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: geos-chem-support@as.harvard.edu
      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.
2.5.2.1 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. 
2.5.2.2 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:
2.5.3.1 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. 
2.5.3.2 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)
2.5.4.1 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           $(ROOT_LIBRARY_DIR)/lib
where root_library_dir is the directory into which you installed the libraries, as described above. Then to accept the changes, type source ~/.cshrc at the Unix prompt. 
2.5.4.2 With sh or bash
If you use Bourne-shell (sh), then add the following lines to your .profile file. If you use Bourne-Again shell (bash), then add these same lines to your .bashrc file.
ROOT_LIBRARY_DIR=root_library_dir
GC_BIN=$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.
4.2.31 The SST_200508 subdirectory
NOTES:
   1. The raw SST data from NOAA was converted into binary punch (bpch) file format by Rokjin Park (rjp.snu.ac.kr). Rokjin Park also regridded these files to the GMAO 1° x 1° grid.
   2. Binary punch files were created for each year (1985-2004), with each file containing 12 months of monthly-mean data.
REFERENCES:
   1. Reynolds, R.W., N.A. Rayner, T.M. Smith, D.C. Stokes, and W. Wang, An Improved In Situ and Satellite SST Analysis for Climate, J. Climate, 15, 1609-1625, 2002.
Files
Description
SST.geos.1x1.1985
SST.geos.1x1.1986
SST.geos.1x1.1987
SST.geos.1x1.1988
SST.geos.1x1.1989
SST.geos.1x1.1990
SST.geos.1x1.1991
SST.geos.1x1.1992
SST.geos.1x1.1993
SST.geos.1x1.1994
SST.geos.1x1.1995
SST.geos.1x1.1996
SST.geos.1x1.1997
SST.geos.1x1.1998
SST.geos.1x1.1999
SST.geos.1x1.2000
SST.geos.1x1.2001
SST.geos.1x1.2002
SST.geos.1x1.2003
SST.geos.1x1.2004
SST.geos.1x1.2005
SST.geos.1x1.2006
SST.geos.1x1.2007
SST.geos.1x1.2008
NOAA OI.v2 sea surface temperatures on the GMAO 1° x 1° grid. Each data file has 12 months of data. At present, years 1985-2008 are available. Additional years may be added as the data becomes available.
The NOAA OI.v2 SST monthly fields are derived by a linear interpolation of the weekly optimum interpolation (OI) version 2 fields to daily fields then averaging the daily values over a month.
  
4.2.32 The strat_chem_201206 directory
Please see Chapter 4.3.25 for more information about the contents of the strat_chem_201206/ subdirectory.
The GEOS_1x1/strat_chem_201206/ subdirectory contains the 2 x 2.5 files, which are then regridded to nested-grid resolution.
4.2.33 The Streets_200607 subdirectory
NOTES:
   1. There are actually two types of data. The data files below marked Streets_XXX_FF_2000.generic.1x1 are from the Streets SE Asia inventory. However, the CO in this inventory was too low over China. Therefore, we replace the CO over China with the CO from the file Streets_CO_FF_2001.generic.1x1.
REFERENCES:
   1. GEOS-Chem wiki: David Streets regional inventory for China/SE Asia
   2. Streets, D.G, Q. Zhang, L. Wang, K. He, J. Hao, Y. Wu, Y. Tang, and G.C. Carmichael, Revisiting China's CO emissions after the Transport and Chemical Evolution over the Pacific (TRACE-P) mission: Synthesis of inventories, atmospheric modeling, and observations, J. Geophys. Res, 111, D14306, doi:10.1029/2006JD007118, 2006.
   3. Streets, D.G., T.C. Bond, G.R. Carmichael, S.D. Fernandes, Q. Fu, Z. Klimont, S.M. Nelson, N.Y. Tsai, M.Q. Wang, J-H. Woo, and K.F. Yarber, An inventory of gaseous and primary aerosol emissions in Asia in the year 2000, J. Geophys. Res, 108, D21, doi:10.1029/2002JD003093, 2003.
Files
Description
China_mask.generic.1x1
China mask file for 2001 emissions of CO, on the generic 1° x 1° grid. 
This masking file is meant to be used with:
Streets_CO_FF_2000.generic.1x1.
NH3-Streets-SeasonalScalar.generic.1x1
Seasonal scale factors used to apply seasonal variation to NH3 following the methodology of Lex Bouwman.
SE_Asia_mask.generic.1x1
SE Asia mask for 2000 emissions on the generic 1° x 1° grid. 
This masking file is meant to be used with the emissions in the files named: Streets_XXX_FF_2000.generic.1x1, where XXX = NOx, SO2, NH3, CH4, CO2
Streets_CH4_FF_2000.generic.1x1
CH4 emissions for 2000 over SE Asia, on the generic 1° x 1° grid. Units are [kg CH4/yr].
Streets_CO2_FF_2000.generic.1x1 
CO2 emissions for 2000 over SE Asia, on the generic 1° x 1° grid. . This file includes the large point source emissions. Units are [kg CO2/yr].
Streets_CO_BF_2001_monthly.generic.1x1
Monthly CO biofuel emissions for 2001 over SE Asia, on the generic 1° x 1° grid. 
Streets_CO_FF_2000.generic.1x1
CO emissions for 2000 over SE Asia, on the generic 1° x 1° grid. 
Streets_CO_FF_2001.generic.1x1
CO emissions for 2000, over China only, on the generic 1° x 1° grid. 
NOTE: This file "overwrites" the emissions in the file Streets_CO_FF_2000.generic.1x1 over China only. 
Streets_CO_FF_2001_monthly.generic.1x1
Monthly CO emissions for 2001, over China only, on the generic 1° x 1° grid. 
Streets_NH3_FF_2000.generic.1x1
NH3 emissions for 2000 over SE Asia on the generic 1° x 1° grid. Units are [kg NH3/yr].
Streets_NOx_BF_2004_monthly.generic.1x1
Monthly NOx biofuel emissions for 2004 over SE Asia on the generic 1° x 1° grid. This file includes the large point source emissions. Units are [kg NO2/yr]. 
Streets_NOx_FF_2000.generic.1x1
NOx emissions for 2000 over SE Asia on the generic 1° x 1° grid. This file includes the large point source emissions. Units are [kg NO2/yr]. 
Streets_NOx_FF_2004_monthly.generic.1x1
Monthly NOx emissions for 2004 over SE Asia on the generic 1° x 1° grid. This file includes the large point source emissions. Units are [kg NO2/yr]. 
Streets_SO2_FF_2000.generic.1x1
SO2 emissions for 2000 over SE Asia on the generic 1° x 1° grid. This file includes the large point source emissions. Units are [kg NO2/yr].
4.2.34 The Streets_200812 subdirectory
NOTES:
   1. The bpch files in this directory were created from 2 separate inventories (original resolution: 0.5° x 0.5° resolution):
         o Inventory 1: Speciated VOC emissions (ACET,ALD2,ALK4,C2H6,C3H8,CH2O,ISOP,MEK,PRPE) for various sectors -- specially created for GEOS-Chem by D. Streets.
         o Inventory 2: Emissions for SO2, NOx, CO, total VOC, PM10, PM2.5, BC, and OC for various sectors. This was the Streets INTEX-B inventory.
   2. Even though Inventory 2 has total VOC, we cannot use this for GEOS-Chem. GEOS-Chem requires VOC's to be speciated into the various hydrocarbons (ACET,ALD2,ALK4,C2H6,C3H8,CH2O,ISOP,MEK,PRPE), so we use Inventory 1.
   3. IMPORTANT: Biofuel emissions are not separated from anthropogenic emissions.
REFERENCES:
   1. GEOS-Chem wiki: David Streets regional inventory for China/SE Asia
Files
Description
Streets_<VOC>_dob_2006.generic.1x1
Streets_<VOC>_dof_2006.generic.1x1
Streets_<VOC>_dop_2006.generic.1x1
Streets_<VOC>_ind_2006.generic.1x1
Streets_<VOC>_pow_2006.generic.1x1
Streets_<VOC>_tra_2006.generic.1x1
Files for speciated VOC's, taken from Inventory 1, for each of the various emission sectors. 
<VOC> = ACET, ALD2, ALK4, C2H6, C3H8, CH2O, ISOP, MEK, PRPE
Emission sectors: 
   * dob = domestic biofuel
   * dof = domestic fossil fuel
   * dop = domestic non-combustion
   * ind = industry
   * pow = power plants
   * tra = transportation
Data is placed on the generic 1° x 1° grid.
Streets_<SPEC>_ind_2006.generic.1x1
Streets_<SPEC>_pow_2006.generic.1x1
Streets_<SPEC>_res_2006.generic.1x1
Streets_<SPEC>_tra_2006.generic.1x1
Files for the various species: 
<SPEC> = (NOX,CO,SO2) 
taken from Inventory 2, for each of the various emission sectors:
   * ind = industry
   * pow = power plants
   * res = residential 
   * tra = transportation
Data is placed on the generic 1° x 1° grid.
Streets_<SPEC>_2006.generic.1x1
Files including all sectors for each species from Inventory 1 and Inventory 2. 
NOTE: These are not used in GEOS-Chem.
SE_Asia_mask.generic.1x1
SE Asia mask for emissions on the generic 1° x 1° grid.
4.2.35 The TOMS_201203 subdirectory
NOTES:
   1. This is an update of the TOMS_200906 subdirectory.
REFERENCES:
   1. GEOS - Chem wiki: Overhead TOMS/SBUV merged O3 columns
   2. Data: http://acdb-ext.gsfc.nasa.gov/Data_services/merged/
Files
Description
TOMS_O3col_YYYY.geos.1x1
12 months of TOMS/SBUV data on the GMAO 1° x 1° grid for years 
YYYY= 1971 ... 2010
4.2.36 The VISTAS_200811 subdirectory
NOTES:
   1. NOx inventory from Visibility Improvement State and Tribal Association of the Southeast (VISTAS), which "is a collaborative effort of state governments, tribal governments, and various federal agencies established to initiate and coordinate activities associated with the management of regional haze, visibility and other air quality issues in the Southeastern United States."
REFERENCES:
   1. Data: http://www.vistas-sesarm.org/index.asp
Files
Description
ARP-SeasonalVariation-YYYY-1.1x1
ARP-SeasonalVariation-YYYY-2.1x1
ARP-SeasonalVariation-YYYY-3.1x1
ARP-SeasonalVariation-YYYY-4.1x1
ARP-SeasonalVariation-YYYY-5.1x1
ARP-SeasonalVariation-YYYY-6.1x1
ARP-SeasonalVariation-YYYY-7.1x1
ARP-SeasonalVariation-YYYY-8.1x1
ARP-SeasonalVariation-YYYY-9.1x1
ARP-SeasonalVariation-YYYY-10.1x1
ARP-SeasonalVariation-YYYY-11.1x1
ARP-SeasonalVariation-YYYY-12.1x1
Ozone seasonal regulation factors on the GMAO 1° x 1° grid.
Vistas-NOx-1.1x1
Vistas-NOx-2.1x1
Vistas-NOx-3.1x1
Vistas-NOx-4.1x1
Vistas-NOx-5.1x1
Vistas-NOx-6.1x1
Vistas-NOx-7.1x1
Vistas-NOx-8.1x1
Vistas-NOx-9.1x1
Vistas-NOx-10.1x1
Vistas-NOx-11.1x1
Vistas-NOx-12.1x1
NOx emissions on the GMAO 1° x 1° grid.
Vistas-Ratio-NOx-1.1x1
Vistas-Ratio-NOx-2.1x1
Vistas-Ratio-NOx-3.1x1
Vistas-Ratio-NOx-4.1x1
Vistas-Ratio-NOx-5.1x1
Vistas-Ratio-NOx-6.1x1
Vistas-Ratio-NOx-7.1x1
Vistas-Ratio-NOx-8.1x1
Vistas-Ratio-NOx-9.1x1
Vistas-Ratio-NOx-10.1x1
Vistas-Ratio-NOx-11.1x1
Vistas-Ratio-NOx-12.1x1

wkday_an_scalar.nei99.geos.1x1
wkend_an_scalar.nei99.geos.1x1
Weekend/weekday factors on the GMAO 1° x 1° grid.
4.2.37 The volcano_SO2_201010 subdirectory
NOTES:
   1. The data in this directory reflect the latest updates from Thomas Diehl as of Oct 2010. 
   2. The data in this directory now supersede the previous data files stored in volcano_SO2_200909.
   3. Data is now available from 1979 - 2009.
REFERENCES:
   1. GEOS-Chem wiki: Volcanic SO2 emissions from Aerocom
   2. Data: http://www-lscedods.cea.fr/aerocom/AEROCOM_HC/volc/
Files
Description
YYYY/SO2_volc.erup.YYYYMM.generic.1x1
Monthly file of eruptive emissions on the generic 1° x 1° grid
for years YYYY= 1979 ... 2009. Units are in kg/event/day.
YYYY/SO2_volc.nonerup.YYYYMM.generic.1x1
Monthly file of non-eruptive emissions on the generic 1° x 1° grid
for years YYYY= 1979 ... 2009. Units are in kg/event/day.
4.2.38 The volcano_SO2_201206 subdirectory
NOTES:
   1. The contents of this directory contain the same data as in volcano_201010, except data is stored in netCDF format.
   2. The data in this directory reflect the latest updates from Thomas Diehl as of Oct 2010. 
   3. The data in this directory now supersede the previous data files stored in volcano_SO2_200909.
   4. Data is now available from 1979 - 2009.
REFERENCES:
   1. GEOS-Chem wiki: Volcanic SO2 emissions from Aerocom
   2. Data: http://www-lscedods.cea.fr/aerocom/AEROCOM_HC/volc/
Files
Description
YYYY/Volcano_SO2_YYYYMM.nc
Monthly file of eruptive emissions on the generic 1° x 1° grid
for years YYYY= 1979 ... 2009 

4.3 The GEOS_2x2.5, GEOS_4x5, and GCAP_4x5 directories
The GEOS_2x2.5, GEOS_4x5, and GCAP_4x5 data directories contain (in general) the same data files for both the GEOS 2° x 2.5° and 4° x 5° grids. For purposes of clarity we will discuss them together as a group.
Directory 
Contents
GEOS_2x2.5
Contains data files at 2° x 2.5° horizontal resolution for GEOS - 4, GEOS - 5, MERRA, and GEOS - 5.7.2 vertical grids. Data files are stored into various subdirectories of this root directory.
NOTE: The Dalhousie archive (rain.ucis.dal.ca) stores MERRA data at 2° x 2.5° resolution. The Harvard archive (ftp.as.harvard.edu) only stores MERRA data at 4° x 5° resolution.
GEOS_4x5
Contains data files for 4° x 5° horizontal resolution for GEOS - 4, GEOS - 5, MERRA, and GEOS - 5.7.2 vertical grids. Data files are stored into various subdirectories of this root directory.
GCAP_4x5
Contains data files for 4° x 5° horizontal resolution for the GCAP vertical grid. Data files are stored into various subdirectories of this root directory.
The following extensions are used to denote different GCAP and GEOS model types:
Extension
Model Type
Grid Type
geos.2x25
any GEOS 
2° x 2.5° grid, surface data only (144 x 91)
geos4.2x25 
GEOS - 4
2° x 2.5° grid, 55 vertical levels (met) or 30 vertical levels (data) 
geos5.2x25
GEOS - 5
2° x 2.5° grid, 72 vertical levels (met) or 47 vertical levels (data) 
gcap.4x5
GCAP
4° x 5° GCAP grid, 23 vertical levels
geos.4x5
any GEOS 
4° x 5° grid, surface only (72 x 46)
geos4.4x5
GEOS - 4
4° x 5° grid, 55 vertical levels (met) or 30 vertical levels (data) 
geos5.4x5
GEOS - 5
4° x 5° grid, 72 vertical levels (met) or 47 vertical levels (data) 
merra.2x25
MERRA
2° x 2.5° grid, 72 vertical levels (met) or 47 vertical levels (data) 
merra.4x5
MERRA
4° x 5° grid, 72 vertical levels (met) or 47 vertical levels (data) 
NOTES:
   1. 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.
   2. Files with a .geos*.2x25 extension are located in subdirectories of GEOS_2x2.5.
   3. Files with a .geos*.4x5 or *.merra.4x5 extension are located in subdirectories of GEOS_4x5.
   4. Files with a .gcap.4x5 extension are located in subdirectories of GCAP_4x5.
   5. Each subdirectory of GEOS_2x2.5, GEOS_4x5, and GCAP_4x5 now contains a README file for further reference. 
   6. Assume that all files listed below are in binary punch (bpch) format unless specified otherwise.
   7. The GEOS - 5.7.2 and MERRA 72-layer full vertical grids are identical to the GEOS-5 72-layer full vertical grid
   8. The GEOS - 5.7.2 and MERRA 47-layer full vertical grids are identical to the GEOS-5 47 layer full vertical grid
                                       

4.3.1 The aircraft_NOx_200202 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Aircraft NOx emissions inventory
   2. Wang, Y., D.J. Jacob, and J.A. Logan, Global simulation of tropospheric O3-NOx-hydrocarbon chemistry, 1. Model formulation, J. Geophys. Res., 103/D9, 10,713-10,726, 1998.
Files
Description
airjan.2x25
airfeb.2x25
airmar.2x25
airapr.2x25
airmay.2x25
airjun.2x25
airjul.2x25
airaug.2x25
airsep.2x25
airoct.2x25
airnov.2x25
airdec.2x25

airjan.4x5
airfeb.4x5
airmar.4x5
airapr.4x5
airmay.4x5
airjun.4x5
airjul.4x5
airaug.4x5
airsep.4x5
airoct.4x5
airnov.4x5
airdec.4x5
Monthly mean emissions of Aircraft NOx (based on Wang et al, 1998) for the GCAP 4° x 5° grid and the GMAO 2° x 2.5° and 4° x 5° grids.
Units are kg NOx/4h. Files are in plain-text format.
 
4.3.2 The biofuel_200202 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Biofuel emissions
   2. Yevich, R. and J. A. Logan, An assesment of biofuel use and burning of agricultural waste in the developing world, Global Biogeochem. Cycles, 17(4), 1095, doi:10.1029/2002GB001952, 2003.
Files
Description
biofuel.geos.2x25
biofuel.geos.4x5
biofuel.gcap.4x5
Biofuel burning emissions (for the GCAP 4° x 5° grid and the GMAO 2° x 2.5° and 4° x 5° grids) from Jennifer Logan, Rose Yevich, and Bryan Duncan. 
Revised version, Feb 2002, now includes emissions of 10 tracers:
NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6
4.3.3 The bromine_201205 subdirectory
Please see Chapter 4.2.5 for more information about the contents of the bromine_201205/ subdirectory.
The GEOS_1x1/bromine_201205/ subdirectory contains the 2° x 2.5° files, which are then regridded to the model resolution.
4.3.4 The C3H8_C2H6_200109 subdirectory
Files
Description
C3H8_C2H6_ngas.geos.2x25
C3H8_C2H6_ngas.geos.4x5
C3H8_C2H6_ngas.gcap.4x5
Anthropogenic propane and ethane emissions computed from natural gas by James Wang and Yaping Xiao.
4.3.5 The carbon_200411 subdirectory
NOTES:
   1. This an update of the now obsolete carbon_200404/ subdirectory.
REFERENCES:
   1. GEOS-Chem wiki: Carbonaceous aerosols
   2. Park, R. J., D. J. Jacob, M. Chin and R. V. Martin, Sources of carbonaceous aerosols over the United States and implications for natural visibility, J. Geophys. Res., 108(D12), 4355, doi:10.1029/2002JD003190, 2003.
Files
Description
BCOC_TBond_biofuel.geos.2x25
BCOC_TBond_biofuel.geos.4x5
Emissions of black carbon and organic carbon aerosols from biofuels (baseline year: 2001), according to the Tami Bond et al (2004) inventory. Units are kg C/year.
BCOC_TBond_biomass.geos.2x25
BCOC_TBond_biomass.geos.4x5
Emissions of black carbon and organic carbon aerosols from biomass burning for baseline year 2001, according to the Tami Bond et al (2004) inventory. Units are kg C/year.
BCOC_TBond_fossil.geos.2x25
BCOC_TBond_fossil.geos.4x5
Emissions of black carbon and organic carbon aerosols from fossil fuels (baseline year: 2001), according to the Tami Bond et al (2004) inventory. Units are kg C/year.
BCOC_anthsrce.geos.2x25
BCOC_anthsrce.geos.4x5
Monthly mean emissions (baseline year: 1998) of black carbon and elemental carbon from fossil fuels, according to the inventory of Cooke et al (1998), with seasonality imposed by R. Park (2004). Units are kg C/month.
BCOC_biofuel.geos.2x25
BCOC_biofuel.geos.4x5
Monthly mean emissions (baseline year: 1998) of black carbon and elemental carbon from biofuels, according to the inventory of Cooke et al (1998), with seasonality imposed by R. Park (2004). Units are kg C/month.
emis_fac.EC-OC.2x25
emis_fac.EC-OC.4x5
Emission factors that are used to compute the yield of black carbon and organic carbon from the GEOS - Chem biomass burning inventory. Contact: Rokjin Park (rjpsnu.ac.kr).
NVOC.geos.2x25
NVOC.geos.4x5
Emissions of non-volatile organic carbon (kg C/month). This is used for the secondary organic aerosol emissions. 
4.3.6 The carbon_200909 subdirectory
NOTES:
   1. This subdirectory contains updates for Bond's inventory for biofuel and fossil emissions compared to carbon_200411/
REFERENCES:
   1. GEOS-Chem wiki: Carbonaceous aerosols
   2. Bond, T.C. et al.: Historical emissions of black and organic carbon aerosol from energy-related combustion, 1850-2000, Global Biogeochem. Cycles, 21 GB2018, doi: 10.1029/2006GB002840, 2007.
Files
Description
BCOC_TBond_biofuel.2000.geos.2x25
BCOC_TBond_biofuel.2000.geos.4x5
Bond et al. 2007 biofuel emissions of EC and OC in [kg C/month]. 
BCOC_TBond_fossil.2000.geos.2x25
BCOC_TBond_biofuel.2000.geos.4x5
Bond et al. 2007 biofuel emissions of EC and OC in [kg C/month].
4.3.7 The CH3I subdirectory
NOTES:
   1. The CH3I simulation has not been used regularly in a couple of years. If you wish to work with this simulation then you will be responsible for bringing it up to the state of the science. 
Files
Description
ch4_rice.geos.2x25
ch4_rice.geos.4x5
Monthly methane emissions from rice paddies for CH3I simulation (Fung et al, 1991)
ch4_wetl.geos.2x25
ch4_wetl.geos.4x5
Monthly methane emissions from wetlands for CH3I simulation (Fung et al, 1991)
ocean_ch3i.geos.2x25
ocean_ch3i.geos.4x5
Aqueous concentrations of ocean CH3I
ocean_DOC.geos.4x5
Monthly mean values of Dissolved Organic Carbon (for CH3I simulation). 
ocean_npp.geos.2x25
ocean_npp.geos.4x5
Net Primary Productivity from the ocean (for CH3I simulation). 
radswg.geos.4x5
Contains monthly averaged solar insolation at the ground (for CH3I simulation).
4.3.8 The CH4_200911 subdirectory
NOTES:
   1. This is an update of the now obsolete CH4_200202 and CH4_200909 subdirectories
REFERENCES:
   1. GEOS-Chem wiki: CH4 simulation
   2. Termites and Soil Absorption: Regridded from 4x5 product described by Fung et. al. 1991
   3. Coal, gas_oil, livestock, rice, waste, other: From EDGAR version 4 inventory (http://edgar.jrc.ec.europa.eu/index.php)
Files
Description
coal.2004.geos.2x25
gas_oil.2004.geos.2x25
livestock.2004.geos.2x25
other.2004.geos.2x25
rice.2004.geos.2x25
soilabs.2004.geos.2x25
termites.2004.geos.2x25
waste.2004.geos.2x25

coal.2004.geos.4x5
gas_oil.2004.geos.4x5
livestock.2004.geos.4x5
other.2004.geos.4x5
rice.2004.geos.4x5
soilabs.2004.geos.4x5
termites.2004.geos.4x5
waste.2004.geos.4x5
Yearly methane emissions from coal mining, gas leakage and venting, livestock, rice paddies, soil absorption, termites, waste and other are included on GMAO 2° x 2.5° grid and GMAO 4° x 5° grid.
Units are molecules CH4/cm[2]/s.
GWETTOP/GWETTOP.YYYY.geos4.2x25
GWETTOP/GWETTOP.YYYY.geos5.2x25

GWETTOP/GWETTOP.YYYY.geos4.4x5
GWETTOP/GWETTOP.YYYY.geos5.4x5
Monthly and annual mean soil wetness.
For GEOS4, the data are for the years YYYY=2000 ... 2006
For GEOS5, the data are for the years YYYY=2004 ... 2009
wetlands/Carbon_litter.geos.2x25

wetlands/Carbon_litter.geos.4x5
Carbon emissions from litter as calculated in a 20th century simulation by the LPJ Vegetation Model
wetlands/Carbon_soil.geos.2x25

wetlands/Carbon_soil.geos.4x5
Carbon emissions from soil as calculated in a 20th century simulation by the LPJ Vegetation Model
wetlands/Wet_frac.geos.2x25

wetlands/Wet_frac.geos.4x5
Wet fraction in each grid cell follows the map in Bergamaschi et. al. 2007
wetlands/TSKIN.YYYY.geos4.2x25
wetlands/TSKIN.YYYY.geos5.2x25

wetlands/TSKIN.YYYY.geos4.4x5
wetlands/TSKIN.YYYY.geos5.4x5
Monthly and annual mean skin temperature
For GEOS4, the data are for the years YYYY=2000 ... 2006
For GEOS5, the data are for the years YYYY=2004 ... 2009
4.3.9 The CH4_201203 subdirectory
NOTES:
   1. This is an update of the CH4_200911 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: CH4 simulation
   2. Termites and Soil Absorption: Regridded from 4x5 product described by Fung et. al. 1991
   3. Coal, gas_oil, livestock, rice, waste, other: From EDGAR version 4 inventory (http://edgar.jrc.ec.europa.eu/index.php)
Files
Description
resident.2x25.2004.bpch

resident.4x5.2004.bpch 
Yearly methane emissions from biofuel burning are included on GMAO 2° x 2.5° grid and GMAO 4° x 5° grid.
Units are molecules CH4/cm[2]/s.
gmi.ch4loss.geos5_47L.2x25.bpch

gmi.ch4loss.geos5_47L.4x5.bpch 
CH4 loss frequencies. These values constitute a linearized stratospheric CH4 chemistry scheme. Loss frequencies from 4° x 5° output are from the GMI model. (Courtesy of Lee Murray)
Values are for "generic" year 1985. Units are 1/s.
GWETTOP/GWETTOP.geos5.2x25.YYYY.bpch

GWETTOP/GWETTOP.geos5.4x5.YYYY.bpch
Monthly and annual mean soil wetness.
For GEOS - 5, the data are for the years YYYY=2004 ... 2011
wetlands/Carbon_litter.2x25.bpch

wetlands/Carbon_litter.4x5.bpch
Carbon emissions from litter as calculated in a 20th century simulation by the LPJ Vegetation Model
wetlands/Carbon_soil.2x25.bpch

wetlands/Carbon_soil.4x5.bpch
Carbon emissions from soil as calculated in a 20th century simulation by the LPJ Vegetation Model
wetlands/Wetfrac.2x25.bpch

wetlands/Wetfrac.4x5.bpch
Wet fraction in each grid cell follows the map in Bergamaschi et. al. 2007
wetlands/TSKIN.geos5.2x25.YYYY.bpch

wetlands/TSKIN.geos5.4x5.YYYY.bpch
Monthly and annual mean skin temperature
For GEOS - 5, the data are for the years YYYY=2004 ... 2011
4.3.10 The CO2_201003 subdirectory
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.geos.2x25
Aviation_Regions.geos.4x5
File that defines the aircraft regions for the GMAO 2° x 2.5° and 4° x 5° grids.
Net_terrestrial_exch_5.29Pg.geos.2x25
Net_terrestrial_exch_5.29Pg.geos.4x5
Net terrestrial exchange data from TRANSCOM 3 climatology (cf. Baker et al 2006) on the GMAO 2° x 2.5° and 4° x 5° grids.
biofuel/biofuel_CO2.2x25-1985
biofuel/biofuel_CO2.4x5-1985
CO2 biofuel emissions (base year 1985) from Yevich & Logan 2003, on the generic 1° x 1° grid.
biofuel/biofuel_CO2.2x25-1995
biofuel/biofuel_CO2.4x5-1995
CO2 biofuel emissions from Yevich & Logan 2003, on the the GMAO 2° x 2.5° and 4° x 5° grids.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
ChemSrc/CH4_source.geos.2x25.bpch
ChemSrc/CH4_source.geos.4x5.bpch
Chemical source of CH4 [kg] archived by Ray Nassar. The data is on the GMAO 2° x 2.5° and 4° x 5° grids.
ChemSrc/CO2_prod_rates_YYYY.geos4.2x25.30L
ChemSrc/CO2_prod_rates_YYYY.geos4.4x5.30L
Chemical source of CO2 [molec/cm3/s] archived by Ray Nassar, for years YYYY = 2001..2006. The data is on the GMAO GEOS - 4 30-level grid at both 2° x 2.5° and 4° x 5° horizontal resolution.
ChemSrc/CO2_prod_rates_YYYY.geos5.2x25.47L
ChemSrc/CO2_prod_rates_YYYY.geos5.4x5.47L
Chemical source of CO2 [molec/cm3/s] archived by Ray Nassar, for years YYYY = 2004..2009. The data is on the GMAO GEOS - 5 47-level grid at both 2° x 2.5° and 4° x 5° horizontal resolution. 
ChemSrc/Isoprene-2004.geos.2x25
ChemSrc/Isoprene-2004.geos.4x5
Chemical source of Isoprene [molec/cm2/s] archived by Kevin Wecht. The data is on the GMAO 2° x 2.5° and 4° x 5° grids.
ChemSrc/Monoterpene-2004.geos5.2x25
ChemSrc/Monoterpene-2004.geos5.4x5
Chemical source of Monoterpenes [molec/cm2/s] archived by Kevin Wecht. The data is on the GMAO 2° x 2.5° and 4° x 5° grids.
fossilfuel_andres/annual/ff.YYYY.geos.2x25
fossilfuel_andres/annual/ff.YYYY.geos.4x5
Annual CO2 fossil fuel emissions from Robert J. Andres, for years YYYY = 1985 to 2006. The data is on the GMAO 2° x 2.5° and 4° x 5° grids.
NOTE: This data is now obsolete and is superseded by the data files contained in annual_v2010.
fossilfuel_andres/annual_v2010/ff.YYYY.geos.2x25
fossilfuel_andres/annual_v2010/ff.YYYY.geos.4x5
Updated annual CO2 fossil fuel emissions [molec/cm2/s] from the CDIAC inventory (version 2010, by Robert J. Andres), for years YYYY = 1979..2009. The data are on the GMAO 2° x 2.5° and 4° x 5° grids.
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.
fossilfuel_andres/monthly_v2010/ff.YYYYMM.geos.2x25
fossilfuel_andres/monthly_v2010/ff.YYYYMM.geos.4x5
Updated monthly CO2 fossil fuel emissions [molec/cm2/s] from the CDIAC inventory (version 2010, by Robert J. Andres), for years YYYY = 1979..2009 and months MM = 01..12. The data are on the GMAO 2° x 2.5° and 4° x 5° grids.
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.
Ocean/Taka2009_OceanCO2_MM.geos.2x25
Ocean/Taka2009_OceanCO2_MM.geos.4x5
Monthly mean oceanic CO2 exchange [molec/cm2/s] from Takahashi et al, 2009, for months MM = 01..12. The data are on the GMAO 2° x 2.5° and 4° x 5° grids.
Ocean/Taka2009_OceanCO2_annual.geos.2x25
Ocean/Taka2009_OceanCO2_annual.geos.4x5
Annual mean oceanic CO2 exchange [molec/cm2/s] from Takahashi et al, 2009. The data are on the GMAO 2° x 2.5° and 4° x 5° grids.
4.3.11 The dust_200605 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Mineral dust aerosols
   2. Fairlie, T. D., D.J. Jacob, and R.J. Park, The impact of transpacific transport of mineral dust in the United States, Atmos. Environ., 41, 1251-1266, 2007.
Files
Description
dst_tibds.geos.2x25
dst_tibds.geos.4x5
dst_tibds.gcap.4x5
Time-invariant fields which are used as input by the DEAD dust emissions routines (cf. C. Zender). These have been converted to binary punch format by Duncan Fairlie and Bob Yantosca.
dst_tvbds.geos.2x25
dst_tvbds.geos.4x5
dst_tvbds.gcap.4x5
Time-variant (e.g. monthly mean) fields which are used as input by the DEAD dust emissions routines (cf. C. Zender). These have been converted to binary punch format by Duncan Fairlie and Bob Yantosca. 
GOCART_src_fn.geos.2x25 
GOCART_src_fn.geos.4x5
GOCART_src_fn.gcap.4x5
File containing the GOCART dust source function (i.e. frac of grid box suitable for mobilization). Supplied by Duncan Fairlie and converted to bpch format by Bob Yantosca.
4.3.12 The EPA_NEI_200411 subdirectory
NOTES:
   1. The anthropogenic emissions from the EPA/NEI99 in this directory have been superseded by the data in the EPA_NEI_200708 and EPA_NEI_200806 directories. However, you should consider using the more recent EPA/NEI05 inventory.
   2. The biofuel emissions in this directory are still used by GEOS - Chem.
   3. The newer EPA/NEI05 inventory only contains anthropogenic emissions. GEOS - Chem will therefore use the biofuel emissions data contained in this directory (EPA_NEI_200411) when you select the EPA/NEI05 inventory.
REFERENCES:
   1. GEOS - Chem wiki: Anthropogenic Emissions
   2. GEOS - Chem wiki: EPA/NEI99 North American emissions inventory
   3. GEOS - Chem wiki: EPA/NEI05 North American emissions inventory
Files
Description
wkday_avg_bf.199901.geos.4x5
wkday_avg_bf.199902.geos.4x5
wkday_avg_bf.199903.geos.4x5
wkday_avg_bf.199904.geos.4x5
wkday_avg_bf.199905.geos.4x5
wkday_avg_bf.199906.geos.4x5
wkday_avg_bf.199907.geos.4x5
wkday_avg_bf.199908.geos.4x5
wkday_avg_bf.199909.geos.4x5
wkday_avg_bf.199910.geos.4x5
wkday_avg_bf.199911.geos.4x5
wkday_avg_bf.199912.geos.4x5 
EPA / NEI99 weekday biofuel 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, MSA, BCPI, OCPI, NH4
wkend_avg_bf.199901.geos.4x5
wkend_avg_bf.199902.geos.4x5
wkend_avg_bf.199903.geos.4x5
wkend_avg_bf.199904.geos.4x5
wkend_avg_bf.199905.geos.4x5
wkend_avg_bf.199906.geos.4x5
wkend_avg_bf.199907.geos.4x5
wkend_avg_bf.199908.geos.4x5
wkend_avg_bf.199909.geos.4x5
wkend_avg_bf.199910.geos.4x5
wkend_avg_bf.199911.geos.4x5
wkend_avg_bf.199912.geos.4x5
EPA / NEI99 weekday biofuel 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, MSA, BCPI, OCPI, NH4
4.3.13 The EPA_NEI_200708 subdirectory
NOTES:
   1. These directories are for the EPA/NEI99 emissions inventory. You should consider using the newer EPA/NEI2005 inventory.
   2. These directories include the same data than GEOS_1x1/EPA_NEI_200708 subdirectory but at resolutions 4° x 5° and 2° x 2.5°.
4.3.14 The EPA_NEI_200806 subdirectory
NOTES:
   1. These directories are for the EPA/NEI99 emissions inventory. You should consider using the newer EPA/NEI2005 inventory.
   2. Mask file in this directory is the same than in GEOS_1x1/EPA_NEI_200806 subdirectory but at resolutions 4° x 5° and 2° x 2.5°.
   3. The data are the same as EPA_NEI_200708, except for NOx (50% decrease over ozone season only from power plant and industry sectors) and CO (decrease of 60%). Base year for the updated NOx and CO is 2004, since they result from model comparison with ICARTT observations.
4.3.15 The fossil_200104 subdirectory
NOTES:
   1. The GEIA/Piccot inventory is the default inventory for the hydrocarbon emissions (EDGAR is used for NOx, CO, SOx).
   2. You should make sure to turn on the regional emissions inventories (e.g. CAC, BRAVO, EMEP, EPA/NEI, Streets, etc.). These will "overwrite" the GEIA/Piccot emissions in the various regions of the world with more up-to-date emissions.
REFERENCES:
   1. GEOS-Chem wiki: GEIA/Piccot anthropogenic emissions inventory
   2. Bey I., D. J. Jacob, R. M. Yantosca, J. A. Logan, B. Field, A. M. Fiore, Q. Li, H. Liu, L. J. Mickley, and M. Schultz, Global modeling of tropospheric chemistry with assimilated meteorology: Model description and evaluation , J. Geophys. Res., 106 , 23,073-23,096, 2001.
Files
Description
merge_nobiofuels.geos.2x25
merge_nobiofuels.geos.4x5
merge_nobiofuels.gcap.4x5
Anthropogenic emissions, with contributions from biofuels removed so as to avoid double-counting. Version released April 2001, by Jennifer Logan, Rose Yevich, and Amanda Staudt. Contains 10 emission species.
NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, ETHE, SOx
MELD_N96_70_HC
File containing day of week scale factors for anthropogenic emissions for the GMAO 4° x 5° grid (a similar file is available for the GCAP 4° x 5° grid). File is in plain-text format.
MELD2x25
File containing day of week scale factors for anthropogenic emissions for the GMAO 2° x 2.5° grid. File is in plain-text format.
4.3.16 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.2x25
BCOC/BCOC_anthsrce.YYYY.geos.4x5
BCOC/BCOC_anthsrce.YYYY.gcap.4x5
Monthly black carbon and organic carbon emissions [kg] from anthropogenic sources.
Data is available for the years 1850 to 2050 and is on the GMAO 2° x 2.5° grid, the GMAO 4° x 5° grid, and the GCAP 4° x 5° grid.
BCOC/BCOC_biofuel.YYYY.geos.2x25
BCOC/BCOC_biofuel.YYYY.geos.4x5 BCOC/BCOC_biofuel.TTTT.gcap.4x5
Monthly black carbon and organic carbon emissions [kg] from biofuel burning.
Data is available for the years 1850 to 2050 and is on the GMAO 2° x 2.5° grid, the GMAO 4° x 5° grid, and the GCAP 4° x 5° grid.
4.3.17 The hydrogen_200704 subdirectory
REFERENCES:
   1. Curci, G., G. Visconti, D.J. Jacob, and M.J. Evans, Tropospheric fate of Tunguska generated nitrogen oxides, Geophys. Res. Lett., 31, L06123, 2004.
   2. Deutsch et al., Nature, 445, 163-167 (2007).
Files
Description
H2COyield.geos3.2x25
H2COyield.geos3.4x5

H2COyield.geos4.2x25
H2COyield.geos4.4x5
Files containing relative H2/CO yield from photochemical production. This has been archived monthly (PH2/PCO using the PRODLOSS diagnostic and turning H2 on as an active species) from a full chemistry simulation at 4x5, v7 - 03 - 03, year 2001, GEOS - 3 met fields.
Data has been regridded to the GEOS - 3 2° x 2.5° grid and GEOS - 4 2° x 2.5° and 4° x 5° grids.
Ocean_H2_annual.geos3.2x25
Ocean_H2_annual.geos3.4x5

Ocean_H2_annual.geos4.2x25
Ocean_H2_annual.geos4.4x5
Ocean H2 emissions are based on the N2 oceanic fixation rates determined by Curtis Deutsch (University of Washington) by assimilating observed nutrient distributions in the oceans (see citation above).
Data has been regridded to the GEOS - 3 2° x 2.5° grid and GEOS - 4 2° x 2.5° and 4° x 5° grids.
stratO1D.geos3.2x25
stratO1D.geos3.4x5

stratO1D.geos4.2x25
stratO1D.geos4.4x5
The O1D fields were obtained from Gabriele Curci GEOS - Chem simulation in the stratosphere (GEOS - Chem v5 - 03).
Data has been regridded to the GEOS - 3 2° x 2.5° grid and GEOS - 4 2° x 2.5° and 4° x 5° grids.
4.3.18 The lightning_NOx_201101 subdirectory
NOTE: In GEOS - Chem v9 - 01 - 01, the following updates were made that impact the emissions of lightning NOx:
   1. Bug fix for incorrect cloud-top-height determination
   2. Addition of updated vertical release profiles (cf. Ott et al 2010)
   3. Removal of obsolete options from the source code (lightning_nox_mod.f)
REFERENCES:
   1. GEOS - Chem wiki: Lightning NOx emissions
   2. L.T. Murray, Changes affecting lightning NOx emissions in GEOS - Chem v9 - 01 - 01, January 2011
   3. Allen D., K.E. Pickering, B. Duncan, M. Damon, Impact of lightning NO emissions on North American photochemistry as determined using the Global Modeling Initiative GMI) model, J Geophys Res, 115, D22301, 2010.
   4. Allen, D.J., and K.E. Pickering, Evaluation of lightning flash rate parameterizations for use in a global chemical transport model, J Geophys Res, 107(D23), 4711, 2002
   5. Murray, L.T., J.A. Logan, D.J. Jacob, and R.C. Hudman, Spatial and interannual variability in lightning constrained by LIS/OTD satellite data for 1998-2006: implications for tropospheric ozone and OH, in preparation
   6. Ott L.E., K.E. Pickering, G.L. Stenchikov, D.J. Allen, A.J. DeCaria, B. Ridley, R.-F. Lin, S. Lang, W.-K. Tao, Production of lightning NOx and its vertical distribution calculated from three-dimensional cloud-scale chemical transport model simulations, J Geophys Res, 115, D04301, 2010.
   7. Pickering K.E., Y. Wang, W.-K. Tao, C. Price, J.-F. Müller, Vertical distributions of lightning NOx for use in regional and global chemical transport models, J Geophys Res, 103(D23), 31203-31216, 1998
   8. Price, C., and D.H. Rind, A simple lightning parameterization for calculating global lightning distributions, J Geophys Res, 97(D9), 9919-9933, 1992
   9. Price, C., and D.H. Rind, Modeling global lightning distributions in a general circulation model, Mon Weather Rev, 122(8), 1930-1939, 1994
   10. Sauvage B., R.V. Martin, A. van Donkelaar, X. Liu, K. Chance, L. Jaeglé, P. I. Palmer, S. Wu, and T.-M. Fu, Remote sensed and in situ constraints on processes affecting tropical tropospheric ozone. Atmos Chem Phys, 7, 815-838, 2007
Files
Description
light_dist.ott2010.dat
File containing vertical probability functions from Ott et al 2010
OTD-LIS-Local-Redist.CTH.v5.geos4.4x5
OTD-LIS-Local-Redist.CTH.v5.geos4.4x5
OTD/LIS flash redistribution factors for GEOS - 4 meteorology. Data is provided on the global 2° x 2.5° and 4° x 5° grids.
OTD-LIS-Local-Redist.CTH.v5.geos5.1.0.05x0666.CH
OTD-LIS-Local-Redist.CTH.v5.geos5.1.0.05x0666.NA
OTD-LIS-Local-Redist.CTH.v5.geos5.1.0.2x25
OTD-LIS-Local-Redist.CTH.v5.geos5.1.0.4x5
OTD/LIS flash redistribution factors for GEOS - 5.1.0 meteorology (model dates prior to 01 Sep 2008). Data is provided on the global 2° x 2.5° and 4° x 5° grids, as well as for the 0.5° x 0.666° nested grids (China and North America).
OTD-LIS-Local-Redist.CTH.v5.geos5.2.0.05x0666.CH
OTD-LIS-Local-Redist.CTH.v5.geos5.2.0.2x25
OTD-LIS-Local-Redist.CTH.v5.geos5.2.0.4x5
OTD/LIS flash redistribution factors for GEOS - 5.2.0 meteorology (model dates from 01 Sep 2008 onwards). Data is provided on the global 2° x 2.5° and 4° x 5° grids, as well as for the 0.5° x 0.666° nested China grid.
OTD-LIS-Local-Redist.CTH.v5.merra.4x5
OTD-LIS-Local-Redist.CTH.v5.merra.2x25
OTD/LIS flash redistribution factors for MERRA meteorology. At present, data is provided on the global 2° x 2.5° and 4° x 5° grid.
4.3.19 The mercury_201007 subdirectory
NOTES:
   1. For more information about these files, or about the mercury simulation in general, please contact the Hg and POPs Working Group.
   2. Some other data for the mercury simulation is kept on the 1° x 1° grid. Please see the description for the GEOS_1x1/mercury_201002/ directory.
   3. As of Oct 2011, the GEOS_2x2.5/mercury_201002 has been moved to to GEOS_2x2.5/mercury_201007 so that the file path is consistent with the GEOS_4x5 subdirectory.
REFERENCES:
   1. GEOS - Chem wiki: Mercury simulation
   2. GEOS - Chem wiki: Global Terrestrial Mercury Model
   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, Atmospheric Chemistry and Physics, submitted, 2010.
   4. Selin, N.E. and D.J. Jacob. Seasonal and spatial patterns of mercury wet deposition in the United States: North American vs. intercontinental sources, Atmospheric Environment, 42, 5193-5204, 2008.
   5. Smith‐Downey, N. V, E. M. Sunderland, and D. J. Jacob, Anthropogenic impacts on global storage and emissions of mercury from terrestrial soils: Insights from a new global model, J. Geophys. Res., 115, G03008, doi:10.1029/2009JG001124, 2010.
   6. Soerensen, A.L., E.M. Sunderland, C.D. Holmes, D.J. Jacob, R.M. Yantosca, H. Skov, J.H. Christensen, and R.P. Mason, An improved global model for air-sea exchange of mercury: High concentrations over the North Atlantic, Environ. Sci. Technol., 44, 8574-8580, 2010.
Files
Description
BrOx.GC.geos5.2x25
BrOx.GC.geos5.4x5
Br and BrO mixing ratios from GEOS - Chem using the tropospheric bromine chemistry mechanism (courtesy J. Parrella). The 2° x 2.5° data were regridded from 4° x 5° data for a 2007 simulation.
BrOx.GMI.geos5.2x25
BrOx.GMI.geos4.4x5
BrOx.GMI.geos5.4x5
Br and BrO mixing ratios from GMI combo model. These are regridded from the Aura4 simulations of 2007 (courtesy J. Logan, I. Megretskaia). 
BrOx.TOMCAT_org.geos5.2x25
BrOx.TOMCAT_org.geos4.4x5
BrOx.TOMCAT_org.geos5.4x5
Br and BrO mixing ratios from University of Cambridge p-TOMCAT model (courtesy Xin Yang). These are from a simulation with only organic Br-y precursors (no sea-salt aerosol).
Br_3Dglobal.geos4.4x5
Br_3Dglobal.geos5.4x5
Br and BrO mixing ratios from surface through stratosphere. Tropospheric values are from p-TOMCAT (courtesy Xin Yang) and stratospheric values are from GMI combo model (Aura runs, courtesy J. Logan and I. Megretskaia).
NOTE: These files are not used.
Chl_2003.geos.2x25
Chl_2003.geos.4x5
Mean monthly chlorophyl A concentrations in the ocean. Data is from the MODIS satellite in mg m-3 for 2003. Obtained from http://oceancolor.gsfc.nasa.gov (cf. Soerenson et al, 2010).
MERGE.O3.47L.geos5.2x25
MERGE.O3.47L.geos5.4x5
MERGE.O3.geos4.4x5
O3 mixing ratios for surface through stratosphere. Tropospheric values are from GEOS-Chem v7 full chemistry (sulfate_sim_200507) and stratospheric values are from GMI combo model (Aura runs, courtesy J. Logan and I. Megretskaia). 
MLD_DReqDT.geos.2x25 MLD_DReqDT.geos.4x5
Mean monthly mixed layer depths of the surface ocean in meters. Data is from de Boyer Montégut et al. (2004).
NPP_2003.geos.2x25
NPP_2003.geos.4x5
Mean monthly Net Primary Production from MODIS satellite data in mgC m-2 d-1 for 2003 taken from Behrenfeld et al. (1997).
OH_3Dglobal.geos5.2x25
OH_3Dglobal.geos4.4x5
OH_3Dglobal.geos5.4x5
OH concentration for surface through stratosphere. Tropospheric values are from GEOS-Chem v7-02-03 (OHmerge/v7-02-03.2001) and stratospheric values are from GMI combo model (Aura runs, courtesy J. Logan and I. Megretskaia). 
artisanal.bpch
Mercury from artisanal mining inventory documented in Selin et al., 2008. This is not used when running with the GCAP and GEIA 2005 emission inventories as artisanal mining is already included.
jBrO.daytime.geos5.2x25
jBrO.daytime.geos4.4x5
jBrO.daytime.geos5.4x5
Photolysis frequency for BrO, averaged over daylight hours. Calculated in a preliminary GEOS - Chem Br-y simulation for 2002 (courtesy J. Parella). This simulation did not include wet scavenging of Br-y species as this was not yet included in the Br-y model. BrO J-values are used to calculate [Br]/[BrO] ratio in the marine boundary layer.
jvalues.noon.geos5.2x25
jvalues.noon.geos5.4x5
Photolysis frequency for NO2, instantaneous at local noon. Calculated in GEOS-Chem full chemistry simulation for 2008 (courtesy J. Mao). NO2 J-values (with imposed diurnal cycle) are used to calculate the reduction rate of Hg(II) in clouds. 
nasatransp_4x5.*.bpch
Monthly mean climatological evapotranspiration fields [Mintz and Walker, 1993]. These were used in Selin et al., 2008 to scale vegetation mercury emissions.
NOTE: This process is not included in more recent versions of the model and these files may be obsolete.
newnatural.bpch
Natural sources of Hg, scaled to the location of mercury mines as described in Selin et al., 2007.
soilhg.preind.cdh.bpch
soilhg.presentday.cdh.bpch
Files containing soil concentrations of Hg on land for pre-industrial years and present day.
GTMM_data/
Directory containing data used by the Global Terrestrial Mercury Model to run offline (courtesy Smith-Downey et al., 2010). 
mean_metfields/geos4/mean_YYYYMM.bpch
mean_metfields/geos5/mean_YYYYMM.bpch
mean_metfields/merra/mean_YYYYMM.bpch
Monthly-mean values of surface temperature, total surface precipitation, and net shortwave radiation (GEOS - 4, GEOS - 5, and MERRA). These are read in by the Global Terrestrial Mercury Model (GTMM).
Data is for months MM = 01 .. 12 and years YYYY = 2001 to 2006 (GEOS-4), 2004 to 2009 (GEOS-5), 1979 to 2009 (MERRA).
4.3.20 The mercury_201110 subdirectory
NOTES:
   1. For more information about these files, or about the mercury simulation in general, please contact the Hg and POPs Working Group.
Files
Description
soilHg.102311.preind.bpch
soilHg.merra.preind.bpch
Files containing soil concentrations of mercury from the preindustrial which are consistent with the emissions and chemical mechanism in GEOS - Chem v9 - 01 - 02 and higher versions. These are created using the methodology of Selin et al., 2008.
Data files are available for GEOS - 5 2° x 2.5°, and GEOS - 5 4° x 5° and MERRA 4° x 5°.
soilHg.102311.presentday.bpch
soilHg.merra.presentday.bpch
Files containing soil concentrations of mercury for the present-day which are consistent with the chemical mechanism in GEOS - Chem v9 - 01 - 02 and higher versions and the 2005 GEIA emissions inventory, using the methodology of Selin et al., 2008.
Data files are available for GEOS - 5 2° x 2.5°, and GEOS - 5 4° x 5° and MERRA 4° x 5°.
4.3.21 The pco_lco_200203 subdirectory
NOTES:
   1. The new stratospheric P/K update (benchmarked in v9-01-03o) now renders this directory obsolete. GEOS - Chem does not use these files for the full-chemistry simulation any longer. 
   2. Some of the offline simulations (e.g. Tagged CH4) may still use these files. Therefore we shall keep this directory for the time being.
REFERENCES:
   1. Schneider, H. R., D. B. A. Jones, G.-Y. Shi, and M. B. McElroy. Analysis of residual mean transport in the stratosphere. Part I: Model description and comparison with satellite data, submitted to J. Geophys. Res., 1998.
Files
Description
COprod.gcap.4x5
COloss.gcap.4x5
Stratospheric P(CO) and L(CO) rates obtained from Hans Schneider's 2D model, regridded to the GCAP 4° x 5° grid.
COprod.geos4.2x25
COprod.geos4.4x5
COloss.geos4.2x25
COloss.geos4.4x5
Stratospheric P(CO) and L(CO) rates obtained from Hans Schneider's 2D model, regridded to the GEOS - 4 2° x 2.5° and 4° x 5° grids.
COprod.geos5.2x25
COprod.geos5.4x5
COloss.geos5.2x25
COloss.geos5.4x5 
Stratospheric P(CO) and L(CO) rates obtained from Hans Schneider's 2D model, regridded to the GEOS - 5 2° x 2.5°, and 4° x 5° grids.
4.3.22 The RETRO_201103 subdirectory
NOTES:
   1. IMPORTANT: Biofuel emissions are not separated from anthropogenic emissions.
REFERENCES:
   1. GEOS-Chem wiki: Implementation of RETRO Anthropogenic Emissions
   2. Reinhart, W., and D. Millet, Implementation of RETRO Anthropogenic Emissions Inventory into the GEOS-Chem Model, May 2011.
   3. Bolshcer, M, et al., RETRO Deliverable D1-6, RETRO Documentation, 2007.
   4. Pulles, T, et al., Assessment of Global Emissions from Fuel Combustion in the Final Decades of the 20th Century, TNO report A-R0132/B, 2007. 
Files
Description
YYYYMM.2x2.5
YYYYMM.4x5 
Files containing monthly emissions data (base year 2000) from the RETRO inventory for the following species: ALD2, ALK4, BENZ, C2H2, C2H4, C2H6, C3H8, C2HO, HCOOH, MEK, PRPE, TOLU, XYLE. Units are atoms C/cm2/s.
Data is on the GMAO 4° x 5° grid. Retro emissions were prepared by Wes Reinhart. 
4.3.23 The RnPbBe_200203 subdirectory
REFERENCES:
   1. Liu, H., D.J. Jacob, I. Bey, and R.M. Yantosca, Constraints from [210]Pb and [7]Be on wet deposition and transporting a global threee-dimensional chemical tracer model driven by assimilated meteorological fields, J. Geophys. Res., 106, 12,109 - 12,128, 2001.
Files
Description
7Be.Lal
Source of 7Be (Lal & Peters. 1967, used for [222]Rn-[210]Pb-[7]Be simulations). File is in plain-text format.
4.3.24 The soil_NOx_200203 subdirectory
NOTES:
   1. We plan to introduce a new soil NOx emissions scheme post v9 - 01 - 03. This new scheme will render the soil_NOx_200203 directory obsolete
REFERENCES:
   1. GEOS-Chem wiki: Soil NOx emissions
   2. Wang, Y., D.J. Jacob, and J.A. Logan, Global simulation of tropospheric O3-NOx-hydrocarbon chemistry, 1. Model formulation, J. Geophys. Res., 103/D9, 10,713-10,726, 1998. [PDF]
Files
Description
climatprep2x25.dat
climatprep4x5.dat
Monthly soil precipitation for soil NOx emissions (Wang et al, 1998). File is in plain-text format.
fert_scale.dat
Fertilizer NOx emissions (Wang et al, 1998). File is in plain-text format.
soiltype.dat
Mapping from Olson land type to soil land type (Wang et al, 1998). File is in plain-text format.
4.3.25 The strat_chem_201206 subdirectory
NOTES:
   1. This directory contains the input files for applying linearized stratospheric chemistry production and loss in strat_chem_mod.F90. These were generated with the GMI Combo model and saved to netCDF format by Lee Murray. 
   2. The files and new stratospheric chemistry scheme are described in detail on the Stratospheric Chemistry page on the GEOS - Chem wiki.
REFERENCES:
   1. Murray, L.T., D.J. Jacob, J.A. Logan, R.C. Hudman, and W.J. Koshak, Optimized regional and interannual variability of lightning in a global chemical transport model constrained by LIS/OTD satellite data, submitted to J. Geophys. Res., 2012. 
   2. Allen, D., K. Pickering, B. Duncan, and M. Damon (2010), Impact of lightning NO emissions on North American photochemistry as determined using the Global Modeling Initiative (GMI) model, J. Geophys. Res., 115, doi: 10.1029/2010JD014062.
   3. Considine, D. B., J. A. Logan, and M. A. Olsen (2008), Evaluation of near-tropopause ozone distributions in the Global Modeling Initiative combined stratosphere/ troposphere model with ozonesonde data, Atmos. Chem. Phys., 8(9), 2365-2385.
   4. Duncan, B. N., J. A. Logan, I. Bey, I. A. Megretskaia, R. M. Yantosca, Novelli, P. C., N. B. Jones, and C. P. Rinsland (2007), Global budget of CO, 1988-1997: Source estimates and validation with a global model, J. Geophys. Res., 112, doi: 10.1029/2007JD008459.
Files
Description
gmi.clim.*.geos4.2x25.nc
gmi.clim.*.geos4.4x5.nc
These files contain 3D climatological monthly mean production rates, loss frequencies, and concentrations for each of the species simulated by the GMI "Combo" model. GMI archives the reaction rates for each kinetic and photolysis reaction, which have been stoichiometrically summed for each individual species, and averaged over all years by L. Murray.
In addition to these individual species: 
A3O2, ACET, ACTA, ALD2, ALK4, A3O2, B3O2, Br, BrCl, BrO, BrONO2, C2H6, C3H8, CCl4, CF2Br2, CF2ClBr, CF3Br, CFC113, CFC114, CFC115, CH2O, CH3Br, CH3CCl3, CH3Cl, CH4, CO, Cl, Cl2, CL2O2, ClO, ClONO2, EOH, ETP, GCO3, GLYC, GLYX, GP, GPAN, H,H2, H24O2, H2O, H2O2, HAC, HBR, HCFC141b, HCFC142b, HCFC22, HCOOH, HCl, HNO2, HNO3, HNO4, HO2, HOBr, HOCl, IALD, IAO2, IAP, INO2, INPN, ISN1, ISNP, ISOP, KO2, MACR, MAN2, MAO3, MAOP, MAP, MCO3, MEK, MGLY, MO2, MOH, MP, MRO2, MRP, MVK, MVN2, N, N2O, N2O5, NO, NO2, NO3, NOx, O, O1D, O3, OClO, OH, Ox, PAN, PMN, PO2, PP, PPN, PRN1, PRPE, PRPN, R4N1, R4N2, R4O2, R4P, RA3P, RB3P, RCHO, RCOOH, RIO1, RIO2, RIP, ROH, RP, VRO2, VRP.
we have determined production rates and loss frequencies for:
   1. The NOx family = N + NO + NO2 + NO3 + HNO2 
   2. The Ox family = O + O1D + O3
Ox was determined for completeness; we recommend that you use GEOS - Chem with the Linoz (recommended) or Synoz options for stratospheric O3. 
NOTES:
   1. The GMI "Combo" model uses a different vertical resolution for GEOS - 4 meteorology than does GEOS - Chem. We have regridded these files to the GEOS - 4 native vertical grid (55 layers) used by GEOS - Chem.
   2. We created these files from the archived GMI "Combo" monthly mean output (2004 - 2007) located at:
ftp://dirac.gsfc.nasa.gov/pub/gmidata2/users/mrdamon/Aura4-Final
gmi.clim.*.geos5.2x25.nc
gmi.clim.*.geos5.4x5.nc
These files contain 3D climatological monthly mean production rates, loss frequencies, and concentrations for each of the species simulated by the GMI "Combo" model. GMI archives the reaction rates for each kinetic and photolysis reaction, which have been stoichiometrically summed for each individual species, and averaged over all years by L. Murray.
The data in these files are placed on the GEOS - 5 native vertical grid (72 layers) used by GEOS - Chem. GEOS - Chem will read these data files when being driven by MERRA or GEOS - 5.7.2 meteorology.
See the above row in this table for a list of included species. 
NOTES:
   1. We created these files from the archived GMI "Combo" monthly mean output (2004 - 2010) located at:
ftp://dirac.gsfc.nasa.gov/pub/gmidata2/users/steenrod/MERRA
gmi.clim.*.merra.2x25.nc
gmi.clim.*.merra.4x5.nc
Symbolic links to the gmi.clim.*.geos5.2x25 and gmi.clim.*.geos5.4x5 files. 
The MERRA vertical grid is the same as the GEOS - 5 native vertical grid (72 layers). We need to add the symbolic links so that GEOS - Chem will find these files when being driven by the MERRA meteorology.
4.3.26 The sulfate_sim_200508 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Sulfate aerosols
   2. Andreae, M.O. & P. Merlet, Emission of trace gases and aerosols from biomass burning, Global Biogeochem. Cycles, 15, 955-966, 2001.
   3. Duncan, B.N., R.V. Martin, A.C. Staudt, R. Yevich, J.A. Logan, Interannual and Seasonal Variability of Biomass Burning Emissions Constrained by Satellite Observations, J. Geophys. Res., 108(D2), 4040, doi:10.1029/2002JD002378, 2003.
Files
Description
DMS_seawater.geos.2x25
DMS_seawater.geos.4x5
DMS_seawater.gcap.4x5 
Monthly average DMS seawater concentrations [nm/ML] on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids. From Andreae.
NH3_anthsrce.geos.2x25
NH3_anthsrce.geos.4x5
NH3_anthsrce.gcap.4x5
Binary punch file containing anthropogenic NH3 emissions for the year 1990 [kg N/month] on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids. From GEIA.
NH3_biofuel.geos.2x25
NH3_biofuel.geos.4x5
NH3_biofuel.gcap.4x5
Binary punch files containing NH3 biofuel burning emissions [kg NH3/month] on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids. From GEIA.
NH3_natusrce.geos.2x25
NH3_natusrce.geos.4x5
NH3_natusrce.gcap.4x5
Binary punch files containing natural-source NH3 emissions for the year 1990 [kg N/month] on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids. From GEIA.
NH3emis.monthly.geos.2x25
NH3emis.monthly.geos.4x5
NH3emis.monthly.gcap.4x5
Binary punch files containing anthropogenic NH3 emissions for the year 1990 [kg N/month] on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids. From GEIA.
NOTE: These files appear to be obsolete now.
SST.geos.2x25
SST.geos.4x5
SST.gcap.4x5
Annual average monthly mean sea surface temperatures on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids. From Mian Chin.
NOTE: These files are superseded by the files contained w/in the SST_200508 directory.
aircraft.2x25.1992.apr
aircraft.2x25.1992.aug
aircraft.2x25.1992.dec
aircraft.2x25.1992.feb
aircraft.2x25.1992.jan
aircraft.2x25.1992.jul
aircraft.2x25.1992.jun
aircraft.2x25.1992.mar
aircraft.2x25.1992.may
aircraft.2x25.1992.nov
aircraft.2x25.1992.oct
aircraft.2x25.1992.sep

