on the on the GMAO 1° x 1° grid containing scale factors for EDGAR SOx emissions for years 1985-1995.
These scale factors scale the emissions from 2000 to the given year.
SOx/ship_SOx_scale.JAN.geos.1x1
SOx/ship_SOx_scale.FEB.geos.1x1
SOx/ship_SOx_scale.MAR.geos.1x1
SOx/ship_SOx_scale.APR.geos.1x1
SOx/ship_SOx_scale.MAY.geos.1x1
SOx/ship_SOx_scale.JUN.geos.1x1
SOx/ship_SOx_scale.JUL.geos.1x1
SOx/ship_SOx_scale.AUG.geos.1x1
SOx/ship_SOx_scale.SEP.geos.1x1
SOx/ship_SOx_scale.OCT.geos.1x1
SOx/ship_SOx_scale.NOV.geos.1x1
SOx/ship_SOx_scale.DEC.geos.1x1
Files on the on the GMAO 1° x 1° grid containing monthly scale factors for EDGAR ship SO2 emissions, which are defined as:
( Corbett monthly ship SO2 ) / ( Ann. total of Corbett SO2 )
SOx/anth_SOx_scale.DJF.generic.1x1
SOx/anth_SOx_scale.MAM.generic.1x1
SOx/anth_SOx_scale.JJA.generic.1x1
SOx/anth_SOx_scale.SON.generic.1x1
Files on the generic 1° x 1° grid contaning SEASONAL SCALE FACTORS which are computed as ( GEIA SOx per season ) / ( GEIA SOx per year )
   * WINTER seasonal ratios (DJF)
   * SPRING seasonal ratios (MAM)
   * SUMMER seasonal ratios (JJA)
   * AUTUMN seasonal ratios (SON)
BENZ/BENZ_1985_FF_IND_EDGAR2.1x1geos.bpch
C2H2/C2H2_1985_FF_IND_EDGAR2.1x1geos.bpch
C2H4/C2H4_1985_FF_IND_EDGAR2.1x1geos.bpch
TOLU/TOLU_1985_FF_IND_EDGAR2.1x1geos.bpch
XYLE/XYLE_1985_FF_IND_EDGAR2.1x1geos.bpch
Files on the GMAO 1° x 1° grid for species only used for dicarbonyl chemistry (73 tracers). Files were prepared by May Fu.

REFERENCE:
   1. http://www.mnp.nl/edgar/model/edgar2/precursor_gases/edgar_20_nmvoc.jsp
4.2.10 The EMEP_200510 subdirectory
NOTES:
   1. For years prior to 1985, GEOS - Chem will use EMEP emissions for 1985.
   2. For NOx, CO, and SOx from 1990 onward data from EMEP_200911 subdirectory are used.
REFERENCES:
   1. GEOS-Chem wiki: EMEP anthropogenic and ship emissions
   2. Emission data reported to UNECE/EMEP: Quality assurance and trend analysis and presentation of WebDab, MSC-W Status Report 2002. [PDF]
Files
Description
EMEP.geos.1x1.1985
EMEP.geos.1x1.1986
EMEP.geos.1x1.1987
EMEP.geos.1x1.1988
EMEP.geos.1x1.1989
EMEP.geos.1x1.1990
EMEP.geos.1x1.1991
EMEP.geos.1x1.1992
EMEP.geos.1x1.1993
EMEP.geos.1x1.1994
EMEP.geos.1x1.1995
EMEP.geos.1x1.1996
EMEP.geos.1x1.1997
EMEP.geos.1x1.1998
EMEP.geos.1x1.1999
EMEP.geos.1x1.2000
EMEP European anthropogenic emissions on the GMAO 1° x 1° grid.
Species: NOx, CO, ALK4, MEK, ALD2, PRPE, C2H6.
EMEP raw data were supplied to us by Marion Auvray and Isabelle Bey at EPFL, Lausanne, Switzerland. Brendan Field created these binary punch files from the raw data.

4.2.11 The EMEP_200911 subdirectory
NOTES:
   1. This is an update of the now obsolete EMEP_200806 subdirectory.
   2. These data where gathered from the EMEP website and compiled by Aaron van Donkelaar
   3. These emissions are used complementary to emissions in the EMEP_200510 subdirectory.
REFERENCES:
   1. GEOS-Chem wiki: EMEP anthropogenic and ship emissions
   2. Data: http://www.ceip.at/
Files
Description
EMEP_mask.geos.1x1
Updated mask file for EMEP emissions, submitted by G.C.M. Vinken.
Prior to this fix, the mask used by GEOS - Chem corresponded to the emissions in the EMEP_200510 directory. This mismatch caused no ship emissions to be released over a region of the North Atlantic and north of Norway. The updated mask now corresponds with the new border of the EMEP emissions domain and thus fixes the problem.
EMEP-1990.geos.1x1
EMEP-1991.geos.1x1
EMEP-1992.geos.1x1
EMEP-1993.geos.1x1
EMEP-1994.geos.1x1
EMEP-1995.geos.1x1
EMEP-1996.geos.1x1
EMEP-1997.geos.1x1
EMEP-1998.geos.1x1
EMEP-1999.geos.1x1
EMEP-2000.geos.1x1
EMEP-2001.geos.1x1
EMEP-2002.geos.1x1
EMEP-2003.geos.1x1
EMEP-2004.geos.1x1
EMEP-2005.geos.1x1
EMEP-2006.geos.1x1
EMEP-2007.geos.1x1
EMEP anthropogenic emissions of CO, NH3, NOx, and SOx [molec/cm2/s] for year 1990 to 2007 on the GMAO 1° x 1° grid.