aircraft.4x5.1992.apr
aircraft.4x5.1992.aug
aircraft.4x5.1992.dec
aircraft.4x5.1992.feb
aircraft.4x5.1992.jan
aircraft.4x5.1992.jul
aircraft.4x5.1992.jun
aircraft.4x5.1992.mar
aircraft.4x5.1992.may
aircraft.4x5.1992.nov
aircraft.4x5.1992.oct
aircraft.4x5.1992.sep
SO2 emissions from aircraft on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids.
These are fuel burned in [kg/box/day], from AEAP for 1992. SO2 emission is calculated by assuming an emission index EI of 1.0, i.e., 1g of SO2 emitted per kg of fuel burned. It is also assumed that there is no diurnal variation of emission rate.
shipSOx.geos.2x25
shipSOx.geos.4x5
shipSOx.gcap.4x5
SO2 emissions from ship exhaust, from Corbett et al. 
The native resolution of the data is 2 x 2 degrees. These were regridded to the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids by Becky Alexander.
scalefoss.SOx.2x25.1998
scalefoss.SOx.4x5.1998
Fossil fuel scale factors used to scale up GEIA SOx emissions from the baseline year 1985 to 1998. From Rokjin Park.
volcano.con.2x25
volcano.con.4x5
Non-eruptive volcanic SO2 emission from GEIA in [Mg SO2/box/day] on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids. Text format. 
volcano.erup.1994.2x25
volcano.erup.1994.4x5
Eruptive volcanic SO2 emission from GEIA in [Mg SO2/box/day] on the GCAP 4° x 5°, GMAO 2° x 2.5°, and GMAO 4° x 5° grids. Text format. 
In addition to the above files, monthly-mean oxidant files for the offline aerosol simulation are stored in the sulfate_sim_200508/offline subdirectory. A listing of these files follows:
Files
Description
JH2O2.geos4.2x25
JH2O2.geos4.4x5

JH2O2.geos5.2x25
JH2O2.geos5.4x5
Files containing J(H2O2) values (JV-MAP-$, tracer=3) saved out from 1-yr benchmark simulations done with GEOS - Chem v7 - 02 - 03.
Data is saved up to the tropopause only. Units are [s-1].
Files are provided for the GEOS - 4, and GEOS - 5 / MERRA / GEOS - 5.7.2 vertical grids at both 2° x 2.5° and 4° x 5° horizontal resolution.
For more information about how the individual files were created, contact Bob Yantosca.
NO3.geos4.2x25
NO3.geos4.4x5

NO3.geos5.2x25
NO3.geos5.4x5
Files containing / NO3 values (CHEM-L=$, tracer=5) saved out from 1-yr benchmark simulations done with GEOS - Chem v7 - 02 - 03.
Units are [v/v] (mixing ratio).
Files are provided for the GEOS - 4, and GEOS - 5 / MERRA / GEOS - 5.7.2 vertical grids (reduced resolution) at 2° x 2.5° and 4° x 5° horizontal resolution.
For more information about how the individual files were created, contact Bob Yantosca.
O3.geos4.2x25
O3.geos4.4x5

O3.geos5.2x25
O3.geos5.4x5
Files containing O3 values (IJ-AVG-$, tracer=51) saved out from 1-yr benchmark simulations done with GEOS - Chem v7 - 02 - 03.
Units are [v/v] (mixing ratio).
Files are provided for the GEOS - 4, and GEOS - 5 / MERRA / GEOS - 5.7.2 vertical grids (reduced resolution) at 2° x 2.5° and 4° x 5° horizontal resolution.
GEOS - 4 data are saved on 30-level reduced grids.
For more information about how the individual files were created, contact Bob Yantosca.
PH2O2.geos4.2x25
PH2O2.geos4.4x5

PH2O2.geos5.2x25
PH2O2.geos5.4x5
Files containing P(H2O2) values (PORL-L=$, tracer=5) saved out from 1-yr benchmark simulations done with GEOS - Chem v7 - 02 - 03.
Data is saved up to the tropopause only. Units are [molec/cm3/s].
Files are provided for the GEOS - 4, and GEOS - 5 / MERRA / GEOS - 5.7.2 vertical grids (reduced resolution) at 2° x 2.5° and 4° x 5° horizontal resolution.
For more information about how the individual files were created, contact Bob Yantosca.
THNO3.geos4.2x25
THNO3.geos4.4x5

THNO3.geos5.2x25
THNO3.geos5.4x5
Files containing THNO3 (= HNO3 + NIT) values (IJ-AVG-$, tracer=7) saved out from 1-yr benchmark simulations done with GEOS - Chem v7 - 02 - 03.
Files are provided for the GEOS - 3, GEOS - 4, and GEOS - 5 vertical grids (reduced resolution) at 2° x 2.5° and 4° x 5° horizontal resolution.
For more information about how the individual files were created, contact Bob Yantosca.
4.3.27 The tagged_CO_200106 subdirectory
REFERENCES:
   1. GEOS-Chem wiki: Tagged CO simulation
Files
Description
acetone.geos.2x25
acetone.geos.4x5
Monthly mean emissions of direct biogenic acetone and acetone from grasslands for the GMAO 2° x 2.5° and 4° x 5° grids.
This data was archived from a 1994 GEOS - Chem model simulation (GEOS - 1)
ch3oh96.geos.2x25
isop96.geos.2x25
mono96.geos.2x25

ch3oh96.geos.4x5
isop96.geos.4x5
mono96.geos.4x5
Surface concentrations of CH3OH, isoprene, and monoterpenes from 1996 for the GMAO 2° x 2.5° and 4° x 5° grids.
tagco_mask.geos.2x25
tagco_mask.geos.4x5
Contains country mask for ICARTT Tagged CO runs for the GMAO 2° x 2.5° and 4° x 5° grids. (1 = USA/Canada, 2 = Mexico, 3 = Europe, 4 = Asia)
4.3.28 The TOMS_201203 subdirectory
NOTES:
   1. This is an update of the TOMS_200906 subdirectory
REFERENCES:
   1. GEOS - Chem wiki: Overhead TOMS/SBUV merged O3 columns
Data source and version:
------------------------

Data are taken from:
http://acdb-ext.gsfc.nasa.gov/Data_services/merged/index.html

Version 8 Merged Ozone Data Sets
Total Ozone Revision 05
DATA THROUGH: MAR 2009
LAST MODIFIED: 01 MAY 2009

Resolution: 5 x 10 deg.

Contact person for the merged data product:
Dr. Richard Stolarski (Richard.S.Stolarski@nasa.gov)
Stacey Frith (Stacey.M.Frith@nasa.gov)
Files
Description<
TOMS_O3col_YYYY.gcap.4x5             
File containing 12 months of combined TOMS/SBUV gridded data on the GCAP 4° x 5° horizontal grid.
Available years YYYY = 1971 - 2010.
TOMS_O3col_YYYY.geos.2x25
File containing 12 months of combined TOMS/SBUV gridded data on the GMAO 2° x 2.5° horizontal grid.
Available years YYYY = 1971 - 2010.
TOMS_O3col_YYYY.geos.4x5
File containing 12 months of combined TOMS/SBUV gridded data on the GMAO 4° x 5° horizontal grid.
Available years YYYY = 1971 - 2010.
4.3.29 The uvalbedo_200111 subdirectory
REFERENCES:
   1. Herman, J.R. and E.A. Celarier, Earth surface reflectivity climatology at 340-380 nm from TOMS data, J. Geophys. Res., 102(D23),
28,003-28,011 (1997)
Files
Description
uvalbedo.geos.2x25
uvalbedo.geos.4x5
uvalbedo.gcap.4x5
Monthly mean UV albedoes (340 nm - 380 nm, from TOMS) for the GMAO 2° x 2.5°, GMAO 4° x 5°, and GCAP 4° x 5° grids. These files are used for FAST - J photolysis

4.4 Obsolete data
The following data directories are now considered obsolete in GEOS - Chem v9 - 01 - 01. We keep these in the GEOS - Chem shared data directories for backwards compatibility with older versions.
Obsolete directory name
Notes
acetone_200108
   * Rendered obsolete by the new acetone algorithm of Emily Fischer (benchmarked in v9-01-03b)
ann_mean_trop_200202
   * The dynamic tropopause feature of GEOS - Chem makes these data obsolete. 
   * You must use the dynamic tropopause option with GEOS - 5 and MERRA met fields.
biofuel_200007
   * Replaced by biofuel_200002
biofuel_200104
   * Replaced by biofuel_200202
biofuel_obsolete
   * Replaced by biofuel_200202
biogenic_200203
   * Rendered obsolete by MEGAN v2.1 and the new acetone algorithm of Emily Fischer (benchmarked in v9-01-03b)
biomass_200009
   * Rendered obsolete by GFED3 biomass emissions
biomass_200110
   * Rendered obsolete by GFED3 biomass emissions
biomass_obsolete
   * Replaced by biomass_200110
CH4_200202
   * Replaced by CH4_200911
CH4_200909
   * Replaced by CH4_200911
CO2_200508
   * Replaced by CO2_201003
CO2_201003/fossilfuel_andres/annual
   * Replaced by CO2_201003/fossilfuel_andres/annual_v2010
CO2_201003/fossilfuel_andres/monthly
   * Replaced by CO2_201003/fossilfuel_andres/monthly_v2010
dust_200203
   * Replaced by dust_200605
drydep_200203
   * GEOSChem now reads dry deposition input information (formerly stored in ASCII files drydep.coef, drydep.table) from a netCDF file located in the GEOS_1x1/Olson_Land_Map_201203 directory.
EMEP_200806
   * These data are now obsolete.
   * There is a reference to this directory in the code to run the European nested-grid simulation. However, Harvard does not store the data for this simulation. For more information, please refer to the Regional Air Quality Working Group wiki page.
EPA_NEI_200406
   * Replaced by EPA_NEI_200411 and later directories
EPA_NEI_200411 
(anthro emissions only)
   * The anthropogenic emissions in this directory are now replaced by the data stored in the EPA_NEI_200708 and EPA_NEI_200806 directories.
   * Subsequent updates of EPA/NEI99 and EPA/NEI05 inventories only contained revisions for the anthropogenic emissions data. Therefore, the biofuel emissions data contained in this directory will be applied if you are choose to use EPA/NEI99 or EPA/NEI05 North American emissions.
fastj_200203
   * FAST - J files are now kept in the GEOS - Chem run directory.
   * GEOS - Chem now reads a netCDF version of jv_atms.dat from the GEOS_1x1/FastJ_201204 directory.
   * These files probably do not reflect the various updates to the aerosol optical properties that were recently made.
fossil_obsolete
   * Replaced by fossil_200104
GFED2_200601
   * Rendered obsolete by GFED3 biomass emissions
GFED2_3hr_200901
   * Rendered obsolete by GFED3 biomass emissions
GFED2_8day_200712
   * Rendered obsolete by GFED3 biomass emissions
Kzz
   * This feature has been removed from GEOS - Chem
leaf_area_index_200202
   * GEOS - Chem now reads Olson map (1992 or 2001) from netCDF files in GEOS_1x1/Olson_Land_Map_201203.
   * GEOS - Chem now reads MODIS LAI data from netCDF files in GEOS_1x1/MODIS_LAI_201204.
leaf_area_index_200412
   * GEOS - Chem now reads Olson map (1992 or 2001) from netCDF files in GEOS_1x1/Olson_Land_Map_201203.
   * GEOS - Chem now reads MODIS LAI data from netCDF files in GEOS_1x1/MODIS_LAI_201204.
lightning_NOx_200203
   * Replaced by lightning_NOx_201101
lightning_NOx_200605
   * Replaced by lightning_NOx_201101
lightning_NOx_200709
   * Replaced by lightning_NOx_201101
lightning_NOx_200907
   * Replaced by lightning_NOx_201101
lightning_NOx_200911
   * Replaced by lightning_NOx_201101
mercury_200412
   * Replaced by mercury_200501 and mercury_201007
MODIS_LAI_200910
   * GEOS - Chem now reads Olson map (1992 or 2001) from netCDF files in GEOS_1x1/Olson_Land_Map_201203.
   * GEOS - Chem now reads MODIS LAI data from netCDF files in GEOS_1x1/MODIS_LAI_201204.
MODIS_LAI_200911
   * GEOS - Chem now reads Olson map (1992 or 2001) from netCDF files in GEOS_1x1/Olson_Land_Map_201203.
   * GEOS - Chem now reads MODIS LAI data from netCDF files in GEOS_1x1/MODIS_LAI_201204.
MODIS_LAI_200911
   * GEOS - Chem now reads Olson map (1992 or 2001) from netCDF files in GEOS_1x1/Olson_Land_Map_201203.
   * GEOS - Chem now reads MODIS LAI data from netCDF files in GEOS_1x1/MODIS_LAI_201204.
O3_climatology_200202
   * This feature has been removed from GEOS - Chem.
Prior_To_20010409
   * Contains ancient versions of CO prod/loss, P(NOy), and fossil fuel scale factor data from prior to April 2001. Data is on GEOS - 1 and GEOS - STRAT grids.
pco_lco_200203
   * Rendered obsolete by the new stratospheric P/k update (benchmarked in v9-01-03o).
   * NOTE: Some offline simulations may still use these data files for the time being.
pnoy_200106
   * Rendered obsolete by the new stratospheric P/k update (benchmarked in v9-01-03o).
scalefoss_200202
   * These directories are now obsolete, and are preserved here only for versions of GEOS - Chem prior to v8 - 01 - 04. They are superseded by the new scale factors from Aaron van Donkelaar in anth_scale_factors_200905.
   * For more information, please see the GEOS - Chem wiki: Scale factors for anthropogenic emissions
slowj_200003
   * This feature has been removed from GEOS - Chem
stratOH_200203
   * Rendered obsolete by the new stratospheric P/k update (benchmarked in v9-01-03o).
stratjv_200203
   * Rendered obsolete by the new stratospheric P/k update (benchmarked in v9-01-03o).
Streets_200803
   * Replaced by Streets_200812
sulfate_sim_200106
   * Replaced by sulfate_sim_200508
sulfate_sim_200210
   * Replaced by sulfate_sim_200508
TOMS_200307
   * Replaced by TOMS_200906
TOMS_200701
   * Replaced by TOMS_200906
TOMS_O3col_200202
   * This feature has been removed from GEOS - Chem
volcano_SO2_200909
   * Replaced by volcano_SO2_201010

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Chapter 5
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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5. GEOS - Chem run directories

5.1 Overview
This section describes the contents of the GEOS - Chem run directory. Compiling GEOS - Chem creates an executable file. You will place this executable into the run directory so that you can start a new GEOS - Chem simulation. 
The run directory also contains the various input files with which you select the proper options for your GEOS - Chem simulation. We recommend that you create a unique run directory for each of your GEOS - Chem simulations. Otherwise you risk having important output overwritten by subsequent model runs.
We have made available for download (via Git) several sample run directories, grouped by simulation, met field type, and horizontal resolution. Please see Chapter 2.3 for instructions on how to download each individual run directory. You can download one or more run directories to get started.
Here we present a list of GEOS - Chem's input files. You can modify these to customize your simulation. Detailed descriptions of each file then follow in the subsequent sections.
GEOS - Chem user input files
input.geos
File containing all GEOS - Chem user options. In this file, you may specify the following options:
   * Start & end time of the simulation
   * Names of the input& output files
   * Which diagnostics to save to disk
   * Which processes (e.g. chemistry, transport, dry deposition, etc.) to turn on, etc.
Planeflight.dat 
Specifies flight tracks for which you want to save out specific tracers, chemical species, or met field quantities. 
GEOS - Chem chemistry mechanism files
chemga.dat
File containing some aerosol parameters for SMVGEAR II or KPP.
globchem.dat
File that defines the GEOS - Chem NOx-Ox-hydrocarbon-aerosol chemical mechanism. This file contains the list of chemical species and reactions used by the chemical solver (SMVGEAR II or KPP). 
At present, you may pick from a few different chemistry mechanisms:
   1. standard: 53 advected tracers, our default simulation.
   2. SOA: 59 advected tracers, with secondary organic aerosols
   3. dicarbonyls: 75 advected tracers, with dicarbonyl chemistry
   4. isoprene: 56 advected tracers, with the Caltech isoprene scheme. 
NOTE: This scheme has not been fully tested yet!
mglob.dat
Setup file for SMVGEAR II, containing convergence criteria and other parameters.
GEOS - Chem photolysis mechanism files
jv_spec.dat
Contains cross-section and quantum yields (at 400nm) for FAST - JX photolysis species.
jv_spec_aod.dat
Contains aerosol optical properties at an arbitrary wavelength (currently 550nm). This allows you to request photolysis diagnostics at a different wavelength than 400nm. You may update this file accordingly.
ratj.d
Links "GEOS - Chem species" to "FAST - JX" species. FAST - JX photolysis species are defined in the data file jv_spec.dat, GEOS - Chem species in globchem.dat.
NOTE: For now, GEOS - Chem v9 - 01 - 03 still uses the older FAST - J photolysis code, but we now feed it the updated cross-section inputs from the more recent FAST - JX code.

5.2 GEOS - Chem user input files
You must modify these files to customize your GEOS - Chem simulation. These files contain definitions of tracers, starting and ending times, diagnostics, and other relevant quantities. You should make it a habit of thoroughly checking these files before submitting a long GEOS - Chem run.

5.2.1 The input.geos file
GEOS - Chem combines all the input options and switches into a single input file, input.geos. All user-defined input switches and settings which customize GEOS - Chem output options are now defined within this file. 
An input.geos file ships with each of the GEOS - Chem run directories. We invite you to download the run directory for the simulation(s) that you are interested in and view the corresponding input.geos file.
We have also provided input.geos files for certain offline simulations (for which we do not typically archive run directories). To view, click on one of the following links.
   1. Tagged Ox simulation
   2. Tagged CO simulation
   3. Offline sulfate/carbon/dust/seasalt aerosol simulation
   4. H2 and HD simulation 
Note that the input.geos file is grouped into menus. Each menu controls the options for a particular aspect of a GEOS - Chem simulation. Here is a list of menus and the options which they control. You can click on the name of a menu for more information.
Simulation Menus
Simulation Menu
Specifies the start & stop times of the run, the restart file names, and the directory path information.
Tracer Menu
Specifies information about each tracer, including name, molecular weight, and, for family tracers, individual constituent species.
Operations Menus
Transport Menu
Specifies options for TPCORE transport.
Convection Menu
Specifies options for cloud convection and PBL mixing.
Emissions Menu
Specifies options for anthropogenic, biomass, biofuel, and biogenic emissions.
Future Menu 
Specifies options for future emissions scenarios.
NOTE: This is currently only implemented for use with the GCAP met fields.
Aerosol Menu
Specifies options for emissions and chemistry of sulfate, carbon, secondary organic, dust, and sea salt aerosols.
Deposition Menu
Specifies options for both dry deposition and wet deposition.
Chemistry Menu
Specifies options for chemistry.
CO2 Menu
Specifies options for the CO2 simulation.
Mercury Menu 
Specifies options for the mercury simulation, with or without the Global Terrestrial Mercury Model.
Methane Menu
Specifies options for the methane simulation.
Diagnostic Menus
Output Menu
Specifies dates on which diagnostic output will be saved to the binary punch file.
GAMAP Menu
Specifies the path names for the GAMAP diaginfo.dat and tracerinfo.dat files, both of which are now written by GEOS - Chem.
Diagnostic Menu
Specifies which binary punch file diagnostics to turn on, and which tracers to save to disk.
Planeflight Menu
Specifies the names of the files for the ND40 plane flight diagnostic.
ND48 Menu
Specifies options for the ND48 station timeseries diagnostic.
ND49 Menu
Specifies options for the ND49 instantaneous timeseries diagnostic.
ND50 Menu
Specifies options for the ND50 24-hour average timeseries diagnostic.
ND51 Menu
Specifies options for the ND51 "satellite" timeseries diagnostic.
ND51b Menu
Specifies options for the ND51b "satellite" timeseries diagnostic.
ND63 Menu
Specifies options for the ND63 ship timeseries diagnostic.
Prod & Loss Menu
Specifies options for the ND65 (chemical prod & loss) and ND20 (save PO3, LO3 to disk for tagged Ox simulation) diagnostics.
Other Menus
Archived OH Menu
Specifies the directory path for offline OH data files.
O3 P/L Menu
Specifies the directory path for PO3 and LO3 rate files (for tagged Ox simulation)
Nested Grid Menu
Specifies options for the nested grid simulations
Unix Cmds Menu
Specifies Unix commands which are used for unzipping data on the fly.
The menus must occur in this order:
   1. Simulation Menu 
   2. Tracer Menu
   3. Then any of the Operations Menus
   4. Then any of the Diagnostic Menus
   5. Other Menus can go anywhere; by convention we will list them at the end of the file.
For each of the menus in input.geos, we shall describe the options and switches that you must set in order to perform a NOx - Ox - Hydrocarbon - aerosol simulation (a.k.a. "full chemistry simulation"). Menus that are optional shall be noted as such.

5.2.1.1 The SIMULATION MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% SIMULATION MENU %%% :
02: Start YYYYMMDD, HHMMSS  : 20050701 000000
03: End   YYYYMMDD, HHMMSS  : 20050801 000000
04: Run directory           : ./
05: Input restart file      : restart.v9-01-03-geos5-Run1.YYYYMMDDhh
06: Make new restart file?  : T
07: Output restart file(s)  : restart.v9-01-03-geos5-Run1.YYYYMMDDhh
08: Root data directory     : /as/data/geos/GEOS_4x5/
09:  => GCAP       subdir   : AGRID/YYYY/MM/
10:  => GEOS-4     subdir   : GEOS_4_v4/YYYY/MM/
11:  => GEOS-5     subdir   : GEOS_5/YYYY/MM/
12:  => GEOS-5.7.x subdir   : GEOS_5.7/YYYY/MM/
13:  => MERRA      subdir   : MERRA/YYYY/MM/
14: Dir w/ 1x1 emissions etc: /as/data/geos/GEOS_1x1/
15: Temporary directory     : ./
16: Unzip met fields?       : F
17: Wait for met fields?    : F
18: Use variable tropopause?: T
19: Global offsets I0, J0   : 0 0
Line
Description
1
Header line 
2
Specify the starting date and time of the GEOS - Chem simulation. The date must be in YYYYMMDD format (4-digit year, month, and day). The time must be in hhmmss format (hour, minute, and seconds). Note that since the GEOS - Chem dynamic timestep (see Transport Menu) is usually 10, 15, or 30 minutes, you can always set the seconds to zero. 
3
Specify the ending date (YYYYMMDD format) and time (hhmmss format) of the GEOS - Chem simulation.
4
Specify the name of the GEOS - Chem run directory (e.g. where the executable file and input files reside).
5
Specify the name of the restart file, which contains the initial tracer concentrations. If you just specify the file name, GEOS - Chem will look for the restart file in the run directory. You may also specify an entire directory path. Also, you may include the following tokens in the file name: 
   * YYYY: Replaced by 4-digit year (e.g. 2008)
   * MM: Replaced by 2-digit month (01-12)
   * DD: Replaced by 2-digit day (01-31)
   * hh: Replaced by 2-digit hour (0-23)
   * mm: Replaced by 2-digit minutes (0-59)
   * ss: Replaced by 2-digit seconds (0-59)
NOTE: Since the typical GEOS - Chem simulations start and end at the top of the hour, a restart file name such as restart.YYYYMMDDhh should suffice for most applications.
6
If you want to create new restart files then set this to T. A new restart file will be saved at the same time when diagnostics are saved to the binary punch file. See Output Menu for more information.
7
Specify the name or file path for the output restart file(s). As described above, GEOS - Chem will replace the YYYY, MM, DD, hh, mm, ss tokens in the file name with the appropriate date or time values.
8
Specify DATA_DIR (located in source code file directory_mod.F). DATA_DIR is the root-level data directory path. The various shared data inputs (e.g. emissions, offline OH, offline dust & aerosol concentrations, etc). are stored in subdirectories of DATA_DIR. Also, the met fields are stored in subdirectories of DATA_DIR.
9 
Specify the directory path where GCAP met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable GEOS_1_DIR in source code file directory_mod.F.)
10
Specify the directory path where GEOS - 4 met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable GEOS_4_DIR in source code file directory_mod.F.
11
Specify the directory path where GEOS - 5 met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable GEOS_5_DIR in source code file directory_mod.F.
12
Specify the directory path where GEOS - 5.7.2 met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable GEOS_57_DIR in source code file directory_mod.F.
13
Specify the directory path where MERRA met fields are stored. You may include the YYYY and MM tokens as described above. This is stored in the variable MERRA_DIR in source code file directory_mod.F.
14
Specify DATA_DIR_1x1 (located in source code file directory_mod.F). DATA_DIR_1x1 is the root-level data directory path where emission files on the GMAO 1° x 1°, generic 1° x 1°, and native grids are stored. GEOS - Chem v9 - 01 - 03 has the ability to regrid emissions (etc.) files on-the-fly from these 1° x 1° and native grids to the current model grid using the MAP A2A regridding algorithm.
15
Specify TEMP_DIR (located in source code file directory_mod.F). TEMP_DIR is the path of a temporary directory into which met field files will be unzipped.
NOTE: You only need to specify this if you are unzipping met fields on the fly. This was usually done with GEOS - 3 met fields, which are now obsolete.
16
Specify LUNZIP (located in source code file logical_mod.F). LUNZIP determines whether GEOS - Chem will unzip met field files on the fly. If you have stored your met fields in gzipped format in order to save space, then you must set LUNZIP to T. If you have stored your met fields as unzipped, then set LUNZIP to F.
NOTE: You only need to specify this if you are unzipping met fields on the fly. This was usually done with GEOS - 3 met fields, which are now obsolete.
17
Specify LWAIT (located in source code file logical_mod.F). If you are unzipping met field files on the fly (i.e. if LUNZIP is set to T), then you may also specify if you want GEOS - Chem to wait until the met field fi les are completely unzipped before proceeding. It may be necessary to set LWAIT to T if you are using a simulation such as Radon or Tagged Ox where the chemistry takes less time than it does to unzip the met fields.
NOTE: You only need to specify this if you are unzipping met fields on the fly. This was usually done with GEOS - 3 met fields, which are now obsolete.
18
Specify if you want to use the variable tropopause option. This should always be set to T if you are using GEOS - 4 or GEOS - 5 met fields.
19
Specify the global offsets I0 and J0 (located in source code file grid_mod.F). For a global run, I0 and J0 must both be set to zero. However, for nested grid runs, we must set I0 and J0 to the appropriate offsets.

5.2.1.2 The TRACER Menu
Line numbers are not part of the input.geos file, but have been included for reference.
See Appendix 1 for the list of tracers for the different "full-chemistry" options.
01: %%% TRACER MENU %%%     :
02: Type of simulation      : 3
03: Number of Tracers       : 53
04: Tracer Entries -------> : TR#   Name  g/mole   Tracer Members; () = emitted
05: Tracer #1               :   1   NOx     46.0   NO2  (NO)  NO3   HNO2
06: Tracer #2               :   2   Ox      48.0   (O3)  NO2  2NO3
07: Tracer #3               :   3   PAN    121.0
08: Tracer #4               :   4   CO      28.0   (CO)
09: Tracer #5               :   5   ALK4    12.0   (4C)
10: Tracer #6               :   6   ISOP    12.0   (5C)
11: Tracer #7               :   7   HNO3    63.0   (HNO3)
12: Tracer #8               :   8   H2O2    34.0
13: Tracer #9               :   9   ACET    12.0   (3C)
14: Tracer #10              :  10   MEK     12.0   (4C)
15: Tracer #11              :  11   ALD2    12.0   (2C)
16: Tracer #12              :  12   RCHO    58.0
17: Tracer #13              :  13   MVK     70.0
18: Tracer #14              :  14   MACR    70.0
19: Tracer #15              :  15   PMN    147.0
20: Tracer #16              :  16   PPN    135.0
21: Tracer #17              :  17   R4N2   119.0
22: Tracer #18              :  18   PRPE    12.0   (3C)
23: Tracer #19              :  19   C3H8    12.0   (3C)
24: Tracer #20              :  20   CH2O    30.0   (CH2O)
25: Tracer #21              :  21   C2H6    12.0   (2C)
26: Tracer #22              :  22   N2O5   105.0
27: Tracer #23              :  23   HNO4    79.0
28: Tracer #24              :  24   MP      48.0
29: Tracer #25              :  25   DMS     62.0
30: Tracer #26              :  26   SO2     64.0
31: Tracer #27              :  27   SO4     96.0
32: Tracer #28              :  28   SO4s    96.0
33: Tracer #29              :  29   MSA     96.0
34: Tracer #30              :  30   NH3     17.0
35: Tracer #31              :  31   NH4     18.0
36: Tracer #32              :  32   NIT     62.0
37: Tracer #33              :  33   NITs    62.0
38: Tracer #34              :  34   BCPI    12.0
39: Tracer #35              :  35   OCPI    12.0
40: Tracer #36              :  36   BCPO    12.0
41: Tracer #37              :  37   OCPO    12.0
42: Tracer #38              :  38   DST1    29.0
43: Tracer #39              :  39   DST2    29.0
44: Tracer #40              :  40   DST3    29.0
45: Tracer #41              :  41   DST4    29.0
46: Tracer #42              :  42   SALA    36.0
47: Tracer #43              :  43   SALC    36.0
48: Tracer #44              :  44   Br2    160.0   (Br2)
49: Tracer #45              :  45   Br      80.0
50: Tracer #46              :  46   BrO     96.0
51: Tracer #47              :  47   HOBr    97.0
52: Tracer #48              :  48   HBr     81.0
53: Tracer #49              :  49   BrNO2  126.0
54: Tracer #50              :  50   BrNO3  142.0
55: Tracer #51              :  51   CHBr3  253.0   (CHBr3)
56: Tracer #52              :  52   CH2Br2 174.0   (CH2Br2)
57: Tracer #53              :  53   CH3Br   95.0
Line
Description
1
Header line 
2
Specify the type of GEOS - Chem simulation that you wish to perform. The choices are:
   1. Rn - Pb - Be simulation
   2. CH3I simulation (NOTE: this is old and in need of updating) 
   3. NOx - Ox - Hydrocarbon - aerosol simulation w/ SMVGEAR or KPP solver (a.k.a. "full chemistry")
   4. HCN simulation
   5. ### unused ###
   6. Tagged Ox simulation
   7. Tagged CO simulation
   8. C2H6 simulation
   9. CH4 simulation
   10. Offline aerosol simulation (sulfate, carbon, secondary organics, dust, and sea salt aerosols)
   11. Mercury simulation (with or without the Global Terrestrial Mercury Model option)
   12. CO2 simulation
   13. H2 and HD simulation (NOTE: this is in need of updating)
NOTE: In this example, the TRACER MENU is set up for a NOx - Ox - Hydrocarbon - aerosol (or "full chemistry") simulation.
3
Specify N_TRACERS (located in source code file tracer_mod.F). N_TRACERS is the number of tracers that will be included in the GEOS - Chem simulation.
NOTE: If you are performing a "full-chemistry" simulation:
   1. with standard chemistry, then set N_TRACERS to 53 (as shown in the example above).
   2. with secondary organic aerosols (SOA), then set N_TRACERS to 59.
   3. with dicarbonyl chemistry, then set N_TRACERS to 75.
   4. with the Caltech isoprene chemistry, then set N_TRACERS to 56.
4
Header line
5
Entry for the NOx tracer. You must list the following information:
   * Tracer number
   * Tracer name (up to 14 characters)
   * Molecular weight in g/mole
For most types of simulations this is all you need to list. However, for the NOx - Ox - Hydrocarbon - aerosol simulation (a.k.a. "full chemistry") simulation, you must also list the following information, which will be passed to the SMVGEAR chemistry solver routines:
   * If this is a family tracer, then you must specify the names of the individual species which constitute this tracer. In this example, NOx is a family consisting of NO2 + NO + NO3 + HNO2, so you must list these species names after the molecular weight as shown above. These can be separated by spaces (i.e. no commas or semicolons are needed).
   * You must also denote species which have emission reactions in the SMVGEAR chemical mechanism by placing parentheses around the species name. In this case, all of the anthropogenic emissions which go into the NOx family are actually emissions of NO, so you must denote this by (NO).
   * A number in front of an individual species name denotes the coefficient by which that species is to be multiplied. In the case of NOx, all of the species have a coefficient of one, and thus may be omitted.
6
Entry for the Ox tracer. As with NOx, you must list the tracer number, name, and molecular weight. You must also list this additional information:
   * Ox is a family tracer (which consists of O3 + NO2 + 2NO3). Therefore in the example above, you must list constituent species as shown above. Note that the coefficient in front of the NO3 is 2, which denotes that 2 molecules of NO3 are included in the Ox family.
   * You must also denote species which have emission reactions in the SMVGEAR chemical mechanism by placing parentheses around the species name. In this case, all of the anthropogenic emissions which go into the Ox family are actually emissions of O3, so you must denote this by (O3).
7
Entry for the PAN tracer: As with NOx, you must list the tracer number, name, and molecular weight. However, PAN is not a family tracer (i.e. it has no constituent species other than itself). It also does not have an emission reaction defined in the SMVGEAR chemical mechanism. So this is all the information you need to give.
8
Entry for the CO tracer: As with NOx you must list the tracer number, name, and molecular weight. Although CO is not a family tracer (i.e. it has no constituent species other than itself), it is an emitted tracer in the SMVGEAR chemical mechanism. Therefore you need to list (CO) in parentheses after the molecular weight in g/mole.
9 
Entry for the ALK4 (C4 lumped alkanes) tracer: As with NOx you must list the tracer number, name, and molecular weight.
In GEOS - Chem, several of the hydrocarbon tracers are not carried in molecules of tracer, but in equivalent atoms of carbon. ALK4 is one of these types of hydrocarbon tracers. Also, ALK4 has an emission reaction defined within the SMVGEAR chemistry mechanism. You can therefore denote this by placing (4C) after the molecular weight in g/mole. The 4C denotes that ALK4 consists of 4 carbon atoms, and the parentheses denote that ALK4 has an emission reaction in the SMVGEAR chemistry mechanism.
10
Entry for the ISOP (isoprene) tracer. This is a hydrocarbon tracer which consists of 5 carbon atoms.
11 - 12
Entries for HNO3 and H2O2 tracers
13 - 15
Entries for hydrocarbon tracers: ACET (3 carbons), MEK (4 carbons), ALD2 (2 carbons)
16 - 21
Entries for RCHO, MVK, MACR, PMN, PPN, R4N2.
22 - 23
Entries for they hydrocarbon tracers PRPE (C3 lumped alkenes -- 3 carbons) and C3H8 (3 carbons).
24
Entry for CH2O (formaldehyde). This has an emission reaction defined in the SMVGEAR chemistry mechanism so we must list its name in parentheses after the molecular weight. 
25
Entry for hydrocarbon tracer C2H6 (2 carbons).
26 - 57
Entries for the rest of the GEOS - Chem tracers.
Note: Br2, CHBr3, and CH2Br2 have emissions reactions defined within the SMVGEAR chemistry mechanism, so we must list these names in parentheses after the molecular weight.

5.2.1.3 The TRANSPORT MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% TRANSPORT MENU %%%  :
02: Turn on Transport       : T
03:  => Use Flux Correction?: F
04:  => Fill Negative Values: T
05:  => IORD, JORD, KORD    : 3 3 7
06: Transport Timestep [min]: 30
Line
Description
1
Header line 
2
Specify LTRAN (located in source code file logical_mod.F). Set LTRAN to T to turn on TPCORE transport, or set to F to turn off TPCORE transport.
3
Specify LMFCT (located in source code file logical_mod.F). Setting LFMCT to T turns on flux-corrected transport in TPCORE.
NOTE: This has no effect for GEOS - 4 and GEOS - 5 simulations.
4
Specify LFILL (located in source code file logical_mod.F). Setting LFILL to T will cause TPCORE to fill negative values with zeroes.
5
Specify the IORD, JORD, KORD transport options for TPCORE (located in source code file transport_mod.F). These settings determine how TPCORE performs transport in the E/W, N/S, and vertical directions. Recommended values are 3, 3, 7. 
6
Specify the transport timestep (TS_DYN) in minutes. Recommended values: 30 min (4° x 5°), 15 min (2° x 2.5°) and 10 min (1° x 1° or higher resolution). The transport timestep should be the smallest timestep used. 

5.2.1.4 The CONVECTION MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% CONVECTION MENU %%% :
02: Turn on Cloud Conv?     : T
03: Turn on PBL Mixing?     : T
04:  => Use non-local PBL?  : T
05: Convect Timestep (min)  : 30
Line
Description
1
Header line 
2
Specify LCONV (located in source code file logical_mod.F). Set LCONV to T to turn on cloud convection.
3
Specify LTURB (located in source code file logical_mod.F). Set LTURB to T to turn on PBL mixing.
4
Specify LNLPBL (located in source code file logical_mod.F). The options are as follows:
   * To use the non-local PBL mixing scheme (aka VDIFF), then LNLPBL to T.
   * To use the full mixing in the PBL (aka TURBDAY), then set LNLPBL to F
NOTE: If LTURB (Line 3) is set to F, then neither PBL mixing option will be executed, regardless of the setting of LNLPBL.
5
Specify the convection timestep (TS_CONV) in minutes. The convection timestep should equal the the transport timestep (i.e. TS_CONV = TS_DYN). This is required for the central chemistry timestep algorithm.

5.2.1.5 The EMISSIONS MENU 
Line numbers are not part of the input.geos file, but have been included for reference.
01: %% EMISSIONS MENU %%%  :
02: Turn on emissions?      : T
03: Emiss timestep (min)    : 60 
04: Include anthro emiss?   : T
05:  => Scale to (1985-2005): -1
06:  => Use EMEP emissions? : T
07:  => Use BRAVO emissions?: T
08:  => Use EDGAR emissions?: T
09:  => Use STREETS emiss?  : T
10:  => Use CAC emissions?  : T
11:  => Use NEI2005 emiss?  : T
12:  => Use RETRO emiss?    : T
13: Use EPA/NEI99 (anth+bf)?: F
14:     w/ ICARTT modif.?   : F
15:     w/ VISTAS NOx emis? : F
16: Include biofuel emiss?  : T
17: Include biogenic emiss? : T
18:  => Use MEGAN inventory?: T
19:  => Use PCEEA model?    : F
20:  => Use MEGAN for MONO? : T
21:  => Isoprene scaling    : 1
22: Include biomass emiss?  : T
23:  => Seasonal biomass?   : T
24:  => Scaled to TOMSAI?   : F
25:  => Use GFED2 biomass?  :---
26:     => monthly GFED2?   : F
27:     => 8-day GFED2?     : F 
28:     => 3-hr GFED2?      : F
29:     => synoptic GFED2?  : F
30:  => Use GFED3 biomass?  :---
31:     => monthly GFED3?   : T 
32:     => daily GFED3?     : F 
33:     => 3-hr GFED3?      : F
34: Individual NOx sources  :---
35:  => Use aircraft NOx?   : T
36:  => Use lightning NOx?  : T
37:     => Spat-seas constr?: T
38:  => Use soil NOx        : T
39:  => Use fertilizer NOx  : T
40: NOx scaling             : 1
41: Use ship SO2 emissions? :---
42:  => global EDGAR ?      : T
43:  => global ICOADS ?     : T
44:  => EMEP over EUROPE ?  : T
45:  => ship SO2 Corbett ?  : F
46:  => ship SO2 Arctas ?   : T
47: Use COOKE BC/OC (N. Am.): F   
48: Use AVHRR-derived LAI?  : F
49: Use MODIS-derived LAI?  : T
50: Use historical emiss?   : F
51:  => What decade?        : 2000
52: Bromine switches        :---
53:  => Use Warwick VSLS?   : T
54:  => Use seasalt Br2?    : T
55:  => 1ppt MBL BRO Sim.?  : F
56:  => Bromine scaling     : 1
Line
Description
1
Header line 
2
Specify LEMIS (located in source code file logical_mod.F). Set LEMIS to T to turn on emissions in a GEOS - Chem simulation. Set LEMIS to F to turn off all emissions in a GEOS - Chem simulation.
3
Specify the emission timestep (TS_EMIS) in minutes. The emissions timestep should be the same as the chemistry time step (i.e. TS_EMIS = TS_CHEM). This is required for the central chemistry timestep algorithm.
4
Specify LANTHRO (located in source code file logical_mod.F). Set LANTHRO to T to include anthropogenic emission, or to F to shut off all anthropogenic emission. 
5
Specify FSCALYR, the emission year for anthropogenic emissions (located in source code file CMN_O3). For each selected inventory (see below), if a dataset exists for that year, it is used. If not, the closest available year is used, and -for NOx, CO, and SOx only- emissions are scaled to the emission year. Scale factors are available for 1985-2006. Before 1985, 1985 is used and after 2006, 2006 is used. It is recommended to set this input to -1 to let GEOS - Chem automatically scale data to the year simulated.
6
Specify LEMEP (located in source code file logical_mod.F). Set LEMEP to T to include EMEP European anthropogenic emissions, or to F otherwise. 
7
Specify LBRAVO (located in source code file logical_mod.F). Set LBRAVO to T to include BRAVO anthropogenic emissions over Mexico, or to F otherwise.
8
Specify LEDGAR (located in source code file logical_mod.F). Set LEDGAR to T to include EDGAR anthropogenic emissions, or to F otherwise.
9
Specify LSTREETS (located in source code file logical_mod.F). Set LSTREETS to T to include David Streets SE Asian anthropogenic emissions, or to F otherwise.
10
Specify LCAC (located in source code file logical_mod.F). Set LCAC to T to include CAC anthropogenic emissions over Canada, or to F otherwise.
11
Specify LNEI05 (located in source code file logical_mod.F). Set LNEI05 to T to overwrite anthropogenic emissions over the continental USA with those from the EPA/NEI05 inventory, or F to keep the default emissions over the continental USA.
NOTE: We recommend using the newer EPA/NEI05 emissions rather than the EPA/NEI99 emissions.
12
Specify LRETRO (located in source code file logical_mod.F). Set LRETRO to T to include RETRO anthropogenic VOC emissions, or to F otherwise.
13
Specify LNEI99 (located in source code file logical_mod.F). Set LNEI99 to T to overwrite anthropogenic and biofuel emissions over the continental USA with those from the EPA/NEI99 inventory, or F to keep the default emissions over the continental USA.
NOTE: If LNEI99 and LNEI05 are both set to T, then LNEI05 is used.
14
Specify LICARTT (located in source code file logical_mod.F). Set LICARTT to T to use the ICARTT fix for EPA/NEI99 emissions.
15
Specify LVISTAS (located in source code file logical_mod.F). Set LVISTAS to T to include VISTAS anthropogenic NOx emissions.
16
Specify LBIOFUEL (located in source code file logical_mod.F). Set LBIOFUEL to T to include biofuel emissions, or to F to shut off all biofuel emission.
17
Specify LBIOGENIC (located in source code file logical_mod.F). Set LBIOGENIC to T to include biogenic emissions (e.g. ISOPRENE, MONOTERPENES), or to F to shut off all biogenic emission.
18
Specify LMEGAN (located in source code file logical_mod.F). Set LMEGAN to T to use biogenic emissions from the MEGAN inventory for Isoprene and other VOC's.
NOTE: The GEIA biogenic emissions are now deprecated. They have been removed in GEOS - Chem v9 - 01 - 03.
19
Specify LPECCA (located in source code file logical_mod.F).
If you turn off the PCEEA model (by setting the line => Use PCEEA model? : F), then MEGAN will use the existing canopy model, but with updated leaf-age and temperature algorithms. This option is closest to the previous implementation of MEGAN in GEOS - Chem v8 - 02 - 03 and prior versions.
If you turn on the PCEEA model (by setting the line => Use PCEEA model? : T), then MEGAN will follow the approach of Guenther et al, 2006. It will not use a canopy model, but will take into account the light dependency of monoterpene emissions.
20
Specify LMONO (located in source code file logical_mod.F). Set LMONO to T to use biogenic emissions from the MEGAN inventory for Monoterpenes and Methyl Butenol, or to F to use the default GEIA biogenic emissions. 
21
Set ISOP_SCALING (located in source code file emissions_mod.F). Set ISOP_SCALING to any REAL value to scale overall isoprene emissions. If you do not want to scale isoprene emissions, then leave ISOP_SCALING set to 1.
22
Specify LBIOMASS (located in source code file logical_mod.F). Set LBIOMASS to T to include biomass burning emissions, or to F to shut off all biomass burning emissions.
23
Specify LBBSEA (located in source code file logical_mod.F). Set LBBSEA to T if you wish to use seasonal (aka climatological) biomass burning emissions. Set LBBSEA to F if you wish to use biomass burning emissions for specific years (in order to establish interannual variability).
NOTE: This option is mostly obsolete. We recommend using the GFED3 biomass emissions.
24
Specify LTOMSAI (located in source code file logical_mod.F). Set LTOMSAI to T if you wish to scale biomass burning to TOMS Aerosol Index data.
NOTE: This option is mostly obsolete. We recommend using the GFED3 biomass emissions.
25
Header line
26
Specify LGFED2BB (located in source code file logical_mod.F). Set LGFED2BB to T if you wish to use the monthly-mean GFED2 biomass emissions, or to F otherwise. 
NOTE: We recommend using the newer GFED3 biomass emissions rather than the GFED2 emissions.
27
Specify L8DAYBB (located in source code file logical_mod.F). Set L8DAYBB to T if you wish to use the weekly-mean GFED2 biomass emissions, or to F otherwise.
28
Specify L3HRBB (located in source code file logical_mod.F). Set L3HRBB to T if you wish to use the 3-hourly-mean GFED2 biomass emissions, or to F otherwise.
29
Specify LSYNOPB (located in source code file logical_mod.F). Set LSYNOPB to T if you wish to use the 3-hourly synoptic GFED2 biomass emissions, or to F otherwise.
30
Header line
31
Specify LGFED3BB (located in source code file logical_mod.F). Set LGFED3BB to T if you wish to use the monthly-mean GFED3 biomass emissions, or to F otherwise. 
NOTE: For most applications, the monthly-mean GFED3 data should suffice.
32
Specify LDAYBB3 (located in source code file logical_mod.F). Set LDAYBB3 to T if you wish to use the daily-mean GFED3 biomass emissions, or to F otherwise.
NOTE: To use daily GFED3, you must also set LGFED3BB to T.
33
Specify L3HRBB3 (located in source code file logical_mod.F). Set L3HRBB3 to T if you wish to use the 3-hourly-mean GFED3 biomass emissions, or to F otherwise.
NOTE: To use 3-hourly GFED3, you must also set LGFED3BB and LDAYBB3 to T.
34
Header line
35
Specify LAIRNOX (located in source code file logical_mod.F). Set LAIRNOX to T to include aircraft NOx emissions, or to F to shut off all aircraft NOx emissions. 
36
Specify LLIGHTNOX (located in source code file logical_mod.F). Set LLIGHTNOX to T to include lightning NOx emissions, or to F to shut off all lightning NOx emissions. 
37
Specify LOTDSCALE (located in source code file logical_mod.F) to apply the OTD/LIS redistribution. This will place a spatial and seasonal constraint on lightning emissions.
NOTE: All of the other lightning redistribution options are now obsolete and have been removed.
38
Specify LSOILNOX (located in source code file logical_mod.F). Set LSOILNOX to T to include soil NOx emissions, or to F to shut off soil NOx emissions other than fertilizer NOx emissions. 
39
Set LFERTILIZERNOX (located in source code file logical_mod.F). Set LFERTILIZERNOX to T to include fertilizer NOx emissions, or to F to shut off fertilizer NOx emissions.
40
Set NOx_SCALING (located in source code file emissions_mod.F). Set NOx_SCALING to any REAL value to scale overall NOx emissions.
41
Header line
42
Specify LEDGARSHIP (located in source code file logical_mod.F). Set LEDGARSHIP to T to use EDGAR ship emissions, or to F otherwise.
43
Specify LICOADSSHIP (located in source code file logical_mod.F). Set LICOADSSHIP to T to use ICOADS ship emissions, or to F otherwise.
44
Specify LEMEPSHIP (located in source code file logical_mod.F). Set LEMEPSHIP to T to use EMEP ship emissions for Europe, or to F otherwise.
45
Specify LSHIPSO2 (located in source code file logical_mod.F). Set LSHIPSO2 to T to include SO2 emissions from ship exhaust, or to F to shut off SO2 emissions from ship exhaust.
46
Specify LARCSHIP (located in source code file logical_mod.F). Set LARCSHIP to T to include ARCTAS SO2 and CO2 ship emissions, or to F otherwise.
47
Specify LCOOKE (located in source code file logical_mod.F). Set LCOOKE to T to use Cooke anthropogenic and biofuel emissions for BC/OC over North America. 
48
Specify LAVHRRLAI (located in source code file logical_mod.F). Set LAVHRRLAI to T to use leaf area indices obtained from the AVHRR satellite, or F to continue using the default LAI inventory (from Yuhang Wang, 1998).
NOTE: This switch is now obsolete and is slated to be removed. GEOS - Chem now reads MODIS LAI data from netCDF files. The AVHRR LAI option has been removed.
49
Specify LMODISLAI (located in source code file logical_mod.F). Set LMODISLAI to T to use leaf area indices obtained from the MODIS satellite.
NOTE: This switch is now obsolete and is slated to be removed. GEOS - Chem now reads MODIS LAI data from netCDF files. The AVHRR LAI option has been removed.
50
Specify LHIST (located in source code file logical_mod.F). Set LHIST to T to use historical emissions inventories of SO2, NOx, BC, and POA, or to F otherwise.
51
Specify HISTYR, the emission year for historical emissions of SO2, NOx, BC, and POA (located in source code file input_mod.F).
52
Header line
53
Specify LWARWICK_VSLS (located in source code file logical_mod.F). Set LWARWICK_VSLS to T to use surface CHBr3 emissions from Warwick et al. (2006), scenario 3 (400 Gg CHBr3/year).
54
Specify LSSABr2 (located in source code file logical_mod.F). Set LSSABr2 to T to use sea salt Br2 emissions. Following Yang et al. (2005), sea-salt debromination is treated as emission of Br2.
55
Specify LFIX_PBL_BrO (located in source code file logical_mod.F). Set LFIX_PBL_BrO to T to set Bro concentrations in the PBL equal to 1 ppt during the day.
56
Set Br_SCALING (located in source code file bromocarb_mod.F). Set Br_SCALING to any REAL value to scale overall bromine emissions. If you do not want to scale bromine emissions, then leave Br_SCALING set to 1.

5.2.1.6 The FUTURE MENU 
NOTE: At present, this menu controls options that only affect simulations with GCAP met fields. 
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% FUTURE MENU %%%     :
02: Use future emissions?   : F
03: Which IPCC future year? : 2050
04: Which IPCC scenario?    : A1
Line
Description
1
Header line
2
Specify LFUTURE (located in source code file logical_mod.F). Set LFUTURE to T to scale present-day emissions to one of the IPCC future scenarios, or F otherwise. 
3
Specify FUTURE_YEAR, which is the year to which the current emissions will be scaled. Current options are 2030 and 2050. 
4
Specify FUTURE_SCEN, which is the IPCC scenario to be used. Current options are: A1, B1. 

5.2.1.7 The AEROSOL MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% AEROSOL MENU %%%    :
02: Online SULFATE AEROSOLS : T
03: Online CRYST/AQ AEROSOLS: F
04: Online CARBON  AEROSOLS : T
05: Online 2dy ORG AEROSOLS : F
06: Online DUST    AEROSOLS : T
07:  => Use DEAD emissions? : T
08: Online SEASALT AEROSOLS : T
09:  => SALA radius bin [um]: 0.01 0.5
10:  => SALC radius bin [um]: 0.5  8.0
11: Online dicarb. chem.    : F
Line
Description
1
Header line 
2
Specify LSULF (located in source code file logical_mod.F). Set LSULF to T to turn on emissions and chemistry for sulfate aerosols (DMS, SO2, SO4, MSA, NH3, NH4, NIT).
3
Specify LCRYST (located in source code file logical_mod.F). Set LCRYST to T to turn on emissions and chemistry for crystalline sulfur and aqueous aerosols (AS, AHS, LET, SO4aq, NH4aq).
NOTE: This feature has not been implemented in GEOS - Chem v9 - 01 - 03. For the time being, set LCRYST to F.
4
Specify LCARB (located in source code file logical_mod.F). Set LCARB to T to turn on emissions and chemistry for carbonaceous aerosols (BCPI, BCPO, OCPI, OCPO).
5
Specify LSOA (located in source code file logical_mod.F). Set LSOA to T to turn on emissions and chemistry for secondary organic aerosols. Turning on the secondary organic aerosols will add 9 tracers to the simulation.
NOTE: If you are going to use the SOA tracers, you must also change the setting of LISOPOH in the "globchem.dat" file from "D" (dead) to "A" (active).
6
Specify LDUST (located in source code file logical_mod.F). Set LDUST to T to turn on emissions and chemistry for mineral dust aerosol tracers (DST1, DST2, DST3, DST4).
7
Specify LDEAD (located in source code file logical_mod.F). Set LDEAD to T to use the dust source function from the DEAD model (cf. C. Zender). Set LDEAD to F to use the dust source function from the GOCART (cf. Paul Ginoux). 
8
Specify LSSALT (located in source code file logical_mod.F). Set LSSALT to T to turn on emissions and chemistry for sea salt aerosols (SALA, SALC).
9
Specify the edges which denote accumulation mode sea salt tracer in microns. (This is stored in variable SALA_REDGE_um in tracer_mod.F). Recommended setting: 0.01 to 0.5 microns.
10
Specify the edges which denote coarse mode sea salt tracer in microns. (This is stored in variable SALC_REDGE_um in tracer_mod.F). Recommended setting: 0.5 to 8 microns. 
11
Specify LDICARB (located in source code file logical_mod.F). Set LDICARB to T if you are using the dicarbonyl chemistry simulations (75 tracers), to F otherwise.
NOTES:
   1. You may define the limits of the accumulation and coarse mode sea salt aerosol radius bins (in variables SALA_REDGE_um and SALC_REDGE_um) as you wish. However, the recommended values of 0.1 - 0.5 and 0.5 - 4 microns, respectively, were chosen in order to conform to the cross-sections and other optical settings as defined in the FAST - J input file jv_spec.dat. Therefore, unless you use the recommended values, you will not be able to archive aerosol optical depths for these aerosol types with the ND21, ND48, ND49, ND50, and ND51 diagnostics. 

5.2.1.8 The DEPOSITION MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% DEPOSITION MENU %%% :
02: Turn on Dry Deposition? : T
03: Turn on Wet Deposition? : T
Line
Description
1
Header line 
2
Specify LDRYD (located in source code file logical_mod.F). Set LDRYD to T to turn on dry deposition, or F to turn off dry deposition.
3
Specify LWETD (located in source code file logical_mod.F). Set LWETD to T to turn on wet deposition, or F to turn off wet deposition.

5.2.1.9 The CHEMISTRY MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% CHEMISTRY MENU %%%  :
02: Turn on Chemistry?      : T
03: Use linear. strat. chem?: T
04:  => Use Linoz for O3?   : T
05: Chemistry Timestep [min]: 60
06: Read and save CSPEC_FULL: T
07: Use solver coded by KPP : F
Line
Description
1
Header line 
2
Specify LCHEM (located in source code file logical_mod.F). Set LCHEM to T to turn on chemistry, or F to turn off chemistry.
3
Specify LSCHEM (located in source code file logical_mod.F). Set LSCHEM to T to turn on stratospheric chemistry, or F to turn off stratospheric chemistry.
4
Specify LLINOZ (located in source code file logical_mod.F). Set LLINOZ to T to use Linoz for O3 chemistry in the stratosphere, otherwise Synoz will be used.
5
Specify the chemistry timestep (TS_CHEM) in minutes. We suggest using a chemistry timestep double the transport time step (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep should be a multiple of the transport timestep (i.e. TS_CHEM = X * TS_DYN, where X is an integer). See this wiki page for more information.
6
Specify LSVCSPEC (located in source code file logical_mod.F). Set LSVCSPEC to T to save all species (CSPEC_FULL array) in a restart file in addition to the standard restart file, which saves only the transported tracers or to F otherwise. If the option Make new restart file is set to F in the simulation menu, then no restart file will be saved regardless of LSVCSPEC value. 
NOTE: If you are going to be running a very long GEOS - Chem simulation, and must split the job into several stages (i.e. in order to submit to a queue system), then you should set LSVCSPEC to T. This will make sure that the chemical species stored in the CSPEC array will not get reset to the background defaults (from globchem.dat) when the next run stage starts.
7
Specify LKPP (located in source code file logical_mod.F). Set LKPP to T to use a chemistry solver coded by the KPP pre-processor. If set to F, the chemistry solver SMVGEAR II is used. 

5.2.1.10 The CO2 MENU
This menu only controls options for the CO2 and tagged CO2 simulations. This is an optional menu and may be omitted from input.geos if you are not concerned with these simulations.
For more information, please see:
   1. GEOS - Chem wiki: CO2 simulation page
   2. A more detailed account of all settings can be found in: 

Nassar, R., D.B.A. Jones, P. Suntharalingam, J.M. Chen, R.J. Andres, K.J. Wecht, R.M. Yantosca, S.S. Kulawik, K.W. Bowman, J.R. Worden, T. Machida, and H. Matsueda, Modeling CO2 with improved emission inventories and CO2 production from the oxidation of other carbon species, Geoscientific Model Development, 3, 689-716, 2010.
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% CO2 SIM MENU %%%    :
02: Fossil Fuel Emissions   :---
03:   Generic FF emissions  : F
04:   Annual FF emissions   : F
05:   Monthly FF emissions  : T
06: 3-D Chemical Oxid Source: F
07: Biomass Burn emissions  :---
08:   Seasonal only biomass : F
09:   GFED2 monthly biomass : F
10:   GFED2 8-day biomass   : T
11:   GFED3 monthly biomass : F
12:   GFED3 daily biomass   : F
13: Biofuel emissions       : T
14: Terrestrial Exchange    :---
15:   CASA daily avg NEP    : F
16:   CASA diurnal cycle NEP: T
17:   Net Ter Ex original   : F
18:   Net Ter Ex climatology: T
19: Ocean Exchange          :---
20:   Takahashi 1997        : F
21:   Takahashi 2009 annual : F
22:   Takahashi 2009 monthly: T
23: Ship & Plane Emissions  :---
24:   EDGAR ship emissions  : F
25:   ICOADS ship emissions : T
26:   Aviation emissions    : T
27: Tagged CO2 runs         :---
28:   Save Fossil CO2 Bkgrd : F
29:   Tag Bios/Ocean CO2 reg: F
30:   Tag Land FF CO2 reg   : F
31:   Tag Global Ship CO2   : F
32:   Tag Global Plane CO2  : F 
Line
Description
1
Header line 
2
Fossil Fuel sub-header line (select only one option in this section)
3
Annually averaged fossil fuel emissions for 1995 from CDIAC [Andres et al., 1996]
4
Year-specific annually averaged fossil fuel emissions from CDIAC [Andres et al., 1996], with 2007-2009 scaled based on [Boden et al., 2009; LeQuere, 2009] 
5
Month and year-specific monthly averaged fossil fuel emissions from CDIAC [Andres et al., 1996], with 2007-2009 scaled based on [Boden et al., 2009; LeQuere, 2009]
6
3-D CO2 chemical source from oxidation of CO, CH4 and NMHCs based on Suntharalingam et al. [2005], with appropriate surface emission corrections.
7
Biomass Burning sub-header line (select only one option in this section)
8
Seasonally approximated biomass burning emissions from Duncan et al. [2003]
9
Global Fire Emission Database (GFED) version 2 âEuro" monthly (1997-2008). NOTE: The choice of GFED emissions in the CO2 MENU must be consistent with the choice in the EMISSIONS MENU.
10
Global Fire Emission Database (GFED) version 2 âEuro" 8-day (2001-2007). NOTE: The choice of GFED emissions in the CO2 MENU must be consistent with the choice in the EMISSIONS MENU.
11
Global Fire Emission Database (GFED) version 3 âEuro" monthly (1997-2010). NOTE: The choice of GFED emissions in the CO2 MENU must be consistent with the choice in the EMISSIONS MENU.
12
Global Fire Emission Database (GFED) version 3 âEuro" daily (2003-2010). NOTE: The choice of GFED emissions in the CO2 MENU must be consistent with the choice in the EMISSIONS MENU.
13
Biofuel Emissions âEuro" Yevich and Logan [2003]
14
Terrestrial Exchange sub-header line (select one balanced biosphere option and one Net Terrestrial Exchange option)
15
CASA model daily average Net Ecosystem Production (balanced âEuro" no net annual flux) [Potter et al., 1993; Olsen and Randerson, 2004]
16
CASA model 3-hourly Net Ecosystem Production (balanced âEuro" no net annual flux) [Potter et al., 1993; Olsen and Randerson, 2004]
17
Net Terrestrial Exchange (original) of -1.01 PgC/yr 
18
Net Terrestrial Exchange (climatology) of -5.29 PgC/yr [Baker et al., 2006] adjusted for biomass/biofuel burning
19
Ocean Exchange sub-header line (select only one option in this section)
20
Annual ocean flux climatology of non-El NiÃ+-o years from Takahashi et al. [1997]
21
Annual ocean flux climatology of non-El NiÃ+-o years from Takahashi et al. [2009]
22
Monthly ocean flux climatology of non-El NiÃ+-o years from Takahashi et al. [2009]
23
Ship and Plane sub-header (select no more than one ship option and one aviation option)
24
International ship CO2 emissions (annually-averaged) with simplified distribution from EDGAR scaled to scaled to annual values for 1985-2006 [Endresen et al. 2007].
25
International ship CO2 emissions based on the International Comprehensive Ocean Atmosphere Data Set (ICOADS) with monthly variability [Corbett & Koehler, 2003, 2004; Wang et al., 2008] scaled to annual values for 1985-2006 [Endresen et al. 2007].
26
Aviation emission 3-D distribution from fuel burn (GEOS - Chem sulfate aerosol simulation) scaled to annual CO2 values for 1985-2002 [Sausen & Schumann, 2000; Kim et al., 2005; 2007; Wilkerson et al., 2010] and estimates for 2002-2009. An associated surface correction automatically removes domestic aviation emissions from the main fossil fuel source in continental size regions. 
27
Tagged CO2 sub-header line (select all that apply)
28
Save CO2 background
29
Tag biosphere regions (28), ocean regions (11) and the Rest of the World (ROW) as specified in the Regions_land.dat and Regions_ocean.dat files
NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.
30
Tag fossil fuel regions (28) as specified in the Regions_land.dat file and ROW
NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.
31
Tag global ship emissions as a single tracer
NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.
32
Tag global aviation emissions as a single tracer
NOTE: Tagged tracers should be customized by each user and the present configuration will not work for resolutions other than 2x2.5.

5.2.1.11 The MERCURY MENU
This menu only controls options for the mercury simulation (with or without the Global Terrestrial Mercury Model). This is an optional menu and may be omitted from input.geos if you are not concerned with this simulation.
For more information, please see:
   1. GEOS - Chem wiki: Mercury simulation
   2. GEOS - Chem wiki: Global Terrestrial Mercury Model
   3. Global Terrestrial Mercury Model User's Manual (which describes the contents of the GTMM run directory)
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% MERCURY MENU %%%    : 
02: Use anthro Hg emiss for : 2000
03: Error check tag/tot Hg? : F
04: Use dynamic ocean Hg?   : T
05: Preindustrial sim?      : F
06: Ocean Hg restart file   : ocean.totHg.YYYYMMDDhh
07: Use GTMM soil model?    : F
08: GTMM Hg restart file    : GTM.totHg.YYYYMMDDhh
Line
Description
1
Header line
2
Specify ANTHRO_Hg_YEAR (located in source code file mercury_mod.F), which is the baseline year of the anthropogenic mercury emissions that are used in the tagged mercury simulation. Current options are either 1995 or 2000.
3
Specify USE_CHECKS (located in source code file file ocean_mercury_mod.F). Set USE_CHECKS to T to stop with an error message if the sum of tagged tracers does not equal the total tracer, or F otherwise. This is useful for debugging.
4
Specify LDYNOCEAN (located in source code file logical_mod.F). Set LDYNOCEAN to T to use the online ocean mercury model (in source code file ocean_mercury_mod.F) or F to read ocean mercury concentrations from monthly mean files on disk.
5
Set to T if you want to run a preindustrial simulation (turn off anthropogenic emissions), to F otherwise.
6
If you have set LDYNOCEAN to T (i.e. you are using the online ocean mercury model), then you can specify the name of the ocean mercury restart file. This file saves the concentrations of oceanic mercury tracers for continuing the run at a later stage.
7
Set to T if you want to run GTMM online in GEOS - Chem. Note, that to use GTMM online, you need to first run GTMM offline up to equilibrium and to compile GEOS - Chem with GTMM enabled. For more information, please refer to this document.
8
If you are using the GTMM online, then you can specify the name of the GTMM mercury restart file. This file saves the monthly depositions of mercury tracers for continuing the run at a later stage.
NOTES:
   1. In order for GTMM to work properly, the Mercury Menu should come before the Diagnostic Menu.

5.2.1.12 The CH4 MENU (a.k.a. methane menu)
NOTE: This menu controls options for the tagged CH4 simulation only. This is an optional menu and may be omitted from input.geos if you are not concerned with this simulation.
For more information, please see:
   1. GEOS - Chem wiki: CH4 simulation
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% CH4 MENU %%%        :
02: Compute CH4 budget?     : F
03: Use Gas & Oil emis?     : T
04: Use Coal Mine emis?     : T
05: Use Livestock emis?     : T
06: Use Waste emis?         : T
07: Use Biofuel emis?       : T
08: Use Rice emis?          : T
09: Use Ot. Anthro emis?    : T
10: Use Biomass emis?       : T
11: Use Wetlands emis?      : T
12: Use Soil Absorption?    : T
13: Use Ot. Natural emis?   : T
Line
Description
1
Header line
2
Specify LCH4BUD (located in source code file logical_mod.F). Set LCH4BUD to T to calculate a monthly budget for CH4. The CH4 budget is not working well, we recommend setting LCH4BUD to F.
3
Specify LGAO (located in source code file logical_mod.F). Set LGAO to F to turn off CH4 emissions from gas and oil.
4
Specify LCOL (located in source code file logical_mod.F). Set LCOL to F to turn off CH4 emissions from coal.
5
Specify LLIV (located in source code file logical_mod.F). Set LLIV to F to turn off CH4 emissions from livestock.
6
Specify LWAST (located in source code file logical_mod.F). Set LWAST to F to turn off CH4 emissions from waste.
7
Specify LBFCH4 (located in source code file logical_mod.F). Set LBFCH4 to F to turn off CH4 emissions from biofuels.
8
Specify LRICE (located in source code file logical_mod.F). Set LRICE to F to turn off CH4 emissions from rice fields.
9
Specify LOTANT (located in source code file logical_mod.F). Set LOTANT to F to turn off other CH4 anthropogenic emissions.
10
Specify LBMCH4 (located in source code file logical_mod.F). Set LBMCH4 to F to turn off CH4 emissions from biomass burning.
11
Specify LWETL (located in source code file logical_mod.F). Set LWETL to F to turn off CH4 emissions from wetlands
12
Specify LSOABS (located in source code file logical_mod.F). Set LSOABS to F to turn off CH4 absorption by soils.
13
Specify LOTNAT (located in source code file logical_mod.F). Set LOTNAT to F to turn off other CH4 natural emissions.

5.2.1.13 The OUTPUT MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% OUTPUT MENU %%%     : 123456789.123456789.123456789.1--1=ZERO+2=BPCH
02: Schedule output for JAN : 3000000000000000000000000000000
03: Schedule output for FEB : 30000000000000000000000000000
04: Schedule output for MAR : 3000000000000000000000000000000
05: Schedule output for APR : 300000000000000000000000000000
06: Schedule output for MAY : 3000000000000000000000000000000
07: Schedule output for JUN : 300000000000000000000000000000
08: Schedule output for JUL : 3000000000000000000000000000000
09: Schedule output for AUG : 3000000000000000000000000000000
10: Schedule output for SEP : 300000000000000000000000000000
11: Schedule output for OCT : 3000000000000000000000000000000
12: Schedule output for NOV : 300000000000000000000000000000
13: Schedule output for DEC : 3000000000000000000000000000000
Line
Description
1
Header line 
2
Schedule diagnostic output for JANUARY. Place a 3 in the column corresponding to the day of the month (1 - 31) on which you want diagnostic output saved to the binary punch file. 
In the example above, the columns which indicate January 1st and February 1st both have a 3 listed there. This will cause GEOS - Chem to archive diagnostic data for the entire month of January and then save it to disk at 0 GMT on February 1st. (GEOS - Chem is smart enough not to write anything to disk at 0 GMT on January 1st, since this is the starting time of the simulation.)
3
Schedule diagnostic output for FEBRUARY. 
4
Schedule diagnostic output for MARCH.
5
Schedule diagnostic output for APRIL.
6
Schedule diagnostic output for MAY. 
7
Schedule diagnostic output for JUNE. 
8
Schedule diagnostic output for JULY. 
9
Schedule diagnostic output for AUGUST. 
10
Schedule diagnostic output for SEPTEMBER. 
11
Schedule diagnostic output for OCTOBER. 
12
Schedule diagnostic output for NOVEMBER.
13
Schedule diagnostic output for DECEMBER. 

5.2.1.14 The GAMAP MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% GAMAP MENU %%%      :
02: diaginfo.dat path       : diaginfo.dat
03: tracerinfo.dat path     : tracerinfo.dat
Line
Description
1
Header line 
2
Path name of the diaginfo.dat file for GAMAP. GEOS - Chem will create this file, which will be customized to the particular simulation that is being done. 
This may be either a relative path name (i.e. diaginfo.dat) 
or absolute path name (i.e. /home/bmy/T/run.v9-01-03/diaginfo.dat).
3
Path name of the tracerinfo.dat file for GAMAP. GEOS - Chem will create this file, which will be customized to the particular simulation that is being done. 
This may be either a relative path name (i.e. tracerinfo.dat) 
or absolute path name (i.e. /home/bmy/T/run.v9-01-03/tracerinfo.dat).

5.2.1.15 The DIAGNOSTIC MENU
Line numbers are not part of the input.geos file, but have been included for reference.
For more information about GEOS - Chem diagnostics, please see Appendix 5. 
01: %% DIAGNOSTIC MENU %%% : 
02: Binary punch file name  : ctm.bpch
03: Diagnostic Entries ---> :  L   Tracers to print out for each diagnostic
04: ND01: Rn/Pb/Be source   :  0   all        
05: ND02: Rn/Pb/Be decay    :  0   all             
06: ND03: Hg emissions, P/L :  0   all                
07: ND04: CO2 sources       :  0   all                
08: ND05: Sulfate prod/loss :  0   all               
09: ND06: Dust aer source   :  0   all                
10: ND07: Carbon aer source :  0   all                
11: ND08: Seasalt aer source:  0   all                
12: ND09: -                 :  0   all                
13: ND10: -                 :  0   all                
14: ND11: Acetone sources   :  0   all                 
15: ND12: BL fraction       :  0   all              
16: ND13: Sulfur sources    :  0   all                
17: ND14: Cld conv mass flx :  0   all                
18: ND15: BL mix mass flx   :  0   all                
19: ND16: LS/Conv prec frac :  0   all               
20: ND17: Rainout fraction  :  0   all            
21: ND18: Washout fraction  :  0   all            
22: ND19: CH4 loss          :  0   all            
23: ND21: Optical depths    :  0   all            
24: ND22: J-Values          :  0   1 7 8 20 99            
25:       => JV time range  :      11 13
26: ND24: E/W transpt flx   :  0   all
27: ND25: N/S transpt flx   :  0   all
28: ND26: U/D transpt flx   :  0   all
29: ND27: Strat NOx,Ox,HNO3 :  0   1 2 7
30: ND28: Biomass emissions :  0   1 4 5 9 10 11 18 19 20 21 26 30 34 35
31: ND29: CO sources        :  0   all
32: ND30: Land Map          :  0   all
33: ND31: Surface pressure  :  0   all
34: ND32: NOx sources       :  0   all
35: ND33: Column tracer     :  0   all
36: ND34: Biofuel emissions :  0   1 4 5 9 10 11 18 19 20 21
37: ND35: Tracers at 500 mb :  0   all
38: ND36: Anthro emissions  :  0   1 4 5 9 10 11 18 19 20 21
39: ND37: Updraft scav frac :  0   all
40: ND38: Cld Conv scav loss: 47   7 8 20 24 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43
41: ND39: Wetdep scav loss  :  0   7 8 20 24 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43
42: ND41: Afternoon PBL ht  :  0   all
43: ND42: SOA concentrations:  0   all
44: ND43: Chem OH,NO,HO2,NO2: 47   all
45:   ==> OH/HO2 time range :       0 24   
46:   ==> NO/NO2 time range :      10 14
47: ND44: Drydep flx/vel    :  0   1 2 3 7 8 15 16 17 20 22 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 47 48 50 
48: ND45: Tracer Conc's     : 47   all 
49:   ==> ND45 Time range   :       0 24
50: ND46: Biogenic emissions:  0   all
51: ND47: 24-h avg trc conc :  0   all
52: ND52: GAMMA HO2         :  0   all
53: ND53: -                 :  0   all
54: ND54: Time in t'sphere  :  0   all
55: ND55: Tropopause height :  0   all
56: ND56: Lightning flashes :  0   all
57: ND57: Potential T       :  0   all
58: ND58: CH4 Emissions     :  0   all
59: ND59: -                 :  0   all
60: ND60: Wetland Frac      :  0   all
61: ND61: -                 :  0   all
62: ND62: Inst column maps  :  0   all
63: ND64: -                 :  0   all
64: ND66: DAO 3-D fields    :  0   all
65: ND67: DAO 2-D fields    :  0   all
66: ND68: Airmass/Boxheight :  0   all
67: ND69: Surface area      :  0   all
68: ND70: Debug output      :  0   all
Line
Description
1
Header line 
2
Specify the name of the binary punch file. You may use date & time tokens YYYY, MM, DD, hh, mm, ss and GEOS - Chem will replace these with the appropriate values. 
3
Header line. 
4
ND01 (Rn - Pb - Be source) diagnostic settings. You must list the following information:
   * Number of levels to save:
         o Entering 0 will turn off this diagnostic.
         o Entering 1 will archive data from level 1 (the surface level).
         o Entering 20 will archive data from level from 1 (surface) up to and including level 20. 
         o Entering 30 will archive data from level from 1 (surface) up to and including level 30, etc.

Note that the code is smart enough to prevent you from saving out more vertical levels than there are present for a given diagnostic.
   * Tracer numbers to save. If you want to save all tracers for a given diagnostic, just type the word all. If you want to save specific tracer numbers then list them individually (separated by spaces).
You must list this information (number of levels and tracer numbers) for all other diagnostics in this menu. It is recommended to save out all tracers for a given diagnostic, unless you need to save disk space. 
5
ND02 (Rn - Pb - Be decay) diagnostic settings.
6
ND03 (Mercury emissions, production & loss) diagnostic settings.
7
ND04 (CO2 prod/loss) diagnostic settings.
8
ND05 (sulfate prod & loss) diagnostic settings.
9
ND06 (mineral dust emissions) diagnostic settings.
10
ND07 (carbonaceous aerosol emissions) diagnostic settings.
11
ND08 (sea salt aerosol emissions) diagnostic settings.
12
ND09 (Free diagnostic) 
13
ND10 (sources, production and loss of H2 and HD) diagnostic settings 
14
ND11 (sea salt aerosol emissions) diagnostic settings.
15
ND12 (fraction of each layer in the PBL fraction) diagnostic settings.
16
ND13 (sulfate aerosol emissions) diagnostic settings.
17
ND14 (mass flux from cloud convection) diagnostic settings.
18
ND15 (mass flux from PBL mixing) diagnostic settings.
19
ND16 (fraction of grid box undergoing large scale & convective precip) diagnostic settings.
20
ND17 (fraction of soluble tracer lost to rainout) diagnostic settings.
21
ND18 (fraction of soluble tracer lost to washout) diagnostic settings.
22
ND19 (CH4 loss) diagnostic settings. For CH4 simulation only.
23
ND21 (optical depths of cloud, dust, and aerosols) diagnsotic settings.
24
ND22 (J-value photolysis rates) diagnostic settings. 
25
Specify the averaging period (in local time) for the ND22 diagnostic. In the example above, J-value data from grid boxes where it is between 11:00 and 13:00 local time will be averaged and then saved to disk.
26
ND24 (E/W transport mass fluxes) diagnostic settings
27
ND25 (N/S transport mass fluxes) diagnostic settings
28
ND26 (vertical transport mass fluxes) diagnostic settings
29
ND27 (flux of tracer from the stratosphere) diagnostic settings
30
ND28 (biomass burning emissions) diagnostic settings. NOTE: the only tracers that have biomass burning emissions defined are:
#
Tracer (standard simulation)
#
Tracer (dicarbonyl simulaton)
#
Tagged Simulations
1
NOx (Odd nitrogen)
 
All of the standard simulation tracers PLUS:
1-N
CO2 (Carbon monoxide)
4
CO (Carbon monoxide)
57
GLYX (Glyoxal)
1-N
CH4 (methane)
5
ALK4 (Lumped >= C4 Alkanes)
58
MGLY (Methylglyoxal)
 
 
9
ACET (Acetone)
59
BENZ (Benzene)
 
 
10
MEK (Methyl Ethyl Ketone)
60
TOLU (Toluene)
 
 
11
ALD2 (Acetaldehyde)
61
XYLE (Xylene)
 
 
18
PRPE (Lumped >= C3 Alkenes)
65
C2H4 (Ethene)
 
 
19
C3H8 (Propane)
66
C2H2 (Acetylene)
 
 
20
CH2O (Formaldehyde)
68
GLYC (Glycoaldehyde)
 
 
21
C2H6 (Ethane)
69
HAC (Hydroxyacetone)
 
 
26
SO2 (Sulfur Dioxide)
 
 
 
 
30
NH3 (Ammonia)
 
 
 
 
34
BCPI (Black Carbon)
 
 
 
 
35
OCPI (Organic Carbon)
 
 
 
 

31
ND29 (sources of CO) diagnostic settings
32
ND30 (surface map) diagnostic settings
33
ND31 (surface pressure) diagnostic settings.
34
ND32 (sources of NOx) diagnostic settings.
35
ND33 (column tracer) diagnostic settings. NOTE: This is more or less obsolete.
36
ND34 (biofuel emissions) diagnostic settings. NOTE: the only tracers that have biofuel emissions defined are: 
#
Tracer (standard simulation)
#
Tracer (dicarbonyl simulaton)
1
NOx (Odd nitrogen)
 
All of the standard simulation tracers PLUS:
4
CO (Carbon monoxide)
57
GLYX (Glyoxal)
5
ALK4 (Lumped >= C4 Alkanes)
58
MGLY (Methylglyoxal)
9
ACET (Acetone)
59
BENZ (Benzene)
10
MEK (Methyl Ethyl Ketone)
60
TOLU (Toluene)
11
ALD2 (Acetaldehyde)
61
XYLE (Xylene)
18
PRPE (Lumped >= C3 Alkenes)
65
C2H4 (Ethene)
19
C3H8 (Propane)
66
C2H2 (Acetylene)
20
CH2O (Formaldehyde)
68
GLYC (Glycoaldehyde)
21
C2H6 (Ethane)
69
HAC (Hydroxyacetone)

37
ND35 (500 hPa tracers) diagnostic settings. NOTE: This is more or less obsolete now.
38
ND36 (anthropogenic emissions) diagnostic settings. NOTE: the only tracers that have anthropogenic emissions defined are: 
#
Tracer (standard simulation)
1
NOx (Odd nitrogen)
4
CO (Carbon monoxide)
5
ALK4 (Lumped >= C4 Alkanes)
9
ACET (Acetone)
10
MEK (Methyl Ethyl Ketone)
11
ALD2 (Acetaldehyde)
18
PRPE (Lumped >= C3 Alkenes)
19
C3H8 (Propane)
20
CH2O (Formaldehyde)
21
C2H6 (Ethane)

39
ND37 (fraction of soluble tracer scavenged in updrafts in cloud convection) diagnostic settings.
40
ND38 (rainout loss of soluble tracer in convective updrafts) diagnostic settings.
41
ND39 (washout loss of soluble tracer in convective updrafts) diagnostic settings.
42
ND41 (afternoon PBL height) diagnostic settings.
43
ND42 (secondary organic aerosol concentration) diagnostic settings.
44
ND43 (chemically produced quantities) diagnostic settings.
45
Specify the averaging period (in local time) for OH and HO2 in the ND43 diagnostic. It is recommended to average OH and HO2 from 00:00 to 24:00 hours local time (i.e. all day long). This is shown in the example above. 
46
Specify the averaging period (in local time) for NO and NO2 in the ND43 diagnostic. It is recommended to average NO and NO2 from 10:00 to 14:00 hours local time (i.e. around noon time). This is shown in the example above. 
47
ND44 (dry deposition fluxes& velocities) diagnostic settings.
48
ND45 (tracer concentrations) diagnostic settings.
49
Specify the averaging period (in local time) for tracers in the ND45 diagnostic. It is recommended to average tracers from 00:00 to 24:00 hours local time (i.e. all day long). This is shown in the example above. 
50
ND46 (biogenic emissions) diagnostic settings.
51
ND47 (24-hour tracer concentrations) diagnostic settings.
52
ND52 (gamma(HO2) for the HO2 uptake by aerosols)
53
Free diagnostic (reserved for future use)
54
ND54 diagnostic -- computes the time that a given grid box spends in the troposphere.
55
ND55 (tropopause height) diagnostic settings. 
56
ND56 (lightning flashes) diagnostic settings. 
57
ND57 (Potential temperature) diagnostic settings
58
ND58 (CH4 Emissions) diagnostic settings. For CH4 simulation only
59
Free diagnostic (reserved for future use).
60
ND60 (Wetland Frac) diagnotic settings. For CH4 simulation only
61
Free diagnostic (reserved for future use).
62
ND62 (instantaneous column maps) diagnostic settings.
63
Free diagnostic (reserved for future use).
64
ND66 (3-D met fields) diagnostic settings.
65
ND67 (2-D met fields) diagnostic settings.
66
ND68 (boxheight & air mass) diagnostic settings.
67
ND69 (grid box surface area) diagnostic settings.
68
ND70 (turn on debug output) diagnostic settings.

5.2.1.16 The PLANEFLIGHT MENU
We have IDL codes that can create a Planeflight.dat file from the DC8 and P3B navigation files from ARCTAS, ICARTT, and other aircraft missions. Click here for more information.
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% PLANEFLIGHT MENU %%%:
02: Turn on plane flt diag? : F
03: Flight track info file  : Planeflight.dat.YYYYMMDD
04: Output file name        : plane.log.YYYYMMDD
Line
Description
1
Header line 
2
Set this to T to turn on the plane flight following diagnostic (a.k.a. ND40 diagnostic). Set this switch to F to turn off the plane flight diagnostic.
3
Specify the name of the input file (usually called Planeflight.dat.YYYYMMDD) for the plane flight diagnostic. This file is described below. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS - Chem will replace these with the appropriate values. 
If the plane flight diagnostic is turned on, then GEOS - Chem will look for a new Planeflight.dat.YYYYMMDD file for each YYYYMMDD date. Then it will save out various quantities along the flight track(s) define within the Planeflight.dat.YYYYMMDD file.
4
Specify the name of the output file (usually called plane.log) for the plane flight diagnostic. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS - Chem will replace these with the appropriate values. 

5.2.1.17 The ND48 MENU
Note: this diagnostic is somewhat obsolete. We recommend using ND49 to save the region where your stations are, then post-process the output to get the quantities at the stations position.
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% ND48 MENU %%%       :
02: Turn on ND48 stations   : T
03: Station Timeseries file : stations.YYYYMMDD
04: Frequency [min]         : 60
05: Number of stations      : 3
06: Station #1 (I,J,Lmax,N) : 23 34 1 1
07: Station #2 (I,J,Lmax,N) : 23 34 1 97
08: Station #3 (I,J,Lmax,N) : 23 34 1 98
Line
Description
1
Header line 
2
Set this to T to turn on the ND48 station timeseries diagnostic. This allows you to save timeseries data of various quantities at specific grid boxes. Set this to F to turn off the ND48 station timeseries diagnostic.
3
Specify the name of the file which will contain output from the ND48 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS - Chem will replace these with the appropriate values. 
4
Specify the frequency in minutes at which data will be archived by the ND48 station timeseries diagnostic. Recommended values: 60 minutes or 120 minutes. 
5
Specify the number of ND48 stations at which timeseries data will be saved to disk.
6 - 8
For each ND48 station, you must provide the following information (separated by spaces):
   * Longitude index
   * Latitude index
   * Number of levels to save 
         * If you type 1, it will just save the surface level. 
         * If you type 10, then it will save all levels from level 1 (surface) to level 10. 
   * ND48 diagnostic quantity number 
#
ND48 diagnostic quantity
Units
1 - N_TRACERS
GEOS - Chem advected tracers 
[v/v]
76
OH concentration 
[molec/cm3] 
77
NO2 concentration 
[v/v] 
78
PBL heights 
[m]
79
PBL heights
[levels]
80
Air density 
[molec/cm3]
81
Cloud fractions 
[unitless]
82
Column optical depths 
[unitless]
83
Cloud top heights 
[hPa]
84
Sulfate aerosol optical depth 
[unitless]
85
Black carbon aerosol optical depth 
[unitless]
86
Organic carbon aerosol optical depth 
[unitless]
87
Accumulation mode seasalt optical depth 
[unitless]
88
Coarse mode seasalt optical depth 
[unitless]
89
Total dust optical depth
[unitless]
90
Total seasalt tracer concentration 
[unitless] 
91
Pure O3 (not Ox) concentration 
[v/v]
92
NO concentration 
[v/v] 
93
NOy concentration
[v/v] 
94
Grid box height 
[m]
95
Relative humidity 
[%] 
96
Sea level pressure 
[hPa] 
97
Zonal wind (a.k.a. U-wind) 
[m/s]
98
Meridional wind (a.k.a. V-wind) 
[m/s] 
99
Pressure at level edges (PEDGE-$) 
[hPa]
100
Temperature 
[K]


5.2.1.18 The ND49 MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% ND49 MENU %%%       :
02: Turn on ND49 diagnostic : T
03: Inst 3-D timeser. file  : tsYYYYMMDD.bpch
04: Tracers to include      : 94
05: Frequency [min]         : 120
06: IMIN, IMAX of region    : 70 30
07: JMIN, JMAX of region    : 23 46
08: LMIN, LMAX of region    : 1 20
Line
Description
1
Header line 
2
Set this to T to turn on the ND49 instantaneous 3D timeseries diagnostic. This allows you to archive instantaneous timeseries data for various quantities from a 3D region of the globe.
3
Specify the name of the file which will contain output from the ND49 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS - Chem will replace these with the appropriate values. 
4
Specify the ND49 diagnostic quantities to save to disk. Separate each number with a space. 
#
ND49 diagnostic quantity
Units
1 - N_TRACERS
GEOS - Chem advected tracers 
[v/v]
76
OH concentration 
[molec/cm3] 
77
NO2 concentration 
[v/v] 
78
PBL heights 
[m]
79
PBL heights
[levels]
80
Air density 
[molec/cm3]
81
Cloud fractions 
[unitless]
82
Column optical depths 
[unitless]
83
Cloud top heights 
[hPa]
84
Sulfate aerosol optical depth 
[unitless]
85
Black carbon aerosol optical depth 
[unitless]
86
Organic carbon aerosol optical depth 
[unitless]
87
Accumulation mode seasalt optical depth 
[unitless]
88
Coarse mode seasalt optical depth 
[unitless]
89
Total dust optical depth
[unitless]
90
Total seasalt tracer concentration 
[unitless] 
91
Pure O3 (not Ox) concentration 
[v/v]
92
NO concentration 
[v/v] 
93
NOy concentration
[v/v] 
94
Grid box height 
[m]
95
Relative humidity 
[%] 
96
Sea level pressure 
[hPa] 
97
Zonal wind (a.k.a. U-wind) 
[m/s]
98
Meridional wind (a.k.a. V-wind) 
[m/s] 
99
Pressure at level edges (PEDGE-$) 
[hPa]
100
Temperature 
[K]
101
PAR direct 
[W/m2]
102
PAR diffuse 
[W/m2]
103
Daily LAI 
[cm2/cm2]
104
Temperature at 2m
[K]
105
Isoprene emissions 
[atoms C/cm2/s]
106
Total Monoterpene emissions 
[atoms C/cm2/s]
107
Methyl Butenol emissions 
[atoms C/cm2/s]
108
Alpha-Pinene emissions 
[atoms C/cm2/s]
109
Beta-Pinene emissions
[atoms C/cm2/s]
110
Limonene emissions 
[atoms C/cm2/s]
111
Sabinene emissions 
[atoms C/cm2/s]
112
Myrcene emissions
[atoms C/cm2/s]
113
3-Carene emissions
[atoms C/cm2/s]
114
Ocimene emissions
[atoms C/cm2/s]
115 - 121
Size-resolved dust optical depth (i.e. the 7 FAST-J dust bins) 
[unitless]

5
Specify the frequency (in minutes) at which ND49 will save data for a 3D region of the globe data to disk. Recommended value: 180 min (3 hours). You may save data at a higher temporal resolution (e.g. every 60 min) but this will create HUGE data files! 
6
Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:
   * For GCAP 4° x 5° grid: 1 72 
   * For GMAO 4° x 5° grid: 1 72 
   * For GMAO 2° x 2.5° grid: 1 144 
Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude.
7
Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:
   * For GCAP 4° x 5° grid: 1 45
   * For GMAO 4° x 5° grid: 1 46
   * For GMAO 2° x 2.5° grid: 1 91
8
Specify LMIN and LMAX, the indices which determine the vertical extent of the 3D region of the globe.

5.2.1.19 The ND50 MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% ND50 MENU %%%       :
02: Turn on ND50 diagnostic : T
03: 24-hr avg timeser. file : ts_24h_avg.YYYYMMDD.bpch
04: Output as HDF5?         : F
05: Tracers to include      : 94
06: IMIN, IMAX of region    : 1 72
07: JMIN, JMAX of region    : 1 46
08: LMIN, LMAX of region    : 1 20
Line
Description
1
Header line 
2
Set this to T to turn on the ND50 24-hour 3D timeseries diagnostic. This allows you save to archive 24-hour averaged data from a 3D region of the globe.
3
Specify the name of the file which will contain output from the ND49 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS - Chem will replace these with the appropriate values. 
4
To output the ND50 diagnostic quantities in HDF5 format.
Note: HDF5 must be installed on your system for using this option.
(The GEOS - Chem support team does not provide help for the installation of this library)
5
Specify the ND50 diagnostic quantities to save to disk. Separate each number with a space. 
#
ND50 diagnostic quantity
Units
1 - N_TRACERS
GEOS - Chem advected tracers 
[v/v]
76
OH concentration 
[molec/cm3] 
77
NO2 concentration 
[v/v] 
78
PBL heights 
[m]
79
PBL heights
[levels]
80
Air density 
[molec/cm3]
81
Cloud fractions 
[unitless]
82
Column optical depths 
[unitless]
83
Cloud top heights 
[hPa]
84
Sulfate aerosol optical depth 
[unitless]
85
Black carbon aerosol optical depth 
[unitless]
86
Organic carbon aerosol optical depth 
[unitless]
87
Accumulation mode seasalt optical depth 
[unitless]
88
Coarse mode seasalt optical depth 
[unitless]
89
Total dust optical depth
[unitless]
90
Total seasalt tracer concentration 
[unitless] 
91
Pure O3 (not Ox) concentration 
[v/v]
92
NO concentration 
[v/v] 
93
NOy concentration
[v/v] 
94
Grid box height 
[m]
95
Relative humidity 
[%] 
96
Sea level pressure 
[hPa] 
97
Zonal wind (a.k.a. U-wind) 
[m/s]
98
Meridional wind (a.k.a. V-wind) 
[m/s] 
99
Pressure at level edges (PEDGE-$) 
[hPa]
100
Temperature 
[K]
115 - 121
Size-resolved dust optical depth (i.e. the 7 FAST-J dust bins) 
[unitless]

6
Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:
   * For GCAP 4° x 5° grid: 1 72 
   * For GMAO 4° x 5° grid: 1 72 
   * For GMAO 2° x 2.5° grid: 1 144 
Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude.
7
Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:
   * For GCAP 4° x 5° grid: 1 45
   * For GMAO 4° x 5° grid: 1 46
   * For GMAO 2° x 2.5° grid: 1 91
8
Specify LMIN and LMAX, the indices which determine the vertical extent of the 3D region of the globe.

5.2.1.20 The ND51 MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% ND51 MENU %%%       :
02: Turn on ND51 diagnostic : T
03: LT avg timeseries file  : ts_satellite.YYYYMMDD.bpch
04: Output as HDF5?         : F
05: Tracers to include      : 94
06: GMT Hour for disk write : 0
07: Avg Period [LT hours]   : 10 12
08: IMIN, IMAX of region    :  1 72
09: JMIN, JMAX of region    : 23 46
10: LMIN, LMAX of region    :  1  1
Line
Description
1
Header line 
2
Set this to T to turn on the ND51 "satellite" 3D timeseries diagnostic. ND51 allows you to archive 3D data blocks for various quantities which have been time-averaged between 2 local times. This is useful for comparing model data to sun-synchronous satellites such as GOME or MOPITT which have morning overpass times. 
3
Specify the name of the file which will contain output from the ND51 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS - Chem will replace these with the appropriate values. 
4
To output the ND50 diagnostic quantities in HDF format.
Note: HDF5 must be installed on your system for using this option.
(The GEOS - Chem support team does not provide help for the installation of this library)
5
Specify the ND51 diagnostic quantities to save to disk. Separate each number with a space. 
#
ND51 diagnostic quantity
Units
1 - N_TRACERS
GEOS - Chem advected tracers 
[v/v]
76
OH concentration 
[molec/cm3] 
77
NO2 concentration 
[v/v] 
78
PBL heights 
[m]
79
PBL heights
[levels]
80
Air density 
[molec/cm3]
81
Cloud fractions 
[unitless]
82
Column optical depths 
[unitless]
83
Cloud top heights 
[hPa]
84
Sulfate aerosol optical depth 
[unitless]
85
Black carbon aerosol optical depth 
[unitless]
86
Organic carbon aerosol optical depth 
[unitless]
87
Accumulation mode seasalt optical depth 
[unitless]
88
Coarse mode seasalt optical depth 
[unitless]
89
Total dust optical depth
[unitless]
90
Total seasalt tracer concentration 
[unitless] 
91
Pure O3 (not Ox) concentration 
[v/v]
92
NO concentration 
[v/v] 
93
NOy concentration
[v/v] 
94
Grid box height 
[m]
95
Relative humidity 
[%] 
96
Sea level pressure 
[hPa] 
97
Zonal wind (a.k.a. U-wind) 
[m/s]
98
Meridional wind (a.k.a. V-wind) 
[m/s] 
99
Pressure at level edges (PEDGE-$) 
[hPa]
100
Temperature 
[K]
101
PAR direct 
[W/m2]
102
PAR diffuse 
[W/m2]
103
Daily LAI 
[cm2/cm2]
104
Temperature at 2m
[K]
105
Isoprene emissions 
[atoms C/cm2/s]
106
Total Monoterpene emissions 
[atoms C/cm2/s]
107
Methyl Butenol emissions 
[atoms C/cm2/s]
108
Alpha-Pinene emissions 
[atoms C/cm2/s]
109
Beta-Pinene emissions
[atoms C/cm2/s]
110
Limonene emissions 
[atoms C/cm2/s]
111
Sabinene emissions 
[atoms C/cm2/s]
112
Myrcene emissions
[atoms C/cm2/s]
113
3-Carene emissions
[atoms C/cm2/s]
114
Ocimene emissions
[atoms C/cm2/s]
115 - 121
Size-resolved dust optical depth (i.e. the 7 FAST-J dust bins) 
[unitless]

6
Specify the time of day (in GMT hours) at which the ND51 timeseries file will be written to disk. Recommended value: 0 GMT each day. 
7
Specify the ND51 time averaging window (in local time hours). Only data from grid boxes where the local time falls within this window will be included in the diagnostic averaging process. Recommended values: 10:00 to 12:00 LT. This will cover both GOME and MOPITT overpasses.
8
Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:
   * For GCAP 4° x 5° grid: 1 72 
   * For GMAO 4° x 5° grid: 1 72 
   * For GMAO 2° x 2.5° grid: 1 144 
Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude.
9
Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:
   * For GCAP 4° x 5° grid: 1 45
   * For GMAO 4° x 5° grid: 1 46
   * For GMAO 2° x 2.5° grid: 1 91
10
Specify LMIN and LMAX, the indices which determine the vertical extent of the 3D region of the globe.

5.2.1.21 The ND51b MENU
ND51b allows you to output quantities along a second satellite path. ND51b setup is identical to ND51 setup.

5.2.1.22 The ND63 MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% ND63 MENU %%%       :
02: Turn on ND63 diagnostic : T
03: LT avg timeseries file  : paranox_ts.YYYYMMDD.bpch
04: Tracers to include      : 1
05: Frequency [min]         : 120
06: IMIN, IMAX of region    : 70 30
07: JMIN, JMAX of region    : 23 46
Line
Description
1
Header line 
2
Set this to T to turn on the ND63 ship timeseries diagnostic.
3
Specify the name of the file which will contain output from the ND63 timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS - Chem will replace these with the appropriate values. 
4
Specify the ND63 diagnostic quantities to save to disk. 
#
ND63 diagnostic quantity
Units
1
Fraction of NOx remaining 
[unitless]
2
Integrated Ozone Production Efficiency, or OPE 
[unitless]
3
Fraction of NOx * ship emissions 
[kg/box/timestep]
4
Integrated OPE * ( 1 - fraction of NOx) * ship emissions 
[kg/box/timestep]
5
Ship emissions 
[kg/box/timestep]

5
Specify the frequency (in minutes) at which the ND63 timeseries file will be written to disk.
6
Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:
   * For GCAP 4° x 5° grid: 1 72 
   * For GMAO 4° x 5° grid: 1 72 
   * For GMAO 2° x 2.5° grid: 1 144 
Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude.
7
Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:
   * For GCAP 4° x 5° grid: 1 45
   * For GMAO 4° x 5° grid: 1 46
   * For GMAO 2° x 2.5° grid: 1 91


5.2.1.23 The PROD & LOSS MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% PROD & LOSS MENU %%%:
02: Turn on P/L (ND65) diag?: T
03: # of levels for ND65    : 47
04: Save O3 P/L (ND20)?     : F
05: Number of P/L families  : 7
06: 1st  chemical family    : POX: O3 NO2 2NO3 PAN PMN PPN HNO4 3N2O5 HNO3 BrO HOBr BrNO2 2BrNO3
07: 2nd  chemical family    : LOX: O3 NO2 2NO3 PAN PMN PPN HNO4 3N2O5 HNO3 BrO HOBr BrNO2 2BrNO3
08: 3rd  chemical family    : PCO: CO
09: 4th  chemical family    : LCO: CO
10: 5th  chemical family    : PBrOx: Br BrO
11: 6th  chemical family    : PBry: 2Br2 Br BrO HOBr HBr BrNO2 BrNO3
12: 7th  chemical family    : LBry: 2Br2 Br BrO HOBr HBr BrNO2 BrNO3
Line
Description
1
Header line 
2
Set this switch to T if you wish to save out chemical production for family tracers (a.k.a. the ND65 diagnostic), or F otherwise.
3
Specify the number of levels to save for the chemical family production & loss diagnostic. 
   * If you type 1, it will just save the surface level. 
   * If you type 20, then it will save all levels from level 1 (surface) to level 20, etc.
If you are performing a full-chemistry simulation, then you may only archive production and loss data within the troposphere. This is because SMVGEAR does not do chemistry in the stratosphere. For other types of simulations (e.g. tagged Ox, tagged CO), you may archive production and loss data from all levels.
4
Set this switch to T if you wish to archive P(Ox) and L(Ox) rates from a full chemistry simulation into binary punch format, so that these rates can be used to drive a future tagged Ox simulation (a.k.a. ND20 diagnostic). 
5
Specify the number of production and loss families to archive. You must list each family below.
6
Entry for the POx chemical production family (assuming we are performing a full-chemistry simulation). The family name comes first and must be followed by a colon. Then you must list the individual species which constitute the POx family. A number in front of a species name is the coefficient by which that species will be multiplied. (You do not have to list the coefficient if it is 1.) Since the family name POx begins with a P, it is interpreted to be a chemical production family.
7
Entry for the LOx chemical production family (assuming we are performing a full-chemistry simulation). You may proceed as described above. Since the family name LOx begins with an L, it is interpreted to be a chemical loss family. 
8
Entry for the PCO chemical production family.
9
Entry for the LCO chemical production family.
10
Entry for the PBrOx chemical production family.
11
Entry for the PBry chemical production family.
12
Entry for the LBry chemical production family.