EMEP-SHIP-1990.geos.1x1
EMEP-SHIP-1991.geos.1x1
EMEP-SHIP-1992.geos.1x1
EMEP-SHIP-1993.geos.1x1
EMEP-SHIP-1994.geos.1x1
EMEP-SHIP-1995.geos.1x1
EMEP-SHIP-1996.geos.1x1
EMEP-SHIP-1997.geos.1x1
EMEP-SHIP-1998.geos.1x1
EMEP-SHIP-1999.geos.1x1
EMEP-SHIP-2000.geos.1x1
EMEP-SHIP-2001.geos.1x1
EMEP-SHIP-2002.geos.1x1
EMEP-SHIP-2003.geos.1x1
EMEP-SHIP-2004.geos.1x1
EMEP-SHIP-2005.geos.1x1
EMEP-SHIP-2006.geos.1x1
EMEP-SHIP-2007.geos.1x1
EMEP ship emissions of CO, NH3, NOx, and SOx [molec/cm2/s] for year 1990 to 2007 on the GMAO 1° x 1° grid.
SeasonalVariation/EMEP-SeasonalVariation-1.1x1
SeasonalVariation/EMEP-SeasonalVariation-2.1x1
SeasonalVariation/EMEP-SeasonalVariation-3.1x1
SeasonalVariation/EMEP-SeasonalVariation-4.1x1
SeasonalVariation/EMEP-SeasonalVariation-5.1x1
SeasonalVariation/EMEP-SeasonalVariation-6.1x1
SeasonalVariation/EMEP-SeasonalVariation-7.1x1
SeasonalVariation/EMEP-SeasonalVariation-8.1x1
SeasonalVariation/EMEP-SeasonalVariation-9.1x1
SeasonalVariation/EMEP-SeasonalVariation-10.1x1
SeasonalVariation/EMEP-SeasonalVariation-11.1x1
SeasonalVariation/EMEP-SeasonalVariation-12.1x1
Monthly variations. Courtesy of the GENEMIS project coordinated by the Institute of Energy Economics and the Rational Use of Energy (IER) at the University of Stuttgart.
4.2.12 The EPA_NEI_200708 subdirectory
NOTES:
   1. The files in the EPA_NEI_200708 directory were updated to account for transport emissions in California. The files in EPA_NEI_200411 did not contain these emissions.
   2. The files in the EPA_NEI_200708 directory contain NH3 emissions, whereas the files in the EPA_NEI_200411 directory did not.
   3. For more information, please see the Anthropogenic Emissions page on the GEOS - Chem Wiki.
   4. The mask file for USA in this subdirectory is used when not using BRAVO and CAC inventories.
Files
Description
wkday_avg_an.199901.geos.1x1
wkday_avg_an.199902.geos.1x1
wkday_avg_an.199903.geos.1x1
wkday_avg_an.199904.geos.1x1
wkday_avg_an.199905.geos.1x1
wkday_avg_an.199906.geos.1x1
wkday_avg_an.199907.geos.1x1
wkday_avg_an.199908.geos.1x1
wkday_avg_an.199909.geos.1x1
wkday_avg_an.199910.geos.1x1
wkday_avg_an.199911.geos.1x1
wkday_avg_an.199912.geos.1x1
EPA / NEI99 weekday anthropogenic emissions files on the GMAO 1° x 1° grid.
The following species are included:
NOx, CO, ALK4, ACET, MEK, PRPE, C2H6, C3H8, CH2O, SO2, SO4, NH3
wkend_avg_an.199901.geos.1x1
wkend_avg_an.199902.geos.1x1
wkend_avg_an.199903.geos.1x1
wkend_avg_an.199904.geos.1x1
wkend_avg_an.199905.geos.1x1
wkend_avg_an.199906.geos.1x1
wkend_avg_an.199907.geos.1x1
wkend_avg_an.199908.geos.1x1
wkend_avg_an.199909.geos.1x1
wkend_avg_an.199910.geos.1x1
wkend_avg_an.199911.geos.1x1
wkend_avg_an.199912.geos.1x1
EPA / NEI99 weekend anthropogenic emissions files on the GMAO 1° x 1° grid.
The following species are included:
NOx, CO, ALK4, ACET, MEK, PRPE, C2H6, C3H8, CH2O, SO2, SO4, NH3
usa_mask.geos.1x1
Mask file (on the GMAO 1° x 1° grid) which is used for emissions over the continental USA. Grid boxes that lie totally within the USA are assigned a value of 1, other boxes are assigned a value of zero.
4.2.13 The EPA_NEI_200806 subdirectory
NOTES:
   1. For more information, see the GEOS-Chem wiki: EPA/NEI99 North American inventory
   2. As of 04/30/2009, the data are not available on any 1x1 grid. The data are directly read on the GMAO 2° x 2.5° grid or on the GMAO 4° x 5° grid.
   3. The mask file for USA in this subdirectory is used when using BRAVO and CAC inventories.
Files
Description
usa_mask.geos.1x1
Mask file (on the GMAO 1° x 1° grid) which is used for emissions over the continental USA. Grid boxes where there is EPA emissions are assigned a value of 1, other boxes are assigned a value of zero.
4.2.14 The FastJ_201204 subdirectory
References:
   1. GEOS-Chem wiki: Photolysis mechanism
Files
Description
fastj.jv_atms_dat.nc
NetCDF file, which contains the default temperature and ozone profiles for the FAST-J photolysis scheme. This file is equivalent to the old ASCII file jv_atms.dat that shipped with GEOS - Chem run directories.
4.2.15 The GFED2_200601 subdirectory
NOTES:
   1. For GEOS - Chem v9 - 01 - 02 and higher versions, GFED2 emissions data in this subdirectory are superseded by GFED3 emissions data in GFED3_201110. The emissions data in this subdirectory are kept for compatability with older model versions.
   2. The GFED2 emissions in this directory are monthly mean biomass emissions.
   3. GEOS - Chem reads the GFED2 C emissions data on the generic 1x1 grid, then converts to equivalent biomass emissions for each species, and then regrids to the current model grid. Therefore, to change GFED2 biomass emissions, all one has to do is to change the emission factors for the various vegetation types.
REFERENCES:
   1. GEOS-Chem wiki: GFED2 monthly biomass burning emissions
   2. Original GFED2 database from Jim Randerson.
   3. Giglio, L., G.R. van der Werf, J.T. Randerson, G.J. Collatz, and P. Kasibhatla, Global estimation of burned area using MODIS active fire observations, Atm. Chem. Phys., 6, 957-974, 2006.
   4. G.R. van der Werf, J.T. Randerson, L. Giglio, G.J. Collatz,P.S. Kasibhatla, and A.F. Arellano, Jr., Interannual variability in global biomass burning emissions from 1997 to 2004, Atm. Chem. Phys., 6, 3423-3441, 2006.
Files
Description
YYYY/GFED2_C_YYYY01.generic.1x1
YYYY/GFED2_C_YYYY02.generic.1x1
YYYY/GFED2_C_YYYY03.generic.1x1
YYYY/GFED2_C_YYYY04.generic.1x1
YYYY/GFED2_C_YYYY05.generic.1x1
YYYY/GFED2_C_YYYY06.generic.1x1
YYYY/GFED2_C_YYYY07.generic.1x1
YYYY/GFED2_C_YYYY08.generic.1x1
YYYY/GFED2_C_YYYY09.generic.1x1
YYYY/GFED2_C_YYYY10.generic.1x1
YYYY/GFED2_C_YYYY11.generic.1x1
YYYY/GFED2_C_YYYY12.generic.1x1
Files containing GFED2 monthly mean carbon emissions on the generic 1° x 1° grid. Units are g/m2.
Emissions are available from 1997 thru 2008.
NOTE: This data is now superseded by the data contained in GFED3_201110.
GFED2_emission_factors.txt
Text file containing the GFED2 emission factors for each species as a function of vegetation type. Includes emission factors for the following:
Gas-phase species:
NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6
Aerosol species:
SO2, NH3, BC, OC
and also CO2 (for offline simulations).
NOTE: This file is used by older versions than version 8-02-01
GFED2_emission_factors_73t.txt
Text file containing the same emission factors for the same species than GFED2_emission_factors.txt and the GFED2 emission factors for species used in dicarbonyl simulation.
Includes emission factors for the following:
Gas-phase species:
NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6, GLYX, MGLY, BENZ, TOLU, XYLE, C2H4, C2H2, GLYC, HAC
Aerosol species:
SO2, NH3, BC, OC
and also CO2 (for offline simulations).
NOTE: This file is used by version 8-02-01 and newer.
GFED2_vegmap.generic.1x1
GFED2 vegetation map on the generic 1° x 1° grid.
Values are:
   * 3 = boreal forest
   * 2 = tropical forest
   * 1 = savanna / herb / other land
   * 0 = water
4.2.16 The GFED2_3hr_200901 subdirectory
NOTES:
   1. For GEOS - Chem v9 - 01 - 02 and higher versions, GFED2 emissions data in this subdirectory are superseded by GFED3 emissions data in GFED3_201110. The emissions data in this subdirectory are kept for compatability with older model versions.
   2. These data were generated for a specific research project. We recommend using either the monthly or 8-day data.
   3. The GFED2 emissions in this directory are 3-hourly data. The "3hr" data are obtained from applying a 3hr diurnal variation to the 8-day averages. The "synoptic" data distribute the 8-day average data in their respective 8 days according to the meteorological ISI index, then apply a 3hr diurnal cycle.
   4. As of 04/30/2009, there are only 4 months of data available: June, July, August and September 2004.
Files
Description
2004/GFED2.3hr.C_200406.generic.1x1
2004/GFED2.3hr.C_200407.generic.1x1
2004/GFED2.3hr.C_200408.generic.1x1
2004/GFED2.3hr.C_200409.generic.1x1
Files containing 3-hour carbon fluxes based on GFED2 for June, July, August, and September of 2004. Units are g C/m[2]/3hr.