5.2.1.24 The ARCHIVED OH MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% ARCHIVED OH MENU %%%:
02: Dir w/ archived OH files: /as/data/geos/GEOS_MEAN/OHmerge/v5-07-08/
Line
Description
1
Header line 
2
Specify OH_DIR (located in source code file directory_mod.F). OH_DIR is directory path where the offline monthly-mean OH files are stored.

5.2.1.25 The O3 P/L MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01:%%% O3 P/L MENU %%%      :
02: Dir w/ O3 P/L rate files: /as/data/geos/GEOS_MEAN/O3_PROD_LOSS/2003.v6-01-05/
Line
Description
1
Header line 
2
Specify O3_PL_DIR (located in source code file directory_mod.F). O3_PL_DIR is directory path where the P(Ox) and L(Ox) rates are stored, or where they will be created. These rates, which have been archived from a full-chemistry simulation, are required to drive a tagged Ox simulation. 

5.2.1.26 The NESTED GRID MENU
NOTE: This menu controls options for the various GEOS - Chem nested grid simulations. This is an optional menu and may be omitted from input.geos if you are not concerned with these simulations.
For more information, please see:
   1. GEOS - Chem wiki: Nested-grid simulations
   2. GEOS - Chem wiki: Setting up nested-grid simulations
   3. GEOS - Chem wiki: Available met data for nested-grid simulations
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% NESTED GRID MENU %%%:  
02: Save TPCORE BC's        : F
03: Input BCs at 2x2.5?     : T
04: Over North America?     : F
05: TPCORE NA BC directory  : BC_2x25_NA/
06: Over Europe?            : F
07: TPCORE EU BC directory  : BC_2x25_EU/
08: Over China?             : F
09: TPCORE CH BC directory  : BC_2x25_CH/
10: Over SEAC4RS region?    : F
11: TPCORE SEAC4RS BC dir.  : BC_2x25_SEAC4RS
12: Over Custom Region?     : F
13: TPCORE BC directory     : BC_2x25/
14: BC timestep [min]       : 180
15: LL box of BC region     :   9  26
16: UR box of BC region     :  29  41
17: 1x1 offsets I0_W, J0_W  :   3   3
Line
Description
1
Header line 
2
Specify LWINDO (located in source code file logical_mod.F). Set LWINDO to T if you wish to save out boundary conditions from a GEOS - Chem simulation, or F otherwise. Before you run at the nested-grid resolution, you must first save out boundary conditions from a global GEOS - Chem simulation (usually 2° x 2.5°).
3
Specify LWINDO2x25 (located in source code file logical_mod.F):
   * If you are using boundary conditions saved from a 2° x 2.5° GEOS - Chem simulation, then set Set LWINDO2x25 to T.
   * If you are using boundary conditions saved from a 4° x 5° GEOS - Chem simulation, then set Set LWINDO2x25 to F.
4
Specify LWINDO_NA (located in source code file logical_mod.F). Set LWINDO_NA to T if you wish to perform a GEOS - Chem nested grid simulation over the North American domain.
5
Specify TPBC_DIR_NA (located in source code file directory_mod.F). TPBC_DIR_NA is the directory path where you have stored the boundary conditions for your North American nested-grid simulation.
6
Specify LWINDO_EU (located in source code file logical_mod.F). Set LWINDO_EU to T if you wish to perform a GEOS - Chem nested grid simulation over the European domain.
7
Specify TPBC_DIR_EU (located in source code file directory_mod.F). TPBC_DIR_EU is the directory path where you have stored the boundary conditions for your European nested-grid simulation.
8
Specify LWINDO_CH (located in source code file logical_mod.F). Set LWINDO_CH to T if you wish to perform a GEOS - Chem nested grid simulation over the China/SE Asia domain.
9
Specify TPBC_DIR_CH (located in source code file directory_mod.F). TPBC_DIR_CH is the directory path where you have stored the boundary conditions for your China/SE Asia nested-grid simulation.
10
Specify LWINDO_SE (located in source code file logical_mod.F). Set LWINDO_SE to T if you wish to perform a GEOS - Chem nested grid simulation over the SEAC4RS region.
11
Specify TPBC_DIR_SE (located in source code file directory_mod.F). TPBC_DIR_SE is the directory path where you have stored the boundary conditions for your SEAC4RS nested-grid simulation.
12
Specify LWINDO_CU (located in source code file logical_mod.F). Set LWINDO_CU to T if you wish to perform a GEOS - Chem nested grid simulation a domain that you have customized yourself.
13
Specify TPBC_DIR_CU (located in source code file directory_mod.F). TPBC_DIR_CU is the directory path where you have stored the boundary conditions for your custom-domain nested-grid simulation.
14
Specify the frequency in minutes at which the 2° x 2.5° or 4° x 5° boundary conditions will be saved to disk. Recommended value: 180 min (3 hours).
15
Specify I1_BC and J1_BC (located in source code file tpcore_bc_mod.F). I1_BC and J1_BC are the longitude and latitude indices of the grid box at the LOWER LEFT CORNER of the region in which 4° x 5° boundary conditions are being saved. In the example listed above, I1_BC=51 and J1_BC=21 denotes the grid box (70°E, 10°S).
16
Specify I2_BC and J2_BC (located in source code file tpcore_bc_mod.F). I2_BC and J2_BC are the longitude and latitude indices of the grid box at the UPPER RIGHT CORNER of the 4° x 5° window region in which boundary conditions are being saved. In the example listed above, I2_BC=67 and J2_BC=37 denotes the grid box (150°E, 54°N).
17
Specify I0_W and J0_W (located in source code file tpcore_bc_mod.F). I0_W and J0_W are the 1° x 1° nested grid longitude and latitude offsets (in # of boxes) of the which are used to define an inner window reion in which transport is actually done. The region in which transport is done in the 1° x 1° window is smaller than the actual size of them 1° x 1° nested grid met fields in order to account for the boundary conditions. Please see the comments to the source code file tpcore_bc_mod.F for more information. Recommended values: I0_W=3 and J0_W=3.

5.2.1.27 The UNIX CMDS MENU
Line numbers are not part of the input.geos file, but have been included for reference.
01: %%% UNIX CMDS MENU %%%  :
02: Background symbol       : &
03: Redirect symbol         :  >
04: Unix remove command     : rm -f
05: Unix pathname separator : /
06: Unix wildcard character : *
07: Unix unzip command      : gzip -dc
08: Zip file suffix         : .gz
Line
Description
1
Header line 
2
Specify BACKGROUND (located in source code file unix_cmds_mod.F). Set BACKGROUND to the symbol which is used to place Unix jobs in the background. Recommended value: "&".
3
Specify REDIRECT (located in source code file unix_cmds_mod.F). Set REDIRECT to the symbol which is used to redirect output from one file to another. Recommended value: "  >". (NOTE: leave a space before the greater than sign.)
4
Specify REMOVE_CMD (located in source code file unix_cmds_mod.F). Set REMOVE_CMD to the string which defines the Unix remove file command. Recommended value: "rm -f".
5
Specify SEPARATOR (located in source code file unix_cmds_mod.F). Set SEPARATOR to the symbol which is used as the directory path separator. Recommended value: "/".
6
Specify STAR (located in source code file unix_cmds_mod.F). Set STAR to the symbol which is used as the Unix wild card character. Recommended value: "*".
7
Specify UNZIP_CMD (located in source code file unix_cmds_mod.F). Set UNZIP_CMD to the string which defines the file unzipping command. Recommended value: "gzip -dc".
8
Specify ZIP_SUFFIX (located in source code file unix_cmds_mod.F). Set ZIP_SUFFIX to the file extension string which is used to denote compressed files. Recommended value: ".gz".

5.2.2 The Planeflight.dat.YYYYMMDD file
We have IDL codes that can create a Planeflight.dat file from the DC8 and P3B navigation files from ARCTAS, ICARTT, and other aircraft missions. Click here for more information. 
Sometimes it is necessary to compare GEOS - Chem output against aircraft observations. The plane flight following diagnostic (a.k.a. ND40 diagnostic) allows you to save out GEOS - Chem diagnostic quantities for grid boxes corresponding to aircraft flight tracks. This prevents you from having to save out huge 3-D punch files with lots of species.
The Planeflight.dat.YYYYMMDD files allow you to specify the diagnostic quantities (tracers, reaction rates, met fields, or chemical species) that you want to print out for a specific longitude, latitude, altitude, and time. A sample Planeflight.dat.YYYYMMDD file is given below. Of course if you have lots of flight track data points, your file will be much longer. 
In GEOS - Chem v7 - 03 - 06 and higher versions, the plane flight following diagnostic has been modified to be consistent with the method of saving out plane flight data used in the ICARTT mission. If the plane flight following diagnostic is switched on, then it will look for a new Planeflight.dat.YYYYMMDD file each day. If a Planeflight.dat.YYYYMMDD file is found for a given day, then GEOS - Chem will save out diagnostic quantities along the flight track(s) specified within the file.
01: Planeflight.dat
02: Bob Yantosca
03: 26 Apr 2004
04: -------------------------------------------------------------------------------
05: 9 < -- # of variables to be output (list them below, one per line)
06: -------------------------------------------------------------------------------
07: TRA_004
08: O3
09: REA_O1D
10: REA_001
11: REA_299
12: GMAO_TEMP
13: GMAO_ABSH
14: GMAO_SURF
15: AODB_SULF
16: AODC_BLKC
17: -------------------------------------------------------------------------------
18: Now give the times and locations of the flight
19: -------------------------------------------------------------------------------
20: Point Type  DD-MM-YYYY HH:MM   LAT    LON    PRESS
21:     1 P3B04 01-01-2003 00:00   42.00  290.00 500.00
22:     2 DC801 01-01-2003 00:00   42.00  290.00 500.00
23:     3 P3B04 01-01-2003 01:00   41.00  290.00 500.00
24:     4 DC801 01-01-2003 01:00   42.00  289.00 500.00
25:     5 P3B04 01-01-2003 02:00   40.00  290.00 500.00
26: 99999 END   0- 0- 0    0 :0    0.00   0.00   0.00
Line
Description
1 - 4
Header lines with comments
5
Number of diagnostic quantities to print out. 
6
Separator line 
7 - 16
Here we list the diagnostic quantities that we want to print out at each flight track location. (For clarity, only a few flight track locations are listed, but in reality, you can list thousands of locations.) 
Name
Planeflight diagnostic quantity
TRA_nnn
Advected tracer (where nnn is the tracer number from input.geos)
REA_nnn
Chemistry reaction # (where nnn is the reaction number printed out in globchem.dat and smv2.log)
O3, OH, NO, etc.
Chemical species (use the same names as in the globchem.dat mechanism file)
GMAO_TEMP
Temperature from the met fields
GMAO_ABSH
Absolute humidity derived from the met fields
GMAO_SURF
Aerosol surface area
GMAO_PSFC 
Surface pressure
GMAO_UWND 
Zonal winds
GMAO_VWND 
Meridional winds
GMAO_IIEV 
GEOS-Chem grid box index, longitude
GMAO_JJEV
GEOS-Chem grid box index, latitude
GMAO_LLEV 
GEOS-Chem grid box index, altitude
GMAO_ICEnn
SEAICEnn fields (i.e. the fraction of each grid box that has nn% to nn+10% of sea ice coverage)
NOTE: You can only use this option for MERRA and GEOS-5.7.x met fields.
AODB_SULF
Sulfate optical depth -- column from surface up to location of aircraft
AODB_BLKC 
Black carbon optical depth -- column from surface up to location of aircraft
AODB_ORGC
Organic carbon optical depth -- column from surface up to location of aircraft
AODB_ORGC
Organic carbon optical depth -- column from surface up to location of aircraft
AODB_ORGC 
Organic carbon optical depth -- column from surface up to location of aircraft
AODB_SALC 
Coarse mode sea salt optical depth -- column from surface up to location of aircraft
AODC_SULF
Sulfate optical depth -- tropospheric column
AODC_BLKC 
Black carbon optical depth -- tropospheric column
AODC_ORGC 
Organic carbon optical depth -- tropospheric column
AODC_SALA 
Accumulation mode sea salt optical depth -- tropospheric column
AODC_SALC
Coarse mode sea salt optical depth -- tropospheric column
As shown above, you may specify multiple flight tracks in a Planeflight.dat file. The only restriction is that flight track locations must be listed in increasing order of GMT.
17 - 19
Separator Lines 
20
Comment line which shows you where to line up each column field of the flight track points.
21 - 25
Here we list quantities which define each flight track point. Make sure that each field lines up with the guides in the line above. 
Guide
Quantity
Point
Flight track data point number (used internally for reference)
Type
A short string that denotes the aircraft type and flight number. 
Date
List the day, month, and year (GMT date) for each flight track point.
HH:MM
List the hour and minute (GMT time) for each flight track point.
Lat
List the latitude (-90 to 90 degrees) for each flight track point.
Lon
List the longitude (-180 to 180 degrees) for each flight track point.
Press
List the pressure in hPa for each flight track point.
GEOS - Chem will loop through each of the flight track points listed in Planeflight.dat and print out each of the diagnostic quantities. GEOS - Chem will pick the nearest model box to each flight track point for comparison. In the future we may introduce a more intelligent interpolation scheme.
Note that it is OK to list flight track points from more than one aircraft in the same Planeflight.dat.YYYYMMDD file (as is shown above). However, all flight track points must be listed in increasing order of GMT time or else they will not be interpreted correctly by GEOS - Chem.
26
Ending line

5.3. GEOS - Chem chemistry mechanism files
In this section are included GEOS - Chem input files which only need to be modified every once and a while. These include files which describe the chemistry and photolysis mechanisms. You should only have to modify these files if you wish to change the chemical mechanism or photolysis mechanism.

5.3.1 The mglob.dat file
The mglob.dat file contains convergence criteria and other parameters for SMVGEAR II (and hence is only needed for the full-chemistry simulations). A copy of mglob.dat ships with each of the GEOS - Chem run directories for full-chemistry simulations (e.g. standard, SOA, dicarbonyls, isoprene).
The three most important parameters in this file are:
NREAD   : Number of reactants and products per chemical reaction in globchem.dat file
ERRMAXU : Relative error convergence criterion for SMVGEAR II urban domain
YLOWU   : Absolute error convergence criterion for SMVGEAR II urban domain
NREAD should be 20 if using the standard or SOA chemistry options. NREAD should be 24 if using the isoprene simulation.
Recommended values: ERRMAXU = 1.0E-01; YLOWU = 1.0E+06
You should not normally have to modify this file, unless the chemistry does not converge at a particular location. 

5.3.2 The globchem.dat file
This globchem.dat defines the chemistry mechanism that SMVGEAR II will use. If you feel that something should be changed in this file, please consult first with Daniel Jacob and the GEOS - Chem Oxidants and Chemistry Working Group.
A copy of globchem.dat ships with each of the GEOS - Chem run directories for full-chemistry simulations (e.g. standard, SOA, dicarbonyls, isoprene).
NOTES: 
   1. The chemistry mechanisms for SOA simulation and dicarbonyls simulation are based on the standard mechanism, with the appropriate modifications.

5.3.3 The chemga.dat file
The chemga.dat file defines some aerosol properties for the full-chemistry run with the SMVGEAR solver. This file is read in by SMVGEAR routine chemset.F. You should not modify these without first consulting with Daniel Jacob.
A copy of chemga.dat ships with each of the GEOS - Chem run directories for full-chemistry simulations (e.g. standard, SOA, dicarbonyls, isoprene).

5.4. GEOS - Chem photolysis mechanism files
In this section are included GEOS - Chem input files which only need to be modified every once and a while. These include files which describe the chemistry and photolysis mechanisms. You should only have to modify these files if you wish to change the chemical mechanism or photolysis mechanism.
NOTE: GEOS - Chem v9 - 01 - 03 uses the older FAST - J photolysis code. However, we have updated FAST - J so that it uses the same photolysis species as the newer FAST - JX code.

5.4.1 The ratj.d file
The ratj.d file lists the species names and branching ratios for FAST - JX photolysis species. Unless you are changing the chemistry mechanism, you should not have to change this file. The photolysis reactions listed in ratj.d should correspond to those listed in globchem.dat. If they do not, then FAST - JX will stop execution with an indexing error message.
A copy of ratj.d ships with each of the GEOS - Chem run directories for full-chemistry simulations (e.g. standard, SOA, dicarbonyls, isoprene).
NOTES:
   1. The pound sign (#) is treated as a comment character. If you want to place comments at the top of the file, make sure the first column begins with a #. Also, everything below the 9999 will not be read in. You can use this space for comments as well.
   2. If you are trying to run a CH3I simulation, then you should use this version of ratj.d, which includes information for methyl iodide. This file will open in a new browser window.

5.4.2 The jv_atms.dat file
The jv_atms.dat file contains climatology for O3 and temperature, as used with the FAST - J photolysis code. You should not modify this file unless you wish to change some parameters for the photolysis.
NOTES: 
   * As of GEOS - Chem v9 - 01 - 03, the jv_atms.dat file is no longer shipped with the GEOS - Chem run directories, but is now stored in netCDF format in the FastJ_201204 data directory.

5.4.3 The jv_spec.dat file
The jv_spec.dat file contains cross-sections and quantum yields for FAST - JX photolysis species. You should not have to modify this file unless you wish to change some parameters for the photolysis.
A copy of jv_spec.dat ships with each of the GEOS - Chem run directories for full-chemistry simulations (e.g. standard, SOA, dicarbonyls, isoprene).
For more information on the format of jv_spec.dat, see HERE. This file will open in a new browser window.

5.4.4 The jv_spec_aod.dat file
The jv_spec_aod.dat file contains the optical properties for aerosols at a single wavelength to be used in the online calculation of the aerosol optical depth diagnostics. The default properties are provided at 550 nm. These properties have been calculated using the same size and optical properties as the jv_spec.dat file used for the FAST - J photolysis calculations. 
The user can exchange this set of properties with those at another wavelength. We recommend that the wavelength used be included in the first line of the header for traceability (this line is output to the GEOS - Chem log file during run time). 
A complete set of optical properties from 250-2000 nm for aerosols is available at:
ftp ftp.as.harvard.edu
cd pub/geos-chem/data/aerosol_optics/hi_spectral_res
mget *
A copy of jv_spec_aod.dat (with optical properties for 550 nm) ships with each of the GEOS - Chem run directories for full-chemistry simulations (e.g. standard, SOA, dicarbonyls, isoprene).

5.5 Output Files
Here follows a list of the files that GEOS - Chem will create in the user's run directory. Some files include a YYYYMMDD date string as part of the file name.

5.5.1 Files created by GEOS - Chem
File 
Description 
paranox_ts.YYYYMMDD.bpch
Output file (binary punch format) from the ND63 ship timeseries.
A new file (timestamped with YYYYMMDD) will be created for each new day.
stations.YYYYMMDD
Output file (binary punch format) from the ND48 station timeseries diagnostic.
A new file (timestamped with YYYYMMDD) will be created for each new day.
NOTE: You can use the GAMAP routine GC_COMBINE_ND48 to work with this file. Click here for more information. This diagnostic is somewhat obsolete. We recommend using ND49 to save a region of the world and post-process the output to get the output at the stations positions.
tsYYYYMMDD.bpch
Output file (binary punch format) from the ND49 instantaneous timeseries diagnostic.
A new file (timestamped with YYYYMMDD) will be created for each new day.
NOTE: You can use the GAMAP routine GC_COMBINE_ND49 to work with this file. Click here for more information.
ts_24hr_avg.YYYYMMDD.bpch
Output file (binary punch format) from the ND50 24-hr average timeseries diagnostic.
A new file (timestamped with YYYYMMDD) will be created for each new day.
NOTE: You can use the GAMAP routine GC_COMBINE_ND49 to work with this file. Click here for more information.
ts_satellite.YYYYMMDD.bpch
Output file (binary punch format) from the ND51 local-time-averaged timeseries, also known as satellite timeseries).
A new file (timestamped with YYYYMMDD) will be created for each new day.
NOTE: You can use the GAMAP routine GC_COMBINE_ND49 to work with this file. Click here for more information.
restart.YYYYMMDD
Restart file (binary punch format) for gas-phase and aerosol tracers for year/month/date YYYYMMDD. 
This file saves instantaneous concentrations of all tracers on all levels for continuation of the run at a later stage.
NOTE: You may use the GAMAP routines REGRIDV_RESTART and REGRIDH_RESTART to vertically and horizontally regrid restart files from one grid to another.
restart.cspec.YYYYMMDDhh
Restart file (binary punch format) for all chemical species for year/month/day/hour YYYYMMDDhh. 
This file saves instantaneous concentrations of all tracers on all levels for continuation of the run at a later stage.
NOTE: If you are going to be running a very long GEOS - Chem simulation, and must split the job into several stages (i.e. in order to submit to a queue system), then you should set LSVCSPEC to T. This will make sure that the chemical species stored in the CSPEC array will not get reset to the background defaults (from globchem.dat) when the next run stage starts.
soaprod.YYYYMMDDhh 
Restart file (binary punch format) for APROD and GPROD quantities for year/month/date YYYYMMDD.
This file saves the various quantities stored in the APROD and GPROD arrays in GEOS - Chem source code file carbon_mod.F for continuation of the run at a later stage.
This is necessary if you are performing a simulation with secondary organic aerosol tracers or with dicarbonyls.
NOTE: You can use the GAMAP routines REWRITE_AGPROD, REGRIDV_RESTART, and REGRIDH_RESTART to regrid these files from one horizontal resolution to another. Click here for more information.
ocean_Hg.YYYYMMDDhh
Restart file (binary punch format) for the online mercury model for year/month/date YYYYMMDD.
This file saves the concentrations of tagged mercury tracers in the ocean (from GEOS - Chem source code file ocean_mercury_mod.F) for continuation of the run at a later stage.
NOTE: You may use the GAMAP routines REGRIDV_RESTART and REGRIDH_RESTART to vertically and horizontally regrid restart files from one grid to another.
ctm.bpch
File (binary punch format) containing time-averaged diagnostic output from GEOS - Chem. Most of the GEOS - Chem diagnostics will place their output in this file.
A single file containing multiple data blocks will be created.
diaginfo.dat
File (text format) that lists diagnostic categories contained in the ctm.bpch file. This file facilitates reading and plotting of the data with the GAMAP package.
For more information, please see the GAMAP Online User's Guide, Chapter 7.2.
tracerinfo.dat
File (text format) that lists the tracer numbers for each diagnostic category contained in the ctm.bpch file. This file facilitates reading and plotting of the data with the GAMAP package.
For more information, please see the GAMAP Online User's Guide, Chapter 7.3.
smv2.log
File (text format) containing echo-back of input from SMVGEAR II. Check this file to see if SMVGEAR read the globchem.dat file properly. 
This file will also contain information about reactions and species used by the ND65 prod-loss diagnostic. (This file is only produced when SMVGEAR is used, i.e. for full NOx-Ox-hydrocarbon chemistry only.)
plane.log.YYYYMMDD
File (text format) containing output from the ND40 planeflight diagnostic, scheduled via the Planeflight.dat file (see above).
NOTE: You can use GAMAP routines CTM_READ_PLANEFLlGHT and PLANE_PLOT to read and plot output from this file.

5.5.2 Sending GEOS - Chem output to a log file
The standard practice is to redirect GEOS - Chem output to a file named log, geos.log or something similar. This log file will contain the standard output from the model run, as well as any warnings or error messages. This log file can be checked periodically to indicate the run status. See Chapter 6: Running GEOS - Chem.
Bob Yantosca's TESTRUN package makes it easy to run GEOS - Chem and to send both stdout and stderr output to the same log file.

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6. Running the GEOS - Chem Model 

6.1 Input File Checklists for GEOS - Chem Model Simulations
After you have completed the following steps:
   1. Downloaded the GEOS - Chem source code (see Chapter 2.2)
   2. Downloaded the GEOS - Chem run directories (see Chapter 2.3)
   3. Downloaded the GEOS - Chem shared data directories (see Chapter 2.4)
   4. Installed the netCDF library with the GEOS-Chem-Libraries installer program (if necessary, see Chapter 2.5)
   5. Compiled the GEOS - Chem source code into an executable file (see Chapter 3)
you can finally run GEOS - Chem. But first doublecheck that you have customized the input files in your run directory for the simulation that you wish to perform. We provide below some convenient checklists that you can follow..

6.1.1 Checklist for NOx - Ox - Hydrocarbon - aerosol chemistry simulation with SMVGEAR or KPP
You have several chemistry mechanism options for the NOx - Ox - Hydrocarbon - aerosol (a.k.a. "full-chemistry") simulation:
   1. the standard mechanism (now including bromine species)
   2. the secondary organic aerosol (SOA) mechanism,
   3. the dicarbonyls mechanism, and
   4. the Caltech isoprene mechanism . 
We present a checklist of how to select options for each of these mechanisms in your input.geos file.
Simulation Menu: 
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu: 
Type of simulation      : 3
Number of Tracers       : 53
And then list the tracer names, molecular weights, and constituent species as described in Chapter 5.2.1.2.
To run the SOA mechanism, increase the number of transported tracers to 59. A list of the tracer names can be found HERE.
To run the dicarbonyls mechanism, increase the number of transported tracers to 75. A list of the tracer names can be found HERE. 
To run the Caltech isoprene mechanism, increase the number of transported tracers to 56. A list of the tracer names can be found HERE. 
Aerosol Menu:
Online SULFATE AEROSOLS : T
Online CRYST/AQ AEROSOLS: F
Online CARBON AEROSOLS  : T
Online 2dy ORG AEROSOLS : F
Online DUST AEROSOLS    : T
 => Use DEAD emissions? : T
Online SEASALT AEROSOLS : T
 => SALA radius bin [um]: 0.01 0.5
 => SALC radius bin [um]: 0.5  8.0
Online dicarb. chem.    : F
If you have included the SOA mechanism, you must toggle the 4th entry:
Online 2dy ORG AEROSOLS : T
If you have included the dicarbonyls mechanism, you must toggle the 4th and 11th entries:
Online 2dy ORG AEROSOLS : T
Online dicarb. chem.    : T
If you switch the other aerosol types (sulfate, carbon, dust, seasalt) to to F (false), GEOS - Chem will attempt to read these from disk as monthly-mean quantities. NOTE: These offline aerosol fields may not be archived for the GEOS5 ( = MERRA = GEOS-5.7.x) vertical grids.
The crystalline sulfur and aqueous aerosols have not been implemented into GEOS - Chem at this point. They will be added into a future version.
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 30
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is computationally expensive.
Convection Menu: 
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : T
Convect Timestep (min)  : 30
Set the convection timestep to the same value as the transport timestep. 
Select the non-local PBL mixing option, which performs the boundary layer mixing more accurately.
Chemistry Menu: 
Turn on Chemistry?      : T
Use linear. strat. chem?: T
 => Use Linoz for O3?   : T
Chemistry Timestep [min]: 60
Read and save CSPEC_FULL: T
USE solver coded by KPP : F
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Select the linear stratospheric chemistry option. We also recommend choosing the Linoz stratospheric ozone chemistry option as well. If you turn off Linoz, then GEOS - Chem will revert to using Synoz (synthetic stratospheric ozone algorithm) instead. 
We recommend that you generate chemical species restart files by setting Read and save CSPEC_FULL to T (true). You may have to split your GEOS - Chem simulation into several stages in order to fit within the time limits imposed by your batch queuing system. Turning this option on will preserve the chemical species concentrations (stored in the CSPEC array) for the start of the next run stage.
You can switch from SMVGEAR II to KPP by toggling the USE solver coded by KPP option to T (true). If you use KPP, pick the Rosenbrock solver option. The Rosenbrock solver scales better than the SMVGEAR II solver.
Deposition Menu: 
Turn on Dry Deposition? : T
Turn on Wet Deposition? : T
Dry deposition occurs on every chemistry timestep (typically 60 minutes). Wet deposition takes place on every transport timestep (see above).
Emissions Menu: 
%%% EMISSIONS MENU %%%  :
Turn on emissions?      : T
Emiss timestep (min)    : 60 
Include anthro emiss?   : T
 => Scale to (1985-2005): -1
 => Use EMEP emissions? : T
 => Use BRAVO emissions?: T
 => Use EDGAR emissions?: T
 => Use STREETS emiss?  : T
 => Use CAC emissions?  : T
 => Use NEI2005 emiss?  : T
 => Use RETRO emiss?    : T
Use EPA/NEI99 (anth+bf)?: F
    w/ ICARTT modif.?   : F
    w/ VISTAS NOx emis? : F
Include biofuel emiss?  : T
Include biogenic emiss? : T
 => Use MEGAN inventory?: T
 => Use PCEEA model?    : F
 => Use MEGAN for MONO? : T
 => Isoprene scaling    : 1
Include biomass emiss?  : T
 => Seasonal biomass?   : T
 => Scaled to TOMSAI?   : F
 => Use GFED2 biomass?  :---
    => monthly GFED2?   : F 
    => 8-day GFED2?     : F 
    => 3-hr GFED2?      : F
    => synoptic GFED2?  : F
 => Use GFED3 biomass?  :---
    => monthly GFED3?   : T 
    => daily GFED3?     : F 
    => 3-hr GFED3?      : F
Individual NOx sources  :---
 => Use aircraft NOx?   : T
 => Use lightning NOx?  : T
    => Spat-seas constr?: T
 => Use soil NOx        : T
 => Use fertilizer NOx  : T
NOx scaling             : 1
Use ship SO2 emissions? :---
 => global EDGAR ?      : T
 => global ICOADS ?     : T
 => EMEP over EUROPE ?  : T
 => ship SO2 Corbett ?  : F
 => ship SO2 Arctas ?   : T
Use COOKE BC/OC (N. Am.): F   
Use AVHRR-derived LAI?  : F
Use MODIS-derived LAI?  : T
Use historical emiss?   : F
 => What decade?        : 2000
Bromine switches        :---
 => Use Warwick VSLS?   : T
 => Use seasalt Br2?    : T
 => 1ppt MBL BRO Sim.?  : F
 => Bromine scaling     : 1
You will want to turn on all of these different emission types, including the regional inventories (NEI05 for the USA, BRAVO for Mexico, STREETS for South-East Asia, EMEP for Europe). See Chapter 5.2.1.5. for a detailed description of each of these options.
Set the emission timestep to the same value as the chemistry timestep. The chemistry solver treats emissions as reactions having net production; therefore, emissions must be done as often as chemistry.
Output Menu: 
%%% OUTPUT MENU %%%     : 123456789.123456789.123456789.1--1=ZERO+2=BPCH
Schedule output for JAN : 3000000000000000000000000000000
Schedule output for FEB : 30000000000000000000000000000
Schedule output for MAR : 3000000000000000000000000000000
Schedule output for APR : 300000000000000000000000000000
Schedule output for MAY : 3000000000000000000000000000000
Schedule output for JUN : 300000000000000000000000000000
Schedule output for JUL : 3000000000000000000000000000000
Schedule output for AUG : 3000000000000000000000000000000
Schedule output for SEP : 300000000000000000000000000000
Schedule output for OCT : 3000000000000000000000000000000
Schedule output for NOV : 300000000000000000000000000000
Schedule output for DEC : 3000000000000000000000000000000
Place a 3 in the column corresponding to the months and days for which you want output. 
Most of the time you will want to generate monthly-mean diagnostic output. To do this, simply make sure that the first day of the each month has a "3" listed there. For example, the above menu settings will direct GEOS - Chem to write the monthly-mean diagnostic output from January to disk at 0 GMT on February 1st, etc.
Diagnostic Menu:
We list below the most important diagnostics for the Tagged Ox simulation. We assume GEOS-5 meteorology with the "reduced" grid (47 vertical levels).
%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : ctm.bpch
Diagnostic Entries ---> : L Tracers to print out for each diagnostic
...
ND05: Sulfate prod/loss : 47 all
ND06: Dust aer source   : 1  all
ND07: Carbon aer source : 47 all
ND08: Seasalt aer source: 1  all
...
ND11: Acetone sources   : 47 all 
...
ND13: Sulfur sources    : 47 all
...
ND21: Optical depths    : 47 all
ND22: J-Values          : 47 1 7 8 20 99    
      => JV time range  :    11 13
ND24: E/W transpt flx   : 47 all
ND25: N/S transpt flx   : 47 all
ND26: U/D transpt flx   : 47 all
...
ND28: Biomass emissions : 1  1 4 5 9 10 11 18 19 20 21 26 30 34 35
ND29: CO sources        : 1  all
...
ND31: Surface pressure  : 48 all
ND32: NOx sources       : 1  all
...
ND34: Biofuel emissions : 1  1 4 5 9 10 11 18 19 20 21
...
ND36: Anthro emissions  : 1  1 4 5 9 10 18 19 21
...
ND38: Cld Conv scav loss: 47 all
ND39: Wetdep scav loss  : 47 7 8 20 24 26 27 28 29 30 31 32 34 35 36 37 38 39 40 41 42 43
...
ND43: Chem OH,NO,HO2,NO2: 47 all
 ==> OH/HO2 time range  :     0 24
 ==> NO/NO2 time range  :    10 14
ND44: Drydep flx/vel    : 1  1 2 3 7 8 15 17 20 22 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 47 48 50
ND45: Tracer Conc's     : 47 all
 ==> ND45 Time range    :    0 24
ND46: Biogenic emissions: 1  all
...
ND68: Airmass/Boxheight : 47 all
ND69: Surface area      : 1  all
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu: 
At present, you can only use this diagnostic with the SMVGEAR II solver. If you turn on this diagnostic while using the KPP solver, you will receive an error message asking you to change the settings in input.geos. We are looking to implement this diagnostic into KPP, so stay tuned!
%%% PROD & LOSS MENU %%%:
Turn on P/L (ND65) diag?: T
# of levels for ND65    : 47
Save O3 P/L (ND20)?     : F
Number of P/L families  : 7 
1st chemical family     : POX: O3 NO2 2NO3 PAN PMN PPN HNO4 3N2O5 HNO3 BrO HOBr BrNO2 2BrNO3
2nd chemical family     : LOX: O3 NO2 2NO3 PAN PMN PPN HNO4 3N2O5 HNO3 BrO HOBr BrNO2 2BrNO3
3rd chemical family     : PCO: CO
4th chemical family     : LCO: CO
5th  chemical family    : PBrOx: Br BrO
6th  chemical family    : PBry: 2Br2 Br BrO HOBr HBr BrNO2 BrNO3
7th  chemical family    : LBry: 2Br2 Br BrO HOBr HBr BrNO2 BrNO3
You should save the chemical production and loss of at least the Ox family tracer and CO tracer. List the constituent species of each family.
If you also wish to archive the P(Ox) and L(Ox) rates for a future offline tagged Ox simulation, then you can set the SAVE O3 P/L (ND20)? switch to T and specify the number of levels to save to disk.
For more information about the Prod& Loss Menu, refer to Chapter 5.2.1.22. 
Input files
Make sure you have properly modified these input files. Most of the time these will be preset for the particular mechanism you are using.
   *             globchem.dat. (See Chapter 5.3.2)
   *             ratj.d. (See Chapter 5.4.1)
   *             jv_spec.dat. (See Chapter 5.4.3)
   *             mglob.dat (See Chapter 5.3.1).
Restart files:
For each full-chemistry simulation, you need at least the tracer restart file. We also recommend saving out the chemical species restart file as well (refer to the Chemistry Menu section above). Use the gamap routine from the GAMAP package to check the integrity of your restart file before starting a simulation. 
Also, for SOA and dicarbonyl simulations, you need a soaprod.YYYYMMDDhh restart file. Refer to Chapter 5.5.1 for more information.

6.1.2 Checklist for Radon - Lead - Beryllium simulation
We present a checklist of how to customize input.geos for the Radon-Lead-Beryllium simulation:
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
Type of simulation      : 1
Number of Tracers       : 3
Tracer Entries -------> : TR#  Name  g/mole Tracer Members; () = emitted 
Tracer #1               : 1    Rn    222.0
Tracer #2               : 2    Pb    210.0
Tracer #3               : 3    Be7   7.0
Specify each tracer and its molecular weight in this menu.
Aerosol Menu:
None of the options in this menu affect the Radon-Lead-Beryllium simulation, so set these to F (false).
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 30
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is computationally expensive. 
Convection Menu:
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : F
Convect Timestep (min)  : 30
Set the convection timestep to the same value as the transport timestep. 
At present you cannot use the non-local PBL mixing scheme with the Radon-Lead-Beryllium simulation. We are working to correct this situation.
Chemistry Menu:
Turn on Chemistry?      : T
Use linear. strat. chem?: F
 => Use Linoz for O3?   : F
Chemistry Timestep [min]: 60
Read and save CSPEC_FULL: F
USE solver coded by KPP : F
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
The other chemistry options do not affect the Radon - Lead - Beryllium simulation, so set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T
Turn on Wet Deposition? : T
Dry deposition occurs on every chemistry timestep. Wet deposition takes place on every transport timestep.
Emissions Menu:
Turn on emissions?      : T
Emiss timestep (min)    : 60
Set the emission timestep to the same value as the chemistry timestep. 
The rest of the switches in the emissions menu do not affect the Radon - Lead - Beryllium simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
We list below the most important diagnostics for the Radon-Lead-Beryllium simulation. We assume GEOS-5 meteorology with the "reduced" grid (47 vertical levels).
%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : ctm.bpch
Diagnostic Entries ---> : L  Tracers to print out for each diagnostic
ND01: Rn/Pb/Be source   : 47 all
ND02: Rn/Pb/Be decay    : 47 all
...
ND24: E/W transpt flx   : 47 1 2 3
ND25: N/S transpt flx   : 47 1 2 3
ND26: U/D transpt flx   : 47 1 2 3
...
ND31: Surface pressure  : 48 1
...
ND38: Cld Conv scav loss: 47 1 2 3
ND39: Wetdep scav loss  : 47 1 2 3
...
ND44: Drydep flx/vel    : 1  all
ND45: Tracer Conc's     : 47 all
 --> ND45 Time range    :    0 24
...
ND68: Airmass/Boxheight : 47 all
ND69: Surface area      : 1  all
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.

6.1.3 Checklist for Total Ox and Tagged Ox simulations
We present a checklist of how to customize input.geos for the Tagged Ox simulation. NOTE: We will update this simulation in the next version.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
You need to carry 2 tracers to run the total Ox simulation: Total Ox and Stratospherically produced Ox. Specfify these in the Tracer Menu section as follows:
%%% TRACER MENU %%%     :
Type of simulation      : 6
Number of Tracers       : 2 
Tracer Entries -------> : TR#   Name     g/mole  Tracer Members; () = emitted
Tracer #1               : 1     Ox       48.0
Tracer #2               : 2     OxStrt   48.0
You may also specify geographically-tagged tracers:
%%% TRACER MENU %%%     :
Type of simulation      : 6
Number of Tracers       : 13 
Tracer Entries -------> : TR#   Name     g/mole  Tracer Members; () = emitted
Tracer #1               : 1     Ox       48.0
Tracer #2               : 2     OxUT     48.0
Tracer #3               : 3     OxMT     48.0
Tracer #4               : 4     OxROW    48.0
Tracer #5               : 5     OxPacBL  48.0
Tracer #6               : 6     OxNABL   48.0
Tracer #7               : 7     OxAtlBL  48.0 
Tracer #8               : 8     OxEurBL  48.0
Tracer #9               : 9     OxAfrBL  48.0
Tracer #10              : 10    OxAsBL   48.0
Tracer #11              : 11    OxStrat  48.0
Tracer #12              : 12    OxInit   48.0
Tracer #13              : 13    OxUSA    48.0
Aerosol Menu:
None of the options in this menu affect the tagged Ox simulation. Set all of these to F (false).
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 30
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is more computationally expensive. 
Convection Menu:
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : F
Convect Timestep (min)  : 30
Set the convection timestep to the same value as the transport timestep. 
At present you cannot use the non-local PBL mixing scheme with the tagged Ox simulation. We are working to correct this.
Chemistry Menu:
Turn on Chemistry?      : T
Use linear. strat. chem?: T
 => Use Linoz for O3?   : T
Chemistry Timestep [min]: 60
Read and save CSPEC_FULL: F
USE solver coded by KPP : F
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information. 
Select the linear stratospheric chemistry and Linoz stratospheric ozone chemistry options. These will ensure that the stratospheric ozone gets computed correctly.
The other chemistry options do not have any effect on the tagged Ox simulation, so set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T
Turn on Wet Deposition? : F
Dry deposition will be done on every chemistry timestep. Wet deposition is not done for the tagged Ox simulation because Ox is not water-soluble.
Emissions Menu:
Turn on emissions?      : T
Emiss timestep (min)    : 60
Set the emission timestep to the same value as the chemistry timestep. The rest of the switches in the Emissions Menu do not affect the tagged Ox simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
We list below the most important diagnostics for the Tagged Ox simulation. We assume GEOS-5 meteorology with the "reduced" grid (47 vertical levels).
%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : ctm.bpch
Diagnostic Entries ---> : L  Tracers to print out for each diagnostic
...
ND24: E/W transpt flx   : 47 all
ND25: N/S transpt flx   : 47 all
ND26: U/D transpt flx   : 47 all
...
ND31: Surface pressure  : 1  all
...
ND36: Anthro emissions  : 0  1 4 5 9 10 18 19 21
...
ND44: Drydep flx/vel    : 1  all
ND45: Tracer Conc's     : 47 all
  ==> ND45 Time range   :    0 24
...
ND68: Airmass/Boxheight : 47 all
ND69: Surface area      : 1  all
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
IMPORTANT NOTE! For GEOS - Chem v9 - 01 - 03 and earlier versions, the Total Ox and Tagged Ox simulations will not work unless you switch on the PROD & LOSS diagnostic! We shall correct this issue in the next version.
For the Ox simulation, the number of production & loss families is TWICE the number of advected tracers. Therefore, if you are using the Total Ox simulation, you should have 4 prod & loss families:
%%% PROD & LOSS MENU %%%:
Turn on P/L (ND65) diag?: T
# of levels for ND65    : 38
Save O3 P/L (ND20)?     : F
Number of P/L families  : 26
Prod/Loss Family #1     : POx:      Ox
Prod/Loss Family #2     : POxUT:    OxStrt
Prod/Loss Family #3     : LOx:      Ox
Prod/Loss Family #4     : LOxStrt:  OxStrt
If, on the other hand, you are using the full tagged Ox simulation, then you should have 26 prod & loss families:
%%% PROD & LOSS MENU %%%:
Turn on P/L (ND65) diag?: T
# of levels for ND65    : 47
Save O3 P/L (ND20)?     : F
Number of P/L families  : 26
Prod/Loss Family #1     : POx:      Ox
Prod/Loss Family #2     : POxUT:    OxUT
Prod/Loss Family #3     : POxMT:    OxMt
Prod/Loss Family #4     : POxROW:   OxROW
Prod/Loss Family #5     : POxPacBL: OxPacBL
Prod/Loss Family #6     : POxNABL:  OxNABL
Prod/Loss Family #7     : POxAtlBL: OxAtlBL
Prod/Loss Family #8     : POxEurBL: OxEurBL
Prod/Loss Family #9     : POxAfrBL: OxAfrBL
Prod/Loss Family #10    : POxAsBL:  OxAsBL
Prod/Loss Family #11    : POxStrat: OxStrat
Prod/Loss Family #12    : POxInit:  OxInit
Prod/Loss Family #13    : POxUSA:   OxUSA
Prod/Loss Family #14    : LOx:      Ox
Prod/Loss Family #15    : LOxUT:    OxUT
Prod/Loss Family #16    : LOxMT:    OxMt
Prod/Loss Family #17    : LOxROW:   OxROW
Prod/Loss Family #18    : LOxPacBL: OxPacBL
Prod/Loss Family #19    : LOxNABL:  OxNABL
Prod/Loss Family #20    : LOxAtlBL: OxAtlBL
Prod/Loss Family #21    : LOxEurBL: OxEurBL
Prod/Loss Family #22    : LOxAfrBL: OxAfrBL
Prod/Loss Family #23    : LOxAsBL:  OxAsBL
Prod/Loss Family #24    : LOxStrat: OxStrat
Prod/Loss Family #25    : LOxInit:  OxInit
Prod/Loss Family #26    : LOxUSA:   OxUSA
The order of the production and loss families should be the same as for the advected tracers (i.e. total Ox first, then OxUT, then OxMT, etc).
If you are running GEOS - 5 or MERRA simulation with 47 levels, then typically the P(Ox) and L(Ox) data will be saved on 38 levels. The number of levels for ND65 also determines the size of the arrays used in the Total Ox and Tagged Ox simulation. This is why we use specify 38 levels in the text above.
For more information about the Prod& Loss Menu, refer to Chapter 5.2.1.22. 

6.1.4 Checklist for Tagged CO simulation
We present a checklist of how to customize input.geos for the current "standard" 17-tracer Tagged CO simulation. In practice, the number of tagged CO tracers varies widely depending on which geographical regions are being studied.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%%     :
Type of simulation      : 7
Number of Tracers       : 17
Tracer Entries -------> : TR#   Name    g/mole Tracer Members; () = emitted
Tracer #1               : 1     CO      28.0   (CO)
Tracer #2               : 2     COus    28.0
Tracer #3               : 3     COeur   28.0
Tracer #4               : 4     COasia  28.0
Tracer #5               : 5     COoth   28.0
Tracer #6               : 6     CObbam  28.0
Tracer #7               : 7     CObbaf  28.0
Tracer #8               : 8     CObbas  28.0
Tracer #9               : 9     CObboc  28.0
Tracer #10              : 10    CObbeu  28.0
Tracer #11              : 11    CObbna  28.0
Tracer #12              : 12    COch4   28.0
Tracer #13              : 13    CObiof  28.0
Tracer #14              : 14    COisop  28.0
Tracer #15              : 15    COmono  28.0
Tracer #16              : 16    COmeoh  28.0
Tracer #17              : 17    COacet  28.0
Note that the first tracer is total CO and is just named CO. The names of the other tagged CO tracers specify the geographical region from which they are emitted.
Aerosol Menu:
None of the options in this menu affect the tagged CO simulation, so set them all to F (false).
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 30
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is computationally expensive.
Convection Menu:
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : T
Convect Timestep (min)  : 30
Set the convection timestep to the same value as the transport timestep. 
Chemistry Menu:
Turn on Chemistry?      : T
Use linear. strat. chem?: T
 => Use Linoz for O3?   : F
Chemistry Timestep [min]: 60
Read and save CSPEC_FULL: F
USE solver coded by KPP : F
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Select the linear stratospheric chemistry option, which will properly set the stratospheric boundary conditions for CO. You can skip the Linoz stratospheric chemistry algorithm, which only applies to ozone.
The rest of the options in this menu have no affect on the tagged CO simulation, so set them to F (false).
Deposition Menu:
Turn on Dry Deposition? : T
Turn on Wet Deposition? : F
CO will dry-deposit to the surface, so you must turn dry deposition on to account for this. CO is not water-soluble, so turn off wet deposition.
Emissions Menu:
%%% EMISSIONS MENU %%%  :
Turn on emissions?      : T
Emiss timestep (min)    : 60 
Include anthro emiss?   : T
 => Scale to (1985-2005): -1
 => Use EMEP emissions? : T
 => Use BRAVO emissions?: T
 => Use EDGAR emissions?: T
 => Use STREETS emiss?  : T
 => Use CAC emissions?  : T
 => Use NEI2005 emiss?  : T
 => Use RETRO emiss?    : T
Use EPA/NEI99 (anth+bf)?: F
    w/ ICARTT modif.?   : F
    w/ VISTAS NOx emis? : F
Include biofuel emiss?  : T
Include biogenic emiss? : F
 => Use MEGAN inventory?: T
 => Use PCEEA model?    : F
 => Use MEGAN for MONO? : T
 => Isoprene scaling    : 1
Include biomass emiss?  : T
 => Seasonal biomass?   : F
 => Scaled to TOMSAI?   : F
 => Use GFED2 biomass?  :---
    => monthly GFED2?   : F 
    => 8-day GFED2?     : F 
    => 3-hr GFED2?      : F
    => synoptic GFED2?  : F
 => Use GFED3 biomass?  :---
    => monthly GFED3?   : T 
    => daily GFED3?     : F 
    => 3-hr GFED3?      : F
Individual NOx sources  :---
 => Use aircraft NOx?   : F
 => Use lightning NOx?  : F
    => Spat-seas constr?: T
 => Use soil NOx        : F
 => Use fertilizer NOx  : F
NOx scaling             : 1
Use ship SO2 emissions? :---
 => global EDGAR ?      : F
 => global ICOADS ?     : F
 => EMEP over EUROPE ?  : F
 => ship SO2 Corbett ?  : F
 => ship SO2 Arctas ?   : T
Use COOKE BC/OC (N. Am.): F   
Use AVHRR-derived LAI?  : F
Use MODIS-derived LAI?  : T
Use historical emiss?   : F
 => What decade?        : 2000
Bromine switches        :---
 => Use Warwick VSLS?   : F
 => Use seasalt Br2?    : F
 => 1ppt MBL BRO Sim.?  : F
 => Bromine scaling     : 1
Set the emission timestep to the same value as the chemistry timestep. 
You will want to turn on all of the different anthropogenic emission types, including the regional inventories (NEI05 for the USA, BRAVO for Mexico, STREETS for South-East Asia, EMEP for Europe). See Chapter 5.2.1.5. for a detailed description of each of these options. Turn off all options for species other than CO.
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
We list below the most important diagnostics for the Tagged CO simulation. We assume GEOS-5 meteorology with the "reduced" grid (47 vertical levels).
%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : ctm.bpch
Diagnostic Entries ---> : L  Tracers to print out for each diagnostic
ND24: E/W transpt flx   : 47 all
ND25: N/S transpt flx   : 47 all
ND26: U/D transpt flx   : 47 all
ND28: Biomass emissions : 1  4
ND29: CO sources        : 1  all
ND31: Surface pressure  : 48 all
ND34: Biofuel emissions : 1  4
ND36: Anthro emissions  : 0  4
ND45: Tracer Conc's     : 47 all
  ==> ND45 Time range   :    0 24
ND68: Airmass/Boxheight : 47 all
ND69: Surface area      : 1  all
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
%%% PROD & LOSS MENU %%%:
Turn on P/L (ND65) diag?: T
# of levels for ND65    : 47
Save O3 P/L (ND20)?     : F
Number of P/L families  : 22
Prod/Loss Family #1     : LCO: CO
Prod/Loss Family #2     : PCOus: COus
Prod/Loss Family #3     : PCOeur: COeur
Prod/Loss Family #4     : PCOasia: COasia
Prod/Loss Family #5     : PCOoth: COoth
Prod/Loss Family #6     : PCObbam: CObbam
Prod/Loss Family #7     : PCObbaf: CObbaf
Prod/Loss Family #8     : PCObbas: CObbas
Prod/Loss Family #9     : PCObboc: CObboc
Prod/Loss Family #10    : PCObbeu: CObbeuP
Prod/Loss Family #11    : PCObbna: CObbna
Prod/Loss Family #12    : PCOch4: COch4
Prod/Loss Family #13    : PCObiof: CObiof
Prod/Loss Family #14    : PCOisop: COisop
Prod/Loss Family #15    : PCOmono: COmono
Prod/Loss Family #16    : PCOmeoh: COmeoh
Prod/Loss Family #17    : PCOacet: COacet
Prod/Loss Family #18    : PISOP: ISOP
Prod/Loss Family #19    : PCH4: CH4
Prod/Loss Family #20    : PCH3OH: CH3OH
Prod/Loss Family #21    : PMONO: MONO
Prod/Loss Family #22    : PACET: ACET
For the tagged CO simulation, you must define the following production and loss families:
   *             Loss of total CO by OH (LCO)
   *             Production of each of the tagged CO tracers
   *             Production of CO from Isoprene (PISOP)
   *             Production of CO from CH4 (PCH4)
   *             Production of CO from methanol (PCH3OH)
   *             Production of CO from monoterpenes (PMONO)
   *             Production of CO from Acetone (PACET)
For more information about the Prod & Loss menu, see Chapter 5.2.1.22. 

6.1.5 Checklist for H2 - HD simulation
We present a checklist of how to customize input.geos for the H2-HD simulation.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%%     :
Type of simulation      : 13
Number of Tracers       : 2
Tracer Entries -------> : TR#  Name  g/mole Tracer Members; () = emitted
Tracer #1               : 1    H2    2.0
Tracer #2               : 2    HD    3.0 
Specify each tracer and its molecular weight here.
Aerosol Menu:
None of the options in this menu affect the H2-HD simulation, so set them all to F (false).
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 30
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is computationally expensive.
Convection Menu:
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : F
Convect Timestep (min)  : 30
Set the convection timestep to the same value as the transport timestep. 
At present, you cannot use the non-local PBL mixing scheme with the H2 - HD simulation. 
Chemistry Menu:
Turn on Chemistry?      : T
Use linear. strat. chem?: T
 => Use Linoz for O3?   : F
Chemistry Timestep [min]: 60
Read and save CSPEC_FULL: F
USE solver coded by KPP : F
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Select the linear stratospheric chemistry option, which will apply the stratospheric boundary conditions for the H2-HD simulation. 
All of the other Chemistry Menu options do not affect the H2-HD simulation, so set them all to F (false).
Deposition Menu:
Turn on Dry Deposition? : T
Turn on Wet Deposition? : T
Dry deposition will be done on every chemistry timestep. Wet deposition will be done on every transport timestep. Therefore you do not have to list timesteps for these operations here.
Emissions Menu:
Turn on emissions?      : T
Emiss timestep (min)    : 60
Set the emission timestep to the same value as the chemistry timestep. The other switches in this menu do not affect the H2-HD simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
We list below the most important diagnostics for the H2-HD simulation. We assume GEOS-5 meteorology with the "reduced" grid (47 vertical levels).
%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : ctm.bpch
Diagnostic Entries ---> : L   Tracers to print out for each diagnostic
ND10: H2 prod/loss/emiss: 47  all
ND24: E/W transpt flx   : 47  all
ND25: N/S transpt flx   : 47  all
ND26: U/D transpt flx   : 47  all
ND28: Biomass emissions : 1   4
ND29: CO sources        : 1   all
ND31: Surface pressure  : 48  all
ND34: Biofuel emissions : 1   4
ND36: Anthro emissions  : 0   4
ND45: Tracer Conc's     : 47  all
 ==> ND45 Time range    :     0 24
ND68: Airmass/Boxheight : 47  all
ND69: Surface area      : 1   all
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
%%% PROD & LOSS MENU %%%:
Turn on P/L (ND65) diag?: F
For the H2-HD simulation, production and loss of H2 and Deuterium are archived with the ND10 diagnostic. 
For more information about the Prod & Loss menu, see Chapter 5.2.1.22. 