2004/GFED2.synoptic.C_200406.generic.1x1
2004/GFED2.synoptic.C_200407.generic.1x1
2004/GFED2.synoptic.C_200408.generic.1x1
2004/GFED2.synoptic.C_200409.generic.1x1
Files containing synoptic 3-hour carbon fluxes based on GFED2 for June, July, August, and September of 2004. Units are g C/m[2]/3hr
4.2.17 The GFED2_8day_200712 subdirectory
NOTES:
   1. For GEOS - Chem v9 - 01 - 02 and higher versions, GFED2 emissions data in this subdirectory are superseded by GFED3 emissions data in GFED3_201110. The emissions data in this subdirectory are kept for compatability with older model versions.
   2. The GFED2 emissions in this directory are 8-day averages.
   3. As of 04/30/2009, the GFED2_emission_factors.txt file, the GFED2_emission_factors_73t.txt file and the GFED2_vegmap.generic.1x1 file are the same versions as are found in the GFED2_200601 subdirectory, which contains monthly emissions. At some point we may upgrade to a newer version of the vegetation map file from Prasad Kasibhatla, but that has not been done as of 04/30/2009.
   4. GEOS-Chem reads the GFED2 C emissions data on the generic 1x1 grid, then converts to equivalent biomass emissions for each species, and then regrids to the current model grid. Therefore, to change GFED2 biomass emissions, all one has to do is to change the emission factors for the various vegetation types.
REFERENCES:
   1. GEOS-Chem wiki: GFED2 8-day-average biomass burning emissions
   2. Original GFED2 database from Jim Randerson.
   3. Giglio, L., G.R. van der Werf, J.T. Randerson, G.J. Collatz, and P. Kasibhatla, Global estimation of burned area using MODIS active fire observations, Atm. Chem. Phys., 6, 957-974, 2006.
   4. G.R. van der Werf, J.T. Randerson, L. Giglio, G.J. Collatz,P.S. Kasibhatla, and A.F. Arellano, Jr., Interannual variability in global biomass burning emissions from 1997 to 2004, Atm. Chem. Phys., 6, 3423-3441, 2006.
Files
Description
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
YYYY/GFED2_C_YYYYMMDD.generic.1x1
Files containing GFED2 monthly mean carbon emissions on the generic 1° x 1° grid. Units are g/m2.
In the file names, YYYYMMDD is the starting date of the 8-day averaging period. The first 8-day averaging period of any given year starts on January 1st.
Emissions are available from 2001 thru 2007.
GFED2_emission_factors.txt
Text file containing the GFED2 emission factors for each species as a function of vegetation type. Includes emission factors for the following:
Gas-phase species:
NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6
Aerosol species:
SO2, NH3, BC, OC
and also CO2 (for offline simulations).
NOTE: As of May 2009, this file is currently the same as in the GFED_200601 subdirectory.
GFED2_emission_factors_73t.txt
Text file containing the same emission factors for the same species than GFED2_emission_factors.txt and the GFED2 emission factors for species used in dicarbonyl simulation.
Includes emission factors for the following:
Gas-phase species:
NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6, GLYX, MGLY, BENZ, TOLU, XYLE, C2H4, C2H2, GLYC, HAC
Aerosol species:
SO2, NH3, BC, OC
and also CO2 (for offline simulations).
NOTE: As of May 2009, this file is currently the same as in the GFED_200601 subdirectory.
GFED2_vegmap.generic.1x1
GFED2 vegetation map (bpch format) on the generic 1° x 1° grid.
Values are:
   * 3 = boreal forest
   * 2 = tropical forest
   * 1 = savanna / herb / other land
   * 0 = water
NOTE: As of May 2009, this file is currently the same as in the GFED_200601 subdirectory.
4.2.18 The GFED3_201203 subdirectory
NOTES:
   1. This is an update of the now obsolete GFED3_201110 subdirectory.
   2. The GFED3 emissions in this directory are monthly mean, daily, and 3-hourly biomass emissions.
   3. GEOS - Chem reads directly from the GFED3 0.5° x 0.5° native resolution and regrids to the model resolution using the MAP_A2A regriddng package.
REFERENCES:
   1. GEOS-Chem wiki: GFED3
   2. GFED webpage: http://www.globalfiredata.org/
   3. van der Werf, G.R., J.T. Randerson, L. Giglio, G.J. Collatz,M. Mu, P.S. Kasibhatla, D.C. Morton, R.S. DeFries, Y. Jin, and T.T. van Leeuwen, Global fire emissions and the contribution of deforestation, savanna, forest, agricultural, and peat fires (1997 - 2009), Atm. Chem. Phys., Vol 10, 11707 - 11735, 2010.
   4. For methodology: Mu, M., J.T. Randerson, G.R. van der Werf, L. Giglio, P. Kasibhatla, D. Morton, G.J. Collatz, R.S. DeFries, E.J. Hyer, E.M. Prins, D.W.T. Griffith, D. Wunch, G.C. Toon, V. Sherlock, and P.O. Wennberg, Daily and 3-hourly variability in global fire emissions and consequences for atmospheric model predictions of carbon monoxide, Journal of Geophysical Research-Atmospheres, 116: D24303. doi:10.1029/2011JD016245, 2011.
Files
Description
YYYY/3hourly/GFED3_FR_3HR_YYYYMMDDHH
YYYY/Daily/GFED3_FR_DAY_YYYYMMDD
Files containing 3-hourly and daily fire emission fractions on the native GFED3 0.5° x 0.5° grid. Since fire fraction are not available as a function of type of fire type (as is the case for dry matter burnt), the same fractions are applied to all six fire types.
As of March 2012, data from 2003 thru 2010 are available.