6.1.6 Checklist for offline aerosol chemistry simulation
We present a checklist of how to customize input.geos for the offline aerosol simulation (including secondary organic aerosols):
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
Type of simulation      : 10
Number of Tracers       : 29
Tracer Entries -------> : TR#  Name   g/mole Tracer Members; () = emitted
Tracer #1               : 1    DMS    62.00
Tracer #2               : 2    SO2    64.00
Tracer #3               : 3    SO4    96.00
Tracer #4               : 4    MSA    96.00
Tracer #5               : 5    NH3    17.00
Tracer #6               : 6    NH4    18.00
Tracer #7               : 7    NIT    62.00
Tracer #8               : 8    H2O2   34.00
Tracer #9               : 9    BCPI   12.00
Tracer #10              : 10   OCPI   12.00
Tracer #11              : 11   BCPO   12.00
Tracer #12              : 12   OCPO   12.00
Tracer #13              : 13   ALPH   136.23
Tracer #14              : 14   LIMO   136.23
Tracer #15              : 15   ALCO   142.00
Tracer #16              : 16   SOG1   150.00
Tracer #17              : 17   SOG2   160.00
Tracer #18              : 18   SOG3   220.00
Tracer #19              : 19   SOG4   130.00
Tracer #20              : 20   SOA1   150.00
Tracer #21              : 21   SOA2   160.00
Tracer #22              : 22   SOA3   220.00
Tracer #23              : 23   SOA4   130.00
Tracer #24              : 24   DST1   29.00
Tracer #25              : 25   DST2   29.00
Tracer #26              : 26   DST3   29.00
Tracer #27              : 27   DST4   29.00
Tracer #28              : 28   SALA   36.00
Tracer #29              : 29   SALC   36.00
The tracers above consist of sulfate, carbon, mineral dust, sea salt, and secondary organic aerosols. You do not have to use all 23 tracers; you may define any subset of these as you wish. You must also set the appropriate flags T or F in the Aerosol Menu (described below).
Aerosol Menu:
Online SULFATE AEROSOLS : T
Online CRYST/AQ AEROSOLS: F
Online CARBON AEROSOLS  : T
Online 2dy ORG AEROSOLS : T
Online DUST AEROSOLS    : T
 => Use DEAD emissions? : T
Online SEASALT AEROSOLS : T
 => SALA radius bin [um]: 0.01 0.5
 => SALC radius bin [um]: 0.5  8.0
Online dicarb. chem.    : F
   * If you do NOT wish to include sulfate aerosols (DMS, SO2, SO4, MSA, NH3, NH4, NIT), then set the Online SULFATE AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
   * At this point, crystallline sulfur and aqueous aerosols have not been fully implemented into GEOS - Chem. Therefore for the time being, set ONLINE CRYST/AQ AEROSOLS to F (false).
   * If you do NOT wish to include carbonaceous aerosols (BCPI, BCPO, OCPI, OCPO), then set the Online CARBON AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
   * If you do NOT wish to include secondary organic aerosols (ALPH, LIMO, ALCO, SOG1, SOG2, SOG3, SOA4, SOA1, SOA2, SOA3, SOA4), then set the Online 2dy ORG AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
   * If you do NOT wish to include seasalt aerosols (SALA, SALC), then set the Online SEASALT AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
   * If you do not wish to include mineral dust aerosols (DST1, DST2, DST3, DST4), then set the Online DUST AEROSOLS line to F (false). Also remove the lines for these tracers from the Tracer Menu above.
   * NOTE: You may define the limits of the accumulation and coarse mode sea salt aerosol radius bins (in variables SALA_REDGE_um and SALC_REDGE_um) as you wish. However, the recommended values of 0.1 - 0.5 and 0.5 - 4 microns, respectively, were chosen in order to conform to the cross-sections and other optical settings as defined in the FAST - J input file jv_spec.dat. Therefore, unless you use the recommended values, you will not be able to archive aerosol optical depths for these aerosol types with the ND21, ND48, ND49, ND50, and ND51 diagnostics.
   * NOTE: The dicarbonyl chemistry is only implemented for fullchem simulations. So set the Online dicarb. chem.to F.
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 30
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is computationally expensive.
Convection Menu:
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : T
Convect Timestep (min)  : 30
Set the convection timestep to the same value as the transport timestep. 
Select the non-local PBL mixing option, which performs the boundary layer mixing more accurately.
Chemistry Menu:
Turn on Chemistry?      : T
Chemistry Timestep [min]: 60
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
The other chemistry options do not affect the offline aerosols chemistry simulation, so set them to F (false).
Deposition Menu:
Turn on Dry Deposition? : T
Turn on Wet Deposition? : T
Dry deposition occurs on every chemistry timestep. Wet deposition takes place on every transport timestep.
Emissions Menu:
%%% EMISSIONS MENU %%%  :
Turn on emissions?      : T
Emiss timestep (min)    : 60 
Include anthro emiss?   : T
 => Scale to (1985-2005): -1
 => Use EMEP emissions? : T
 => Use BRAVO emissions?: T
 => Use EDGAR emissions?: T
 => Use STREETS emiss?  : T
 => Use CAC emissions?  : T
 => Use NEI2005 emiss?  : T
 => Use RETRO emiss?    : T
Use EPA/NEI99 (anth+bf)?: F
    w/ ICARTT modif.?   : F
    w/ VISTAS NOx emis? : F
Include biofuel emiss?  : T
Include biogenic emiss? : T
 => Use MEGAN inventory?: T
 => Use PCEEA model?    : F
 => Use MEGAN for MONO? : T
 => Isoprene scaling    : 1
Include biomass emiss?  : T
 => Seasonal biomass?   : T
 => Scaled to TOMSAI?   : F
 => Use GFED2 biomass?  :---
    => monthly GFED2?   : F 
    => 8-day GFED2?     : F 
    => 3-hr GFED2?      : F
    => synoptic GFED2?  : F
 => Use GFED3 biomass?  :---
    => monthly GFED3?   : T 
    => daily GFED3?     : F 
    => 3-hr GFED3?      : F
Individual NOx sources  :---
 => Use aircraft NOx?   : T
 => Use lightning NOx?  : T
    => Spat-seas constr?: T
 => Use soil NOx        : T
 => Use fertilizer NOx  : T
NOx scaling             : 1
Use ship SO2 emissions? :---
 => global EDGAR ?      : T
 => global ICOADS ?     : T
 => EMEP over EUROPE ?  : T
 => ship SO2 Corbett ?  : F
 => ship SO2 Arctas ?   : T
Use COOKE BC/OC (N. Am.): F   
Use AVHRR-derived LAI?  : F
Use MODIS-derived LAI?  : T
Use historical emiss?   : F
 => What decade?        : 2000
Bromine switches        :---
 => Use Warwick VSLS?   : F
 => Use seasalt Br2?    : F
 => 1ppt MBL BRO Sim.?  : F
 => Bromine scaling     : 0
Set the emission timestep to the same value as the chemistry timestep.
You will want to turn on all of the different anthropogenic emission types for aerosols, including the regional inventories (NEI05 for the USA, BRAVO for Mexico, STREETS for South-East Asia, EMEP for Europe). See Chapter 5.2.1.5. for a detailed description of each of these options. Turn off all options for species other than aerosols.
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
We list below the most important diagnostics for the offline aerosol simulation. We assume GEOS-5 meteorology with the "reduced" grid (47 vertical levels). 
%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : ctm.bpch
Diagnostic Entries ---> : L   Tracers to print out for each diagnostic
...
ND05: Sulfate prod/loss : 47  all
ND06: Dust aer source   : 1   all
ND07: Carbon aer source : 47  all
ND08: Seasalt aer source: 1   all
...
ND13: Sulfur sources    : 0   all
...
ND21: Optical depths    : 47  all
ND22: J-Values          : 47  all
      -- JV time range  :     11  13
ND24: E/W transpt flx   : 47  all
ND25: N/S transpt flx   : 47  all
ND26: U/D transpt flx   : 47  all
...
ND28: Biomass emissions : 0   1 4 5 9 10 11 18 19 20 21 26 30 34 35
...
ND31: Surface pressure  : 48  all
...
ND34: Biofuel emissions : 0   1 4 5 9 10 11 18 19 20 21
...
ND36: Anthro emissions  : 0   1 4 5 9 10 18 19 21
...
ND38: Cld Conv scav loss: 47  all
ND39: Wetdep scav loss  : 47  all
...
ND44: Drydep flx/vel    : 1   all
ND45: Tracer Conc's     : 47  all
  ==> ND45 Time range   :     0 24
ND46: Biogenic emissions: 0   all
...
ND68: Airmass/Boxheight : 47  all
ND69: Surface area      : 1   all
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Other files:
In order to use the aerosol and dust optical depth diagnostics (ND21, ND48, ND49, ND50, ND51), then GEOS - Chem must read in the chemistry mechanism and photolysis files. 
   *             Make sure you are using the proper globchem.dat and chemga.dat files. For more information, refer to Chapter 5.3.2 and Chapter 5.3.3.
   *             Make sure that you have the proper ratj.d file. For more information, refer to Chapter 5.4.1.
Creating your own oxidant files for an offline aerosol simulation
Thanks to Eric Sofen (U. Washington) for compiling this information! 
NOTE: this assumes a GEOS4 30-level simulation. 
The JH2O2, PH2O2, O3, and NO3 bpch files must extend only up to the tropopause. When you extract the data from the bpch file that is produced by a full chemistry simulation, these files will be either 22 or 30 vertical levels and the tropopause extends up to 17 levels. Use the routine /gamap2/regridding/trop_cut.pro to remove these upper levels. 
THNO3 is a full 30 levels, and consists of HNO3+NIT. 
OH needs to be 55 levels. 22 levels will come from the full-chem simulation, then this gets paired with the stratospheric data from the current OH file in the data directories (e.g. .../data/GEOS_4x5/stratOH_200203/stratOH.geos4.4x5). This is done using IDL routine gamap2/regridding/merge_o3.pro. Bob said of this IDL code, "NOTE, this file is somewhat hardwired, be prepared to dive in & tinker w/ it accordingly." 
You'll also need to modify the GEOS - Chem code so that it looks for your new oxidant files (or, I suppose, overwrite the existing ones). This requires making changes in sulfate_mod.F, global_no3_mod.F, and global_hno3_mod.F. The easiest way to change where the model looks for OH is in the input.geos file.

6.1.7 Checklist for Total Hg and Tagged Hg simulations
We present a checklist of how to customize input.geos for the mercury simulation:
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%%     : 
Type of simulation      : 11
Number of Tracers       : 21 
Tracer Entries -------> : TR# Name       g/mole Tracer Members; () = emitted
Tracer #1               : 1   Hg0        201.0
Tracer #2               : 2   Hg2        201.0
Tracer #3               : 3   HgP        201.0
Tracer #4               : 4   Hg0_an_na  201.0
Tracer #5               : 5   Hg0_an_eu  201.0
Tracer #6               : 6   Hg0_an_as  201.0
Tracer #7               : 7   Hg0_an_rw  201.0
Tracer #8               : 8   Hg0_oc     201.0
Tracer #9               : 9   Hg0_ln     201.0
Tracer #10              : 10  Hg0_nt     201.0
Tracer #11              : 11  Hg2_an_na  201.0
Tracer #12              : 12  Hg2_an_eu  201.0
Tracer #13              : 13  Hg2_an_as  201.0
Tracer #14              : 14  Hg2_an_rw  201.0
Tracer #15              : 15  Hg2_oc     201.0
Tracer #16              : 16  Hg2_ln     201.0
Tracer #17              : 17  Hg2_nt     201.0
Tracer #18              : 18  HgP_an_na  201.0
Tracer #19              : 19  HgP_an_eu  201.0
Tracer #20              : 20  HgP_an_as  201.0
Tracer #21              : 21  HgP_an_rw  201.0
Tracers 1-3 are global totals of Hg0, Hg2, HgP.
Tracers 4-21 are geographically tagged tracers of Hg0, Hg2, HgP. These are named accordingly to reflect which geographical region they are emitted from. 
If you wish to set up a simulation with only the total Hg tracers, then:
   1.             List Tracers 1-3 in the input.geos file
   2.             Omit Tracers 4-21 from the input.geos file
   3.             You also have the option to run with the Global Terrestrial Mercury Model option (if you have compiled GEOS - Chem with the GTMM_Hg C - preprocessor switch). 
   4.             For more information about the Global model, please refer to this document.
If you wish to set up a simulation with the tagged tracers, then 
   1.             Specify Tracers 1-21 in the input.geos file
   2.             NOTE: The Global Terrestrial Mercury Model is not enabled for tagged simulation. GTMM can be used when running the total tracers only.
Aerosol Menu:
None of the switches in this menu affect the mercury simulation, so set them to F (false).
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 30
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is computationally expensive.
Convection Menu:
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : T
Convect Timestep (min)  : 30
Set the convection timestep to the same value as the transport timestep.
Select the non-local PBL mixing option, which performs the boundary layer mixing more accurately.
Chemistry Menu:
Turn on Chemistry?      : T
Chemistry Timestep [min]: 60
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
All of the other options in this menu do not affect the mercury simulation, so set them all to F (false).
Mercury Menu: 
%%% MERCURY MENU %%%    :
Use anthro Hg emiss for : 2000
Error check tag/tot Hg? : F
Use dynamic ocean Hg?   : T
Preindustrial sim?      : F
Ocean Hg restart file   : ocean.totHg.YYYYMMDDhh
Use GTMM soil model?    : F
GTMM Hg restart file    : GTM.totHg.YYYYMMDDhh
Whenever you use the dynamic ocean, you need to specify an ocean restart file. 
For more information about the GTMM model, please refer to this document.
Deposition Menu:
Turn on Dry Deposition? : T
Turn on Wet Deposition? : T
Dry deposition occurs on every chemistry timestep. Wet deposition takes place on every transport timestep.
Emissions Menu:
Turn on emissions?      : T
Emiss timestep (min)    : 60
Set the emission timestep to the same value as the chemistry timestep. 
The rest of the switches in the Emissions Menu do not affect the mercury simulation, so set them all to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
We list below the most important diagnostics for the mercury simulation. We assume GEOS-5 meteorology with the "reduced" grid (47 vertical levels).
%%% DIAGNOSTIC MENU %%% : 
Binary punch file name  : ctm.bpch
Diagnostic Entries ---> : L  Tracers to print out for each diagnostic
...
ND03: Hg emissions, P/L : 47  all
...
ND24: E/W transpt flx   : 47  all
ND25: N/S transpt flx   : 47  all
ND26: U/D transpt flx   : 47  all
...
ND31: Surface pressure  : 48  all
...
ND38: Cld Conv scav loss: 47  all
ND39: Wetdep scav loss  : 47  all
...
ND44: Drydep flx/vel    : 1   all
ND45: Tracer Conc's     : 47  all
 ==> ND45 Time range    :     0 24
 ...
ND68: Airmass/Boxheight : 47  all
ND69: Surface area      : 1   all
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
%%% PROD & LOSS MENU %%%:
Turn on P/L (ND65) diag?: F
# of levels for ND65    : 30
Save O3 P/L (ND20)?     : F
Number of P/L families  : 0
Production & loss of tagged mercury tracers are handled in the ND03 diagnostic, so you can turn off all the switches in the Prod & Loss Menu as shown above.
For more information about the Prod & Loss Menu, refer to Chapter 5.2.1.22.

6.1.8 Checklist for a CH4 offline simulation
We present a checklist of how to customize input.geos for the methane simulation.
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%%     :
Type of simulation      : 9
Number of Tracers       : 12
Tracer Entries -------> : TR# Name       g/mole Tracer Members; () = emitted
Tracer #1               : 1   CH4_tot     16.0   CH4
Tracer #2               : 2   CH4_ga      16.0   CH4
Tracer #3               : 3   CH4_co      16.0   CH4
Tracer #4               : 4   CH4_ef      16.0   CH4
Tracer #5               : 5   CH4_wa      16.0   CH4
Tracer #6               : 6   CH4_bf      16.0   CH4
Tracer #7               : 7   CH4_ri      16.0   CH4
Tracer #8               : 8   CH4_oa      16.0   CH4
Tracer #9               : 9   CH4_bb      16.0   CH4
Tracer #10              : 10  CH4_wl      16.0   CH4
Tracer #11              : 11  CH4_sa      16.0   CH4
Tracer #12              : 12  CH4_on      16.0   CH4
Tracers 1 is global total of CH4. Tracers 2-12 are tagged tracers for each type of emission and are named accordingly.
It is also possible to run a simulation with just the global total tracer CH4_tot.
Aerosol Menu:
The CH4 simulation does not use any of the sulfate, carbon, etc. tracers, so you can set all of the switches in the Aerosol Menu section to F (false).
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 30
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is computationally expensive.
Convection Menu:
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
 => Use non-local PBL?  : F
Convect Timestep (min)  : 30
The convection timestep should be the same as the transport timestep.
Chemistry Menu:
Turn on Chemistry?      : T
Chemistry Timestep [min]: 60
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
Other chemistry options have no effect on the methane simulation, so set them all to F (false).
Methane Menu: 
%%% CH4 MENU %%%        :
Compute CH4 budget?     : F
Use Gas & Oil emis?     : T
Use Coal Mine emis?     : T
Use Livestock emis?     : T
Use Waste emis?         : T
Use Biofuel emis?       : T
Use Rice emis?          : T
Use Ot. Anthro emis?    : T
Use Biomass emis?       : T
Use Wetlands emis?      : T
Use Soil Absorption?    : T
Use Ot. Natural emis?   : T
This menu allows you to turn on/off the individual emission categories for CH4. The CH4 budget computation is thought to be unreliable. If you want to use it anyway, it only works for full month simulations (i.e. you have to start the simulation on the first day of a month and end on a last day of a month).
Deposition Menu:
Turn on Dry Deposition? : F
Turn on Wet Deposition? : F
Methane is not subject to deposition, so you can turn these off.
Emissions Menu:
%%% EMISSIONS MENU %%%  :
Turn on emissions?      : T
Emiss timestep (min)    : 60 
Include anthro emiss?   : T
 => Scale 1985 to year  : -1
 => Use EMEP emissions? : F
 => Use BRAVO emissions?: F
 => Use EDGAR emissions?: F
 => Use STREETS emiss?  : F
 => Use CAC emissions?  : F
 => Use NEI2005 emiss?  : F
 => Use RETRO emiss?    : F
Use EPA/NEI99 (anth+bf)?: F
    w/ ICARTT modif.?   : F
    w/ VISTAS NOx emis? : F
Include biofuel emiss?  : F
Include biogenic emiss? : F
 => Use MEGAN inventory?: F
 => Use PCEEA model?    : F
 => Use MEGAN for MONO? : F
 => Isoprene scaling    : 1
Include biomass emiss?  : T
 => Seasonal biomass?   : F
 => Scaled to TOMSAI?   : F
 => Use GFED2 biomass?  :---
    => monthly GFED2?   : F
    => 8-day GFED2?     : F 
    => 3-hr GFED2?      : F
    => synoptic GFED2?  : F
 => Use GFED3 biomass?  :---
    => monthly GFED3?   : T 
    => daily GFED3?     : T
    => 3-hr GFED3?      : F
Individual NOx sources  :---
 => Use aircraft NOx?   : F
 => Use lightning NOx?  : F
    => Spat-seas constr?: F
 => Use soil NOx        : F
 => Use fertilizer NOx  : F
NOx scaling             : 1
Use ship SO2 emissions? :---
 => global EDGAR ?      : F
 => global ICOADS ?     : F
 => EMEP over EUROPE ?  : F
 => ship SO2 Corbett ?  : F
 => ship SO2 Arctas ?   : F
Use COOKE BC/OC (N. Am.): F   
Use AVHRR-derived LAI?  : F
Use MODIS-derived LAI?  : F
Use historical emiss?   : F
 => What decade?        : 2000
Bromine switches        :---
 => Use Warwick VSLS?   : F
 => Use seasalt Br2?    : F
 => 1ppt MBL BRO Sim.?  : F
 => Bromine scaling     : 1
Set the emissions timestep to the same value as the chemistry timestep.
Only the GFED switches in the Emissions Menu can affect the simulation. They must be consistent with the choice made in the CH4 Menu for the sake of redundancy.
The rest of the switches in the emissions menu do not affect the tagged methane simulation, so set them to F (false).
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
We list below the most important diagnostics for the methane simulation. We assume GEOS-5 meteorology with the "reduced" grid (47 vertical levels).
%%% DIAGNOSTIC MENU %%% :
Binary punch file name  : ctm.bpch
Diagnostic Entries ---> : L  Tracers to print out for each diagnostic
...
ND19: CH4 loss          : 47  all
...
ND24: E/W transpt flx   : 47  all
ND25: N/S transpt flx   : 47  all
ND26: U/D transpt flx   : 47  all
...
ND31: Surface pressure  : 48  all
...
ND45: Tracer Conc's     : 47  all
 ==> ND45 Time range    :     0 24
...
ND58: CH4 Emissions     : 1   all
ND60: Wetland Fraction  : 1   all
ND68: Airmass/Boxheight : 47  all
ND69: Surface area      : 1   all
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.
Prod & Loss Menu:
%%% PROD & LOSS MENU %%%:
Turn on P/L (ND65) diag?: F
# of levels for ND65    : 30
Save O3 P/L (ND20)?     : F
Number of P/L families  : 0
Loss of methane tracers are handled in the ND19 diagnostic, so you can turn off all the switches in the Prod & Loss Menu as shown above.
For more information about the Prod& Loss Menu, refer to Chapter 5.2.1.22.

6.1.9 Checklist for Total CO2 and Tagged CO2 simulations
We present a checklist of how to customize input.geos for the a typical CO2 simulation:
Simulation Menu:
Specify the start and end times of the model run, as well as data and run directories, etc.
Tracer Menu:
%%% TRACER MENU %%%     :
Type of simulation      : 12
Number of Tracers       : 1 
Tracer Entries -------  : TR#  Name  g/mole Tracer Members; () = emitted
Tracer #1               : 1    CO2    44.0
More source tracers can be used if desired for example in the alternate selection, where emission from 1) Total CO2; 2) Fossil Fuel (land) and cement manufacture, 3) Ocean exchange, 4) Balanced Biosphere; 5) Biomass Burning Emissions; 6) Biofuel Burning Emissions; 7) Net Terrestrial Exchange; 8) Ship Emissions; 9) Aviation Emissions; 10) Chemical Source; 11) Chemical Source surface correction. 
NOTE: If the restart file and input.geos do not have the same number of tracers, the run will crash before completion.
Type of simulation      : 12
Number of Tracers       : 10
Tracer Entries -------> : TR#  Name  g/mole Tracer Members; () = emitted
Tracer #1               : 1    CO2    44.0
Tracer #2               : 2    CO2    44.0
Tracer #3               : 3    CO2    44.0
Tracer #4               : 4    CO2    44.0
Tracer #5               : 5    CO2    44.0
Tracer #6               : 6    CO2    44.0
Tracer #7               : 7    CO2    44.0
Tracer #8               : 8    CO2    44.0
Tracer #9               : 9    CO2    44.0
Tracer #10              : 10   CO2    44.0
Tracer #11              : 11   CO2    44.0
Configuration for a full tagged-CO2 run is shown below (appropriate selections at the end of the CO2 menu are also required). 
Tracers 1-11 are as shown above. 
Tracer 12 is the background including only Fossil Fuel CO2. 
Tracers 13-52 are for 40 geographical regions, tracer 53 is shipping and tracer 54 is aviation. 
Remember, if the restart file and input.geos do not have the same number of tracers, the run will crash before completion.
Type of simulation      : 12
Number of Tracers       : 52
Tracer Entries -------> : TR#  Name  g/mole Tracer Members; () = emitted
Tracer #1               : 1    CO2    44.0 
Tracer #2               : 2    CO2    44.0
..
Tracer #53              : 53   CO2    44.0
Tracer #54              : 54   CO2    44.0
Transport Menu:
Turn on Transport       : T
 => Use Flux Correction?: F
 => Fill Negative Values: T
 => IORD, JORD, KORD    : 3 3 7
Transport Timestep [min]: 15
Set the transport timestep to 30 min (4° x 5°), 15 min (2° x 2.5°), or 10 min (1° x 1° or higher resolution). Do not use flux correction -- that is computationally expensive.
Convection Menu:
Turn on Cloud Conv?     : T
Turn on PBL Mixing?     : T
Convect Timestep (min)  : 15
Set the convection timestep to the same value as the transport timestep.
Chemistry Menu:
Turn on Chemistry?      : T
Chemistry Timestep [min]: 30
We recommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting). Typical chemistry timesteps are 60 min (4° x 5°), 30 min (2° x 2.5°), or 20 min (1° x 1° or higher resolution). In all cases, the chemistry timestep must be a multiple of the transport timestep. See this wiki page for more information.
The rest of the switches in this menu do not affect the CO2 simulation, so set them all to F (false).
Emissions Menu:
Turn on emissions?      : T
Emiss timestep (min)    : 30
Set the emission timestep to the same value as the chemistry timestep.
Only the GFED switches in the Emissions Menu can affect the simulation. They must be consistent with the choice made in the CO2 Menu for the sake of redundancy. The rest of the switches in the Emissions Menu do not affect on the CO2 simulation, so set them all to F (false).
CO2 Menu:
%%% CO2 SIM MENU %%%    :
Fossil Fuel Emissions   :---
  Generic FF emissions  : F
  Annual FF emissions   : F
  Monthly FF emissions  : T
3-D Chemical Oxid Source: F
Biomass Burn emissions  :---
  Seasonal only biomass : F
  GFED2 monthly biomass : F
  GFED2 8-day biomass   : F
  GFED3 monthly biomass : T
  GFED3 daily biomass   : F
Biofuel emissions       : T
Terrestrial Exchange    :---
  CASA daily avg NEP    : F
  CASA diurnal cycle NEP: T
  Net Ter Ex original   : F
  Net Ter Ex climatology: T
Ocean Exchange          :---
  Takahashi 1997        : F
  Takahashi 2009 annual : F
  Takahashi 2009 monthly: T
Ship & Plane Emissions  :---
  EDGAR ship emissions  : F
  ICOADS ship emissions : T
  Aviation emissions 3-D: T
Tagged CO2 runs         :---
  Save Fossil CO2 Bkgrd : F
  Tag Bios/Ocean CO2 reg: F
  Tag Land FF CO2 reg   : F
  Tag Global Ship CO2   : F
  Tag Global Plane CO2  : F
The above CO2 menu configuration shows the defaults for a single tracer run. You can select other options (e.g. the chemical source).. 
The tagged tracer options have not been selected. A standard tagged tracer configuration is available in the code for 2° x 2.5° simulations but this can be customized by the user or set up for other resolutions by modification of the code and the Regions_land.dat and Regions_ocean.dat files, which reside in the CO2 run directory.
Output Menu:
Schedule days for diagnostic output as described above in Chapter 6.1.1.
Diagnostic Menu:
The CO2 simulation has its own unique diagnostic (ND04). The CO2 sources 1-7, and 10 are 2-D (surface level) and sources 8-10 are 3-D with all model levels.
%%% DIAGNOSTIC MENU %%% :
ND04: CO2 Sources       :  1   1 2 3 4 5 6 7 8 9 10
For more information about the Diagnostic Menu, refer to Chapter 5.2.1.15.

6.2 Running a Regular GEOS - Chem Job 
We describe below how to run the GEOS - Chem model with the LSF, PBS, and SGE batch queue systems.
Furthermore, we STRONGLY RECOMMEND that you test your simulation with a short (1-day or 2-day) run before submitting a very long-term GEOS - Chem simulation. You will be better able to detect errors or problems in a short run. You will also avoid wasting precious computer time.

6.2.1 Interactive jobs (no queue system) 
If your computer system supports interactive access, then you can run GEOS - Chem from the Unix prompt. (Don't do it yet, please keep reading!) 
At the Unix prompt, type:
geos
You will find that the output from GEOS - Chem is printed to the screen! Therefore, you will need to redirect the screen output to log files. If you use Bourne-again shell (bash), you can type:: 
geos 1>gc.log 2>gc.error &
This will send program output (the Unix stdout stream, aka "1") to gc.log and error output (the Unix stderr stream, aka "2") to gc.error. The & specifies that the job will run in the Unix background.
You can combine these into the same file:
geos 1>gc.log 2>&1
or
geos >& gc.log
This last syntax will also work if you use C-shell (csh) or T-shell (tcsh). Of course, the commands that you use for Unix redirection vary depending on which shell you use. Follow this link for a more detailed discussion about Unix redirection.

6.2.2 LSF Batch Queue System
If your computational cluster uses the LSF batch queue system, you can use the following commands to submit, delete, and check the status of GEOS - Chem jobs: 
bman                         # prints LSF man pages to stdout
bsub or submit               # submit a batch jobs to a queue
bkill                        # kill batch jobs
bjobs                        # Lists all jobs currently running
bqueues                      # Lists available batch queues
bhist                        # shows history list of submitted jobs
lsload                       # shows % of each machine's resources that
                             #  is currently utilized
You can write a simple GEOS - Chem job script to run GEOS - Chem:
#!/bin/tcsh -f               # Script definition line
cd /scratch/bmy/run.v9 - 01 - 03 # cd to your run dir
rm -f log                    # clear pre-existing log files
time geos > log              # time job; pipe output to log file
exit(0)                      # exit normally
and then save that to a file named job. Select the queue in which you will run GEOS - Chem, and type:
 bsub -q queue-name job
You can check the status of the run by looking at the log file. LSF should also email you when your job is done, or if for any reason it dies prematurely.

6.2.3 PBS Batch Queue System
If your comptational cluster uses the PBS batch queue system, you can use the following commands to submit, delete, and check the status of GEOS - Chem jobs:
qsub              # submits a PBS job 
qstat -Q          # list all available batch queues
qstat -a @machine # list all PBS jobs that are running on 'machine'
qstat -f jobid    # list information about PBS Job jobid
qdel jobid        # Kills PBS Job jobid
xpbs              # Graphical user interface for PB
Create a simple GEOS - Chem job script (named job), similar to the above example for LSF:
#!/bin/tcsh -f    # Script definition line
cd run.v9 - 01 - 03   # cd to your run dir
rm -f log         # clear pre-existing log files
time geos > log   # time job; pipe output to log file
exit(0)           # exit normally
and then submit this with the qsub command: 
qsub -q queue-name -o output-file-name job
The job status command qstat -f jobid sometimes provides a little too much information. Bob Yantosca has written a script called pbstat (this is already installed at Harvard) which condenses the output you get from qstat -f jobid. If you type pbstat at the Unix prompt, you will output similar to:
 --------------------------------------------------------
 PBS Job ID number : 10929.sol
 Job owner : pip@sol
 Job name : run.sh
 Job started on : Sun Aug 10 17:22:21 2003
 Job status : Running
 PBS queue and server : q4x64 on amalthea
 Job is running on : hera/0*4 (R12K processors)
 # of CPUs being used : 4 (max allowed is 4)
 CPU utilization : 394% (ideal max is 400%)
 Elapsed walltime : 22:14:43 (max allowed is 64:00:00)
 Elapsed CPU time : 76:20:40
 Memory usage : 10475844kb (max allowed is 1700Mb)
 VMemory usage : 8244704kb
This allows you to obtain information about your run much more easily. If you type pbstat all, you will obtain information about every job which is running. If you type pbstat userid, then you will get information about all of the jobs that user userid is running.

6.2.4 SGE Batch Queue System
If your computational cluster uses the SGE batch queue system, you can use the following commands to submit, delete, and check the status of GEOS - Chem jobs:
qsub                # submits a PBS job
qconf -spl          # list all available batch queues
qstat -f            # list execution queues and shows the status
                    #  of all your jobs on the current cluster
qstat -f -j jobid   # list information about SGE Job jobid
qdel jobid          # Kills PBS Job jobid
qmon                # Graphical user interface for PB
Create a simple GEOS - Chem job script (named job), similar to the above example for PBS: 
#!/bin/tcsh -f      # Script definition line
cd run.v9 - 01 - 03     # cd to your run dir
rm -f log           # clear pre-existing log files
time geos > log     # time job; pipe output to log file
exit(0)             # exit normally
and then submit this with the qsub command:
qsub -pe queue-name NCPUs -o output-file-name job

6.3 Error output
We provide below some general information about GEOS - Chem errors. For the most up-to-date information about specific GEOS - Chem errors and their solutions, please consult the following resources:
   * Chapter 7.2: Debugging GEOS - Chem
   * GEOS - Chem wiki: Common GEOS - Chem error messages
   * GEOS - Chem wiki: Machine issues and portability
   * GEOS - Chem wiki: Outstanding issues
   * GEOS - Chem wiki: Bugs and fixes

6.3.1 I/O (input/output) errors
The GEOS - Chem code supports I/O error trapping. In other words, if an error occurs while reading from a file or writing to a file, the run will display an error message and then exit. Many of the error messages have the following format:
=============================================================== 
I/O Error Number 4001 in file unit 10 
Encountered in routine read_bpch2:3 
===============================================================
This means that an error (#4001) has occurred while reading from logical file unit 10. The routine where the error occurred is routine READ_BPCH2 (which happens to belong to bpch2_mod.F). The string read_bpch2:3 indicates that the third error trap within READ_BPCH2 was where the error occurred. If you grep for the string read_bpch2:3 in bpch2_mod.F, you will be taken to the offending line of code.
In general, Fortran I/O errors fall into 3 classes:
Error number 
Meaning
Greater than 0
An I/O error has occurred. Something went wrong during reading or writing.
Equal to 0
The file was read or written normally. No I/O error has occurred.
Less than 0
The end-of-file was reached normally.
For Fortran I/O errors greater than zero, you can deduce the nature of the error from the error number. For example, if you compile GEOS - Chem with the Intel Fortran Compiler, the code will die with error #29 if it tries to read a file that is not on disk (i.e. a "file-not-found" error). However, if you compile GEOS - Chem with the a different compiler, then the same "file-not-found" error will cause the code to die with a different error number. The number that corresponds to each error depends on the compiler that you are using. Check your compiler documentation for a list of the error codes.
Also be sure to visit the GEOS - Chem wiki for the latest information about bugs and fixes! 

6.3.2 Other errors
Other kind of errors may occur. For a more detailled discussion about catching and debugging them, visit the GEOS - Chem Debugging page.

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Chapter 7
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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7. Coding and Debugging
                                       
7.1 Coding: Practice and Style 
We provide below some guidelines for writing GEOS - Chem source code routines.
                                       
7.1.1 GEOS - Chem program units
We have written GEOS - Chem in Fortran - 90. Three different program units comprise the GEOS - Chem source code:
   1. Traditional subroutines and functions (*.F) contain one subroutine or function per file. Most of these traditional subroutines and functions come from third-party packages (e.g. FAST - J, SMVGEAR, etc.) 
   2. Fortran - 90 Modules (*_mod.F, *_mod.F90) bundle global variables, subroutines, and functions into a coherent package that can be shared by other program units. Modules contain dynamically allocatable arrays, which are more memory-efficient than the older Fortran - 77 COMMON blocks. We have written most GEOS - Chem source code files as modules.
      Note: The *.F90 extension denotes free-format Fortran - 90 layout, as opposed to the 72-character fixed format. 
   3. Header files (*.h) are inlined into subroutines and functions by means of an #include statement. Most of GEOS - Chem's header files came from legacy code and contained obsolete Fortran - 77 style COMMON blocks. We have replaced all header files (except define.h) with Fortran - 90 modules in GEOS - Chem v9 - 01 - 02 and higher versions . These are stored in the Headers/ subdirectory.
GEOS - Chem's Makefiles determine how to compile individual program unit. Each routine (and the modules that it references) are listed in makefiles. This lets the GNU Make utility determine the order of compilation. Refer to Chapter 7.1.3 for more information.
                                       
7.1.2 Fortran Programming Style
We have attempted to create a clear and consistent programming style for GEOS - Chem subroutines and modules. Some of our style points include:
   * A routine header list of arguments and modification history (in ProTeX format)
   * References to other variables or routines contained within modules
   * Use of IMPLICIT NONE to force explicit declaration of all variables
   * Header files in-lined via the C-preprocessor #include facility
   * Comments aligned with mode -- major sections denoted by !=====
   * Copious use of white space to enhance readability
   * Indentation of IF-THEN-ELSE and DO-ENDDO blocks
   * OpenMP parallel DO-loops
   * NEW: Passing data between subroutines with Fortran derived type objects (We are doing this to facilitate connecting GEOS - Chem to the NASA GEOS - 5 GCM.)
When making upgrades to the code, block off the section that you are replacing with comments, and label that with Prior to MM/DD/YY. You can remove the blocked off section once your modified code has been declared stable.
For more information, please be sure to read Appendix 7: GEOS - Chem Style Guide, as well as the floating point and math issues page on the GEOS - Chem wiki.
                                       