YYYY/Monthly/GFED3_DM_AGW_YYYYMM
YYYY/Monthly/GFED3_DM_DEF_YYYYMM
YYYY/Monthly/GFED3_DM_FOR_YYYYMM
YYYY/Monthly/GFED3_DM_PET_YYYYMM
YYYY/Monthly/GFED3_DM_SAV_YYYYMM
YYYY/Monthly/GFED3_DM_TOT_YYYYMM
YYYY/Monthly/GFED3_DM_WDL_YYYYMM
Files containing GFED3 monthly dry matter (DM) emissions on the native GFED3 0.5° x 0.5° grid. Units are g/m2/month. DM burnt is a function of the following fire types:
   * Agricultural waste
   * Deforestation
   * Extratropical forest
   * Peat
   * Savanna
   * Woodland
As of March 2012, emissions from 1997 thru 2010 are available.
GFED3_emission_factors.txt
Text file containing the GFED3 emission factors for each species as a function of vegetation type. Includes emission factors for the following:
Gas-phase species:
NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6
Aerosol species:
SO2, NH3, BC, OC
Other species:
GLYX, MGLY, BENZ, TOLU, XYLE, C2H4, C2H2, GLYC, HAC
and also CO2 and CH4 (for offline simulations).
GFED3_vegmap.generic.1x1
GFED3 humid tropical forest map (bpch format) on the 0.5° x 0.5° GFED3 grid. This is used to assign emission factors for 'deforestation.' 'Deforestation' that occurs outside of humid tropical forest is assigned a woodlands emission factor.
Values are:
   * 1 = humid tropical forest
   * 0 = other
4.2.19 The historical_emissions_201203 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Available Historical and Future Emissions
   2. Leibensperger, E. M., Mickley, L. J., Jacob, D. J., Chen, W.-T., Seinfeld, J. H., Nenes, A., Adams, P. J., Streets, D. G., Kumar, N., and Rind, D.: Climatic effects of 1950 - 2050 changes in US anthropogenic aerosols  -  Part 1: Aerosol trends and radiative forcing, Atmos. Chem. Phys. Discuss., 11, 24085-24125, doi:10.5194/acpd-11-24085-2011, 2011.
Files
Description
BCOC/BCOC_anthsrce.YYYY.geos.1x1
BCOC/BCOC_biofuel.YYYY.geos.1x1
Monthly black carbon and organic carbon emissions [kg] from anthropogenic sources and biofuel burning.
Data is available for the years 1850 to 2050 and is on the generic 1° x 1° grid.
NOx/EDGAR.BCNOX.YYYYgeneric.1x1
NOx/EDGAR.FCNOX.YYYYgeneric.1x1
NOx/EDGAR.INNOX.YYYYgeneric.1x1
Annual NOx emissions from:
   * Biofuel burning
   * Fossil fuel combustion
   * Industrial sources
Data is available for the years 1890 to 2050 and is on the generic 1° x 1° grid.
NOx/lumped_fnox_diurnal_scale_factors.dat
Text file containing lumped diurnal scale factors of NOx.
SO2/EDGAR.BCSO2.YYYYgeneric.1x1
SO2/EDGAR.FCSO2.YYYYgeneric.1x1
SO2/EDGAR.INSO2.YYYYgeneric.1x1
Annual SO2 emissions from:
   * Biofuel burning
   * Fossil fuel combustion
   * Industrial sources
Data is available for the years 1890 to 2050 and is on the generic 1° x 1° grid.
4.2.20 The ICOADS_200907 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: ICOADS ship emissions
   2. Wang, C., J. J. Corbett, and J. Firestone, Improving Spatial representation of Global Ship Emissions Inventories, Environ. Sci. Technol., 42 (1), 193-199, 2008. [link]
   3. Data located at: http://coast.cms.udel.edu/GlobalShipEmissions/
Files
Description
CO_01.geos.1x1
CO_02.geos.1x1
CO_03.geos.1x1
CO_04.geos.1x1
CO_05.geos.1x1
CO_06.geos.1x1
CO_07.geos.1x1
CO_08.geos.1x1
CO_09.geos.1x1
CO_10.geos.1x1
CO_11.geos.1x1
CO_12.geos.1x1
Monthly ship emissions for CO [kg CO/month] on the GMAO 1° x 1° grid
NOx_01.geos.1x1
NOx_02.geos.1x1
NOx_03.geos.1x1
NOx_04.geos.1x1
NOx_05.geos.1x1
NOx_06.geos.1x1
NOx_07.geos.1x1
NOx_08.geos.1x1
NOx_09.geos.1x1
NOx_10.geos.1x1
NOx_11.geos.1x1
NOx_12.geos.1x1
Monthly ship emissions for NOx [kg NOx/month] on the GMAO 1° x 1° grid
SOx_01.geos.1x1
SOx_02.geos.1x1
SOx_03.geos.1x1
SOx_04.geos.1x1
SOx_05.geos.1x1
SOx_06.geos.1x1
SOx_07.geos.1x1
SOx_08.geos.1x1
SOx_09.geos.1x1
SOx_10.geos.1x1
SOx_11.geos.1x1
SOx_12.geos.1x1
Monthly ship emissions for SOx [kg S/month] on the GMAO 1° x 1° grid
4.2.21 The Linoz_200910 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Linoz stratospheric ozone chemistry
Files
Description
Linoz_March2007.dat
Text file containing the climatology for Linoz
4.2.22 The MAP_A2A_Regrid_201203 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: MAP_A2A regridding algorithm
Files
Description
latlon_generic_new.txt
latlon_geos1x1_new.txt
latlon_geos2x25.txt
latlon_geos05x0666.txt
Text files containing the longitude and latitude edge information for the generic 1° x 1° grid, the GMAO 1° x 1° grid, the GMAO 2° x 2.5° grid, and the GMAO 0.5° x 0.666° grid.
MAP_A2A_latlon_generic1x1.nc
MAP_A2A_latlon_geos1x1.nc
MAP_A2A_latlon_geos2x25.nc
MAP_A2A_latlon_geos05x0666.nc
NetCDF files containing the longitude and latitude edge information for the generic 1° x 1° grid the GMAO 1° x 1° grid, the GEOS 2° x 2.5° grid and the GMAO 0.5° x 0.666° grid.
Note: GEOS - Chem does not yet use these netCDF files. We plan to introduce this functionality in the release following GEOS-Chem v9-01-03.
4.2.23 The MEGAN_200909 subdirectory
NOTES:
   1. This is an update of the now obsolete MEGAN_200510 directory.
REFERENCES:
   1. GEOS-Chem wiki: MEGAN v2.1 biogenic emissions
Files
Description
MEGANv2.1_AEF_ALPHA_PINENE.geos.1x1  MEGANv2.1_AEF_BETA_PINENE.geos.1x1  MEGANv2.1_AEF_CARENE.geos.1x1        MEGANv2.1_AEF_ISOPRENE.geos.1x1     MEGANv2.1_AEF_LIMONENE.geos.1x1     MEGANv2.1_AEF_MBO.geos.1x1
MEGANv2.1_AEF_METHANOL.geos.1x1
MEGANv2.1_AEF_MONOTERPENES.geos.1x1
MEGANv2.1_AEF_MYRCENE.geos.1x1
MEGANv2.1_AEF_NITRIC_OXIDE.geos.1x1
MEGANv2.1_AEF_OCIMENE.geos.1x1
MEGANv2.1_AEF_SABINENE.geos.1x1
Annual Emission Factor (AEF) files for
   * Isoprene
   * Methyl Butenol (MBO)
   * Monoterpenes (MTP)
   * Alpha-Pinene
   * Beta-Pinene
   * Carene
   * Limoene
   * Methanol
   * Myrcene
   * Nitric Oxide
   * Ocimene
   * Sabinene
These data were saved into binary punch file (bpch) file format on the GMAO 1° x 1° grid by Mike Barkley.
MEGAN_PFT_BT.geos.1x1
MEGAN_PFT_CR.geos.1x1
MEGAN_PFT_GR.geos.1x1
MEGAN_PFT_NT.geos.1x1
MEGAN_PFT_SH.geos.1x1
Coverage of plant functional types based on MEGAN v2.0 for:
   * broadleaf trees (BT)
   * crops (CR)
   * grasslands (GR)
   * needleleaf trees (NT)
   * shrubs (SH)
These files will be needed as input for MEGAN emission calculations for GEOS - Chem v9 - 01 - 03 and higher.
Files were generated in binary punch file (bpch) file format on the GMAO 1° x 1° grid by Havala Pye with guidance from Dylan Millet.
4.2.24 The MODIS_LAI_201204 subdirectory
NOTES:
   1. The contents of this directory contain the same data as in MODIS_LAI_200911, but with two differences: (1) the data is placed on the 0.5° x 0.5° (Olson 1992) or 0.25° x 0.25° (Olson 2001) native grid and (2) the data is stored as netCDF files.
   2. This is an update of the now obsolete MODIS_LAI_200910 directory.
REFERENCES:
   1. GEOS-Chem wiki: MODIS-derived leaf area indices
Files
Description
For_Olson_1992/MODIS.LAIv.V5.generic.05x05.YYYY.nc
Monthly LAI values on the 0.5° x 0.5° native grid, for years YYYY=1985 (climatological) and 2000 to 2008 (actual years). Data has units of cm2 leaf/cm2 grid box.
For_Olson_2001/MODIS.LAIv.V5.generic.025x025.YYYY.nc
Monthly LAI values on the 0.25° x 0.25° native grid, for years YYYY=2005 to 2009. Data has units of cm2 leaf/cm2 grid box.
4.2.25 The mercury_200511 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Mercury simulation
   2. Esaias, W.E. (1996), Algorithm theoretical basis document for MODIS product MOD-27 ocean primary productivity, report, NASA Goddard Space Flight Cent., Greenbelt, MD.
   3. Frank, D. G. (1999), Mineral Resource Data System (MRDS) data in Arc-View Shape File Format, for Spatial Data Delivery Project, U.S. Geol. Surv., Spokane, Wash.
   4. Hellerman and Rosenstein, Normal monthly wind stess over the world ocean with error estimates, J. Phys. Oceanogr., 13, 1093-1104, 1983.
   5. Kara et al, Mixed layer depth variability over the global ocean, J. Geophys. Res., 108(C3), 3079, 2003, doi:10.1029/2000JC00736.
   6. Selin, N.E., D.J. Jacob, R.J. Park, R.M. Yantosca, S. Strode, L. Jaeglé, and D. Jaffe, Chemical cycling and deposition of atmospheric mercury: Global constraints from observations, J. Geophys. Res., 112, D02308, doi:10.1029/2006JD007450, 2007.