7.1.3 List of GEOS - Chem Modules
As described in Chapter 3, we have separated the GEOS - Chem source code files into various subdirectories. We sought to separate core GEOS - Chem routines from 3rd-party code.
Here we list GEOS - Chem 9 - 01 - 03's directory structure:
Directory name
Description
                                     Help
help
Contains the GEOS - Chem help screen. Type make help to view.
doc
Contains reference documentation (*.pdf, *.ps) generated from ProTeX headers. Type make doc to create this documentation.
                               Core directories
Headers
Contains all Header files (define.h and modules) used by GEOS - Chem.
3rd-party codes may reference files in this directory.
GeosUtil
Contains modules with utility routines: file I/O, horizontal grid, vertical grid, regridding tools, etc.
3rd-party codes may reference files in this directory.
GeosCore
Contains core modules, subroutines, and functions for GEOS - Chem.
3rd-party codes may NOT reference files in this directory. You must pass data to/from these routines as arguments.
                                3rd party codes
ESMF
Contains Grid-Independent GEOS - Chem files for compatibility with the Earth System Model Framework. You can ignore these for the time being.
GTMM
Contains routines for the Global Terrestrial Mercury Model code.
GeosApm
Contains specific routines for APM aerosol microphysics and copies of all GeosCore routines modified by APM.
GeosTomas
Contains specific routines for TOMAS aerosol microphysics and copies of all GeosCore routines modified by TOMAS.
ISORROPIA
Contains routines for ISORROPIA II.
KPP
Contains chemistry solver routines created by the KPP pre-processor. You can use KPP as an alternative to SMVGEAR.
NcdfUtil
Contains routines for netCDF file I/O, taken from Bob Yantosca's NcdfUtilities package.
                                    Outputs
bin
Contains the executable created by the compilation process.
lib
Contains archives of the object files (stored in files with the *.a extension) from each GEOS - Chem subdirectory.
mod
Contains the *.mod files generated by the compiler (one per Fortran - 90 module)
obsolete
Contains obsolete subroutines and module files. We keep these here for future reference.
The GEOS - Chem distribution currently contains over 150 module files. As discussed above, we employ modules to package both variables, subroutines, and functions into a single logical program unit. We list all of the modules and their dependencies below:
Module Name
Purpose
Other Modules Referenced
                              Headers directory 
CMN_DEP_mod.F
Contains common blocks for dry deposition.
CMN_SIZE_mod.F
CMN_DIAG_mod.F
Contains size parameters and global variables for the GEOS - Chem diagnostic arrays.
CMN_SIZE_mod.F
CMN_GCTM_mod.F
Contains GEOS - Chem specific physical constraints and derived quantities.
none
CMN_NOX_mod.F
Contains NOx from soils.
CMN_SIZE_mod.F
CMN_O3_mod.F
Contains common blocks for anthropogenic emissions via SMVGEAR.
CMN_SIZE_mod.F
CMN_SIZE_mod.F
Contains size parameters for GEOS - Chem arrays.
none
CMN_mod.F
Contains global variables (remnant of header file CMN).
CMN_SIZE_mod.F
cmn_fj_mod.F
Contains parameters and global variables used to interface between Harvard chemistry and UC-Irvine FAST-J photolysis programs.
CMN_SIZE_mod.F
commsoil_mod.F
Contains global variables for the soil NOx emissions routines.
CMN_SIZE_mod.F
comode_loop_mod.F
Contains common blocks and variables for SMVGEAR II.
CMN_SIZE_mod.F
jv_cmn_mod.F
Contains global variables for the FAST-J code.
CMN_SIZE_mod.F
cmn_fj_mod.F
jv_mie_mod.F
Contains physical constants for the GEOS - Chem column chemistry code.
none
smv_dimension_mod.F
Contains various placeholder parameters that are required to replace references to GEOS - Chem grid parameters.
none
smv_errcode_mod.F
Contains various success or failure parameters for the GEOS - Chem column chemistry code.
none
smv_physconst_mod.F
Contains physical constants for the GEOS - Chem column chemistry code.
none
                              GeosUtil directory
bpch2_mod.F
Contains the routines used to read data from and write data to binary punch file format (v. 2.0).
CMN_SIZE_mod.F
error_mod.F
file_mod.F
julday_mod.F
charpak_mod.F
Contains selected routines from the CHARPAK package for string manipulation.
none
directory_mod.F
Contains the directory path variables used by 
GEOS - Chem.
none
error_mod.F
Contains error checking subroutines.
ieee_arithmetic.F
(Intel Fortran Compiler only)
file_mod.F
Contains file unit numbers and I/O error trapping routines.
error_mod.F
global_grid_mod.F90
Contains variables and routines for computing grid box longitudes, latitudes, and surface areas on a global grid.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
error_mod.F
grid_mod.F90
Contains variables and routines for computing grid box longitudes, latitudes, and surface areas.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
error_mod.F
hdf_mod.F
Contains routines to write data to HDF5 files.
CMN_SIZE_mod.F
grid_mod.F
error_mod.F 
julday_mod.F
Contains routines for converting YYYYMMDD and HHMMSS to/from astronomical Julian date. (This allows GEOS - Chem to handle transitions such as end-of-month, end-of-year, and end-of-century in a consistent fashion.)
none
pressure_mod.F
Contains variables and routines which specify the grid box pressures for both hybrid or pure-sigma models. This is necessary for running GEOS - Chem with the fvDAS meteorology.
CMN_SIZE_mod.F
error_mod.F
regrid_1x1_mod.F
Does online regridding of data on the GEOS - Chem 1° x 1° grid to 1° x 1°, 2° x 2.5°, or 4° x 5° GEOS or GCAP grids.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
charpak_mod.F
error_mod.F
grid_mod.F
regrid_a2a_mod.F
Does online regridding of data from one horiziontal resolution to another using the MAP_A2A regridding algorithm.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
grid_mod.F
file_mod.F
time_mod.F
Contains routines for computing date & time variables.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
charpak_mod.F
error_mod.F
grid_mod.F
julday_mod.F
transfer_mod.F
Contains routines to copy data from REAL*4 to REAL*8 precision, and also to regrid GEOS - 3 data from 48 vertical levels to 30 vertical levels.
CMN_SIZE_mod.F
error_mod.F
unix_cmds_mod.F
Contains Unix command strings which are used for unzipping of meteorological data files.
none
                              GeosCore directory
RnPbBe_mod.F
Contains variables and routines used for the 222Rn-210Pb-7Be-10Be simulation.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_SIZE_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
file_mod.F
grid_mod.F
logical_mod.F
pressure_mod.F
time_mod.F
tracer_mod.F
tropopause_mod.F
a3_read_mod.F
Contains routines which unzip, open and read the GEOS - Chem A-3 fields from disk.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
logical_mod.F
time_mod.F
transfer_mod.F
unix_cmds_mod.F
a6_read_mod.F
Contains routines which unzip, open and read the GEOS - Chem A-6 fields from disk.
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
logical_mod.F
time_mod.F
transfer_mod.F
unix_cmds_mod.F
acetone_mod.F
Contains subroutines to emit the biogenic flux of acetone into the full chemistry simulation.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
grid_mod.F
megan_mod.F
time_mod.F
transfer_mod.F
aerosol_mod.F
Contains routines which compute aerosol concentrations (kg/m3) and optical depths.
CMN_DIAG_mod.F
cmn_fj_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
comode_loop_mod.F
comode_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
jv_cmn_mod.F
logical_mod.F
time_mod.F
tracer_mod.F
tracerid_mod.F
transfer_mod.F
tropopause_mod.F
aircraft_nox_mod.F
Contains arrays and routines to compute aircraft NOx, emissions for the full chemistry simulation.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
CMN_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
pressure_mod.F
time_mod.F
arctas_ship_emiss_mod.F
Contains variables and routines to read the Arctas Ship emissions.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
tracerid_mod.F
tracer_mod.F
benchmark_mod.F
Contains routines to save out tracer masses in kg for the 1-month fullchem and Rn-Pb-Be benchmark simulations.
CMN_SIZE_mod.F
bpch2_mod.F
file_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
biofuel_mod.F
Contains arrays and routines to compute monthly biofuel burning emissions for NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6 CH4, and CH3I.
CMN_DIAG_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
epa_nei_mod.F
error_mod.F
future_emissions_mod.F
logical_mod.F
streets_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
biomass_mod.F
Contains arrays and routines to compute monthly biomass burning emissions for NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6 CH4, and CH3I.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
diag_mod.F
error_mod.F
gc_biomass_mod.F
gfed2_biomass_mod.F
gfed3_biomass_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
bravo_mod.F
Contains variables and routines to read the BRAVO mexican anthropogenic emission inventory.
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
transfer_mod.F
bromocarb_mod.F
Contains variables and routines for bromine emissions.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_SIZE_mod.F
comode_loop_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
grid_mod.F
logical_mod.F
pbl_mix_mod.F
time_mod.F
tracer_mod.F
c2h6_mod.F
Contains the variables and routines used to perform a standalone simulation for ethane.
CMN_DIAG_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
CMN_mod.F
biofuel_mod.F
biomass_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
geia_mod.F
global_oh_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
cac_anthro_mod.F
Contains variables and routines to read the Criteria Air Contaminant Canadian anthropogenic emissions.
CMN_)3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
carbon_mod.F
Contains variables and routines for carbon aerosol emissions and chemistry.
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
CMN_mod.F
biomass_mod.F
bpch2_mod.F
comode_loop_mod.F
comode_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
drydep_mod.F
error_mod.F
future_emissions_mod.F
gfed2_biomass_mod.F
gfed3_biomass_mod.F
global_no3_mod.F
global_o3_mod.F
global_oh_mod.F
grid_mod.F
logical_mod.F
meganut_mod.F
megan_mod.F
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
tropopause_mod.F
vdiff_pre_mod.F
ch3i_mod.F
Contains the variables and routines used to perform a standalone simulation for methyl iodide.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_SIZE_mod.F
biofuel_mod.F
biomass_mod.F
bpch2_mod.F
comode_loop_mod.F
dao_mod.F
diag_mod.F
diag_pl_mod.F
directory_mod.F
error_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
uvalbedo_mod.F
chemistry_mod.F
Contains a driver program which selects the proper chemistry routine for the various GEOS - Chem simulation types.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
acetone_mod.F
aerosol_mod.F
c2h6_mod.F
carbon_mod.F
ch3i_mod.F
comode_loop_mod.F
comode_mod.F
dao_mod.F
drydep_mod.F
dust_mod.F
error_mod.F
gckpp_comode_mod.F
gckpp_function.F
gckpp_global.F
gckpp_initialize.F
gckpp_integrator.F
gckpp_model.F
gckpp_monitor.F
gckpp_rates.F
gckpp_util.F
global_ch4_mod.F
h2_hd_mod.F
hcn_ch3cn_mod.F
isoropiaii_mod.F
logical_mod.F
mercury_mod.F
optdepth_mod.F
rpmares_mod.F
rnpbbe_mod.F
seasalt_mod.F
strat_chem_mod.o
sulfate_mod.F
tagged_co_mod.F
tagged_ox_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
co2_mod.F
Contains variables and routines used for the CO2 simulation.
CMN_SIZE_mod.F
biomass_mod.F
bpch2_mod.F
dao_mod.F
diag04_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
comode_mod.F
Contains allocatable arrays for SMVGEAR that were previously contained in common blocks in header file comode.h.
CMN_SIZE_mod.F
comode_loop_mod.F
error_mod.F
tracer_mod.F
convection_mod.F
Contains routines which select the proper convection code for GEOS - 1, GEOS - STRAT, GEOS - 3 or GEOS - 4 met data sets.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
dao_mod.F
depo_mercury_mod.F
diag_mod.F
error_mod.F
fvdas_convect_mod.F
gcap_convect_mod.F
gc_type_mod.F
grid_mod.F
logical_mod.F
mercury_mod.F
pressure_mod.F
smv_errcode_mod.F
smv_physconst_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
wetscav_mod.F
dao_mod.F
Contains arrays that hold DAO met fields, as well as subroutines that compute, interpolate, or otherwise process DAO met field data.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
error_mod.F
gc_type_mod.F
grid_mod.F
logical_mod.F
pressure_mod.F
time_mod.F
tracer_mod.F
depo_mercury_mod.F
Contains routines to handle deposition fluxes for mercury.
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
diag03_mod.F
Contains arrays and routines for archiving the ND03 diagnostic -- Hg emissions, mass, and production.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
error_mod.F
file_mod.F
grid_mod.F
time_mod.F
tracerid_mod.F
diag04_mod.F
Contains arrays and routines for archiving the ND04 diagnostic -- CO2 emissions and fluxes.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
error_mod.F
file_mod.F
grid_mod.F
time_mod.F
diag41_mod.F
Contains arrays and routines for archiving the ND41diagnostic -- Afternoon PBL heights.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
error_mod.F
file_mod.F
grid_mod.F
pbl_mix_mod.F
time_mod.F
diag42_mod.F
Contains arrays and routines for archiving the ND42 diagnostic -- secondary organic aerosols (μg/m[3]).
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
diag48_mod.F
Contains variables and routines to save timeseries data at particular lat/lon locations.
CMN_GCTM_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
cmn_fj_mod.F
error_mod.F
file_mod.F
grid_mod.F
jv_cmn_mod.F
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
diag49_mod.F
Contains variables and routines to save instantaneous timeseries data to disk for a 3-D subset of the globe.
CMN_GCTM_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
cmn_fj_mod.F
dao_mod.F
error_mod.F
file_mod.F
grid_mod.F
jv_cmn_mod.F
modis_lai_mod.F90
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
diag50_mod.F
Contains variables and routines to generate 24-hour average timeseries data for a 3-D subset of the globe.
CMN_GCTM_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
cmn_fj_mod.F
comode_loop_mod.F
comode_mod.F
dao_mod.F
error_mod.F
file_mod.F
grid_mod.F
hdf5.F
hdf_mod.F
jv_cmn_mod.F
logical_mod.F
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
tropopause_mod.F
diag51_mod.F
Contains variables and routines to save timeseries data over the United States where the local time is between two user-defined limits. This is useful for comparing with sun-synchronous satellites such as GOME.
CMN_GCTM_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
cmn_fj_mod.F
dao_mod.F
error_mod.F
file_mod.F
grid_mod.F
hdf5.F
hdf_mod.F
jv_cmn_mod.F
logical_mod.F
modis_lai_mod.F90
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
tropopause_mod.F
diag51b_mod.F
Contains similar variables and routines as diag51_mod.F to allow to follow two satellite tracks at a time.
CMN_GCTM_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
cmn_fj_mod.F
dao_mod.F
error_mod.F
file_mod.F
grid_mod.F
hdf5.F
hdf_mod.F
jv_cmn_mod.F
logical_mod.F
modis_lai_mod.F90
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
tropopause_mod.F
diag56_mod.F
Contains arrays and routines for archiving the ND56 diagnostic -- lightning flash rates.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
error_mod.F
file_mod.F
grid_mod.F
time_mod.F
diag63_mod.F
Contains variables and routines to generate timeseries data for PARANOX ship emissions.
CMN_GCTM_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
cmn_fj_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
error_mod.F
file_mod.F
grid_mod.F
jv_cmn_mod.F
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracer_mod.F
tracerid_mod.F
diag_mod.F
Contains declarations for allocatable arrays for use with GEOS - Chem diagnostics and other routines.
none
diag_oh_mod.F
Contains routines to compute the mean OH diagnostic for a full chemistry simulation.
CMN_SIZE_mod.F
comode_loop_mod.F
comode_mod.F
error_mod.F
logical_mod.F
tracerid_mod.F
tracer_mod.F
diag_pl_mod.F
Contains routines to compute chemical production for tracers.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
charpak_mod.F
comode_loop_mod.F
comode_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
drydep_mod.F
Contains variables and routines to compute dry deposition velocities and frequencies.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
CMN_VEL_mod.F
commsoil_mod.F
comode_loop_mod.F
comode_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
meganut_mod.F
pbl_mix_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
dust_dead_mod.F
Contains routines and variables from Charlie Zender's DEAD dust mobilization model. Most routines are from Charlie Zender, but have been modified and/or cleaned up for inclusion into GEOS - Chem. 
CMN_GCTM_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
time_mod.F
transfer_mod.F
dust_mod.F
Contains routines for computing dust aerosol emissions, chemistry, and optical depths.
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
cmn_fj_mod.F
comode_loop_mod.F
comode_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
drydep_mod.F
dust_dead_mod.F
error_mod.F
file_mod.F
grid_mod.F
jv_cmn_mod.F
logical_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
edgar_mod.F
Contains variables and routines to read the EDGAR global anthropogenic emission inventory.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
emep_mod.F
Contains variables and routines to read the EMEP European anthropogenic emission inventory for CO, NOz, and some NMVOCs. The EMEP files come from Marion Auvray and Isabelle Bey at EPFL. 
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
file_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
emissions_mod.F
Contains a driver program which selects the proper emissions subroutine for the various GEOS - Chem simulation types.
CMN_O3_mod.F
CMN_SIZE_mod.F
arctas_ship_emiss_mod.F
biomass_mod.F
bravo_mod.F
c2h6_mod.F
cac_anthro_mod.F
carbon_mod.F
ch3i_mod.F
co2_mod.F
dust_mod.F
edgar_mod.F
emep_mod.F
epa_nei_mod.F
error_mod.F
global_ch4_mod.F
h2_hd_mod.F
hcn_ch3cn_mod.F
icoads_ship_mod.F
logical_mod.F
mercury_mod.F
nei2005_anthro_mod.F
paranox_mod.F
retro_mod.F
rnpbbe_mod.F
seasalt_mod.F
streets_anthro_mod.F
sulfate_mod.F
tagged_co_mod.F
time_mod.F
tracer_mod.F
vistas_anthro_mod.F
epa_nei_mod.F
Contains variables and routines to read the weekday/weekend emissions from the EPA/NEI emissions inventory.
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
file_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
fjx_acet_mod.F
Contains functions for pressure dependency for Acetone photolysis from FAST - JX.
CMN_FJ_mod.F
jv_cmn_mod.F
future_emissions_mod.F
Contains variables and routines for returning scale factors for IPCC A1 & B1 emissions scenarios for future years such as 2030, 2050, etc.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
file_mod.F
transfer_mod.F
fvdas_convect_mod.F
Contains routines (originally from NCAR) which perform shallow and deep convection for the GEOS - 4 met fields. These routines account for shallow and deep convection, updrafts, and downdrafts.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
dao_mod.F
depo_mercury_mod.F
diag_mod.F
grid_mod.F
logical_mod.F
pressure_mod.F
tracerid_mod.F
tracer_mod.F
gamap_mod.F
Contains routines to create GAMAP tracerinfo.dat and diaginfo.dat files which are customized to each particular GEOS - Chem simulation.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
diag03_mod.F
diag04_mod.F
diag41_mod.F
diag42_mod.F
diag48_mod.F
diag49_mod.F
diag50_mod.F
diag51_mod.F
diag51b_mod.F
diag56_mod.F
diag63_mod.F
diag_pl_mod.F
drydep_mod.F
error_mod.F
file_mod.F
hdf_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
wetscav_mod.F
gc_biomass_mod.F
Contains arrays and routines to compute monthly biomass burning emissions for NOx, CO, ALK4, ACET, MEK, ALD2, PRPE, C3H8, CH2O, C2H6, CH4, and CH3I.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
gc_type_mod.F
Contains derived type definitions for GEOS - Chem that will represent the "socket" within external modules. This is used in the grid-independent GEOS-Chem code.
none
gc_type2_mod.F90
Contains derived type definitions for GEOS - Chem. These definitions are used to create objects for: ID flags for advected tracers, coeffifients and arrays that link species and tracers, logical flags that turn various options on/off, etc.
CMN_SIZE_mod.F
comode_loop_mod.F
tracer_mod.F
gc_environment_mod.F90
Contains routines to establish the runtime environment for GEOS - Chem. It is designed to receive model parameter and geophysical environment information and allocate memory based upon it.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_NOx_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
CMN_mod.F
cmn_fj_mod.F
commsoil_mod.F
comode_loop_mod.F
error_mod.F
gc_type_mod.F
gc_type2_mod.F90
jv_cmn_mod.F
pressure_mod.F
vdiff_pre_mod.F
gcap_convect_mod.F
Contains routines (originally from GISS) which perform shallow and deep convection for the GCAP met fields.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
dao_mod.F
diag_mod.F
grid_mod.F
pressure_mod.F
gcap_read_mod.F
Contains subroutines that unzip, open, and read the GCAP PHIS and LWI_GISS fields from disk.
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
logical_mod.F
time_mod.F
transfer_mod.F
unix_cmds_mod.F
geia_mod.F
Contains routines used to read and scale the GEIA/Piccot fossil fuel emissions for NOx, CO, and hydrocarbons.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
file_mod.F
grid_mod.F
time_mod.F
geos57_read_mod.F90
Contains routines used to open and read the GEOS - 5.7.2 fields from disk.
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
time_mod.F
transfer_mod.F
gfed2_biomass_mod.F
Contains variables and routines to compute the GFED2 biomass burning emissions.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
file_mod.F
future_emissions_mod.F
grid_mod.F
julday_mod.F
logical_mod.F
regrid_1x1_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
gfed3_biomass_mod.F
Contains variables and routines to compute the GFED3 biomass burning emissions.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
file_mod.F
future_emissions_mod.F
grid_mod.F
julday_mod.F
logical_mod.F
regrid_1x1_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
global_br_mod.F
Contains variables and routines for reading the global monthly Bromine concentration from disk.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
transfer_mod.F
tropopause_mod.F
global_ch4_mod.F
Contains variables and routines for simulating CH4 chemistry in the troposphere.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
CMN_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
diag_oh_mod.F
directory_mod.F
error_mod.F
file_mod.F
global_oh_mod.F
grid_mod.F
logical_mod.F
pressure_mod.F
regrid_1x1_mod.F
time_mod.F
tracer_mod.F
transfer_mod.F
vdiff_pre_mod.F
global_hno3_mod.F
Contains variables and routines for reading in monthly mean HNO3 concentrations for the offline sulfate simulation.
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
directory_mod.F
error_mod.F
tracer_mod.F
transfer_mod.F
global_no3_mod.F
Contains variables and routines for reading in global monthly mean NO3 concentrations (used for the offline sulfate simulation).
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
transfer_mod.F
global_nox_mod.F
Contains variables and routines for reading the global monthly mean NOx concentration from disk (used for the offline sulfate simulation).
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
transfer_mod.F
unix_cmds_mod.F
global_o1d_mod.F
Contains variables and routines for reading the global monthly mean O1D stratospheric concentration from disk. This is used in the H2/HD simulation. The O1D fields were obtained from Gabriele Curci GEOS - Chem simulation in the stratosphere (v5.03).
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
transfer_mod.F
global_o3_mod.F
Contains variables and routines for reading the global monthly mean O3 concentration from disk.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
transfer_mod.F
global_oh_mod.F
Contains variables and routines for reading the global monthly mean OH concentration from disk.
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
directory_mod.F
error_mod.F
transfer_mod.F
h2_hd_mod.F
Contains variables and routines used for the H2-HD simulation.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
biofuel_mod.F
biomass_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
drydep_mod.F
error_mod.F
geia_mod.F
global_nox_mod.F
global_o1d_mod.F
global_oh_mod.F
grid_mod.F
logical_mod.F
meganut_mod.F
pressure_mod.F
scale_anthro_mod.F
tagged_co_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
tropopause_mod.F
hcn_ch3cn_mod.F
Contains variables and routines that are used for the geographically tagged HCN/CH3CN simulation.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_SIZE_mod.F
biomass_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
geia_mod.F
global_oh_mod.F
grid_mod.F
logical_mod.F
pbl_mix_mod.F
time_mod.F
tracerid_mod.F
transfer_mod.F
i6_read_mod.F
Contains routines which unzip, open and read the GEOS - Chem I-6 fields from disk.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
logical_mod.F
time_mod.F
transfer_mod.F
unix_cmds_mod.F
icoads_ship_mod.F
Contains variables and routines to read the International Comprehensive Ocean-Atmosphere Data Set (ICOADS) ship emissions. Base year is 2002.
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
input_mod.F
Contains routines which read information from the input.geos file and pass it to the various initialization routines of GEOS - Chem modules.
NOTE: This module needs to be compiled last, as it references many other modules.
CMN_DIAG_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
apm_init_mod.F
apm_wets_mod.F
benchmark_mod.F
biofuel_mod.F
biomass_mod.F
bpch2_mod.F
bromocarb_mod.F
charpak_mod.F
depo_mercury_mod.F
diag03_mod.F
diag04_mod.F
diag41_mod.F
diag42_mod.F
diag48_mod.F
diag49_mod.F
diag50_mod.F
diag51_mod.F
diag51b_mod.F
diag56_mod.F
diag63_mod.F
diag_oh_mod.F
diag_pl_mod.F
directory_mod.F
drydep_mod.F
emissions_mod.F
error_mod.F
file_mod.F
future_emissions_mod.F
gamap_mod.F
grid_mod.F
julday_mod.F
land_mercury_mod.F
logical_mod.F
mercury_mod.F
ocean_mercury_mod.F
planeflight_mod.F
restart_mod.F
time_mod.F
tpcore_bc_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
transport_mod.F
unix_cmds_mod.F
wetscav_mod.F
isoropiaII_mod.F
Contains the routines from the ISORROPIAII package, which performs aerosol thermodynamical equilibrium.
CMN_SIZE_mod.F
apm_init_mod.F
dao_mod.F
error_mod.F
global_hno3_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
tropopause_mod.F
land_mercury_mod.F
Contains variables and routines for the land emissions for the GEOS - Chem mercury simulation.
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_SIZE_mod.F
biomass_mod.F
bpch2_mod.F
dao_mod.F
depo_mercury_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
modis_lai_mod.F90
time_mod.F
tracerid_mod.F
transfer_mod.F
lightning_nox_mod.F
Contains variables and routines for emitting NOx from lightning into the atmosphere. Cleaned up for inclusion into GEOS - Chem v9 - 01 - 01 by Lee Murray.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag56_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
pressure_mod.F
time_mod.F
transfer_mod.F
linoz_mod.F
Contains routines to perform the Linoz stratospheric ozone chemistry.
CMN_SIZE_mod.F
CMN_mod.F
dao_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
tropopause_mod.F
logical_mod.F
Contains all of the logical switches used by GEOS - Chem.
none
mapping_mod.F90
Contains a derived-type object to compute the mapping weight and areal mapping..
CMN_SIZE_mod.F
error_mod.F
logical_mod.F
megan_mod.F
Contains variables and routines specifying the algorithms that control the MEGAN inventory of biogenic emissions.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
a3_read_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
file_mod.F
geos57_read_mod.F90
grid_mod.F
julday_mod.F
logical_mod.F
meganut_mod.F
merra_a1_mod.F
modis_lai_mod.F90
regrid_1x1_mod.F
time_mod.F
meganut_mod.F
Contains functions used by MEGAN and other routines.
CMN_SIZE_mod.F
dao_mod.F
mercury_mod.F
Contains variables and routines for the GEOS - Chem mercury simulation. 
CMN_DEP_mod.F
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
depo_mercury_mod.F
diag03_mod.F
diag_mod.F
directory_mod.F
drydep_mod.F
error_mod.F
file_mod.F
global_br_mod.F
global_o3_mod.F
global_oh_mod.F
grid_mod.F
land_mercury_mod.F
logical_mod.F
ocean_mercury_mod.F
pbl_mix_mod.F
pressure_mod.F
regrid_1x1_mod.F
rnpbbe_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
tropopause_mod.F
vdiff_pre_mod.F
merra_a1_mod.F
Contains subroutines for reading the 1-hour time averaged (aka "A1") fields from the MERRA data archive.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
time_mod.F
transfer_mod.F
merra_a3_mod.F
Contains subroutines for reading the 3-hour time averaged (aka "A3") fields from the MERRA data archive.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
time_mod.F
transfer_mod.F
merra_cn_mod.F
Contains subroutines for reading the constant (aka "CN") fields from the MERRA data archive.
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
file_mod.F
time_mod.F
transfer_mod.F
merra_i6_mod.F
Contains subroutines for reading the 6-hour instantaneous (aka "I6") fields from the MERRA data archive.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
directory_mod.F
error_mod.F
file_mod.F
time_mod.F
transfer_mod.F
modis_lai_mod.F90
Reads MODIS LAI data at the native grid and rebins to the proper GEOS - Chem LAI arrays.
CMN_DEP_mod.F
CMN_SIZE_mod.F
directory_mod.F
error_mod.F
logical_mod.F
mapping_mod.F90
time_mod.F
nei2005_anthro_mod.F 
Contains variables and routines to read the NEI2005 anthropogenic emissions.
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
ocean_mercury_mod.F
Contains variables and routines needed to compute the oceanic flux of mercury. Original code by Sarah Strode at UWA/Seattle.
CMN_DEP_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
depo_mercury_mod.F
diag03_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
olson_land_map.F90
Contains routines to read the Olson land map and compute the IREG, ILAND, and IUSE arrays.
CMN_DEP_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
directory_mod.F
error_mod.F
grid_mod.F
logical_mod.F
mapping_mod.F90
optdepth_mod.F
Contains routines to compute optical depths for GEOS - 1, GEOS - STRAT, GEOS - 2, and GEOS - 3 met data sets.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
diag_mod.F
paranox_mod.F
Contains routines to reading and interpolating look up tables that are necessary for the PARANOX ship plume model.
CMN_O3_mod.F
cmn_fj_mod.F
dao_mod.F
directory_mod.F
error_mod.F
file_mod.F
time_mod.F
tracer_mod.F
tracerid_mod.F
pbl_mix_mod.F
Contains routines and variables used to compute the planetary boundary layer (PBL) height and to mix tracers underneath the PBL top.
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
dao_mod.F
diag_mod.F
error_mod.F
grid_mod.F
logical_mod.F
pressure_mod.F
time_mod.F
tracer_mod.F
pjc_pfix_geos5_window_mod.F
Contains routines which implements the Philip Cameron-Smith pressure fixer. Specially modified for the GEOS - 5 nested grid simulation.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
CMN_mod.F
error_mod.F
grid_mod.F
pressure_mod.F
pjc_pfix_geos57_window_mod.F
Contains routines which implements the Philip Cameron-Smith pressure fixer. Specially modified for the GEOS - 5.7.2 nested grid simulation.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
CMN_mod.F
error_mod.F
grid_mod.F
pressure_mod.F
pjc_pfix_mod.F
Contains variables and routines which implement the Philip Cameron-Smith pressure fixer for the GEOS - 4/TPCORE transport code (contained in tpcore_fvdas_mod.F90).
CMN_GCTM_mod.F
CMN_SIZE_mod.F
CMN_mod.F
error_mod.F
grid_mod.F
pressure_mod.F
planeflight_mod.F
Contains variables and routines which are used to "fly" a plane through the GEOS - Chem model simulation. This is useful for comparing model results with aircraft observations. 
CMN_DIAG_mod.F
CMN_FJ_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
comode_loop_mod.F
comode_mod.F
dao_mod.F
error_mod.F
file_mod.F
jv_cmn_mod.F
pressure_mod.F
time_mod.F
tracer_mod.F
tropopause_mod.F
restart_mod.F
Contains variables and routines which are used to read and write GEOS - Chem restart files, which contain tracer concentrations in [v/v] mixing ratio. 
CMN_SIZE_mod.F
CMN_mod.F
bpch2_mod.F
charpak_mod.F
comode_loop_mod.F
comode_mod.F
dao_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracer_mod.F
retro_mod.F
Contains the routines used to read emissions data from the RETRO anthropogenic VOC emissions inventory.
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
file_mod.F
future_emissions_mod.F
grid_mod.F
directory_mod.F
logical_mod.F
scale_anthro_mod.F
time_mod.F
tracer_mod.F
tracerid_mod.F
transfer_mod.F
rpmares_mod.F
Contains variables and routines to compute aerosol thermodynamic equilibrium.
APM_INIT_mod.F
CMN_SIZE_mod.F
dao_mod.F
error_mod.F
global_hno3_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
tropopause_mod.F
scale_anthro_mod.F
Contains routines to scale anthropogenic emissions from a base year to a simulation year.
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
regrid_1x1_mod.F
seasalt_mod.F
Contains arrays and routines for performing either a coupled chemistry/aerosol run or an offline seasalt aerosol simulation. The original code taken from Mian Chin's GOCART model and was modified accordingly for GEOS - Chem. 
CMN_DIAG_mod.F
CMN_GCTM_mod.F
CMN_SIZE_mod.F
dao_mod.F
diag_mod.F
drydep_mod.F
error_mod.F
grid_mod.F
logical_mod.F
pbl_mix_mod.F
pressure_mod.F
ssa_bromine_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
vdiff_pre_mod.F
soaprod_mod.F
Contains variables and routines which are used to read and write APROD and GPROD restart files for SOA simulations.
CMN_DIAG_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
carbon_mod.F
dao_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracer_mod.F
ssa_bromine_mod.F
Contains variables and routines for emissions of Br2. 
CMN_DIAG_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
bromocarb_mod.F
comode_loop_mod.F
diag_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracerid_mod.F
strat_chem_mod.F90
Contains variables and routines for performing a simple linearized chemistry scheme in the stratosphere.
CMN_GCTM_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
dao_mod.F
directory_mod.F
error_mod.F
grid_mod.F
logical_mod.F
linoz_mod.F
pressure_mod.F
tagged_ox_mod.F
time_mod.F
tracer_mod.F
tracerid_mod.F
transfer_mod.F
tropopause_mod.F
streets_anthro_mod.F
Contains variables and routines to read the David Streets et al. Asian anthropogenic emissions.
CMN_O3_mod.F
CMN_SIZE_mod.F
bpch2_mod.F
directory_mod.F
error_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
sulfate_mod.F
Contains the sulfate chemistry routines from Mian Chin's GOCART model and updated routines. 
CMN_DIAG_mod.F
CMN_FJ_mod.F
CMN_GCTM_mod.F
CMN_O3_mod.F
CMN_SIZE_mod.F
arctas_ship_emiss_mod.F
biomass_mod.F
bpch2_mod.F
bravo_mod.F
cac_anthro_mod.F
comode_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
drydep_mod.F
edgar_mod.F
emep_mod.F
epa_nei_mod.F
error_mod.F
file_mod.F
future_emissions_mod.F
gfed2_biomass_mod.F
gfed3_biomass_mod.F
global_hno3_mod.F
global_no3_mod.F
global_oh_mod.F
grid_mod.F
icoads_ship_mod.F
logical_mod.F
nei2005_anthro_mod.F
pbl_mix_mod.F
pressure_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
seasalt_mod.F
streets_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
tropopause_mod.F
uvalbedo_mod.F
vdiff_pre_mod.F
wetscav_mod.F
tagged_co_mod.F
Contains variables and routines used for the geographically tagged CO simulation.
biofuel_mod.F
biomass_mod.F
bpch2_mod.F
dao_mod.F
diag_mod.F
diag_pl_mod.F
directory_mod.F
error_mod.F
global_nox_mod.F
global_oh_mod.F
grid_mod.F
logical_mod.F
meganut_mod.F
megan_mod.F
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
tropopause_mod.F
tagged_ox_mod.F
Contains variables and routines to perform a tagged Ox simulation. P(Ox) and L(Ox) rates need to be archived from a full chemistry simulation before you can run w/ Tagged Ox.
bpch2_mod.F
charpak_mod.F
dao_mod.F
diag_mod.F
diag_pl_mod.F
directory_mod.F
drydep_mod.F
error_mod.F
grid_mod.F
julday_mod.F
logical_mod.F
meganut_mod.F
pbl_mix_mod.F
strat_chem_mod.F90
time_mod.F
tracerid_mod.F
tracer_mod.F
transfer_mod.F
tropopause_mod.F
toms_mod.F
Contains variables and routines for reading the EP-TOMS O3 column data from disk (for use w/ the FAST - J photolysis routines).
bpch2_mod.F
directory_mod.F
error_mod.F
time_mod.F
transfer_mod.F
tpcore_bc_mod.F
Contains variables and routines to read and write boundary conditions from a global simulation. These are needed for TPCORE transport for nested grid 1° x 1° simulations. 
bpch2_mod.F
directory_mod.F
error_mod.F
file_mod.F
grid_mod.F
logical_mod.F
time_mod.F
tracer_mod.F
tpcore_fvdas_mod.F90
Contains routines for the TPCORE transport scheme, as implemented in the GMI model, based on Lin Rood 1995.
none
tpcore_geos5_window_mod.F90
Contains routines for the GEOS - 4/fvDAS transport scheme.  Original code from S-J Lin and Kevin Yeh.
none
tpcore_geos57_window_mod.F90
Contains routines for the GEOS - 4/fvDAS transport scheme.  Original code from S-J Lin and Kevin Yeh.
none
tpcore_mod.F
Contains the TPCORE transport subroutine package by S-J Lin, version 7.1. Also contains the pressure fixer routines for TPCORE from M. Prather (in versions 4.21 and higher). 
dao_mod.F
diag_mod.F
global_ch4_mod.F
grid_mod.F
pressure_mod.F
time_mod.F
tracer_mod.F
tpcore_window_mod.F
Contains the TPCORE transport subroutine package by S-J Lin, version 7.1, modified for nested-grid simulations by Yuxuan Wang.
dao_mod.F
diag_mod.F
global_ch4_mod.F
grid_mod.F
pressure_mod.F
time_mod.F
tracer_mod.F
tracer_mod.F
Contains the GEOS - Chem tracer array STT plus various other related quantities. TRACER_MOD also contains inquiry functions that can be used to determine the type of GEOS - Chem simulation.
error_mod.F
tracerid_mod.F
Contains variables and routines used to identify tracers, emission species, biomass burning species, and biofuel burning species.
charpak_mod.F
error_mod.F
gc_environment_mod.F90
gc_type2_mod.F90
logical_mod.F
tracer_mod.F
transport_mod.F
Contains routines which select the proper transport routines for GEOS - Chem global and window simulations.
dao_mod.F
diag_mod.F
error_mod.F
grid_mod.F
logical_mod.F
pjc_pfix_geos5_window_mod.F
pjc_pfix_geos57_window_mod.F
pjc_pfix_mod.F
pressure_mod.F
time_mod.F
tpcore_bc_mod.F
tpcore_fvdas_mod.F
tpcore_geos5_window_mod.F
tpcore_geos57_window_mod.F
tpcore_mod.F
tpcore_window_mod.F
tracer_mod.F
tropopause_mod.F
Contains routines and variables for reading and returning the value of the annual mean tropopause.
bpch2_mod.F
comode_mod.F
dao_mod.F
diag_mod.F
directory_mod.F
error_mod.F
logical_mod.F
pressure_mod.F
transfer_mod.F
uvalbedo_mod.F
Contains variables and routines for reading the UV Albedo data from disk (for use w/ the FAST - J photolysis routines). 
bpch2_mod.F
directory_mod.F
error_mod.F
transfer_mod.F
vdiff_mod.F
Contains all routines for the non-local PBL mixing scheme.
comode_mod.F
dao_mod.F
depo_mercury_mod.F
diag_mod.F
drydep_mod.F
error_mod.F
grid_mod.F
logical_mod.F
ocean_mercury_mod.F
pbl_mix_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
vdiff_pre_mod.F
vdiff_pre_mod.F
Contains variables used in vdiff_mod.F.
tracer_mod.F
vistas_anthro_mod.F
Contains variables and routines to read the VISTAS anthropogenic emissions.
bpch2_mod.F
directory_mod.F
epa_nei_mod.F
error_mod.F
future_emissions_mod.F
grid_mod.F
logical_mod.F
regrid_1x1_mod.F
scale_anthro_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F
wetscav_mod.F
Contains arrays used in the wet scavenging of tracers in cloud updrafts, rainout, and washout.
dao_mod.F
depo_mercury_mod.F
diag_mod.F
error_mod.F
h2o2.F
ito.F
logical_mod.F
ocean_mercury_mod.F
pressure_mod.F
time_mod.F
tracerid_mod.F
tracer_mod.F

7.1.4 Compilation Sequence for GEOS - Chem
GEOS - Chem's makefiles compile source code files in the following order:
   1. Files in NcdfUtil/
   2. Files in Headers
   3. Files in KPP/
   4. Files in GeosUtil/
   5. Files in ISOROPIA/ 
   6. Files in GeosCore/
If you select the GEOS - Chem mercury simulation with the Global Terrestrial Mercury Model option, then the makefiles will compile files in this order::
   1. Files in GTMM/
   2. Files in NcdfUtil/
   3. Files in Headers
   4. Files in KPP/
   5. Files in GeosUtil/
   6. Files in ISOROPIA/ 
   7. Files in GeosCore/
Each directory has its own makefile. The makefile contains a list of all of the source code files in the subdirectory, plus dependent routines (a.k.a. the "dependencies" list). Source code files that do not refer to any modules have a dependencies listsuch as:
decomp.o                     : decomp.F
Whereas a source code file that refers to several modules (in this case, GeosCore/tropopause_mod.F) has a dependencies list like this:
tropopause_mod.o             : tropopause_mod.F                     \
                               comode_mod.o         dao_mod.o       \
                               diag_mod.o           logical_mod.o
Looking at the List of GEOS - Chem Modules, you will see that GeosCore/tropopause_mod.F refers to 9 other modules. But 5 of those modules are found in different directories (such as Headers/ and GeosUtil/), which are compiled prior to GeosCore/. Therefore you can ignore these when creating the dependencies listing. In the example above, we have only specified the 4 modules that are located in the same directory as tropopause_mod.F.
The order of modules in the dependencies list does not matter. The GNU Make utility will define the order of compilation from the list of files (and their dependencies) that you have specified in each Makefile. You will not have to worry about this unless you add new source code files. If you have questions about how to add dependency lists to makefiles, please let us know.
                                       
7.1.5 OpenMP parallel loop directives 
In the late 1990's, several compiler vendors defined a new open standard for parallel computing, aptly named OpenMP. Most modern Fortran and C compilers include support for OpenMP, which facilitates porting parallel source code to different platforms. GEOS - Chem has used OpenMP parallel computing since version 4.17.
Here is a sample OpenMP parallel DO loop:
Column   1         2         3         4
1234567890123456789012345678901234567890
!$OMP PARALLEL DO
!$OMP+SHARED( A )
!$OMP+PRIVATE( I, J )
!$OMP+SCHEDULE( DYNAMIC )
      DO J = 1, JJPAR
      DO I = 1, IIPAR
	     A(I,J) = A(I,J) * 2.0
      ENDDO
      ENDDO
!$OMP END PARALLEL DO
Notice that the first column of each !$OMP directive has a Fortran comment character (!). This is by design. In order to invoke OpenMP's parallel directives, you must toggle a specific switch in your makefile (usually -mp or -openmp, depending on your compiler). Otherwise, the compiler will interpret the OpenMP parallel directives as Fortran comments. This would cause all OpenMP parallel DO-loops revert to regular Fortran DO loops, executing on a single CPU.
Because the above example uses the traditional fixed-format (Fortran - 77) style, the !$OMP directives must begin at column 1. Otherwise a syntax error will result at compile time. If you are using the free-format (Fortran - 90) style, then you may indent the !OMP directives.
OpenMP parallelization is not equivalent to MPI (message passing interface) parallelization. With OpenMP, you can execute parallel code across CPUs of the same machine or cluster node. You CANNOT use CPUs from physically separated machines. Therefore, OpenMP is incompatible with distributed architectures (e.g. Beowulf, grid computing, cloud computing). Our grid-independent GEOS - Chem project seeks to remove this bottleneck by making make GEOS - Chem compatible with MPI parallelization.
For more information about OpenMP, consult the web site OpenMP.org.
                                       
7.2 GEOS - Chem Debugging
The GEOS - Chem model evovles constantly. Our rapidly-increasing user base frequently submits updates and new features for inclusion into the standard GEOS - Chem repository. As with any software project, mistakes are inevitable. 
The bugs you will encounter when working on GEOS - Chem fall into one of two categories:
   1. True bugs: typos, omissions, reading the wrong file, or other outright mistakes. 
   2. Design limitation bugs: that is, writing code in such a way that precludes future expansion.
You can easily rectify the bugs of the first category. Fixing these usually means correcting a misspelled word, updating an incorrect numerical value, reading from the proper file, etc.
You may struggle to correct the bugs of the second category. You'll find that your simulation works perfectly -- until you try to add in a new species, reaction, offline chemistry simulation, diagnostic, or third-party code package. You may have to invest significant time and effort in modifying GEOS - Chem before it finally does what you want..
Remember that GEOS - Chem includes several disparate software elements: emissions, chemistry and deposition routines from Harvard, transport and convection routines from GSFC, photolysis from UC Irvine, etc. The structure of these codes have largely dicated the overall structure of GEOSChem. At present, we are working to rectify many of these legacy-code issues (a.k.a. "historical baggage.)
                                       
7.2.1 Recent fixes
We strive to fix bugs in GEOS - Chem as soon as we find them. Please see our Bugs and Fixes page on the GEOS - Chem wiki. On this page, you will find a list of bugs by GEOSChem version. Clicking on a link will take you to a wiki post which explains the bug (and how it was fixed) in detail.
When your GEOS - Chem simulation dies with an error, first refer to our Common GEOS - Chem Error Messages wiki page. You may find a solution there.
We invite you to peruse these useful resources:
   1. Appendix 7: GEOS - Chem Style Guide
   2. GEOS - Chem wiki. Floating point math issues
   3. GEOS - Chem wiki: Machine issues & portability
                                       
7.2.2 Debugging Tips
Here are some steps you can take to try to diagnose a particular GEOS - Chem error.
1.
Turn on diagnostic ND70 in the file input.geos. ND70 tells GEOS - Chem to call subroutine DEBUG_MSG from various locations in the code (after advection, chemistry, emissions, dry deposition, etc). DEBUG_MSG writes a short message to the screen and immediately flushes the output to the log file. This will help you be able to pin down where the error occurred.
NOTE: DEBUG_MSG prints and then immediately flushes the error message to disk. Keep in mind that most Unix systems feature buffered I/O -- the screen does not refresh until an internal buffer (usually some multiple of 16KB) fills up with text. If you don't flush an error message to disk, then the last log file output may not reflect the location of the error.
 

2.
Add more calls to DEBUG_MSG as necessary:
CALL DEBUG_MSG( '### after routine X'  )
CALL DEBUG_MSG( '### after function Y' )
 

3.
Check for negative concentrations, NaN or Infinite values, call routine CHECK_STT:
! Put this at the top of the subroutine where you are calling CHECK_STT
USE TRACER_MOD, ONLY: CHECK_STT

. . .

! Check for NaN, infinity, negatives:		
CALL CHECK_STT( 'Where I think there is a problem' )


4.
Check the minimum and maximum values of an array with the MINVAL and MAXVAL intrinsic functions:
PRINT*, '### Min, Max: ', MINVAL( ARRAY ), MAXVAL( ARRAY )
CALL FLUSH( 6 )
Check the sum of an array with the SUM intrinsic function:
PRINT*, '### Sum of X : ', SUM( ARRAY )
CALL FLUSH( 6 )
Don't forget to add a CALL FLUSH(6)to flush the output to the screen or log file.
 

5.
Compile your code with array-out-of-bounds error checking. This makes sure that you are not accessing an array with an invalid index. Consider this example:
REAL*8 :: A(10), B(10)
...
DO I = 1, 10
   B(I) = A(I+1)
ENDDO
The code will try access the 11th element of the A array. But since A only has 10 elements, the code will access the next contiguous memory location, which belongs to a different variable altogether. This will copy a "junk" value into the 10th element of the B array.
Out-of-bounds errors may also manifest themselves as a segmentation fault:
forrtl: severe (174): SIGSEGV, segmentation fault occurred
To invoke array-out-of-bounds checking in your code, issue these commands:
make realclean
make -j4 BOUNDS=yes
(If you use the Intel Fortran Compiler, you can also add the TRACEBACK=yes, which will print out a list of all routines that were being called at the time of the error.)
The compiler will trap out-of-bounds errors at runtime. You may get an error message such as:
forrtl: severe (408): fort: (3):
Subscript #1 of the array PBL_THICK has value -1 
which is less than the lower bound of 1
NOTE: Once you have located and fixed the offending array statement, you should recompile without the array-out-of-bounds checking built in. The error checking causes your code to slow down noticeably. Check for array-out-of-errors in your debugging runs but not in your production runs.
 
 
                                       
7.2.3 Using a debugger
If you have access to a debugger (IDB, DBX, Totalview), then learn how to use at least the basic commands, such as:
   * Examinng data when a program stops
   * Navigating the stack when a program stops
   * Setting breakpoints 
This will save you a lot of time and hassle.
When you use a debugger, you must compile your code with a flag that tells the compiler to generate symbolic debug information. On most compilers, this flag is named -g. You also need to switch off any compiler optimizations (which can modify the sequence in which individual instructions occur) by specifying the -O0 flag.
Add DEBUG=yes (case sensitive) to the make command to apply these options:
make -j4 DEBUG=yes OMP=no    # Without parallelization
make -j4 DEBUG=yes           # With parallelization
                                       
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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Chapter 8
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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8. Using Git to manage the GEOS - Chem source code
In this chapter we list the Git commands that you will most commonly use to manage your local GEOS - Chem repository. For more information (including information about installing Git on your system), please see:
   1. GEOS - Chem wiki: Version control with Git
   2. GEOS - Chem wiki: Using Git with GEOS - Chem
   3. The Git web page: http://www.git-scm.com

8.1 Viewing the revision history
Use the gitk viewer to examine the contents of your Git-backed GEOS - Chem source code directory. You have two choices:
   1. Change into the Code.v9-01-03 directory and start gitk as follows:
            cd Code.v9-01-03
gitk --all &      # This will show ALL open branches 
   2. Or if you are using the git gui GUI browser (more on that below), invoke gitk from the Repository/Visualize All Branch History menu item. 
At the top left of the gitk screen, you will see the graph of revisions. Each dot represents a commit, along with the log message that accompanied each commit. Note that the most recent commit (i.e. the line at the very top), there are 2 green boxes at the top, one named master and one named origin:
   1. origin: Therefore, this indicates the "pristine", unchanged code that you got from the download. 
   2. master: This represents the current state of your local repository. Because you haven't done anything to the code yet, the master and origin branches both point to the same commit. 
If you click on any of the commits in the top left window, in the window below, you will see the log message and a list of changes to the source code. The old code is marked in RED and the new code is marked in GREEN. At right you will also see a list of files that were changed during the commit.
So you can easily see how the code has evolved by using gitk. 

8.2 Making Revisions
8.2.1 Using the GUI browser
Use the git gui for source code management. Start this in your Code.v9-01-03 directory:
cd Code.v9-01-03
git gui & 
On the left there are 2 windows: 
   1. Unstaged Changes: Git is telling you that it doesn't recognize these changes as belonging to the repository. If you modified any files since the last commit, you will see them displayed here. Right above this window you will find the name of the current checked-out branch. 
   2. Staged Changes: Git will add these changes to the repository the next time you make a commit. 
Whenever you need to modify the source code, you should NOT do it on the master branch. Create a new branch for your modifications. Test your modifications in the new branch ad nauseum until you are sure that everything is functioning as it should. When you are done merge your new branch back into the master branch. You can then delete the branch you were testing in.
If you ever need to start over from scratch, you can just go back to the master branch and you will get back the state of the code before your modifications were added. This will save you time.
8.2.2 Creating branches
To create a new branch, go to the Branch/Create on the menu (or type CTRL - N). You will get a dialog box that prompts you for the new branch name. Type a unique name and then click Create. 
You should pick names that have meaning to you. For example, some good branch names are: 
   * Bug_fix_sulfate_mod 
   * CO2_simulation
   * KPP_with_isoprene
   * Methane_simulation
You will be automatically placed into the branch you have just created. 
8.2.3 Committing
With Git, you should commit frequently, such as when you have completed making revisions to a file or group of files. Commits that are made on one branch will not affect the other branches. 
Committing is best done with the git gui. Follow these steps: 
   1. Pick Commit/Rescan from the menu (or type the F5 key). This forces the git gui to show the latest changes.
   2. You should see a list of files in the Unstaged Changes window. Clicking on the icon at the left of a file will send it to the Staged Changes window. Git will add all of the files in Staged Changes to the repository the next time you commit. Note: Clicking on the icon of the files in the Staged Changes moves back the file to the Unstaged Changes window. 
   3. Type a Commit message in the bottom right window. See this example of a good commit message. Some pointers are:
         o The first line should only be 50 characters or less and succinctly describe the commit 
         o Then leave a blank line 
         o Then add more in-depth text that describes the commit 
         o Then click on the Signed-off by button. This will add your name, email address, and a timestamp. 
   4. You will see two radio buttons above the Commit message window. Specify the type of commit:
         o New commit: Assumes we are making a totally new commit (default setting).
         o Amend last commit: If for whatever reason we need to update the last commit message, pick this button.
   5. Click on the Commit button.
Then if you start the gitk viewer, your new commit should be visible.
8.2.4 Switching between branches
Before you switch from one branch to another (aka "checking out a branch"), commit any remaining unstaged files to the current open branch. Unstaged files will remain in your working directory even after you checkout a different branch. This can will lead to confusion.
To check out a new branch, go to Branch/Checkout on the menu and pick the name of the branch you would like to switch to. The current branch name will be displayed just below the menu at top left. 
Once you have created your branch and have checked it out, you can start modifying it with your favorite text editor. (We recommend Emacs.)
We recommend to keep one open branch per new feature that you are adding into GEOS - Chem. This lets you test each individual feature separately. After you have validated each feature, you can merge its branch back into the master.
8.2.5 Merging
Follow this procedure to merge your changes back into the master branch:
   1. Switch back to the master branch by selecting Branch/Checkout from the menu (or type CTRL - O). You will be given a dialog box of available branches. Select master and click Checkout.
   2. Pick Merge/Local Merge from the menu (or type CTRL - M). You will be given a dialog box of available branches. Select the branch you would like to merge into master and click Merge.
This should merge your changes back into master. Then if you start the gitk viewer, the you should see your changes in the master branch.
8.2.6 Tagging
Git lets you tag a particular commit with an alphanumeric string for easy reference. This tag will allow users to just refer to the tag name using git pull. 
Tagging can be done in one of two ways. You can add a tag via the command line: 
git tag GEOS-Chem v9-01-03n
git tag GEOS-Chem v9-01-03o
etc. at the Unix command line.
You may also add a tag via the gitk viewer utility, as follows:
   1. Open the gitk browser:
         o Type gitk (to view the current branch), or 
         o Type gitk --all to view all branches. 
   2. In the top-left window select a commit by clicking on it with the mouse
   3. Right-click to pull up the context menu. Select the Create tag option.
   4. Type in your tag text and click Create.
To remove a tag, you can use the git tag command directly:
git tag -d TAG_NAME
Where TAG_NAME is the name of the tag that you have added.
NOTE: Tagging is something that typically only the GEOS - Chem support team will do.
8.2.7 Deleting branches
Once you have merged your changes back into the master branch, you can delete the branch you just created. In the git gui, go to the Branch/Delete menu item. Select the name of the branch that you wish to delete from the dialog box display.

8.3 Sharing your revisions with others (and vice-versa)
One of the really nice features of Git is that it can create patch files, or files which contain a list of changes that can be imported into someone else's local Git repository. Using patch files obviates the need of having to merge differences between codes manually. 
8.3.1 Creating a patch file to share with others
To create a patch file containing the code differences between a branch of your code with your master branch, type: 
git format-patch master..BRANCH_NAME --stdout > my-patch-file.diff
where BRANCH_NAME is the name of the branch that you want to compare against the master branch. 
You can also create a patch file for a given number of past commits by typing: 
git format-patch -3 --stdout > my-patch-file.diff
If you want the most recent commit then use -1 instead, etc. 
These commands will pipe the output from the git format-patch command to a file named by you (in this case my-patch-file.diff, but you may select whatever name you wish). You can then include the patch file as an email attachment and send it to other GEOS - Chem users or the GEOS - Chem Support Team. 
8.3.2 Checking the validity of a patch file
Other users can send you their source code revisions as patch files. If you want to check the status of a Git patch file (i.e. what it will actually do) before you apply it to your repository, use the git apply command:
git apply --stat my-patch-file.diff
     
GeosCore/aerosol_mod.F |    7 ++++---   
1 files changed, 4 insertions(+), 3 deletions(-)
The sample output listed above indicates that the patch contained 4 insertions and 3 deletions from only one file (aerosol_mod.F).
Note that the git apply --stat command does not apply the patch, but only shows you the stats about what it will do. For more detailed information about the patch, you can open it in either an emacs or vi window and examine it manually.
You can also use git apply command to determine if the patch will install properly or not. Type:
git apply --check my-patch-file.diff
If an error occurs, it usually means that the patch was made from an earlier version of GEOS - Chem. You can rectify this by having the sender recreate the patch with the most recent GEOS - Chem version.
8.3.3 Reading a patch file into your local repository
To ingest a patch file into your local Git repository, first make a new branch. Then follow this procedure: 
   1. Pick Branch/Create from the menu (or type CTRL - N). Give your branch a descriptive name like "Updates_from_xxxx" that will serve as a mnemonic.
   2. Pick Branch/Checkout from the menu (or type CTRL - O) and switch to the branch you just created.
   3. To ingest the other person's source code changes, type:
            git am < their-patch-file.diff
You can then test the other person's revisions in the separate branch until you are sure they are OK. Then you can merge them back into the master branch as described above.
8.3.4 More about patch files
For more information about Git patch files, please see the following links:
   1. Sending Patches with Git: A guide how to use the patch feature of Git to send your changes to another user. 
   2. How to create and apply a patch with Git: Another nice explanation of how to use Git to send patch files.

8.4 Getting updates from the remote repository
We recommend that you use the the git clone command to download each newly-released GEOS - Chem version into a new local directory. 
There may be times, however, when "patches" (i.e. minor fixes) need to be applied to an existing GEOS - Chem version. The easiest way to obtain patches is to use the git pull command, as follows: 
   1. Change to your local code directory (e.g. Code.v9-01-03) 
   2. Make a new branch named patch (or something similar). 
   3. Check out the patch branch. Now we are ready to obtain the updates from the remote server. 
   4. Use the git pull command to download the updated files, as follows: 
            git pull git://git.as.harvard.edu/bmy/GEOS-Chem master
   5. Test compilation to make sure everything is fine.
   6. Check out the master branch. 
   7. Merge the patch branch into your master branch. 
   8. Delete the patch branch. 
This will merge the changes from the master branch of the remote repository into your master branch.

8.5 Reverting to an older state of the code
When you clone GEOS - Chem from the remote repository to your local disk space (with the git clone command), the repository will point to the most recent commit. However, you may want to revert to an older state of the code. Git allows you to do this very easily. 
Let's assume that the latest version of the code is v9 - 01 - 03, but that you want to use the version v8 - 03 - 01. The procedure is as follows: 
   1. Clone GEOS - Chem with:
            git clone git://git.as.harvard.edu/bmy/GEOS-Chem Code.v9-01-03
   2. Open the gitk browser by typing gitk --all & at the command line.
   3. In the top-left window of gitk, find the commit that you want to revert to. Usually this will be denoted with a yellow tag (e.g. v8 - 03 - 01 or v8 - 03 - 01 - benchmark). However, if there are any post-release patches, be sure you select the oldest one.
   4. Right click with the mouse. This will open a context menu. Select Create new branch.
   5. A new dialog box will pop up asking you to name the branch. Type Code.v8 - 03 - 01 and click Create.
   6. Close gitk and open the git gui by typing git gui &.
   7. From the git gui dropdown menu, select Branch / Checkout, and then pick Code.v8 - 03 - 01.
That's it! We now have two branches that represent different GEOS - Chem versions. 
   1. The master branch represents the state of the code as of the v9 - 01 - 03 release.
   2. The Code.v8 - 03 - 01 branch represents the state of the code as of the v8 - 03 - 01 release. 
You can work on the Code.v8 - 03 - 01 branch as you wish. You can create further branches off of the Code.v8 - 03 - 01 branch. You can always revert to the v9 - 01 - 03 state of the code by just switching back to the master branch (with Branch / Checkout from the git gui dropdown menu).

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Chapter 9
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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9. GEOS - Chem Reference

9.1 GEOS - Chem reference guides
GEOS - Chem employs the ProTeX automatic documentation system to create highly detailed reference guides (in both PDF and PostScript formats) from the comments in the source code documentation headers. You can build these reference guides by simply typing:
make doc
(See Chapter 3 for a complete list of Makefile options.)
Here are the current GEOS - Chem v9 - 01 - 03 reference guides in PDF format::
   * Volume 1: GEOS - Chem Makefiles
   * Volume 2: GEOS - Chem Utility Modules
   * Volume 3: "Core" GEOS - Chem Modules and Routines
   * Volume 4: Global Terrestrial Mercury Model

9.2 Acknowledgments and guidelines for offering credit
Development of the GEOS - Chem model and its adjoint is a grass-roots activity by individual scientists pursuing their own research interests and sharing their work for the benefit of all. Good functioning of the GEOS - Chem community and faster sharing of new model features is promoted by users offering co-authorship for recent developments. 
9.2.1 Guidelines for offering credit
We invite you to read our web page: GEOS - Chem Credits and References. This page contains guidelines for giving appropriate credit to developers through co-authorship or citation.
9.2.2 GEOS - Chem code development history
Please refer to the Narrative Description of the GEOS - Chem Model. This page includes a description of the current standard version of GEOS - Chem to assist you in correctly citing relevant model components in your publications.

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 1
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 1: GEOS - Chem Tracers, by Simulation
With GEOS - Chem, you can perform several different types of chemistry simulations. For each simulation, we provide a list of advected tracers below.

A1.1 NOx - Ox - hydrocarbon - aerosol simulations
Advected tracers fall into two categories:
   1. Tracers having lifetimes long enough to be transported out of the grid box in which they are created, or 
   2. "Family tracers", consisting of two or more molecules (e.g. NOx, Ox).
Many advected tracers are also listed as individual species in the chemical mechanism. Please consult Appendix 6 for a complete list of chemical species in GEOS - Chem.
We specify several hydrocarbon tracers (those listed in BOLD ITALICS) as atoms C instead of molecules tracer. We assign to these a molecular weight of 12 g/mole. The number of moles C per moles tracer is listed below.
You can select from different chemistry mechanism options for the NOx - Ox - hydrocarbon - aerosol simulations. In the following table we give the tracers for each option: the standard mechanism, the SOA mechanism, the dicarbonyls mechanism and the Caltech isoprene mechanism.
For more information, please see:
   1. Chapter 6.1.1, Checklist for NOx - Ox - Hydrocarbon - aerosol chemistry simulation with SMVGEAR or KPP
   2. GEOS - Chem Wiki: The "standard" NOx - Ox - Hydrocarbon - aerosol simulation
   3. GEOS - Chem Wiki: Secondary organic aerosols
   4. GEOS - Chem Wiki: Dicarbonyls simulation
   5. GEOS - Chem Wiki: Caltech isoprene mechanism
#
Name
Description
g/mole
mole C/
mole tracer
                              Standard mechanism
1
NOx
NO + NO2+ NO3 + HNO2
46
-
2
Ox
O3 + NO2 + 2NO3
48
-
3
PAN
Peroxyacetyl Nitrate
121
-
4
CO
Carbon Monoxide
28
-
5
ALK4
Lumped >= C4 Alkanes
12
4
6
ISOP
Isoprene
12
5
7
HNO3
Nitric Acid
63
-
8
H2O2
Hydrogen Peroxide
34
-
9
ACET
Acetone
12
3
10
MEK
Methyl Ethyl Ketone
12
4
11
ALD2
Acetaldehyde
12
2
12
RCHO
Lumped Aldehyde >= C3
58
-
13
MVK
Methyl Vinyl Ketone
70
-
14
MACR
Methacrolein
70
-
15
PMN
Peroxymethacroyl Nitrate
147
-
16
PPN
Lumped Peroxypropionyl Nitrate
135
-
17
R4N2
Lumped Alkyl Nitrate
119
-
18
PRPE
Lumped >= C3 Alkenes
12
3
19
C3H8
Propane
12
3
20
CH2O
Formaldehyde
30
-
21
C2H6
Ethane
12
2
22
N2O5
Dinitrogen Pentoxide
105
-
23
HNO4
Pernitric Acid
79
-
24
MP
Methyl Hydro Peroxide
48
-
25
DMS
Dimethyl Sulfide
62
-
26
SO2
Sulfur Dioxide
64
-
27
SO4
Sulfate
96
-
28
SO4s
Sulfate on surface of sea-salt aerosol
96
-
29
MSA
Methyl Sulfonic Acid
96
-
30
NH3
Ammonia
17
-
31
NH4
Ammonium
18
-
32
NIT
Inorganic nitrates
62
-
33
NITs
Inorganic nitrates on surface of sea-salt aerosol
62
-
34
BCPI
Hydrophilic black carbon aerosol
12
1
35
OCPI
Hydrophilic organic carbon aerosol
12
1
36
BCPO
Hydrophobic black carbon aerosol
12
1
37
OCPO
Hydrophobic organic carbon aerosol
12
1
38
DST1
Dust aerosol, Reff = 0.7 microns
29
-
39
DST2
Dust aerosol, Reff = 1.4 microns
29
-
40
DST3
Dust aerosol, Reff = 2.4 microns
29
-
41
DST4
Dust aerosol, Reff = 4.5 microns
29
-
42
SALA
Accumulation mode sea salt aerosol
(Reff = 0.01  -  0.5 microns)
36
-
43
SALC
Coarse mode sea salt aerosol
(Reff = 0.5  -  8 microns)
36
-
44
Br2
Molecular bromine
160
-
45
Br
Bromine radical, or atomic bromine
80
-
46
BrO
Bromine monoxide
96
-
47
HOBr
Hypobromous acid
97
-
48
HBr
Hypobromic acid
81
-
49
BrNO2
Nitryl bromide
126
-
50
BrNO3
Bromine nitrate
142
-
51
CHBr3
Bromoform, or tribromomethane
253
-
52
CH2Br2
Dibromomethane
174
-
53
CH3Br
Methyl bromide
95
-
                                 SOA mechanism
1-37
Same tracers as for the standard mechanism
38
ALPH
A-pinene, B-pinene, sabinene, carene, terpenoid ketones
136.23
-
39
LIMO
Limonene
136.23
-
40
ALCO
Myrcene, terpenoid alcohols, ocimene
142
-
41
SOG1
Lump of gas products of first 3 (ALPH + LIMO + TERP) hydrocarbon oxidation
150
-
42
SOG2
Gas product of ALCO oxidation
160
-
43
SOG3
Gas product of SESQ oxidation 
220
-
44
SOG4
Gas product of ISOP oxidation
130
-
45
SOG5
Gas product of aromatics oxidation
150
-
46
SOA1
Lump of aerosol products of first 3 (ALPH + LIMO + TERP) hydrocarbon oxidation
150
-
47
SOA2
Aerosol product of ALCO oxidation
160
-
48
SOA3
Aerosol product of SESQ oxidation 
220
-
49
SOA4
Aerosol product of ISOP oxidation
130
-
50
SOA5
Aerosol product of aromatics oxidation
150
-
51-56 
Insert tracers 38-43 (dusts and sea salts) from standard simulation. 
57
BENZ
Benzene
12
6
58
TOLU
Toluene
12
7
59
XYLE
Xylene
12
8
                             Dicarbonyls mechanism
1-56
Same tracers as SOA simulation
57
GLYX
Glyoxal
58
-
58
MGLY
Methylglyoxal
72
-
59
BENZ
Benzene
12
6
60
TOLU
Toluene
12
7
61
XYLE
Xylene
12
8
62
MONX
Monoterpenes
12
10
63
SOAG
SOA product of GLYX
58
-
64
SOAM
SOA product of MGLY
72
-
65
C2H4
Ethene
12
2
66
C2H2
Acetylene
12
2
67
MBO
2-methyl-3-bute-2-nol
12
5
68
GLYC
Glycoaldehyde
60
-
69
HAC
Hydroxyacetone
74
-
70 
ACRPAN
APAN (CH2CHC(O)OONO2)
133
-
71 
ENPAN
ENPAN (NO2OCH2C(O)OONO2)
182
-
72
GLPAN
Peroxyacylnitrate from GLCO3
137
-
73
GPAN
Peroxyacylnitrate from GCO3
135
-
74
MPAN
2-methyl-1-oxo-2-propenyl nitroperoxyde
132
-
75
NIPAN
NIPAN (NO2OCH2CCH3CHC(O)OONO2,  C5PAN18)
224
-
                          Caltech isoprene mechanism 
1-43 
Same tracers as standard simulation (without bromine species) 
44 
HCOOH 
Formic acid 
46 
-
45 
ACTA 
Acetic acid
60
-
46 
ISOPN
Isoprene nitrate
147
-
47 
MOBA
5C acid from isoprene 
114
-
48
PROPNN
Propanone nitrate 
109
-
49
HAC
Hydroxyacetone
74
-
50
GLYC
Glycolaldehyde
60
-
51
MMN
Nitrate from MACR + MVK
149
-
52
RIP
Peroxide from RIO2
118
-
53
IEPOX
Isoprene epoxide
118
-
54
PYPAN
Pyruvic acid PAN 
149
-
55
MAP
Peroxyacetic acid
76
-
56
AP
 
76
-
NOTES: 
   1. You may omit the secondary organic aerosol tracers (ALPH, LIMO, ALCO, SOG1, SOG2, SOG3, SOG4, SOG5, SOA1, SOA2, SOA3, SOA4, SOA5, BENZ, TOLU, XYLE) by setting the following switches in the aerosol menu section of the input.geos file.  
       Online 2dy ORG AEROSOLS : F
   2. You may omit the dicarbonyl chemistry tracers (tracers 57 to 75). In this case, you need to set the following switch in the aerosol menu section of the input.geos file: 
       Online dicarb. chem. : F
   3. Each of these chemistry mechanism requires different versions of globchem.dat, jv_spec.dat, mglob.dat and ratj.d. The proper files are included when you download the various GEOS - Chem run directories (see Chapter 2.3).

A1.2 Offine aersosol simulations
You can run a GEOS - Chem "offline" aerosol simulation without having to call the SMVGEAR II or KPP solver. The tracer list is below.
For more information, please see:
   1. Chapter 6.1.6, Checklist for offline aerosol chemistry simulation
   2. GEOS - Chem Wiki: Offline aerosol chemistry simulation
   3. GEOS - Chem Wiki: Sulfate aerosols
   4. GEOS - Chem Wiki: Carbonaceous aerosols
   5. GEOS - Chem Wiki: Secondary organic aerosols
   6. GEOS - Chem Wiki: Mineral dust aerosols
   7. GEOS - Chem Wiki: Sea salt aerosols
#
Name
Description
g/mole
1
DMS
Dimethyl sulfide
62
2
SO2
Sulfur dioxide 
64
3
SO4
Sulfate
96
4
SO4s
Sulfate on surface of sea salt aerosol
96
5
MSA
Methane Sulfionic Acid
96
6
NH3
Ammonia
17
7
NH4
Ammonium
18
8
NIT
Inorganic sulfur nitrates
62
9
NITs
Inorganic sulfur nitrates on surface of sea-salt aerosol
62
10
BCPI
Hydrophilic black carbon aerosol
12
11
OCPI
Hydrophilic organic carbon aerosol
12
12
BCPO
Hydrophobic black carbon aerosol
12
13
OCPO
Hydrophobic organic carbon aerosol
12
14
ALPH
A-pinene, B-pinene, sabinene, carene, terpenoid ketones
136.23
15
LIMO
Limonene
136.23
16
ALCO
Myrcene, terpenoid alcohols, ocimene
142
17
SOG1
Lump of gas products of first 3 (ALPH+LIMO+TERP)
hydrocarbon oxidation
150
18
SOG2
Gas product of ALCO oxidation
160
19
SOG3
Gas product of SESQ oxidation 
220
20
SOG4
Gas product of ISOP oxidation 
130
21
SOG5
Gas product of aromatics oxidation
150
22
SOA1
Lump of aerosol products of first 3 (ALPH+LIMO+TERP)
hydrocarbon oxidation
150
23
SOA2
Aerosol product of ALCO oxidation
160
24
SOA3
Aerosol product of SESQ oxidation 
220
25
SOA4
Aerosol product of ISOP oxidation 
130
26
SOA5
Aerosol product of aromatics oxidation
150
27
DST1
Dust aerosol, Reff = 0.7 microns
29
28
DST2
Dust aerosol, Reff = 1.4 microns
29
29
DST3
Dust aerosol, Reff = 2.4 microns
29
30
DST4
Dust aerosol, Reff = 4.5 microns
29
31
SALA
Accumulation mode sea salt aerosol
(Reff = 0.1  -  2.5 microns)
36
32
SALC
Coarse mode sea salt aerosol
(Reff = 2.5  -  4 microns)
36
NOTE: You may omit the secondary organic aerosol tracers (ALPH, LIMO, ALCO, SOG1, SOG2, SOG3, SOG4, SOG5, SOA1, SOA2, SOA3, SOA4, SOA5) by setting the following switches in the aerosol menu section of the input.geos file.
Online 2dy ORG AEROSOLS : F
If you omit the secondary organic aerosol tracers then there will be a total of 18 tracers.