   7. Strode, S., L. Jaeglé, N.E. Selin, D.J. Jacob, R.J. Park, R.M. Yantosca, R.P. Mason, and F. Slemr, Air-sea exchange in the global mercury cycle, Glob. Biogeochem. Cycles, 21, GB1017, doi:10.1029/2006GB002766, 2007.
Files
Description
GEIA_Hg0.geos.1x1.1995
GEIA_Hg2.geos.1x1.1995
GEIA_HgP.geos.1x1.1995
Anthropogenic emissions of Hg0 (elemental mercury), Hg2 (divalent mercury), and HgP (particulate mercury) from GEIA 1995 inventory. Data are on the GMAO 1° x 1° grid.
GEIA_Hg0.geos.1x1.2000
GEIA_Hg2.geos.1x1.2000
GEIA_HgP.geos.1x1.2000
Anthropogenic emissions of Hg0 (elemental mercury), Hg2 (divalent mercury), and HgP (particulate mercury) from GEIA 1995 inventory. Data are on the GMAO 1° x 1° grid.
Hg_land_reemission.geos.2x25
Hg_land_reemission.geos.4x5
Re-emission of Hg0 on the GMAO 2° x 2.5° and 4° x 5° horizontal grids.
Hg_natural.geos.2x25
Hg_natural.geos.4x5
Emissions of Hg0 from natural sources, on the GMAO 2° x 2.5° and 4° x 5° horizontal grids. Based on Frank et al 1999 (see citation above).
Hg_ocean.geos.2x25
Hg_ocean.geos.4x5
Oceanic emissions of Hg0 on the GMAO 2° x 2.5° and 4° x 5° grids. These files will be read if switch LDYNOCEAN=F in the input.geos file.
ekman_upvel.geos.2x25
ekman_upvel.geos.4x5
Ekman upwelling velocity [cm/s] for the dynamic mercury ocean model, on the GMAO 2° x 2.5° and 4° x 5° horizontal grids. These files will be read if switch LDYNOCEAN=T in the input.geos file.
The velocity is The ekman velocity is calculated as:
k (upward unit vector) dot (del operator) x (tau / rho / f)
where
   * rho is the density of sea water,
   * f is the coriolis parameter, and
   * tau is monthly global wind stress from Hellerman and Rosenstein 1983 (see citation above).
mld.geos.2x25
mld.geos.4x5
Mixed layer depth [cm] for the dynamic mercury ocean model, on the GMAO 2° x 2.5° and 4° x 5° horizontal grids. These files will be read if switch LDYNOCEAN=T in the input.geos file. Based on Kara et al 2003 (see citation above).
modis_npp.geos.2x25
modis_npp.geos.4x5
MODIS net primary productivity files for the dynamic mercury ocean model, on the GMAO 2° x 2.5° and 4° x 5° horizontal grids. These files will be read if switch LDYNOCEAN=T in the input.geos file. Taken from Esaias (1996) (see citation above).
4.2.26 The mercury_201002 subdirectory
NOTES:
   1. Some data for the mercury simulation is also kept on the 4° x 5° grid, in the GEOS_4x5/mercury_201007/ directory.
REFERENCES:
   1. GEOS-Chem wiki: Mercury simulation
   2. Streets, D.; Zhang, Q.; Wu, Y. Projections of Global Mercury Emissions in 2050, Environ. Sci. Technol, 43, 2983-2988. DOI: 10.1021/es802474j, 2009.
   3. Holmes, C.D., D.J. Jacob, E.S. Corbitt, J. Mao, X. Yang, R. Talbot, and F. Slemr, Global atmospheric model for mercury including oxidation by bromine atoms, Atmos. Chem. and Phys., 10, 12037-12057, 2010.
   4. Pacyna, E.G., J.M. Pacyna, K. Sundseth, J. Munthe, K. Kindbom, S. Wilson, F. Steenhuisen, and P. Maxson, Global emission of mercury to the atmosphere from anthropogenic sources in 2005 and projections to 2020, Atmos. Environ., 44, 2487 - 2499, 2010.
Files
Description
GEIA_Hg0.geos.1x1.2005
GEIA_Hg2.geos.1x1.2005
GEIA_HgP.geos.1x1.2005
Anthropogenic emissions of Hg0 (elemental mercury), Hg2 (divalent mercury), and HgP (particulate mercury) from the GEIA 2005 inventory (cf Pacyna et al., 2010). GEIA 2005 emissions include artisinal mining, which was not included in GEIA 2000.
Data are on the GMAO 1° x 1° grid. The binary punch files were prepared by Bess Corbit.
NOTE: As of GEOS - Chem v9 - 01 - 02, GEIA 2005 is the standard anthropogenic emissions inventory for the mercury simulation.
GEIA_Streets_Hg0.geos.1x1.2006
GEIA_Streets_Hg2.geos.1x1.2006
GEIA_Streets_HgP.geos.1x1.2006
Anthropogenic emissions of Hg0 (elemental mercury), Hg2 (divalent mercury), and HgP (particulate mercury) from the GEIA 2000 inventory, scaled to regional totals from David Streets for the year 2006 (cf Streets et al 2009, Holmes et al, 2010). Data are on the GMAO 1° x 1° grid.