A1.3 Total CO2 and Tagged CO2 simulations
Ray Nassar updated the CO2 simulation in GEOS - Chem v8 - 03 - 02.
For more information, please see:
   1. Chapter 6.1.9: Checklist for Total CO2 and Tagged CO2 simulations
   2. GEOS - Chem Wiki: CO2 simulation
#
Name
Description
g/mole
1
CO2
Total CO2
44
         If you wish, you may add tracers for additional CO2 sources:
2
CO2ff
CO2 from fossil fuel emissions 
44
3
CO2oc
CO2 from ocean emissions
44
4
CO2bal
CO2 from balanced biosphere
44
5
CO2bb
CO2 from biomass burning emissions 
44
6
CO2bf
CO2 from biofuel emissions
44
7
CO2nte
CO2 from net terrestrial exchange
44
8
CO2se
CO2 from ship emissions
44
9
CO2av
CO2 from aircraft emissions
44
10
CO2ch
CO2 from chemical source
44
11
CO2corr
CO2 chemical source surface correction
44
For a full tagged CO2 simulation, you can add the following tracers.
NOTE: These extra tracers are only valid for a 2 x 2.5 simulation.
12
CO2bg
CO2 background (including only fossil fuel CO2)
44
13-52
CO2xx
CO2 tracers produced in various geographic regions
44
53
CO2se
CO2 from shipping
44
54
CO2av
CO2 from aviation
44

A1.4 CH4 simulations
Christopher Pickett-Heaps and Kevin Wecht updated the CH4 simulation in GEOS - Chem v8 - 02 - 03. Kevin Wecht has further refined the CH4 simulation since then.
For more information, please see:
   1. Chapter 6.1.8: Checklist for a CH4 offline simulation
   2. GEOS - Chem Wiki: CH4 simulation
#
Name
Description
g/mole
1
CH4
Total CH4
16
2
CH4og
CH4 produced by oil & gas processing
16
3
CH4cm
CH4 produced by coal mining
16
4
CH4ls
CH4 produced by livestock
16
5
CH4wa
CH4 produced by waste
16
6
CH4bf
CH4 produced by biofuel
16
7
CH4ri
CH4 produced by rice
16
8
CH4an
CH4 produced by other anthropogenic processes
16
9
CH4bb
CH4 produced by biomass burning
16
10
CH4we
CH4 produced by wetlands
16
11
CH4sa
CH4 produced by soil absorption
16
12
CH4nat
CH4 produced by other natural sources
16

A1.5 Total Hg and Tagged Hg simulations
You can peform the following GEOS - Chem mercury simulations:
   1. Simulation with the total Hg0, Hg2, and HgP tracers only, with or without the Global Terrestrial Mercury Model option.
   2. Simulation with all tagged Hg0, Hg2, and HgP tracers.
For more information, please see:
   1. Chapter 6.1.7: Checklist for Total Hg and Tagged Hg simulations
   2. GEOS - Chem Wiki: Mercury simulation
   3. GEOS - Chem Wiki: Global Terrestrial Mercury Model
#
Name
Description
g/mole
1
Hg0
Elemental mercury (total tracer) 
201
2
Hg2
Divalent mercury (total tracer)
201
3
HgP
Particulate mercury (total tracer)
201
4
Hg0_an_na
Elemental Mercury (anthro N. Am. tagged tracer)
201
5
Hg0_an_eu
Elemental Mercury (anthro Europe tagged tracer)
201
6
Hg0_an_as
Elemental Mercury (anthro Asia. tagged tracer)
201
7
Hg0_an_rw
Elemental Mercury (anthro rest-of-world tagged tracer)
201
8
Hg0_oc
Elemental Mercury (oceanic tagged tracer)
201
9
Hg0_ln
Elemental Mercury (land re-emission tagged tracer)
201
10
Hg0_nt
Elemental Mercury (natural land source tagged tracer)
201
11
Hg2_an_na
Divalent Mercury (anthro N. Am. tagged tracer)
201
12
Hg2_an_eu
Divalent Mercury (anthro Europe tagged tracer)
201
13
Hg2_an_as
Divalent Mercury (anthro Asia. tagged tracer)
201
14
Hg2_an_rw
Divalent Mercury (anthro rest-of-world tagged tracer)
201
15
Hg2_oc
Divalent Mercury (oceanic tagged tracer)
201
16
Hg2_ln
Divalent Mercury (land re-emission tagged tracer)
201
17
Hg2_nt
Divalent Mercury (natural land source tagged tracer)
201
18
HgP_an_na
Particulate Mercury (anthro N. Am. tagged tracer)
201
19
HgP_an_eu
Particulate Mercury (anthro Europe tagged tracer)
201
20
HgP_an_as
Particulate Mercury (anthro Asia. tagged tracer)
201
21
HgP_an_rw
Particulate Mercury (anthro rest-of-world tagged tracer)
201
22
HgP_oc
Particulate Mercury (oceanic tagged tracer)
201
23
HgP_ln
Particulate Mercury (land re-emission tagged tracer)
201
24
HgP_nt
Particulate Mercury (natural land source tagged tracer)
201

A1.6 Tagged CO simulations
Several GEOS - Chem users have customized the tagged CO simulation to their own purposes. Listed below is the "standard" Tagged CO configuration. 
For more information, please see:
   1. Chapter 6.1.4: Checklist for tagged CO simulation
   2. GEOS - Chem Wiki: Tagged CO simulation
#
Name
Description
g/mole
1
CO
Total CO
28
2
COus
CO from US fossil fuel emissions
28
3
COeur
CO from European fossil fuel emissions
28
4
COasia
CO from Asian fossil fuel emissions
28
5
COoth
CO from fossil fuel emissions -- rest of world
28
6
CObbAm
CO from South American biomass burning
28
7
CObbAf
CO from African biomass burning
28
8
CObbAs
CO from SE Asian biomass burning
28
9
CObbOc
CO from Oceania biomass burning
28
10
CObbEu
CO from European biomass burning
28
11
CObbNA
CO from North American biomass burning
28
12
COch4
CO chemically produced from methane oxidation
28
13
CObiof
CO from biofuel burning (whole world)
28
14
COisop
CO chemically produced from isoprene oxidation
28
15
COmono
CO chemically produced from monoterpenes oxidation
28
16
COmeoh
CO chemically produced from methanol oxidation
28
17
COacet
CO chemically produced from acetone oxidation
28

A1.7 Tagged Ox simulations
NOTE: We shall update the tagged Ox simulation in the version following v9 - 01 - 03.
For more information, please see:
   1. Chapter 6.1.3: Checklist for Tagged Ox simulation
   2. GEOS - Chem Wiki: Tagged Ox simulation
#
Name
Description
g/mole
1
Ox
Total Ox (O3 + NO2 + 2NO3)
46
2
OxUT
Ox produced in the upper troposphere (above 350 hPa)
46
3
OxMT
Ox produced in the middle troposphere (PBL top  -  350 hPa)
46
4
OxROW
Ox produced in the rest of the world
46
5
OxPcBL
Ox produced in the Pacific Ocean boundary layer
46
6
OxNABL
Ox produced in the North American boundary layer
46
7
OxAtBL
Ox produced in the Atlantic Ocean boundary layer
46
8
OxEuBL
Ox produced in the European boundary layer
46
9
OxAfBL
Ox produced in the African boundary layer
46
10
OxAsBl
Ox produced in the Asian boundary layer
46
11
OxStrt
Ox produced in the stratosphere
46
12
OxInit
Ox from the initial condition
46
13
OxUSA
Ox produced over the United States (surface  -  tropopause)
46

A1.8 Rn - Pb - Be simulations
We recommend that you run a RnPbBe simulation whenever you modify the convective updraft scavenging or wet deposition algoritms. For more information about this simulation, please see:
   1. Chapter 6.1.2: Checklist for Radon - Lead - Beryllium simulation
   2. GEOS - Chem Wiki: Rn - Pb - Be simulation
#
Name
Description
g/mole
1
Rn222
Radon-222 isotope
222
2
Pb210
Lead-210 isotope
210
3
Be7
Beryllium-7 isotope
7

A1.9 H2 and HD simulation
The H2/HD simulation has not been used very much recently. If you wish to use this simulation, you will have to invest some time in bringing it back to the state of the science.
   1. Chapter 6.1.5: Checklist for H2 - HD simulation
#
Name
Description
g/mole
1
H2
Divalent hydrogen 
2
2
HD
Deuterium
2.0135

A1.10 CH3I simulations
The CH3I simulation has not been used very much recently. If you wish to use this simulation, you will have to invest some time in bringing it back to the state of the science.
#
Name
Description
g/mole
1
CH3I-oc
Methyl iodide from oceans
141.939
2
CH3I-bb
Methyl iodide from biomass burning
141.939
3
CH3I-bf
Methyl iodide from biofuel burning
141.939
4
CH3I-rc
Methyl iodide from rice paddies
141.939
5
CH3I-wl
Methyl iodide from wetlands
141.939

A1.11 HCN simulations
The HCN simulation has not been used very much recently. If you wish to use this simulation, you will have to invest some time in bringing it back to the state of the science.
#
Name
Description
g/mole
1
HCN
Hydrogen Cyanide
27

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 2
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 2: GEOS - Chem Horizontal Coordinates
We compare the horizontal grids for the met fields that are used to drive GEOS - Chem.

A2.1 GCAP 4° x 5° horizontal grid
          
GCAP 4° x 5° horizontal grid (detail of SE Asia region)
GCAP 4° x 5° longitude edges:
 -182.500 -177.500 -172.500 -167.500 -162.500 -157.500 -152.500 -147.500
 -142.500 -137.500 -132.500 -127.500 -122.500 -117.500 -112.500 -107.500
 -102.500  -97.500  -92.500  -87.500  -82.500  -77.500  -72.500  -67.500
  -62.500  -57.500  -52.500  -47.500  -42.500  -37.500  -32.500  -27.500
  -22.500  -17.500  -12.500   -7.500   -2.500    2.500    7.500   12.500
   17.500   22.500   27.500   32.500   37.500   42.500   47.500   52.500
   57.500   62.500   67.500   72.500   77.500   82.500   87.500   92.500
   97.500  102.500  107.500  112.500  117.500  122.500  127.500  132.500
  137.500  142.500  147.500  152.500  157.500  162.500  167.500  172.500
  177.500
GCAP 4° x 5° longitude centers:
 -180.000 -175.000 -170.000 -165.000 -160.000 -155.000 -150.000 -145.000
 -140.000 -135.000 -130.000 -125.000 -120.000 -115.000 -110.000 -105.000
 -100.000  -95.000  -90.000  -85.000  -80.000  -75.000  -70.000  -65.000
  -60.000  -55.000  -50.000  -45.000  -40.000  -35.000  -30.000  -25.000
  -20.000  -15.000  -10.000   -5.000    0.000    5.000   10.000   15.000
   20.000   25.000   30.000   35.000   40.000   45.000   50.000   55.000
   60.000   65.000   70.000   75.000   80.000   85.000   90.000   95.000
  100.000  105.000  110.000  115.000  120.000  125.000  130.000  135.000
  140.000  145.000  150.000  155.000  160.000  165.000  170.000  175.000
GCAP 4° x 5° latitude edges :
  -90.000  -86.000  -82.000  -78.000  -74.000  -70.000  -66.000  -62.000
  -58.000  -54.000  -50.000  -46.000  -42.000  -38.000  -34.000  -30.000
  -26.000  -22.000  -18.000  -14.000  -10.000   -6.000   -2.000    2.000
    6.000   10.000   14.000   18.000   22.000   26.000   30.000   34.000
   38.000   42.000   46.000   50.000   54.000   58.000   62.000   66.000
   70.000   74.000   78.000   82.000   86.000   90.000
GCAP 4° x 5° latitude centers:
  -88.000  -84.000  -80.000  -76.000  -72.000  -68.000  -64.000  -60.000
  -56.000  -52.000  -48.000  -44.000  -40.000  -36.000  -32.000  -28.000
  -24.000  -20.000  -16.000  -12.000   -8.000   -4.000    0.000    4.000
    8.000   12.000   16.000   20.000   24.000   28.000   32.000   36.000
   40.000   44.000   48.000   52.000   56.000   60.000   64.000   68.000
   72.000   76.000   80.000   84.000   88.000

A2.2 GMAO 4° x 5° horizontal grid
          
GMAO 4° x 5° horizontal grid (detail of SE Asia region)
GMAO 4° x 5° longitude edges: 
 -182.500 -177.500 -172.500 -167.500 -162.500 -157.500 -152.500 -147.500
 -142.500 -137.500 -132.500 -127.500 -122.500 -117.500 -112.500 -107.500
 -102.500  -97.500  -92.500  -87.500  -82.500  -77.500  -72.500  -67.500
  -62.500  -57.500  -52.500  -47.500  -42.500  -37.500  -32.500  -27.500
  -22.500  -17.500  -12.500   -7.500   -2.500    2.500    7.500   12.500
   17.500   22.500   27.500   32.500   37.500   42.500   47.500   52.500
   57.500   62.500   67.500   72.500   77.500   82.500   87.500   92.500
   97.500  102.500  107.500  112.500  117.500  122.500  127.500  132.500
  137.500  142.500  147.500  152.500  157.500  162.500  167.500  172.500
  177.500
GMAO 4° x 5° longitude centers: 
 -180.000 -175.000 -170.000 -165.000 -160.000 -155.000 -150.000 -145.000
 -140.000 -135.000 -130.000 -125.000 -120.000 -115.000 -110.000 -105.000
 -100.000  -95.000  -90.000  -85.000  -80.000  -75.000  -70.000  -65.000
  -60.000  -55.000  -50.000  -45.000  -40.000  -35.000  -30.000  -25.000
  -20.000  -15.000  -10.000   -5.000    0.000    5.000   10.000   15.000
   20.000   25.000   30.000   35.000   40.000   45.000   50.000   55.000
   60.000   65.000   70.000   75.000   80.000   85.000   90.000   95.000
  100.000  105.000  110.000  115.000  120.000  125.000  130.000  135.000
  140.000  145.000  150.000  155.000  160.000  165.000  170.000  175.000
GMAO 4° x 5° latitude edges: 
  -90.000  -88.000  -84.000  -80.000  -76.000  -72.000  -68.000  -64.000
  -60.000  -56.000  -52.000  -48.000  -44.000  -40.000  -36.000  -32.000
  -28.000  -24.000  -20.000  -16.000  -12.000   -8.000   -4.000    0.000
    4.000    8.000   12.000   16.000   20.000   24.000   28.000   32.000
   36.000   40.000   44.000   48.000   52.000   56.000   60.000   64.000
   68.000   72.000   76.000   80.000   84.000   88.000   90.000
GMAO 4° x 5° latitude centers: 
  -89.000  -86.000  -82.000  -78.000  -74.000  -70.000  -66.000  -62.000
  -58.000  -54.000  -50.000  -46.000  -42.000  -38.000  -34.000  -30.000
  -26.000  -22.000  -18.000  -14.000  -10.000   -6.000   -2.000    2.000
    6.000   10.000   14.000   18.000   22.000   26.000   30.000   34.000
   38.000   42.000   46.000   50.000   54.000   58.000   62.000   66.000
   70.000   74.000   78.000   82.000   86.000   89.000

A2.3 GMAO 2° x 2.5° horizontal grid 
         
GMAO 2° x 2.5° horizontal grid (detail of SE Asia region)
GMAO 2° x 2.5° longitude edges:
 -181.250 -178.750 -176.250 -173.750 -171.250 -168.750 -166.250 -163.750
 -161.250 -158.750 -156.250 -153.750 -151.250 -148.750 -146.250 -143.750
 -141.250 -138.750 -136.250 -133.750 -131.250 -128.750 -126.250 -123.750
 -121.250 -118.750 -116.250 -113.750 -111.250 -108.750 -106.250 -103.750
 -101.250  -98.750  -96.250  -93.750  -91.250  -88.750  -86.250  -83.750
  -81.250  -78.750  -76.250  -73.750  -71.250  -68.750  -66.250  -63.750
  -61.250  -58.750  -56.250  -53.750  -51.250  -48.750  -46.250  -43.750
  -41.250  -38.750  -36.250  -33.750  -31.250  -28.750  -26.250  -23.750
  -21.250  -18.750  -16.250  -13.750  -11.250   -8.750   -6.250   -3.750
   -1.250    1.250    3.750    6.250    8.750   11.250   13.750   16.250
   18.750   21.250   23.750   26.250   28.750   31.250   33.750   36.250
   38.750   41.250   43.750   46.250   48.750   51.250   53.750   56.250
   58.750   61.250   63.750   66.250   68.750   71.250   73.750   76.250
   78.750   81.250   83.750   86.250   88.750   91.250   93.750   96.250
   98.750  101.250  103.750  106.250  108.750  111.250  113.750  116.250
  118.750  121.250  123.750  126.250  128.750  131.250  133.750  136.250
  138.750  141.250  143.750  146.250  148.750  151.250  153.750  156.250
  158.750  161.250  163.750  166.250  168.750  171.250  173.750  176.250
  178.750
GMAO 2° x 2.5° longitude centers:
 -180.000 -177.500 -175.000 -172.500 -170.000 -167.500 -165.000 -162.500
 -160.000 -157.500 -155.000 -152.500 -150.000 -147.500 -145.000 -142.500
 -140.000 -137.500 -135.000 -132.500 -130.000 -127.500 -125.000 -122.500
 -120.000 -117.500 -115.000 -112.500 -110.000 -107.500 -105.000 -102.500
 -100.000  -97.500  -95.000  -92.500  -90.000  -87.500  -85.000  -82.500
  -80.000  -77.500  -75.000  -72.500  -70.000  -67.500  -65.000  -62.500
  -60.000  -57.500  -55.000  -52.500  -50.000  -47.500  -45.000  -42.500
  -40.000  -37.500  -35.000  -32.500  -30.000  -27.500  -25.000  -22.500
  -20.000  -17.500  -15.000  -12.500  -10.000   -7.500   -5.000   -2.500
    0.000    2.500    5.000    7.500   10.000   12.500   15.000   17.500
   20.000   22.500   25.000   27.500   30.000   32.500   35.000   37.500
   40.000   42.500   45.000   47.500   50.000   52.500   55.000   57.500
   60.000   62.500   65.000   67.500   70.000   72.500   75.000   77.500
   80.000   82.500   85.000   87.500   90.000   92.500   95.000   97.500
  100.000  102.500  105.000  107.500  110.000  112.500  115.000  117.500
  120.000  122.500  125.000  127.500  130.000  132.500  135.000  137.500
  140.000  142.500  145.000  147.500  150.000  152.500  155.000  157.500
  160.000  162.500  165.000  167.500  170.000  172.500  175.000  177.500
GMAO 2° x 2.5° latitude edges:
  -90.000  -89.000  -87.000  -85.000  -83.000  -81.000  -79.000  -77.000
  -75.000  -73.000  -71.000  -69.000  -67.000  -65.000  -63.000  -61.000
  -59.000  -57.000  -55.000  -53.000  -51.000  -49.000  -47.000  -45.000
  -43.000  -41.000  -39.000  -37.000  -35.000  -33.000  -31.000  -29.000
  -27.000  -25.000  -23.000  -21.000  -19.000  -17.000  -15.000  -13.000
  -11.000   -9.000   -7.000   -5.000   -3.000   -1.000    1.000    3.000
    5.000    7.000    9.000   11.000   13.000   15.000   17.000   19.000
   21.000   23.000   25.000   27.000   29.000   31.000   33.000   35.000
   37.000   39.000   41.000   43.000   45.000   47.000   49.000   51.000
   53.000   55.000   57.000   59.000   61.000   63.000   65.000   67.000
   69.000   71.000   73.000   75.000   77.000   79.000   81.000   83.000
   85.000   87.000   89.000   90.000
GMAO 2° x 2.5° latitude centers:
  -89.500  -88.000  -86.000  -84.000  -82.000  -80.000  -78.000  -76.000
  -74.000  -72.000  -70.000  -68.000  -66.000  -64.000  -62.000  -60.000
  -58.000  -56.000  -54.000  -52.000  -50.000  -48.000  -46.000  -44.000
  -42.000  -40.000  -38.000  -36.000  -34.000  -32.000  -30.000  -28.000
  -26.000  -24.000  -22.000  -20.000  -18.000  -16.000  -14.000  -12.000
  -10.000   -8.000   -6.000   -4.000   -2.000    0.000    2.000    4.000
    6.000    8.000   10.000   12.000   14.000   16.000   18.000   20.000
   22.000   24.000   26.000   28.000   30.000   32.000   34.000   36.000
   38.000   40.000   42.000   44.000   46.000   48.000   50.000   52.000
   54.000   56.000   58.000   60.000   62.000   64.000   66.000   68.000
   70.000   72.000   74.000   76.000   78.000   80.000   82.000   84.000
   86.000   88.000   89.500

A2.4 GMAO 1° x 1.25° horizontal grid
        
GMAO 1 ° x 1.25° horizontal grid (detail of SE Asia region)
This is the native horizontal resolution of the GMAO GEOS - 4 meteorological fields. Some individual MERRA meterological fields also have this native horizontal resolution.
GMAO 1° x 1.25° longitude edges: 
 -180.625 -179.375 -178.125 -176.875 -175.625 -174.375 -173.125 -171.875
 -170.625 -169.375 -168.125 -166.875 -165.625 -164.375 -163.125 -161.875
 -160.625 -159.375 -158.125 -156.875 -155.625 -154.375 -153.125 -151.875
 -150.625 -149.375 -148.125 -146.875 -145.625 -144.375 -143.125 -141.875
 -140.625 -139.375 -138.125 -136.875 -135.625 -134.375 -133.125 -131.875
 -130.625 -129.375 -128.125 -126.875 -125.625 -124.375 -123.125 -121.875
 -120.625 -119.375 -118.125 -116.875 -115.625 -114.375 -113.125 -111.875
 -110.625 -109.375 -108.125 -106.875 -105.625 -104.375 -103.125 -101.875
 -100.625  -99.375  -98.125  -96.875  -95.625  -94.375  -93.125  -91.875
  -90.625  -89.375  -88.125  -86.875  -85.625  -84.375  -83.125  -81.875
  -80.625  -79.375  -78.125  -76.875  -75.625  -74.375  -73.125  -71.875
  -70.625  -69.375  -68.125  -66.875  -65.625  -64.375  -63.125  -61.875
  -60.625  -59.375  -58.125  -56.875  -55.625  -54.375  -53.125  -51.875
  -50.625  -49.375  -48.125  -46.875  -45.625  -44.375  -43.125  -41.875
  -40.625  -39.375  -38.125  -36.875  -35.625  -34.375  -33.125  -31.875
  -30.625  -29.375  -28.125  -26.875  -25.625  -24.375  -23.125  -21.875
  -20.625  -19.375  -18.125  -16.875  -15.625  -14.375  -13.125  -11.875
  -10.625   -9.375   -8.125   -6.875   -5.625   -4.375   -3.125   -1.875
   -0.625    0.625    1.875    3.125    4.375    5.625    6.875    8.125
    9.375   10.625   11.875   13.125   14.375   15.625   16.875   18.125
   19.375   20.625   21.875   23.125   24.375   25.625   26.875   28.125
   29.375   30.625   31.875   33.125   34.375   35.625   36.875   38.125
   39.375   40.625   41.875   43.125   44.375   45.625   46.875   48.125
   49.375   50.625   51.875   53.125   54.375   55.625   56.875   58.125
   59.375   60.625   61.875   63.125   64.375   65.625   66.875   68.125
   69.375   70.625   71.875   73.125   74.375   75.625   76.875   78.125
   79.375   80.625   81.875   83.125   84.375   85.625   86.875   88.125
   89.375   90.625   91.875   93.125   94.375   95.625   96.875   98.125
   99.375  100.625  101.875  103.125  104.375  105.625  106.875  108.125
  109.375  110.625  111.875  113.125  114.375  115.625  116.875  118.125
  119.375  120.625  121.875  123.125  124.375  125.625  126.875  128.125
  129.375  130.625  131.875  133.125  134.375  135.625  136.875  138.125
  139.375  140.625  141.875  143.125  144.375  145.625  146.875  148.125
  149.375  150.625  151.875  153.125  154.375  155.625  156.875  158.125
  159.375  160.625  161.875  163.125  164.375  165.625  166.875  168.125
  169.375  170.625  171.875  173.125  174.375  175.625  176.875  178.125
  179.375
GMAO 1° x 1.25° longitude centers: 
 -180.000 -178.750 -177.500 -176.250 -175.000 -173.750 -172.500 -171.250
 -170.000 -168.750 -167.500 -166.250 -165.000 -163.750 -162.500 -161.250
 -160.000 -158.750 -157.500 -156.250 -155.000 -153.750 -152.500 -151.250
 -150.000 -148.750 -147.500 -146.250 -145.000 -143.750 -142.500 -141.250
 -140.000 -138.750 -137.500 -136.250 -135.000 -133.750 -132.500 -131.250
 -130.000 -128.750 -127.500 -126.250 -125.000 -123.750 -122.500 -121.250
 -120.000 -118.750 -117.500 -116.250 -115.000 -113.750 -112.500 -111.250
 -110.000 -108.750 -107.500 -106.250 -105.000 -103.750 -102.500 -101.250
 -100.000  -98.750  -97.500  -96.250  -95.000  -93.750  -92.500  -91.250
  -90.000  -88.750  -87.500  -86.250  -85.000  -83.750  -82.500  -81.250
  -80.000  -78.750  -77.500  -76.250  -75.000  -73.750  -72.500  -71.250
  -70.000  -68.750  -67.500  -66.250  -65.000  -63.750  -62.500  -61.250
  -60.000  -58.750  -57.500  -56.250  -55.000  -53.750  -52.500  -51.250
  -50.000  -48.750  -47.500  -46.250  -45.000  -43.750  -42.500  -41.250
  -40.000  -38.750  -37.500  -36.250  -35.000  -33.750  -32.500  -31.250
  -30.000  -28.750  -27.500  -26.250  -25.000  -23.750  -22.500  -21.250
  -20.000  -18.750  -17.500  -16.250  -15.000  -13.750  -12.500  -11.250
  -10.000   -8.750   -7.500   -6.250   -5.000   -3.750   -2.500   -1.250
    0.000    1.250    2.500    3.750    5.000    6.250    7.500    8.750
   10.000   11.250   12.500   13.750   15.000   16.250   17.500   18.750
   20.000   21.250   22.500   23.750   25.000   26.250   27.500   28.750
   30.000   31.250   32.500   33.750   35.000   36.250   37.500   38.750
   40.000   41.250   42.500   43.750   45.000   46.250   47.500   48.750
   50.000   51.250   52.500   53.750   55.000   56.250   57.500   58.750
   60.000   61.250   62.500   63.750   65.000   66.250   67.500   68.750
   70.000   71.250   72.500   73.750   75.000   76.250   77.500   78.750
   80.000   81.250   82.500   83.750   85.000   86.250   87.500   88.750
   90.000   91.250   92.500   93.750   95.000   96.250   97.500   98.750
  100.000  101.250  102.500  103.750  105.000  106.250  107.500  108.750
  110.000  111.250  112.500  113.750  115.000  116.250  117.500  118.750
  120.000  121.250  122.500  123.750  125.000  126.250  127.500  128.750
  130.000  131.250  132.500  133.750  135.000  136.250  137.500  138.750
  140.000  141.250  142.500  143.750  145.000  146.250  147.500  148.750
  150.000  151.250  152.500  153.750  155.000  156.250  157.500  158.750
  160.000  161.250  162.500  163.750  165.000  166.250  167.500  168.750
  170.000  171.250  172.500  173.750  175.000  176.250  177.500  178.750
GMAO 1° x 1.25° latitude edges: 
  -90.000  -89.500  -88.500  -87.500  -86.500  -85.500  -84.500  -83.500
  -82.500  -81.500  -80.500  -79.500  -78.500  -77.500  -76.500  -75.500
  -74.500  -73.500  -72.500  -71.500  -70.500  -69.500  -68.500  -67.500
  -66.500  -65.500  -64.500  -63.500  -62.500  -61.500  -60.500  -59.500
  -58.500  -57.500  -56.500  -55.500  -54.500  -53.500  -52.500  -51.500
  -50.500  -49.500  -48.500  -47.500  -46.500  -45.500  -44.500  -43.500
  -42.500  -41.500  -40.500  -39.500  -38.500  -37.500  -36.500  -35.500
  -34.500  -33.500  -32.500  -31.500  -30.500  -29.500  -28.500  -27.500
  -26.500  -25.500  -24.500  -23.500  -22.500  -21.500  -20.500  -19.500
  -18.500  -17.500  -16.500  -15.500  -14.500  -13.500  -12.500  -11.500
  -10.500   -9.500   -8.500   -7.500   -6.500   -5.500   -4.500   -3.500
   -2.500   -1.500   -0.500    0.500    1.500    2.500    3.500    4.500
    5.500    6.500    7.500    8.500    9.500   10.500   11.500   12.500
   13.500   14.500   15.500   16.500   17.500   18.500   19.500   20.500
   21.500   22.500   23.500   24.500   25.500   26.500   27.500   28.500
   29.500   30.500   31.500   32.500   33.500   34.500   35.500   36.500
   37.500   38.500   39.500   40.500   41.500   42.500   43.500   44.500
   45.500   46.500   47.500   48.500   49.500   50.500   51.500   52.500
   53.500   54.500   55.500   56.500   57.500   58.500   59.500   60.500
   61.500   62.500   63.500   64.500   65.500   66.500   67.500   68.500
   69.500   70.500   71.500   72.500   73.500   74.500   75.500   76.500
   77.500   78.500   79.500   80.500   81.500   82.500   83.500   84.500
   85.500   86.500   87.500   88.500   89.500   90.000
GMAO 1° x 1.25° latitude centers: 
  -89.750  -89.000  -88.000  -87.000  -86.000  -85.000  -84.000  -83.000
  -82.000  -81.000  -80.000  -79.000  -78.000  -77.000  -76.000  -75.000
  -74.000  -73.000  -72.000  -71.000  -70.000  -69.000  -68.000  -67.000
  -66.000  -65.000  -64.000  -63.000  -62.000  -61.000  -60.000  -59.000
  -58.000  -57.000  -56.000  -55.000  -54.000  -53.000  -52.000  -51.000
  -50.000  -49.000  -48.000  -47.000  -46.000  -45.000  -44.000  -43.000
  -42.000  -41.000  -40.000  -39.000  -38.000  -37.000  -36.000  -35.000
  -34.000  -33.000  -32.000  -31.000  -30.000  -29.000  -28.000  -27.000
  -26.000  -25.000  -24.000  -23.000  -22.000  -21.000  -20.000  -19.000
  -18.000  -17.000  -16.000  -15.000  -14.000  -13.000  -12.000  -11.000
  -10.000   -9.000   -8.000   -7.000   -6.000   -5.000   -4.000   -3.000
   -2.000   -1.000    0.000    1.000    2.000    3.000    4.000    5.000
    6.000    7.000    8.000    9.000   10.000   11.000   12.000   13.000
   14.000   15.000   16.000   17.000   18.000   19.000   20.000   21.000
   22.000   23.000   24.000   25.000   26.000   27.000   28.000   29.000
   30.000   31.000   32.000   33.000   34.000   35.000   36.000   37.000
   38.000   39.000   40.000   41.000   42.000   43.000   44.000   45.000
   46.000   47.000   48.000   49.000   50.000   51.000   52.000   53.000
   54.000   55.000   56.000   57.000   58.000   59.000   60.000   61.000
   62.000   63.000   64.000   65.000   66.000   67.000   68.000   69.000
   70.000   71.000   72.000   73.000   74.000   75.000   76.000   77.000
   78.000   79.000   80.000   81.000   82.000   83.000   84.000   85.000
   86.000   87.000   88.000   89.000   89.750

A2.5 GMAO 1° x 1° horizontal grid
            
GEOS - Chem 1° x 1° Grid (detail of SE Asia region)
This is the native horizontal resolution of the GMAO GEOS - 3 meteorological fields.
NOTE: The 1° x 1° GEOS - 3 nested grid simulations are now obsolete and have been replaced by the 0.5° x 0.666° GEOS - 5 nested grid simulations for China/SE Asia, North America, and Europe.
GMAO 1° x 1° longitude edges:
 -180.500 -179.500 -178.500 -177.500 -176.500 -175.500 -174.500 -173.500
 -172.500 -171.500 -170.500 -169.500 -168.500 -167.500 -166.500 -165.500
 -164.500 -163.500 -162.500 -161.500 -160.500 -159.500 -158.500 -157.500
 -156.500 -155.500 -154.500 -153.500 -152.500 -151.500 -150.500 -149.500
 -148.500 -147.500 -146.500 -145.500 -144.500 -143.500 -142.500 -141.500
 -140.500 -139.500 -138.500 -137.500 -136.500 -135.500 -134.500 -133.500
 -132.500 -131.500 -130.500 -129.500 -128.500 -127.500 -126.500 -125.500
 -124.500 -123.500 -122.500 -121.500 -120.500 -119.500 -118.500 -117.500
 -116.500 -115.500 -114.500 -113.500 -112.500 -111.500 -110.500 -109.500
 -108.500 -107.500 -106.500 -105.500 -104.500 -103.500 -102.500 -101.500
 -100.500  -99.500  -98.500  -97.500  -96.500  -95.500  -94.500  -93.500
  -92.500  -91.500  -90.500  -89.500  -88.500  -87.500  -86.500  -85.500
  -84.500  -83.500  -82.500  -81.500  -80.500  -79.500  -78.500  -77.500
  -76.500  -75.500  -74.500  -73.500  -72.500  -71.500  -70.500  -69.500
  -68.500  -67.500  -66.500  -65.500  -64.500  -63.500  -62.500  -61.500
  -60.500  -59.500  -58.500  -57.500  -56.500  -55.500  -54.500  -53.500
  -52.500  -51.500  -50.500  -49.500  -48.500  -47.500  -46.500  -45.500
  -44.500  -43.500  -42.500  -41.500  -40.500  -39.500  -38.500  -37.500
  -36.500  -35.500  -34.500  -33.500  -32.500  -31.500  -30.500  -29.500
  -28.500  -27.500  -26.500  -25.500  -24.500  -23.500  -22.500  -21.500
  -20.500  -19.500  -18.500  -17.500  -16.500  -15.500  -14.500  -13.500
  -12.500  -11.500  -10.500   -9.500   -8.500   -7.500   -6.500   -5.500
   -4.500   -3.500   -2.500   -1.500   -0.500    0.500    1.500    2.500
    3.500    4.500    5.500    6.500    7.500    8.500    9.500   10.500
   11.500   12.500   13.500   14.500   15.500   16.500   17.500   18.500
   19.500   20.500   21.500   22.500   23.500   24.500   25.500   26.500
   27.500   28.500   29.500   30.500   31.500   32.500   33.500   34.500
   35.500   36.500   37.500   38.500   39.500   40.500   41.500   42.500
   43.500   44.500   45.500   46.500   47.500   48.500   49.500   50.500
   51.500   52.500   53.500   54.500   55.500   56.500   57.500   58.500
   59.500   60.500   61.500   62.500   63.500   64.500   65.500   66.500
   67.500   68.500   69.500   70.500   71.500   72.500   73.500   74.500
   75.500   76.500   77.500   78.500   79.500   80.500   81.500   82.500
   83.500   84.500   85.500   86.500   87.500   88.500   89.500   90.500
   91.500   92.500   93.500   94.500   95.500   96.500   97.500   98.500
   99.500  100.500  101.500  102.500  103.500  104.500  105.500  106.500
  107.500  108.500  109.500  110.500  111.500  112.500  113.500  114.500
  115.500  116.500  117.500  118.500  119.500  120.500  121.500  122.500
  123.500  124.500  125.500  126.500  127.500  128.500  129.500  130.500
  131.500  132.500  133.500  134.500  135.500  136.500  137.500  138.500
  139.500  140.500  141.500  142.500  143.500  144.500  145.500  146.500
  147.500  148.500  149.500  150.500  151.500  152.500  153.500  154.500
  155.500  156.500  157.500  158.500  159.500  160.500  161.500  162.500
  163.500  164.500  165.500  166.500  167.500  168.500  169.500  170.500
  171.500  172.500  173.500  174.500  175.500  176.500  177.500  178.500
  179.500
GMAO 1° x 1° longitude centers:
 -180.000 -179.000 -178.000 -177.000 -176.000 -175.000 -174.000 -173.000
 -172.000 -171.000 -170.000 -169.000 -168.000 -167.000 -166.000 -165.000
 -164.000 -163.000 -162.000 -161.000 -160.000 -159.000 -158.000 -157.000
 -156.000 -155.000 -154.000 -153.000 -152.000 -151.000 -150.000 -149.000
 -148.000 -147.000 -146.000 -145.000 -144.000 -143.000 -142.000 -141.000
 -140.000 -139.000 -138.000 -137.000 -136.000 -135.000 -134.000 -133.000
 -132.000 -131.000 -130.000 -129.000 -128.000 -127.000 -126.000 -125.000
 -124.000 -123.000 -122.000 -121.000 -120.000 -119.000 -118.000 -117.000
 -116.000 -115.000 -114.000 -113.000 -112.000 -111.000 -110.000 -109.000
 -108.000 -107.000 -106.000 -105.000 -104.000 -103.000 -102.000 -101.000
 -100.000  -99.000  -98.000  -97.000  -96.000  -95.000  -94.000  -93.000
  -92.000  -91.000  -90.000  -89.000  -88.000  -87.000  -86.000  -85.000
  -84.000  -83.000  -82.000  -81.000  -80.000  -79.000  -78.000  -77.000
  -76.000  -75.000  -74.000  -73.000  -72.000  -71.000  -70.000  -69.000
  -68.000  -67.000  -66.000  -65.000  -64.000  -63.000  -62.000  -61.000
  -60.000  -59.000  -58.000  -57.000  -56.000  -55.000  -54.000  -53.000
  -52.000  -51.000  -50.000  -49.000  -48.000  -47.000  -46.000  -45.000
  -44.000  -43.000  -42.000  -41.000  -40.000  -39.000  -38.000  -37.000
  -36.000  -35.000  -34.000  -33.000  -32.000  -31.000  -30.000  -29.000
  -28.000  -27.000  -26.000  -25.000  -24.000  -23.000  -22.000  -21.000
  -20.000  -19.000  -18.000  -17.000  -16.000  -15.000  -14.000  -13.000
  -12.000  -11.000  -10.000   -9.000   -8.000   -7.000   -6.000   -5.000
   -4.000   -3.000   -2.000   -1.000    0.000    1.000    2.000    3.000
    4.000    5.000    6.000    7.000    8.000    9.000   10.000   11.000
   12.000   13.000   14.000   15.000   16.000   17.000   18.000   19.000
   20.000   21.000   22.000   23.000   24.000   25.000   26.000   27.000
   28.000   29.000   30.000   31.000   32.000   33.000   34.000   35.000
   36.000   37.000   38.000   39.000   40.000   41.000   42.000   43.000
   44.000   45.000   46.000   47.000   48.000   49.000   50.000   51.000
   52.000   53.000   54.000   55.000   56.000   57.000   58.000   59.000
   60.000   61.000   62.000   63.000   64.000   65.000   66.000   67.000
   68.000   69.000   70.000   71.000   72.000   73.000   74.000   75.000
   76.000   77.000   78.000   79.000   80.000   81.000   82.000   83.000
   84.000   85.000   86.000   87.000   88.000   89.000   90.000   91.000
   92.000   93.000   94.000   95.000   96.000   97.000   98.000   99.000
  100.000  101.000  102.000  103.000  104.000  105.000  106.000  107.000
  108.000  109.000  110.000  111.000  112.000  113.000  114.000  115.000
  116.000  117.000  118.000  119.000  120.000  121.000  122.000  123.000
  124.000  125.000  126.000  127.000  128.000  129.000  130.000  131.000
  132.000  133.000  134.000  135.000  136.000  137.000  138.000  139.000
  140.000  141.000  142.000  143.000  144.000  145.000  146.000  147.000
  148.000  149.000  150.000  151.000  152.000  153.000  154.000  155.000
  156.000  157.000  158.000  159.000  160.000  161.000  162.000  163.000
  164.000  165.000  166.000  167.000  168.000  169.000  170.000  171.000
  172.000  173.000  174.000  175.000  176.000  177.000  178.000  179.000
GMAO 1° x 1° latitude edges:
  -90.000  -89.500  -88.500  -87.500  -86.500  -85.500  -84.500  -83.500
  -82.500  -81.500  -80.500  -79.500  -78.500  -77.500  -76.500  -75.500
  -74.500  -73.500  -72.500  -71.500  -70.500  -69.500  -68.500  -67.500
  -66.500  -65.500  -64.500  -63.500  -62.500  -61.500  -60.500  -59.500
  -58.500  -57.500  -56.500  -55.500  -54.500  -53.500  -52.500  -51.500
  -50.500  -49.500  -48.500  -47.500  -46.500  -45.500  -44.500  -43.500
  -42.500  -41.500  -40.500  -39.500  -38.500  -37.500  -36.500  -35.500
  -34.500  -33.500  -32.500  -31.500  -30.500  -29.500  -28.500  -27.500
  -26.500  -25.500  -24.500  -23.500  -22.500  -21.500  -20.500  -19.500
  -18.500  -17.500  -16.500  -15.500  -14.500  -13.500  -12.500  -11.500
  -10.500   -9.500   -8.500   -7.500   -6.500   -5.500   -4.500   -3.500
   -2.500   -1.500   -0.500    0.500    1.500    2.500    3.500    4.500
    5.500    6.500    7.500    8.500    9.500   10.500   11.500   12.500
   13.500   14.500   15.500   16.500   17.500   18.500   19.500   20.500
   21.500   22.500   23.500   24.500   25.500   26.500   27.500   28.500
   29.500   30.500   31.500   32.500   33.500   34.500   35.500   36.500
   37.500   38.500   39.500   40.500   41.500   42.500   43.500   44.500
   45.500   46.500   47.500   48.500   49.500   50.500   51.500   52.500
   53.500   54.500   55.500   56.500   57.500   58.500   59.500   60.500
   61.500   62.500   63.500   64.500   65.500   66.500   67.500   68.500
   69.500   70.500   71.500   72.500   73.500   74.500   75.500   76.500
   77.500   78.500   79.500   80.500   81.500   82.500   83.500   84.500
   85.500   86.500   87.500   88.500   89.500   90.000
GMAO 1° x 1° latitude centers:
  -89.750  -89.000  -88.000  -87.000  -86.000  -85.000  -84.000  -83.000
  -82.000  -81.000  -80.000  -79.000  -78.000  -77.000  -76.000  -75.000
  -74.000  -73.000  -72.000  -71.000  -70.000  -69.000  -68.000  -67.000
  -66.000  -65.000  -64.000  -63.000  -62.000  -61.000  -60.000  -59.000
  -58.000  -57.000  -56.000  -55.000  -54.000  -53.000  -52.000  -51.000
  -50.000  -49.000  -48.000  -47.000  -46.000  -45.000  -44.000  -43.000
  -42.000  -41.000  -40.000  -39.000  -38.000  -37.000  -36.000  -35.000
  -34.000  -33.000  -32.000  -31.000  -30.000  -29.000  -28.000  -27.000
  -26.000  -25.000  -24.000  -23.000  -22.000  -21.000  -20.000  -19.000
  -18.000  -17.000  -16.000  -15.000  -14.000  -13.000  -12.000  -11.000
  -10.000   -9.000   -8.000   -7.000   -6.000   -5.000   -4.000   -3.000
   -2.000   -1.000    0.000    1.000    2.000    3.000    4.000    5.000
    6.000    7.000    8.000    9.000   10.000   11.000   12.000   13.000
   14.000   15.000   16.000   17.000   18.000   19.000   20.000   21.000
   22.000   23.000   24.000   25.000   26.000   27.000   28.000   29.000
   30.000   31.000   32.000   33.000   34.000   35.000   36.000   37.000
   38.000   39.000   40.000   41.000   42.000   43.000   44.000   45.000
   46.000   47.000   48.000   49.000   50.000   51.000   52.000   53.000
   54.000   55.000   56.000   57.000   58.000   59.000   60.000   61.000
   62.000   63.000   64.000   65.000   66.000   67.000   68.000   69.000
   70.000   71.000   72.000   73.000   74.000   75.000   76.000   77.000
   78.000   79.000   80.000   81.000   82.000   83.000   84.000   85.000
   86.000   87.000   88.000   89.000   89.750