4.2.27 The mercury_201205 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Mercury simulation
   2. Streets, D.; Zhang, Q.; Wu, Y. Projections of Global Mercury Emissions in 2050, Environ. Sci. Technol, 43, 2983-2988. DOI: 10.1021/es802474j, 2009.
Files
Description
GEIA_Streets_[SCENARIO]_Hg0.geos.1x1.2050
GEIA_Streets_[SCENARIO]_Hg0_[REGION].geos.1x1.2050
GEIA_Streets_[SCENARIO]_Hg2.geos.1x1.2050
GEIA_Streets_[SCENARIO]_Hg2_[REGION].geos.1x1.2050
GEIA_Streets_[SCENARIO]_HgP.geos.1x1.2050
GEIA_Streets_[SCENARIO]_HgP_[REGION].geos.1x1.2050
Anthropogenic emissions of Hg0 (elemental mercury), Hg2 (divalent mercury), and HgP (particulate mercury) from the GEIA 2000 inventory, scaled to regional totals from David Streets future scenarios for the year 2050. SCENARIO is A1B, A2, B1, or B2.
REGION is:
   * Central America (CAM)
   * Canada (CAN)
   * East Africa (EAF)
   * East Asia (EAS)
   * Eastern Europe (EEU)
   * Europe (EUR)
   * Japan (JPN)
   * Middle East (MDE)
   * North Africa (NAF)
   * Oceanic (OCE)
   * South Africa (SAF)
   * South America (SAM)
   * South Asia (SAS)
   * Southeast Asia (SEA)
   * Former USSR (SOV)
   * United States (USA)
   * West Africa (WAF)
Data are on the GMAO 1° x 1° grid.
GEIA_Streets_PRESENT_Hg0.geos.1x1.2006
GEIA_Streets_PRESENT_Hg0_[REGION].geos.1x1.2006
GEIA_Streets_PRESENT_Hg2.geos.1x1.2006
GEIA_Streets_PRESENT_Hg2_[REGION].geos.1x1.2006
GEIA_Streets_PRESENT_HgP.geos.1x1.2006
GEIA_Streets_PRESENT_HgP_[REGION].geos.1x1.2006
Anthropogenic emissions of Hg0 (elemental mercury), Hg2 (divalent mercury), and HgP (particulate mercury) from the GEIA 2000 inventory, scaled to regional totals from David Streets for the year 2006 (cf Streets et al 2009, Holmes et al, 2010). REGION is the same as those listed above.
Data are on the GMAO 1° x 1° grid.
4.2.28 The NEI2005_201007 subdirectory
NOTES:
   1. The NEI 2005 emissions in this directory were reprocessed to fix a bug. These now supersede the older files in the NEI2005_200910 directory.
   2. Emissions are distributed on 5 levels
REFERENCES:
   1. GEOS-Chem wiki: EPA/NEI05 North American Inventory
Files
Description
NEI2005.GEOS3.1x1.AVG.bpch
Emissions for NOx / SO2 / CO / VOC / NIT / BC / OC on 1° x 1° grid for GEOS3
NEI2005.GEOS4.1x1.AVG.bpch
Emissions for NOx / SO2 / CO / VOC / NIT / BC / OC on 1° x 1° grid for GEOS4
NEI2005.GEOS5.1x1.AVG.bpch
Emissions for NOx / SO2 / CO / VOC / NIT / BC / OC on 1° x 1° grid for GEOS5
NEI2005.GEOS5.1t2x2t3.AVG.bpch
Emissions forNOx / SO2 / CO / VOC / NIT / BC / OC on 0.5° x 0.667° grid for GEOS5
usa.mex.mask.nei2005.geos.1x1
Mask to use NEI 2005 emissions over USA and MEXICO
usa.can.mask.nei2005.geos.1x1
Mask to use NEI 2005 emissions over USA and CANADA
usa.can.mex.mask.nei2005.geos.1x1
Mask to use NEI 2005 emissions over USA, MEXICO and CANADA
usa.mask.nei2005.geos.1x1
Mask to use NEI 2005 emissions over USA
4.2.29 The Olson_Land_Map_201203 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Olson land map
Files
Description
Olson_1992_Drydep_Inputs.nc
NetCDF file containing inputs for dry deposition corresponding to the Olson 1992 land map.
Olson_1992_Land_Map.05x05.generic.nc
NetCDF file containing informatin for Olson 1992 land map, such as Olson land types and surface areas.
Olson_1992_Soil_NOx_Inputs_MODIS_Biomes.nc
NetCDF file containing resistances for MODIS/KOPPEN biome types. Units are in s m[-1].
Olson_2001_Drydep_Inputs.nc
NetCDF file containing inputs for dry deposition corresponding to the Olson 2001 land map.
Olson_2001_Land_Map.025x025.generic.nc
NetCDF file containing informatin for Olson 2001 land map, such as Olson land types and surface areas.
4.2.30 PARANOX_201202 subdirectory
NOTES:
   1. These files are in flat binary format, NOT bpch format.
REFERENCES:
   1. GEOS-Chem wiki: PARANOX ship plume model
Files
Description
FracNOx_binary_5hrs_20gs.dat
File containing the fraction of NOx remaining for ship emissions (unitless).
IntOPE_binary_5hrs_20gs.dat
Binary file containing integrated Ozone Production Efficiency (OPE) for ship emissions. Units are in molec O3 produced/molec NOx lost.