A2.6 GMAO 0.5° x 0.667° grid 
         
GEOS - Chem 0.5° x 0.667° Grid (detail of SE Asia region)
This is the native horizontal resolution of the GMAO GEOS - 5 meteorological fields. Some individual MERRA meterological fields also have this native horizontal resolution.
0.5° x 0.667° longitude edges:
 -180.333 -179.667 -179.000 -178.333 -177.667 -177.000 -176.333 -175.667
 -175.000 -174.333 -173.667 -173.000 -172.333 -171.667 -171.000 -170.333
 -169.667 -169.000 -168.333 -167.667 -167.000 -166.333 -165.667 -165.000
 -164.333 -163.667 -163.000 -162.333 -161.667 -161.000 -160.333 -159.667
 -159.000 -158.333 -157.667 -157.000 -156.333 -155.667 -155.000 -154.333
 -153.667 -153.000 -152.333 -151.667 -151.000 -150.333 -149.667 -149.000
 -148.333 -147.667 -147.000 -146.333 -145.667 -145.000 -144.333 -143.667
 -143.000 -142.333 -141.667 -141.000 -140.333 -139.667 -139.000 -138.333
 -137.667 -137.000 -136.333 -135.667 -135.000 -134.333 -133.667 -133.000
 -132.333 -131.667 -131.000 -130.333 -129.667 -129.000 -128.333 -127.667
 -127.000 -126.333 -125.667 -125.000 -124.333 -123.667 -123.000 -122.333
 -121.667 -121.000 -120.333 -119.667 -119.000 -118.333 -117.667 -117.000
 -116.333 -115.667 -115.000 -114.333 -113.667 -113.000 -112.333 -111.667
 -111.000 -110.333 -109.667 -109.000 -108.333 -107.667 -107.000 -106.333
 -105.667 -105.000 -104.333 -103.667 -103.000 -102.333 -101.667 -101.000
 -100.333  -99.667  -99.000  -98.333  -97.667  -97.000  -96.333  -95.667
  -95.000  -94.333  -93.667  -93.000  -92.333  -91.667  -91.000  -90.333
  -89.667  -89.000  -88.333  -87.667  -87.000  -86.333  -85.667  -85.000
  -84.333  -83.667  -83.000  -82.333  -81.667  -81.000  -80.333  -79.667
  -79.000  -78.333  -77.667  -77.000  -76.333  -75.667  -75.000  -74.333
  -73.667  -73.000  -72.333  -71.667  -71.000  -70.333  -69.667  -69.000
  -68.333  -67.667  -67.000  -66.333  -65.667  -65.000  -64.333  -63.667
  -63.000  -62.333  -61.667  -61.000  -60.333  -59.667  -59.000  -58.333
  -57.667  -57.000  -56.333  -55.667  -55.000  -54.333  -53.667  -53.000
  -52.333  -51.667  -51.000  -50.333  -49.667  -49.000  -48.333  -47.667
  -47.000  -46.333  -45.667  -45.000  -44.333  -43.667  -43.000  -42.333
  -41.667  -41.000  -40.333  -39.667  -39.000  -38.333  -37.667  -37.000
  -36.333  -35.667  -35.000  -34.333  -33.667  -33.000  -32.333  -31.667
  -31.000  -30.333  -29.667  -29.000  -28.333  -27.667  -27.000  -26.333
  -25.667  -25.000  -24.333  -23.667  -23.000  -22.333  -21.667  -21.000
  -20.333  -19.667  -19.000  -18.333  -17.667  -17.000  -16.333  -15.667
  -15.000  -14.333  -13.667  -13.000  -12.333  -11.667  -11.000  -10.333
   -9.667   -9.000   -8.333   -7.667   -7.000   -6.333   -5.667   -5.000
   -4.333   -3.667   -3.000   -2.333   -1.667   -1.000   -0.333    0.333
    1.000    1.667    2.333    3.000    3.667    4.333    5.000    5.667
    6.333    7.000    7.667    8.333    9.000    9.667   10.333   11.000
   11.667   12.333   13.000   13.667   14.333   15.000   15.667   16.333
   17.000   17.667   18.333   19.000   19.667   20.333   21.000   21.667
   22.333   23.000   23.667   24.333   25.000   25.667   26.333   27.000
   27.667   28.333   29.000   29.667   30.333   31.000   31.667   32.333
   33.000   33.667   34.333   35.000   35.667   36.333   37.000   37.667
   38.333   39.000   39.667   40.333   41.000   41.667   42.333   43.000
   43.667   44.333   45.000   45.667   46.333   47.000   47.667   48.333
   49.000   49.667   50.333   51.000   51.667   52.333   53.000   53.667
   54.333   55.000   55.667   56.333   57.000   57.667   58.333   59.000
   59.667   60.333   61.000   61.667   62.333   63.000   63.667   64.333
   65.000   65.667   66.333   67.000   67.667   68.333   69.000   69.667
   70.333   71.000   71.667   72.333   73.000   73.667   74.333   75.000
   75.667   76.333   77.000   77.667   78.333   79.000   79.667   80.333
   81.000   81.667   82.333   83.000   83.667   84.333   85.000   85.667
   86.333   87.000   87.667   88.333   89.000   89.667   90.333   91.000
   91.667   92.333   93.000   93.667   94.333   95.000   95.667   96.333
   97.000   97.667   98.333   99.000   99.667  100.333  101.000  101.667
  102.333  103.000  103.667  104.333  105.000  105.667  106.333  107.000
  107.667  108.333  109.000  109.667  110.333  111.000  111.667  112.333
  113.000  113.667  114.333  115.000  115.667  116.333  117.000  117.667
  118.333  119.000  119.667  120.333  121.000  121.667  122.333  123.000
  123.667  124.333  125.000  125.667  126.333  127.000  127.667  128.333
  129.000  129.667  130.333  131.000  131.667  132.333  133.000  133.667
  134.333  135.000  135.667  136.333  137.000  137.667  138.333  139.000
  139.667  140.333  141.000  141.667  142.333  143.000  143.667  144.333
  145.000  145.667  146.333  147.000  147.667  148.333  149.000  149.667
  150.333  151.000  151.667  152.333  153.000  153.667  154.333  155.000
  155.667  156.333  157.000  157.667  158.333  159.000  159.667  160.333
  161.000  161.667  162.333  163.000  163.667  164.333  165.000  165.667
  166.333  167.000  167.667  168.333  169.000  169.667  170.333  171.000
  171.667  172.333  173.000  173.667  174.333  175.000  175.667  176.333
  177.000  177.667  178.333  179.000  179.667
0.5° x 0.667° longitude centers:
 -180.000 -179.333 -178.667 -178.000 -177.333 -176.667 -176.000 -175.333
 -174.667 -174.000 -173.333 -172.667 -172.000 -171.333 -170.667 -170.000
 -169.333 -168.667 -168.000 -167.333 -166.667 -166.000 -165.333 -164.667
 -164.000 -163.333 -162.667 -162.000 -161.333 -160.667 -160.000 -159.333
 -158.667 -158.000 -157.333 -156.667 -156.000 -155.333 -154.667 -154.000
 -153.333 -152.667 -152.000 -151.333 -150.667 -150.000 -149.333 -148.667
 -148.000 -147.333 -146.667 -146.000 -145.333 -144.667 -144.000 -143.333
 -142.667 -142.000 -141.333 -140.667 -140.000 -139.333 -138.667 -138.000
 -137.333 -136.667 -136.000 -135.333 -134.667 -134.000 -133.333 -132.667
 -132.000 -131.333 -130.667 -130.000 -129.333 -128.667 -128.000 -127.333
 -126.667 -126.000 -125.333 -124.667 -124.000 -123.333 -122.667 -122.000
 -121.333 -120.667 -120.000 -119.333 -118.667 -118.000 -117.333 -116.667
 -116.000 -115.333 -114.667 -114.000 -113.333 -112.667 -112.000 -111.333
 -110.667 -110.000 -109.333 -108.667 -108.000 -107.333 -106.667 -106.000
 -105.333 -104.667 -104.000 -103.333 -102.667 -102.000 -101.333 -100.667
 -100.000  -99.333  -98.667  -98.000  -97.333  -96.667  -96.000  -95.333
  -94.667  -94.000  -93.333  -92.667  -92.000  -91.333  -90.667  -90.000
  -89.333  -88.667  -88.000  -87.333  -86.667  -86.000  -85.333  -84.667
  -84.000  -83.333  -82.667  -82.000  -81.333  -80.667  -80.000  -79.333
  -78.667  -78.000  -77.333  -76.667  -76.000  -75.333  -74.667  -74.000
  -73.333  -72.667  -72.000  -71.333  -70.667  -70.000  -69.333  -68.667
  -68.000  -67.333  -66.667  -66.000  -65.333  -64.667  -64.000  -63.333
  -62.667  -62.000  -61.333  -60.667  -60.000  -59.333  -58.667  -58.000
  -57.333  -56.667  -56.000  -55.333  -54.667  -54.000  -53.333  -52.667
  -52.000  -51.333  -50.667  -50.000  -49.333  -48.667  -48.000  -47.333
  -46.667  -46.000  -45.333  -44.667  -44.000  -43.333  -42.667  -42.000
  -41.333  -40.667  -40.000  -39.333  -38.667  -38.000  -37.333  -36.667
  -36.000  -35.333  -34.667  -34.000  -33.333  -32.667  -32.000  -31.333
  -30.667  -30.000  -29.333  -28.667  -28.000  -27.333  -26.667  -26.000
  -25.333  -24.667  -24.000  -23.333  -22.667  -22.000  -21.333  -20.667
  -20.000  -19.333  -18.667  -18.000  -17.333  -16.667  -16.000  -15.333
  -14.667  -14.000  -13.333  -12.667  -12.000  -11.333  -10.667  -10.000
   -9.333   -8.667   -8.000   -7.333   -6.667   -6.000   -5.333   -4.667
   -4.000   -3.333   -2.667   -2.000   -1.333   -0.667    0.000    0.667
    1.333    2.000    2.667    3.333    4.000    4.667    5.333    6.000
    6.667    7.333    8.000    8.667    9.333   10.000   10.667   11.333
   12.000   12.667   13.333   14.000   14.667   15.333   16.000   16.667
   17.333   18.000   18.667   19.333   20.000   20.667   21.333   22.000
   22.667   23.333   24.000   24.667   25.333   26.000   26.667   27.333
   28.000   28.667   29.333   30.000   30.667   31.333   32.000   32.667
   33.333   34.000   34.667   35.333   36.000   36.667   37.333   38.000
   38.667   39.333   40.000   40.667   41.333   42.000   42.667   43.333
   44.000   44.667   45.333   46.000   46.667   47.333   48.000   48.667
   49.333   50.000   50.667   51.333   52.000   52.667   53.333   54.000
   54.667   55.333   56.000   56.667   57.333   58.000   58.667   59.333
   60.000   60.667   61.333   62.000   62.667   63.333   64.000   64.667
   65.333   66.000   66.667   67.333   68.000   68.667   69.333   70.000
   70.667   71.333   72.000   72.667   73.333   74.000   74.667   75.333
   76.000   76.667   77.333   78.000   78.667   79.333   80.000   80.667
   81.333   82.000   82.667   83.333   84.000   84.667   85.333   86.000
   86.667   87.333   88.000   88.667   89.333   90.000   90.667   91.333
   92.000   92.667   93.333   94.000   94.667   95.333   96.000   96.667
   97.333   98.000   98.667   99.333  100.000  100.667  101.333  102.000
  102.667  103.333  104.000  104.667  105.333  106.000  106.667  107.333
  108.000  108.667  109.333  110.000  110.667  111.333  112.000  112.667
  113.333  114.000  114.667  115.333  116.000  116.667  117.333  118.000
  118.667  119.333  120.000  120.667  121.333  122.000  122.667  123.333
  124.000  124.667  125.333  126.000  126.667  127.333  128.000  128.667
  129.333  130.000  130.667  131.333  132.000  132.667  133.333  134.000
  134.667  135.333  136.000  136.667  137.333  138.000  138.667  139.333
  140.000  140.667  141.333  142.000  142.667  143.333  144.000  144.667
  145.333  146.000  146.667  147.333  148.000  148.667  149.333  150.000
  150.667  151.333  152.000  152.667  153.333  154.000  154.667  155.333
  156.000  156.667  157.333  158.000  158.667  159.333  160.000  160.667
  161.333  162.000  162.667  163.333  164.000  164.667  165.333  166.000
  166.667  167.333  168.000  168.667  169.333  170.000  170.667  171.333
  172.000  172.667  173.333  174.000  174.667  175.333  176.000  176.667
  177.333  178.000  178.667  179.333
0.5° x 0.667° latitude edges:
  -90.000  -89.750  -89.250  -88.750  -88.250  -87.750  -87.250  -86.750
  -86.250  -85.750  -85.250  -84.750  -84.250  -83.750  -83.250  -82.750
  -82.250  -81.750  -81.250  -80.750  -80.250  -79.750  -79.250  -78.750
  -78.250  -77.750  -77.250  -76.750  -76.250  -75.750  -75.250  -74.750
  -74.250  -73.750  -73.250  -72.750  -72.250  -71.750  -71.250  -70.750
  -70.250  -69.750  -69.250  -68.750  -68.250  -67.750  -67.250  -66.750
  -66.250  -65.750  -65.250  -64.750  -64.250  -63.750  -63.250  -62.750
  -62.250  -61.750  -61.250  -60.750  -60.250  -59.750  -59.250  -58.750
  -58.250  -57.750  -57.250  -56.750  -56.250  -55.750  -55.250  -54.750
  -54.250  -53.750  -53.250  -52.750  -52.250  -51.750  -51.250  -50.750
  -50.250  -49.750  -49.250  -48.750  -48.250  -47.750  -47.250  -46.750
  -46.250  -45.750  -45.250  -44.750  -44.250  -43.750  -43.250  -42.750
  -42.250  -41.750  -41.250  -40.750  -40.250  -39.750  -39.250  -38.750
  -38.250  -37.750  -37.250  -36.750  -36.250  -35.750  -35.250  -34.750
  -34.250  -33.750  -33.250  -32.750  -32.250  -31.750  -31.250  -30.750
  -30.250  -29.750  -29.250  -28.750  -28.250  -27.750  -27.250  -26.750
  -26.250  -25.750  -25.250  -24.750  -24.250  -23.750  -23.250  -22.750
  -22.250  -21.750  -21.250  -20.750  -20.250  -19.750  -19.250  -18.750
  -18.250  -17.750  -17.250  -16.750  -16.250  -15.750  -15.250  -14.750
  -14.250  -13.750  -13.250  -12.750  -12.250  -11.750  -11.250  -10.750
  -10.250   -9.750   -9.250   -8.750   -8.250   -7.750   -7.250   -6.750
   -6.250   -5.750   -5.250   -4.750   -4.250   -3.750   -3.250   -2.750
   -2.250   -1.750   -1.250   -0.750   -0.250    0.250    0.750    1.250
    1.750    2.250    2.750    3.250    3.750    4.250    4.750    5.250
    5.750    6.250    6.750    7.250    7.750    8.250    8.750    9.250
    9.750   10.250   10.750   11.250   11.750   12.250   12.750   13.250
   13.750   14.250   14.750   15.250   15.750   16.250   16.750   17.250
   17.750   18.250   18.750   19.250   19.750   20.250   20.750   21.250
   21.750   22.250   22.750   23.250   23.750   24.250   24.750   25.250
   25.750   26.250   26.750   27.250   27.750   28.250   28.750   29.250
   29.750   30.250   30.750   31.250   31.750   32.250   32.750   33.250
   33.750   34.250   34.750   35.250   35.750   36.250   36.750   37.250
   37.750   38.250   38.750   39.250   39.750   40.250   40.750   41.250
   41.750   42.250   42.750   43.250   43.750   44.250   44.750   45.250
   45.750   46.250   46.750   47.250   47.750   48.250   48.750   49.250
   49.750   50.250   50.750   51.250   51.750   52.250   52.750   53.250
   53.750   54.250   54.750   55.250   55.750   56.250   56.750   57.250
   57.750   58.250   58.750   59.250   59.750   60.250   60.750   61.250
   61.750   62.250   62.750   63.250   63.750   64.250   64.750   65.250
   65.750   66.250   66.750   67.250   67.750   68.250   68.750   69.250
   69.750   70.250   70.750   71.250   71.750   72.250   72.750   73.250
   73.750   74.250   74.750   75.250   75.750   76.250   76.750   77.250
   77.750   78.250   78.750   79.250   79.750   80.250   80.750   81.250
   81.750   82.250   82.750   83.250   83.750   84.250   84.750   85.250
   85.750   86.250   86.750   87.250   87.750   88.250   88.750   89.250
   89.750   90.000
0.5° x 0.667° latitude centers:
  -89.875  -89.500  -89.000  -88.500  -88.000  -87.500  -87.000  -86.500
  -86.000  -85.500  -85.000  -84.500  -84.000  -83.500  -83.000  -82.500
  -82.000  -81.500  -81.000  -80.500  -80.000  -79.500  -79.000  -78.500
  -78.000  -77.500  -77.000  -76.500  -76.000  -75.500  -75.000  -74.500
  -74.000  -73.500  -73.000  -72.500  -72.000  -71.500  -71.000  -70.500
  -70.000  -69.500  -69.000  -68.500  -68.000  -67.500  -67.000  -66.500
  -66.000  -65.500  -65.000  -64.500  -64.000  -63.500  -63.000  -62.500
  -62.000  -61.500  -61.000  -60.500  -60.000  -59.500  -59.000  -58.500
  -58.000  -57.500  -57.000  -56.500  -56.000  -55.500  -55.000  -54.500
  -54.000  -53.500  -53.000  -52.500  -52.000  -51.500  -51.000  -50.500
  -50.000  -49.500  -49.000  -48.500  -48.000  -47.500  -47.000  -46.500
  -46.000  -45.500  -45.000  -44.500  -44.000  -43.500  -43.000  -42.500
  -42.000  -41.500  -41.000  -40.500  -40.000  -39.500  -39.000  -38.500
  -38.000  -37.500  -37.000  -36.500  -36.000  -35.500  -35.000  -34.500
  -34.000  -33.500  -33.000  -32.500  -32.000  -31.500  -31.000  -30.500
  -30.000  -29.500  -29.000  -28.500  -28.000  -27.500  -27.000  -26.500
  -26.000  -25.500  -25.000  -24.500  -24.000  -23.500  -23.000  -22.500
  -22.000  -21.500  -21.000  -20.500  -20.000  -19.500  -19.000  -18.500
  -18.000  -17.500  -17.000  -16.500  -16.000  -15.500  -15.000  -14.500
  -14.000  -13.500  -13.000  -12.500  -12.000  -11.500  -11.000  -10.500
  -10.000   -9.500   -9.000   -8.500   -8.000   -7.500   -7.000   -6.500
   -6.000   -5.500   -5.000   -4.500   -4.000   -3.500   -3.000   -2.500
   -2.000   -1.500   -1.000   -0.500    0.000    0.500    1.000    1.500
    2.000    2.500    3.000    3.500    4.000    4.500    5.000    5.500
    6.000    6.500    7.000    7.500    8.000    8.500    9.000    9.500
   10.000   10.500   11.000   11.500   12.000   12.500   13.000   13.500
   14.000   14.500   15.000   15.500   16.000   16.500   17.000   17.500
   18.000   18.500   19.000   19.500   20.000   20.500   21.000   21.500
   22.000   22.500   23.000   23.500   24.000   24.500   25.000   25.500
   26.000   26.500   27.000   27.500   28.000   28.500   29.000   29.500
   30.000   30.500   31.000   31.500   32.000   32.500   33.000   33.500
   34.000   34.500   35.000   35.500   36.000   36.500   37.000   37.500
   38.000   38.500   39.000   39.500   40.000   40.500   41.000   41.500
   42.000   42.500   43.000   43.500   44.000   44.500   45.000   45.500
   46.000   46.500   47.000   47.500   48.000   48.500   49.000   49.500
   50.000   50.500   51.000   51.500   52.000   52.500   53.000   53.500
   54.000   54.500   55.000   55.500   56.000   56.500   57.000   57.500
   58.000   58.500   59.000   59.500   60.000   60.500   61.000   61.500
   62.000   62.500   63.000   63.500   64.000   64.500   65.000   65.500
   66.000   66.500   67.000   67.500   68.000   68.500   69.000   69.500
   70.000   70.500   71.000   71.500   72.000   72.500   73.000   73.500
   74.000   74.500   75.000   75.500   76.000   76.500   77.000   77.500
   78.000   78.500   79.000   79.500   80.000   80.500   81.000   81.500
   82.000   82.500   83.000   83.500   84.000   84.500   85.000   85.500
   86.000   86.500   87.000   87.500   88.000   88.500   89.000   89.500
   89.875

A2.6.1 China/SE Asia 0.5° x 0.667° nested grid
The GMAO 0.5 ° x 0.667 ° (GEOS - 5 met fields) nested-grid over China and SE Asia is defined on the following grid (121 longitudes x 133 latitudes):
Longitude centers:
   70.000   70.667   71.333   72.000   72.667   73.333   74.000   74.667   
   75.333   76.000   76.667   77.333   78.000   78.667   79.333   80.000   
   80.667   81.333   82.000   82.667   83.333   84.000   84.667   85.333   
   86.000   86.667   87.333   88.000   88.667   89.333   90.000   90.667   
   91.333   92.000   92.667   93.333   94.000   94.667   95.333   96.000   
   96.667   97.333   98.000   98.667   99.333  100.000  100.667  101.333  
  102.000  102.667  103.333  104.000  104.667  105.333  106.000  106.667  
  107.333  108.000  108.667  109.333  110.000  110.667  111.333  112.000  
  112.667  113.333  114.000  114.667  115.333  116.000  116.667  117.333  
  118.000  118.667  119.333  120.000  120.667  121.333  122.000  122.667  
  123.333  124.000  124.667  125.333  126.000  126.667  127.333  128.000  
  128.667  129.333  130.000  130.667  131.333  132.000  132.667  133.333  
  134.000  134.667  135.333  136.000  136.667  137.333  138.000  138.667  
  139.333  140.000  140.667  141.333  142.000  142.667  143.333  144.000  
  144.667  145.333  146.000  146.667  147.333  148.000  148.667  149.333  
  150.000
Latitude centers:
  -11.000  -10.500  -10.000   -9.500   -9.000   -8.500   -8.000   -7.500   
   -7.000   -6.500   -6.000   -5.500   -5.000   -4.500   -4.000   -3.500   
   -3.000   -2.500   -2.000   -1.500   -1.000   -0.500    0.000    0.500    
    1.000    1.500    2.000    2.500    3.000    3.500    4.000    4.500    
    5.000    5.500    6.000    6.500    7.000    7.500    8.000    8.500    
    9.000    9.500   10.000   10.500   11.000   11.500   12.000   12.500   
   13.000   13.500   14.000   14.500   15.000   15.500   16.000   16.500   
   17.000   17.500   18.000   18.500   19.000   19.500   20.000   20.500   
   21.000   21.500   22.000   22.500   23.000   23.500   24.000   24.500   
   25.000   25.500   26.000   26.500   27.000   27.500   28.000   28.500   
   29.000   29.500   30.000   30.500   31.000   31.500   32.000   32.500   
   33.000   33.500   34.000   34.500   35.000   35.500   36.000   36.500   
   37.000   37.500   38.000   38.500   39.000   39.500   40.000   40.500   
   41.000   41.500   42.000   42.500   43.000   43.500   44.000   44.500   
   45.000   45.500   46.000   46.500   47.000   47.500   48.000   48.500   
   49.000   49.500   50.000   50.500   51.000   51.500   52.000   52.500   
   53.000   53.500   54.000   54.500   55.000

A2.6.2 North America 0.5° x 0.667° nested grid
The GMAO 0.5° x 0.667° (GEOS - 5 met fields) nested-grid over North America is defined on the following grid (151 longitudes x 121 latitudes): 
Longitude centers:
 -140.000 -139.333 -138.667 -138.000 -137.333 -136.667 -136.000 -135.333 
 -134.667 -134.000 -133.333 -132.667 -132.000 -131.333 -130.667 -130.000
 -129.333 -128.667 -128.000 -127.333 -126.667 -126.000 -125.333 -124.667
 -124.000 -123.333 -122.667 -122.000 -121.333 -120.667 -120.000 -119.333
 -118.667 -118.000 -117.333 -116.667 -116.000 -115.333 -114.667 -114.000
 -113.333 -112.667 -112.000 -111.333 -110.667 -110.000 -109.333 -108.667
 -108.000 -107.333 -106.667 -106.000 -105.333 -104.667 -104.000 -103.333
 -102.667 -102.000 -101.333 -100.667 -100.000  -99.333  -98.667  -98.000
  -97.333  -96.667  -96.000  -95.333  -94.667  -94.000  -93.333  -92.667
  -92.000  -91.333  -90.667  -90.000  -89.333  -88.667  -88.000  -87.333
  -86.667  -86.000  -85.333  -84.667  -84.000  -83.333  -82.667  -82.000
  -81.333  -80.667  -80.000  -79.333  -78.667  -78.000  -77.333  -76.667
  -76.000  -75.333  -74.667  -74.000  -73.333  -72.667  -72.000  -71.333
  -70.667  -70.000  -69.333  -68.667  -68.000  -67.333  -66.667  -66.000
  -65.333  -64.667  -64.000  -63.333  -62.667  -62.000  -61.333  -60.667
  -60.000  -59.333  -58.667  -58.000  -57.333  -56.667  -56.000  -55.333
  -54.667  -54.000  -53.333  -52.667  -52.000  -51.333  -50.667  -50.000
  -49.333  -48.667  -48.000  -47.333  -46.667  -46.000  -45.333  -44.667
  -44.000  -43.333  -42.667  -42.000  -41.333  -40.667  -40.000
Latitude centers:
   10.000   10.500   11.000   11.500   12.000   12.500   13.000   13.500
   14.000   14.500   15.000   15.500   16.000   16.500   17.000   17.500
   18.000   18.500   19.000   19.500   20.000   20.500   21.000   21.500
   22.000   22.500   23.000   23.500   24.000   24.500   25.000   25.500
   26.000   26.500   27.000   27.500   28.000   28.500   29.000   29.500
   30.000   30.500   31.000   31.500   32.000   32.500   33.000   33.500
   34.000   34.500   35.000   35.500   36.000   36.500   37.000   37.500
   38.000   38.500   39.000   39.500   40.000   40.500   41.000   41.500
   42.000   42.500   43.000   43.500   44.000   44.500   45.000   45.500
   46.000   46.500   47.000   47.500   48.000   48.500   49.000   49.500
   50.000   50.500   51.000   51.500   52.000   52.500   53.000   53.500
   54.000   54.500   55.000   55.500   56.000   56.500   57.000   57.500
   58.000   58.500   59.000   59.500   60.000   60.500   61.000   61.500
   62.000   62.500   63.000   63.500   64.000   64.500   65.000   65.500
   66.000   66.500   67.000   67.500   68.000   68.500   69.000   69.500
   70.000

A2.6.3 Europe 0.5° x 0.667° nested grid
The GMAO 0.5° x 0.667° (GEOS - 5 met fields) nested-grid over Europe is defined on the following grid (121 longitudes x 81 latitudes): 
Longitude centers:
 -30.000 -29.333 -28.667 -28.000 -27.333 -26.667 -26.000 -25.333
 -24.667 -24.000 -23.333 -22.667 -22.000 -21.333 -20.667 -20.000
 -19.333 -18.667 -18.000 -17.333 -16.667 -16.000 -15.333 -14.667
 -14.000 -13.333 -12.667 -12.000 -11.333 -10.667 -10.000  -9.333
  -8.667  -8.000  -7.333  -6.667  -6.000  -5.333  -4.667  -4.000
  -3.333  -2.667  -2.000  -1.333  -0.667   0.000   0.667   1.333
   2.000   2.667   3.333   4.000   4.667   5.333   6.000   6.667
   7.333   8.000   8.667   9.333  10.000  10.667  11.333  12.000
  12.667  13.333  14.000  14.667  15.333  16.000  16.667  17.333
  18.000  18.667  19.333  20.000  20.667  21.333  22.000  22.667
  23.333  24.000  24.667  25.333  26.000  26.667  27.333  28.000
  28.667  29.333  30.000  30.667  31.333  32.000  32.667  33.333
  34.000  34.667  35.333  36.000  36.667  37.333  38.000  38.667
  39.333  40.000  40.667  41.333  42.000  42.667  43.333  44.000
  44.667  45.333  46.000  46.667  47.333  48.000  48.667  49.333
  50.000
Latitude centers:
  30.000  30.500  31.000  31.500  32.000  32.500  33.000  33.500
  34.000  34.500  35.000  35.500  36.000  36.500  37.000  37.500
  38.000  38.500  39.000  39.500  40.000  40.500  41.000  41.500
  42.000  42.500  43.000  43.500  44.000  44.500  45.000  45.500
  46.000  46.500  47.000  47.500  48.000  48.500  49.000  49.500
  50.000  50.500  51.000  51.500  52.000  52.500  53.000  53.500
  54.000  54.500  55.000  55.500  56.000  56.500  57.000  57.500
  58.000  58.500  59.000  59.500  60.000  60.500  61.000  61.500
  62.000  62.500  63.000  63.500  64.000  64.500  65.000  65.500
  66.000  66.500  67.000  67.500  68.000  68.500  69.000  69.500
  70.000
Longitude edges:
 -30.333 -29.667 -29.000 -28.333 -27.667 -27.000 -26.333 -25.667 
 -25.000 -24.333 -23.667 -23.000 -22.333 -21.667 -21.000 -20.333
 -19.667 -19.000 -18.333 -17.667 -17.000 -16.333 -15.667 -15.000
 -14.333 -13.667 -13.000 -12.333 -11.667 -11.000 -10.333  -9.667
  -9.000  -8.333  -7.667  -7.000  -6.333  -5.667  -5.000  -4.333
  -3.667  -3.000  -2.333  -1.667  -1.000  -0.333   0.333   1.000
   1.667   2.333   3.000   3.667   4.333   5.000   5.667   6.333
   7.000   7.667   8.333   9.000   9.667  10.333  11.000  11.667
  12.333  13.000  13.667  14.333  15.000  15.667  16.333  17.000
  17.667  18.333  19.000  19.667  20.333  21.000  21.667  22.333
  23.000  23.667  24.333  25.000  25.667  26.333  27.000  27.667
  28.333  29.000  29.667  30.333  31.000  31.667  32.333  33.000
  33.667  34.333  35.000  35.667  36.333  37.000  37.667  38.333
  39.000  39.667  40.333  41.000  41.667  42.333  43.000  43.667
  44.333  45.000  45.667  46.333  47.000  47.667  48.333  49.000
  49.667  50.333
Latitude edges:
  29.750  30.250  30.750  31.250  31.750  32.250  32.750  33.250
  33.750  34.250  34.750  35.250  35.750  36.250  36.750  37.250
  37.750  38.250  38.750  39.250  39.750  40.250  40.750  41.250
  41.750  42.250  42.750  43.250  43.750  44.250  44.750  45.250
  45.750  46.250  46.750  47.250  47.750  48.250  48.750  49.250
  49.750  50.250  50.750  51.250  51.750  52.250  52.750  53.250
  53.750  54.250  54.750  55.250  55.750  56.250  56.750  57.250
  57.750  58.250  58.750  59.250  59.750  60.250  60.750  61.250
  61.750  62.250  62.750  63.250  63.750  64.250  64.750  65.250
  65.750  66.250  66.750  67.250  67.750  68.250  68.750  69.250
  69.750  70.250

A2.7 Generic 1° x 1° grid 
              
Generic 1° x 1° grid (detail of SE Asia region)
Many emissions are provided to us on the "generic" 1° x 1° grid. The date line (-180° longitude) is the western edge of the first grid box and -179.5° is the center of the first box. This grid is shifted by 1/2 degree with respect to the GMAO 1° x 1° grid. 
1° x 1° longitude edges:
 -180.000 -179.000 -178.000 -177.000 -176.000 -175.000 -174.000 -173.000
 -172.000 -171.000 -170.000 -169.000 -168.000 -167.000 -166.000 -165.000
 -164.000 -163.000 -162.000 -161.000 -160.000 -159.000 -158.000 -157.000
 -156.000 -155.000 -154.000 -153.000 -152.000 -151.000 -150.000 -149.000
 -148.000 -147.000 -146.000 -145.000 -144.000 -143.000 -142.000 -141.000
 -140.000 -139.000 -138.000 -137.000 -136.000 -135.000 -134.000 -133.000
 -132.000 -131.000 -130.000 -129.000 -128.000 -127.000 -126.000 -125.000
 -124.000 -123.000 -122.000 -121.000 -120.000 -119.000 -118.000 -117.000
 -116.000 -115.000 -114.000 -113.000 -112.000 -111.000 -110.000 -109.000
 -108.000 -107.000 -106.000 -105.000 -104.000 -103.000 -102.000 -101.000
 -100.000  -99.000  -98.000  -97.000  -96.000  -95.000  -94.000  -93.000
  -92.000  -91.000  -90.000  -89.000  -88.000  -87.000  -86.000  -85.000
  -84.000  -83.000  -82.000  -81.000  -80.000  -79.000  -78.000  -77.000
  -76.000  -75.000  -74.000  -73.000  -72.000  -71.000  -70.000  -69.000
  -68.000  -67.000  -66.000  -65.000  -64.000  -63.000  -62.000  -61.000
  -60.000  -59.000  -58.000  -57.000  -56.000  -55.000  -54.000  -53.000
  -52.000  -51.000  -50.000  -49.000  -48.000  -47.000  -46.000  -45.000
  -44.000  -43.000  -42.000  -41.000  -40.000  -39.000  -38.000  -37.000
  -36.000  -35.000  -34.000  -33.000  -32.000  -31.000  -30.000  -29.000
  -28.000  -27.000  -26.000  -25.000  -24.000  -23.000  -22.000  -21.000
  -20.000  -19.000  -18.000  -17.000  -16.000  -15.000  -14.000  -13.000
  -12.000  -11.000  -10.000   -9.000   -8.000   -7.000   -6.000   -5.000
   -4.000   -3.000   -2.000   -1.000    0.000    1.000    2.000    3.000
    4.000    5.000    6.000    7.000    8.000    9.000   10.000   11.000
   12.000   13.000   14.000   15.000   16.000   17.000   18.000   19.000
   20.000   21.000   22.000   23.000   24.000   25.000   26.000   27.000
   28.000   29.000   30.000   31.000   32.000   33.000   34.000   35.000
   36.000   37.000   38.000   39.000   40.000   41.000   42.000   43.000
   44.000   45.000   46.000   47.000   48.000   49.000   50.000   51.000
   52.000   53.000   54.000   55.000   56.000   57.000   58.000   59.000
   60.000   61.000   62.000   63.000   64.000   65.000   66.000   67.000
   68.000   69.000   70.000   71.000   72.000   73.000   74.000   75.000
   76.000   77.000   78.000   79.000   80.000   81.000   82.000   83.000
   84.000   85.000   86.000   87.000   88.000   89.000   90.000   91.000
   92.000   93.000   94.000   95.000   96.000   97.000   98.000   99.000
  100.000  101.000  102.000  103.000  104.000  105.000  106.000  107.000
  108.000  109.000  110.000  111.000  112.000  113.000  114.000  115.000
  116.000  117.000  118.000  119.000  120.000  121.000  122.000  123.000
  124.000  125.000  126.000  127.000  128.000  129.000  130.000  131.000
  132.000  133.000  134.000  135.000  136.000  137.000  138.000  139.000
  140.000  141.000  142.000  143.000  144.000  145.000  146.000  147.000
  148.000  149.000  150.000  151.000  152.000  153.000  154.000  155.000
  156.000  157.000  158.000  159.000  160.000  161.000  162.000  163.000
  164.000  165.000  166.000  167.000  168.000  169.000  170.000  171.000
  172.000  173.000  174.000  175.000  176.000  177.000  178.000  179.000
  180.000
1° x 1° longitude centers:
 -179.500 -178.500 -177.500 -176.500 -175.500 -174.500 -173.500 -172.500
 -171.500 -170.500 -169.500 -168.500 -167.500 -166.500 -165.500 -164.500
 -163.500 -162.500 -161.500 -160.500 -159.500 -158.500 -157.500 -156.500
 -155.500 -154.500 -153.500 -152.500 -151.500 -150.500 -149.500 -148.500
 -147.500 -146.500 -145.500 -144.500 -143.500 -142.500 -141.500 -140.500
 -139.500 -138.500 -137.500 -136.500 -135.500 -134.500 -133.500 -132.500
 -131.500 -130.500 -129.500 -128.500 -127.500 -126.500 -125.500 -124.500
 -123.500 -122.500 -121.500 -120.500 -119.500 -118.500 -117.500 -116.500
 -115.500 -114.500 -113.500 -112.500 -111.500 -110.500 -109.500 -108.500
 -107.500 -106.500 -105.500 -104.500 -103.500 -102.500 -101.500 -100.500  
  -99.500  -98.500  -97.500  -96.500  -95.500  -94.500  -93.500  -92.500  
  -91.500  -90.500  -89.500  -88.500  -87.500  -86.500  -85.500  -84.500  
  -83.500  -82.500  -81.500  -80.500  -79.500  -78.500  -77.500  -76.500 
  -75.500  -74.500  -73.500  -72.500  -71.500  -70.500  -69.500  -68.500  
  -67.500  -66.500  -65.500  -64.500  -63.500  -62.500  -61.500  -60.500  
  -59.500  -58.500  -57.500  -56.500  -55.500  -54.500  -53.500  -52.500 
  -51.500  -50.500  -49.500  -48.500  -47.500  -46.500  -45.500  -44.500 
  -43.500  -42.500  -41.500  -40.500  -39.500  -38.500  -37.500  -36.500 
  -35.500  -34.500  -33.500  -32.500  -31.500  -30.500  -29.500  -28.500 
  -27.500  -26.500  -25.500  -24.500  -23.500  -22.500  -21.500  -20.500
  -19.500  -18.500  -17.500  -16.500  -15.500  -14.500  -13.500  -12.500 
  -11.500  -10.500   -9.500   -8.500   -7.500   -6.500   -5.500   -4.500 
   -3.500   -2.500   -1.500   -0.500    0.500    1.500    2.500    3.500  
    4.500    5.500    6.500    7.500    8.500    9.500   10.500   11.500  
   12.500   13.500   14.500   15.500   16.500   17.500   18.500   19.500  
   20.500   21.500   22.500   23.500   24.500   25.500   26.500   27.500  
   28.500   29.500   30.500   31.500   32.500   33.500   34.500   35.500 
   36.500   37.500   38.500   39.500   40.500   41.500   42.500   43.500 
   44.500   45.500   46.500   47.500   48.500   49.500   50.500   51.500  
   52.500   53.500   54.500   55.500   56.500   57.500   58.500   59.500  
   60.500   61.500   62.500   63.500   64.500   65.500   66.500   67.500 
   68.500   69.500   70.500   71.500   72.500   73.500   74.500   75.500
   76.500   77.500   78.500   79.500   80.500   81.500   82.500   83.500 
   84.500   85.500   86.500   87.500   88.500   89.500   90.500   91.500 
   92.500   93.500   94.500   95.500   96.500   97.500   98.500   99.500 
  100.500  101.500  102.500  103.500  104.500  105.500  106.500  107.500 
  108.500  109.500  110.500  111.500  112.500  113.500  114.500  115.500 
  116.500  117.500  118.500  119.500  120.500  121.500  122.500  123.500 
  124.500  125.500  126.500  127.500  128.500  129.500  130.500  131.500 
  132.500  133.500  134.500  135.500  136.500  137.500  138.500  139.500
  140.500  141.500  142.500  143.500  144.500  145.500  146.500  147.500
  148.500  149.500  150.500  151.500  152.500  153.500  154.500  155.500
  156.500  157.500  158.500  159.500  160.500  161.500  162.500  163.500> 
  164.500  165.500  166.500  167.500  168.500  169.500  170.500  171.500 
  172.500  173.500  174.500  175.500  176.500  177.500  178.500  179.500
1° x 1° latitude edges:
  -90.000  -89.000  -88.000  -87.000  -86.000  -85.000  -84.000  -83.000
  -82.000  -81.000  -80.000  -79.000  -78.000  -77.000  -76.000  -75.000
  -74.000  -73.000  -72.000  -71.000  -70.000  -69.000  -68.000  -67.000
  -66.000  -65.000  -64.000  -63.000  -62.000  -61.000  -60.000  -59.000
  -58.000  -57.000  -56.000  -55.000  -54.000  -53.000  -52.000  -51.000
  -50.000  -49.000  -48.000  -47.000  -46.000  -45.000  -44.000  -43.000
  -42.000  -41.000  -40.000  -39.000  -38.000  -37.000  -36.000  -35.000
  -34.000  -33.000  -32.000  -31.000  -30.000  -29.000  -28.000  -27.000
  -26.000  -25.000  -24.000  -23.000  -22.000  -21.000  -20.000  -19.000
  -18.000  -17.000  -16.000  -15.000  -14.000  -13.000  -12.000  -11.000
  -10.000   -9.000   -8.000   -7.000   -6.000   -5.000   -4.000   -3.000
   -2.000   -1.000    0.000    1.000    2.000    3.000    4.000    5.000
    6.000    7.000    8.000    9.000   10.000   11.000   12.000   13.000
    4.000   15.000   16.000   17.000   18.000   19.000   20.000   21.000
   22.000   23.000   24.000   25.000   26.000   27.000   28.000   29.000
   30.000   31.000   32.000   33.000   34.000   35.000   36.000   37.000
   38.000   39.000   40.000   41.000   42.000   43.000   44.000   45.000
   46.000   47.000   48.000   49.000   50.000   51.000   52.000   53.000
   54.000   55.000   56.000   57.000   58.000   59.000   60.000   61.000
   62.000   63.000   64.000   65.000   66.000   67.000   68.000   69.000
   70.000   71.000   72.000   73.000   74.000   75.000   76.000   77.000
   78.000   79.000   80.000   81.000   82.000   83.000   84.000   85.000
   86.000   87.000   88.000   89.000   90.000
1° x 1° latitude centers:
  -89.500  -88.500  -87.500  -86.500  -85.500  -84.500  -83.500  -82.500
  -81.500  -80.500  -79.500  -78.500  -77.500  -76.500  -75.500  -74.500
  -73.500  -72.500  -71.500  -70.500  -69.500  -68.500  -67.500  -66.500
  -65.500  -64.500  -63.500  -62.500  -61.500  -60.500  -59.500  -58.500
  -57.500  -56.500  -55.500  -54.500  -53.500  -52.500  -51.500  -50.500
  -49.500  -48.500  -47.500  -46.500  -45.500  -44.500  -43.500  -42.500
  -41.500  -40.500  -39.500  -38.500  -37.500  -36.500  -35.500  -34.500
  -33.500  -32.500  -31.500  -30.500  -29.500  -28.500  -27.500  -26.500
  -25.500  -24.500  -23.500  -22.500  -21.500  -20.500  -19.500  -18.500
  -17.500  -16.500  -15.500  -14.500  -13.500  -12.500  -11.500  -10.500
   -9.500   -8.500   -7.500   -6.500   -5.500   -4.500   -3.500   -2.500
   -1.500   -0.500    0.500    1.500    2.500    3.500    4.500    5.500
    6.500    7.500    8.500    9.500   10.500   11.500   12.500   13.500
   14.500   15.500   16.500   17.500   18.500   19.500   20.500   21.500
   22.500   23.500   24.500   25.500   26.500   27.500   28.500   29.500
   30.500   31.500   32.500   33.500   34.500   35.500   36.500   37.500
   38.500   39.500   40.500   41.500   42.500   43.500   44.500   45.500
   46.500   47.500   48.500   49.500   50.500   51.500   52.500   53.500
   54.500   55.500   56.500   57.500   58.500   59.500   60.500   61.500
   62.500   63.500   64.500   65.500   66.500   67.500   68.500   69.500
   70.500   71.500   72.500   73.500   74.500   75.500   76.500   77.500
   78.500   79.500   80.500   81.500   82.500   83.500   84.500   85.500
   86.500   87.500   88.500   89.500

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 3
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 3: GEOS - Chem Vertical Grids
We compare the vertical grids of the meteorological data that GEOS - Chem reads from disk.
                                       
A3.1 Comparison of GCAP, GEOS - 3, GEOS - 4, and GEOS - 5/MERRA vertical grids

GCAP, GEOS - 3, GEOS - 4, and GEOS - 5 vertical levels, up to 3 km
(Solid lines are edges, dotted lines are centers) 
                                       
     
GCAP, GEOS - 3, GEOS - 4, and GEOS - 5 vertical levels, up to 10 km
                                       
     
GCAP, GEOS - 3, GEOS - 4, and GEOS - 5 vertical levels, up to 32 km
                                       
     
GCAP, GEOS - 3, GEOS - 4, and GEOS - 5 vertical levels, up to 80 km
                                       
A3.2 GCAP vertical grid 
The native vertical resolution of the GCAP meteorological fields (which come from the GISS - II GCM) is 23 hybrid sigma-pressure levels, extending from the surface up to 0.002 hPa.
We computed the pressures and altitudes listed below assuming a surface pressure of 1013.25 hPa. Altitudes are approximations based on the US Standard Atmosphere. This shall suffice for purposes of illustration.
GCAP Native Vertical Grid (23 layers)

  L     Sig Edge      Sig Mid    Altitude     Pressure
      (unitless)   (unitless)        (km)        (hPa)
========================================================
        0.000000                    89.247        0.002
 23                  0.000000       77.507        0.017
        0.000000                    73.489        0.031
 22                  0.000000       66.346        0.088
        0.000000                    62.725        0.145
 21                  0.000000       57.209        0.303
        0.000000                    54.014        0.461
 20                  0.000000       48.400        0.960
        0.000000                    45.215        1.460
 19                  0.000000       39.712        3.045
        0.000000                    36.651        4.630
 18                  0.000000       33.388        7.315
        0.000000                    31.209       10.000
 17                  0.000000       28.959       13.900
        0.000000                    27.300       17.800
 16                  0.000000       25.141       24.700
        0.000000                    23.543       31.600
 15                  0.000000       21.439       43.900
        0.000000                    19.876       56.200
 14                  0.000000       18.387       71.200
        0.000000                    17.187       86.200
 13                  0.000000       16.154      101.600
        0.000000                    15.265      117.000
 12                  0.000000       14.431      133.500
        0.000000                    13.690      150.000
 11                  0.000000       12.825      171.737
        0.000000                    12.056      193.473
 10                  0.000000       11.192      220.903
        0.000000                    10.421      248.332
  9                  0.000000        9.524      284.042
        0.000000                     8.721      319.752
  8                  0.000000        7.580      377.198
        0.000000                     6.578      434.645
  7                  0.000000        5.424      509.687
        0.000000                     4.401      584.730
  6                  0.000000        3.509      657.185
        0.000000                     2.692      729.641
  5                  0.000000        2.098      786.052
        0.000000                     1.536      842.463
  4                  0.000000        1.215      876.103
        0.000000                     0.903      909.743
  3                  0.000000        0.692      933.032
        0.000000                     0.485      956.321
  2                  0.000000        0.344      972.365
        0.000000                     0.206      988.408
  1                  0.000000        0.099     1000.829
        0.000000                    -0.006     1013.250
                                       
A3.3 GEOS - 4 vertical grids
The native vertical resolution of GEOS - 4 meteorological fields is 55 hybrid eta levels, extending from the surface up to 0.01 hPa. The first 14 levels from the surface upward are pure sigma levels; the rest are fixed pressure levels.
To conserve memory, you have the option of running GEOS - Chem a reduced vertical resolution of 30 eta levels. GEOS - Chem will combine eta levels above ~50 hPa on-the-fly.
We computed the pressures and altitudes listed below assuming a surface pressure of 1013.25 hPa. Altitudes are approximations based on the US Standard Atmosphere. This shall suffice for purposes of illustration.

A3.3.1 GEOS - 4 native vertical grid
GEOS-4 Native Vertical Grid (55 hybrid pressure-sigma layers)

  L     Eta Edge      Eta Mid     Altitude     Pressure
      (unitless)   (unitless)        (km)        (hPa)
========================================================
        0.000000                    80.581        0.010
 55                  0.000005       78.146        0.015
        0.000010                    76.357        0.020
 54                  0.000016       74.594        0.026
        0.000022                    73.180        0.033
 53                  0.000030       71.812        0.040
        0.000037                    70.657        0.048
 52                  0.000046       69.440        0.057
        0.000055                    68.392        0.066
 51                  0.000067       67.243        0.078
        0.000078                    66.245        0.089
 50                  0.000093       65.115        0.105
        0.000108                    64.130        0.120
 49                  0.000128       63.004        0.140
        0.000148                    62.021        0.159
 48                  0.000173       60.902        0.185
        0.000199                    59.924        0.211
 47                  0.000232       58.816        0.245
        0.000265                    57.846        0.279
 46                  0.000308       56.752        0.322
        0.000350                    55.794        0.365
 45                  0.000405       54.717        0.420
        0.000460                    53.773        0.476
 44                  0.000529       52.716        0.546
        0.000599                    51.788        0.617
 43                  0.000687       50.754        0.706
        0.000775                    49.844        0.795
 42                  0.000886       48.835        0.907
        0.000996                    47.946        1.019
 41                  0.001135       46.962        1.160
        0.001274                    46.092        1.301
 40                  0.001446       45.134        1.476
        0.001619                    44.286        1.651
 39                  0.001834       43.355        1.868
        0.002048                    42.529        2.085
 38                  0.002312       41.627        2.353
        0.002576                    40.825        2.620
 37                  0.002900       39.951        2.948
        0.003224                    39.173        3.276
 36                  0.003619       38.328        3.677
        0.004013                    37.574        4.077
 35                  0.004492       36.759        4.562
        0.004971                    36.030        5.047
 34                  0.005548       35.244        5.632
        0.006126                    34.539        6.217
 33                  0.006818       33.782        6.918
        0.007510                    33.101        7.620
 32                  0.008336       32.372        8.456
        0.009162                    31.716        9.293
 31                  0.010141       31.015       10.285
        0.011120                    30.383       11.277
 30                  0.012287       29.701       12.460
        0.013455                    29.085       13.643
 29                  0.014844       28.423       15.050
        0.016232                    27.824       16.457
 28                  0.017878       27.180       18.124
        0.019523                    26.596       19.792
 27                  0.021467       25.971       21.761
        0.023410                    25.402       23.730
 26                  0.025699       24.794       26.049
        0.027987                    24.240       28.368
 25                  0.030673       23.648       31.089
        0.033358                    23.108       33.810
 24                  0.036499       22.531       36.993
        0.039641                    22.004       40.175
 23                  0.043326       21.438       43.910
        0.047012                    20.920       47.644
 22                  0.051326       20.364       52.016
        0.055641                    19.855       56.388
 21                  0.060682       19.309       61.496
        0.065723                    18.807       66.603
 20                  0.071600       18.269       72.558
        0.077477                    17.773       78.512
 19                  0.084313       17.243       85.439
        0.091149                    16.753       92.366
 18                  0.099191       16.222      100.515
        0.107234                    15.731      108.663
 17                  0.116695       15.198      118.250
        0.126157                    14.706      127.837
 16                  0.137287       14.170      139.115
        0.148418                    13.674      150.393
 15                  0.161513       13.134      163.661
        0.174608                    12.633      176.930
 14                  0.190061       12.086      192.587
        0.205513                    11.578      208.244
 13                  0.223772       11.021      226.745
        0.242032                    10.504      245.246
 12                  0.263587        9.936      267.087
        0.285142                     9.409      288.927
 11                  0.310561        8.830      314.683
        0.335980                     8.291      340.439
 10                  0.365938        7.700      370.793
        0.395895                     7.148      401.146
  9                  0.431179        6.541      436.898
        0.466464                     5.975      472.650
  8                  0.508017        5.351      514.754
        0.549571                     4.768      556.857
  7                  0.598479        4.125      606.413
        0.647387                     3.523      655.968
  6                  0.695218        2.969      704.433
        0.743050                     2.443      752.898
  5                  0.786601        1.986      797.026
        0.830152                     1.549      841.154
  4                  0.866492        1.197      877.974
        0.902831                     0.857      914.795
  3                  0.929330        0.615      941.644
        0.955828                     0.378      968.494
  2                  0.970469        0.249      983.328
        0.985110                     0.122      998.163
  1                  0.992555        0.058     1005.706
        1.000000                    -0.006     1013.250 

A3.3.2 GEOS - 4 reduced vertical grid
GEOS - 4 Reduced Vertical Grid (30 hybrid pressure-sigma layers

  L     Eta Edge     Eta Mid     Altitude     Pressure
      (unitless)   (unitless)        (km)        (hPa)
========================================================
        0.000000                    80.581        0.010
 30                  0.000028       72.180        0.038
        0.000055                    68.392        0.066
 29                  0.000127       63.053        0.139
        0.000199                    59.924        0.211
 28                  0.000399       54.834        0.414
        0.000599                    51.788        0.617
 27                  0.001109       47.135        1.134
        0.001619                    44.286        1.651
 26                  0.002816       40.166        2.864
        0.004013                    37.574        4.077
 25                  0.006588       34.024        6.685
        0.009162                    31.716        9.293
 24                  0.014342       28.654       14.542
        0.019523                    26.596       19.792
 23                  0.023755       25.307       24.080
        0.027987                    24.240       28.368
 22                  0.033814       23.020       34.272
        0.039641                    22.004       40.175
 21                  0.047641       20.836       48.282
        0.055641                    19.855       56.388
 20                  0.066559       18.727       67.450
        0.077477                    17.773       78.512
 19                  0.084313       17.243       85.439
        0.091149                    16.753       92.366
 18                  0.099191       16.222      100.515
        0.107234                    15.731      108.663
 17                  0.116695       15.198      118.250
        0.126157                    14.706      127.837
 16                  0.137287       14.170      139.115
        0.148418                    13.674      150.393
 15                  0.161513       13.134      163.661
        0.174608                    12.633      176.930
 14                  0.190061       12.086      192.587
        0.205513                    11.578      208.244
 13                  0.223772       11.021      226.745
        0.242032                    10.504      245.246
 12                  0.263587        9.936      267.087
        0.285142                     9.409      288.927
 11                  0.310561        8.830      314.683
        0.335980                     8.291      340.439
 10                  0.365938        7.700      370.793
        0.395895                     7.148      401.146
  9                  0.431179        6.541      436.898
        0.466464                     5.975      472.650
  8                  0.508017        5.351      514.754
        0.549571                     4.768      556.857
  7                  0.598479        4.125      606.413
        0.647387                     3.523      655.968
  6                  0.695218        2.969      704.433
        0.743050                     2.443      752.898
  5                  0.786601        1.986      797.026
        0.830152                     1.549      841.154
  4                  0.866492        1.197      877.974
        0.902831                     0.857      914.795
  3                  0.929330        0.615      941.644
        0.955828                     0.378      968.494
  2                  0.970469        0.249      983.328
        0.985110                     0.122      998.163
  1                  0.992555        0.058     1005.706
        1.000000                    -0.006     1013.250

A3.4 GEOS - 5 vertical grids
The native vertical resolution of GEOS - 5 meteorological fields is 72 hybrid eta levels, extending from the surface up to 0.01 hPa. The first 31 levels from the surface upward are pure sigma levels; the rest are fixed pressure levels.
In order to minimize the amount of memory, you can run GEOS - Chem with a reduced vertical resolution of 47 eta levels. This option combines eta levels above ~80 hPa.
We computed the pressures and altitudes listed below assuming a surface pressure of 1013.25 hPa. Altitudes are approximations based on the US Standard Atmosphere. This shall suffice for purposes of illustration.

A3.4.1 GEOS - 5 native vertical grid
GEOS-5 Native Vertical Grid (72 hybrid pressure-sigma levels)

  L     Eta Edge      Eta Mid     Altitude     Pressure
      (unitless)   (unitless)        (km)        (hPa)
========================================================
        0.000000                    80.581        0.010
 72                  0.000005       78.146        0.015
        0.000010                    76.357        0.020
 71                  0.000016       74.594        0.026
        0.000022                    73.180        0.033
 70                  0.000030       71.812        0.040
        0.000037                    70.657        0.048
 69                  0.000046       69.440        0.057
        0.000055                    68.392        0.066
 68                  0.000067       67.243        0.078
        0.000078                    66.245        0.089
 67                  0.000093       65.115        0.105
        0.000108                    64.130        0.120
 66                  0.000128       63.004        0.140
        0.000148                    62.021        0.159
 65                  0.000173       60.902        0.185
        0.000199                    59.924        0.211
 64                  0.000232       58.816        0.245
        0.000265                    57.846        0.279
 63                  0.000308       56.752        0.322
        0.000350                    55.794        0.365
 62                  0.000405       54.717        0.420
        0.000460                    53.773        0.476
 61                  0.000529       52.716        0.546
        0.000599                    51.788        0.617
 60                  0.000687       50.754        0.706
        0.000775                    49.844        0.795
 59                  0.000886       48.835        0.907
        0.000996                    47.946        1.019
 58                  0.001135       46.962        1.160
        0.001274                    46.092        1.301
 57                  0.001446       45.134        1.476
        0.001619                    44.286        1.651
 56                  0.001834       43.355        1.868
        0.002048                    42.529        2.085
 55                  0.002312       41.627        2.353
        0.002576                    40.825        2.620
 54                  0.002900       39.951        2.948
        0.003224                    39.173        3.276
 53                  0.003619       38.328        3.677
        0.004013                    37.574        4.077
 52                  0.004492       36.759        4.562
        0.004971                    36.030        5.047
 51                  0.005548       35.244        5.632
        0.006126                    34.539        6.217
 50                  0.006818       33.782        6.918
        0.007510                    33.101        7.620
 49                  0.008336       32.372        8.456
        0.009162                    31.716        9.293
 48                  0.010141       31.015       10.285
        0.011120                    30.382       11.277
 47                  0.012287       29.701       12.460
        0.013455                    29.085       13.643
 46                  0.014844       28.423       15.050
        0.016232                    27.824       16.457
 45                  0.017878       27.180       18.124
        0.019523                    26.596       19.792
 44                  0.021467       25.971       21.761
        0.023410                    25.402       23.730
 43                  0.025699       24.794       26.049
        0.027987                    24.240       28.368
 42                  0.030673       23.648       31.089
        0.033358                    23.108       33.810
 41                  0.036499       22.531       36.993
        0.039641                    22.004       40.175
 40                  0.043326       21.438       43.910
        0.047011                    20.920       47.644
 39                  0.051326       20.364       52.016
        0.055641                    19.855       56.388
 38                  0.060682       19.309       61.496
        0.065723                    18.807       66.603
 37                  0.071600       18.269       72.558
        0.077477                    17.773       78.512
 36                  0.084313       17.243       85.439
        0.091149                    16.753       92.366
 35                  0.099191       16.222      100.514
        0.107233                    15.731      108.663
 34                  0.116695       15.198      118.250
        0.126157                    14.706      127.837
 33                  0.137287       14.170      139.115
        0.148418                    13.674      150.393
 32                  0.161513       13.134      163.661
        0.174608                    12.633      176.930
 31                  0.190061       12.086      192.587
        0.205513                    11.578      208.244
 30                  0.223772       11.021      226.745
        0.242032                    10.504      245.246
 29                  0.263587        9.936      267.087
        0.285142                     9.409      288.927
 28                  0.309854        8.846      313.966
        0.334566                     8.320      339.005
 27                  0.353349        7.943      358.038
        0.372133                     7.582      377.070
 26                  0.390927        7.237      396.112
        0.409720                     6.905      415.155
 25                  0.428528        6.585      434.212
        0.447337                     6.277      453.269
 24                  0.466153        5.980      472.335
        0.484970                     5.692      491.401
 23                  0.503795        5.413      510.475
        0.522620                     5.142      529.550
 22                  0.541449        4.879      548.628
        0.560278                     4.623      567.706
 21                  0.579115        4.375      586.793
        0.597953                     4.132      605.880
 20                  0.616790        3.896      624.967
        0.635628                     3.665      644.054
 19                  0.654471        3.439      663.146
        0.673314                     3.219      682.239
 18                  0.685878        3.074      694.969
        0.698442                     2.932      707.699
 17                  0.711006        2.792      720.429
        0.723570                     2.654      733.160
 16                  0.736134        2.517      745.890
        0.748698                     2.382      758.621
 15                  0.761265        2.249      771.354
        0.773832                     2.118      784.088
 14                  0.786400        1.988      796.822
        0.798967                     1.860      809.556
 13                  0.809021        1.759      819.743
        0.819075                     1.659      829.929
 12                  0.826616        1.584      837.570
        0.834157                     1.510      845.211
 11                  0.841698        1.436      852.852
        0.849239                     1.363      860.493
 10                  0.856781        1.290      868.135
        0.864323                     1.218      875.776
  9                  0.871864        1.146      883.418
        0.879406                     1.075      891.059
  8                  0.886948        1.004      898.701
        0.894489                     0.934      906.342
  7                  0.902031        0.864      913.984
        0.909573                     0.795      921.626
  6                  0.917116        0.726      929.268
        0.924658                     0.657      936.911
  5                  0.932200        0.589      944.553
        0.939743                     0.521      952.195
  4                  0.947285        0.454      959.837
        0.954828                     0.387      967.480
  3                  0.962370        0.320      975.122
        0.969913                     0.254      982.765
  2                  0.977456        0.189      990.408
        0.984999                     0.123      998.051
  1                  0.992500        0.058     1005.650
        1.000000                    -0.006     1013.250

A3.4.2 GEOS - 5 reduced vertical grid
GEOS-5 Reduced Vertical Grid (47 hybrid pressure-sigma levels)

  L     Eta Edge     Eta Mid     Altitude     Pressure
      (unitless)   (unitless)        (km)        (hPa)
========================================================
        0.000000                    80.581        0.010
 47                  0.000028       72.180        0.038
        0.000055                    68.392        0.066
 46                  0.000127       63.053        0.139
        0.000199                    59.924        0.211
 45                  0.000399       54.834        0.414
        0.000599                    51.788        0.617
 44                  0.001109       47.135        1.134
        0.001619                    44.286        1.651
 43                  0.002816       40.166        2.864
        0.004013                    37.574        4.077
 42                  0.006588       34.024        6.685
        0.009162                    31.716        9.293
 41                  0.014342       28.654       14.542
        0.019523                    26.596       19.792
 40                  0.023755       25.307       24.080
        0.027987                    24.240       28.368
 39                  0.033814       23.020       34.272
        0.039641                    22.004       40.175
 38                  0.047641       20.836       48.282
        0.055641                    19.855       56.388
 37                  0.066559       18.727       67.450
        0.077477                    17.773       78.512
 36                  0.084313       17.243       85.439
        0.091149                    16.753       92.366
 35                  0.099191       16.222      100.514
        0.107233                    15.731      108.663
 34                  0.116695       15.198      118.250
        0.126157                    14.706      127.837
 33                  0.137287       14.170      139.115
        0.148418                    13.674      150.393
 32                  0.161513       13.134      163.661
        0.174608                    12.633      176.930
 31                  0.190061       12.086      192.587
        0.205513                    11.578      208.244
 30                  0.223772       11.021      226.745
        0.242032                    10.504      245.246
 29                  0.263587        9.936      267.087
        0.285142                     9.409      288.927
 28                  0.309854        8.846      313.966
        0.334566                     8.320      339.005
 27                  0.353349        7.943      358.038
        0.372133                     7.582      377.070
 26                  0.390927        7.237      396.112
        0.409720                     6.905      415.155
 25                  0.428528        6.585      434.212
        0.447337                     6.277      453.269
 24                  0.466153        5.980      472.335
        0.484970                     5.692      491.401
 23                  0.503795        5.413      510.475
        0.522620                     5.142      529.550
 22                  0.541449        4.879      548.628
        0.560278                     4.623      567.706
 21                  0.579115        4.375      586.793
        0.597953                     4.132      605.880
 20                  0.616790        3.896      624.967
        0.635628                     3.665      644.054
 19                  0.654471        3.439      663.146
        0.673314                     3.219      682.239
 18                  0.685878        3.074      694.969
        0.698442                     2.932      707.699
 17                  0.711006        2.792      720.429
        0.723570                     2.654      733.160
 16                  0.736134        2.517      745.890
        0.748698                     2.382      758.621
 15                  0.761265        2.249      771.354
        0.773832                     2.118      784.088
 14                  0.786400        1.988      796.822
        0.798967                     1.860      809.556
 13                  0.809021        1.759      819.743
        0.819075                     1.659      829.929
 12                  0.826616        1.584      837.570
        0.834157                     1.510      845.211
 11                  0.841698        1.436      852.852
        0.849239                     1.363      860.493
 10                  0.856781        1.290      868.135
        0.864323                     1.218      875.776
  9                  0.871864        1.146      883.418
        0.879406                     1.075      891.059
  8                  0.886948        1.004      898.701
        0.894489                     0.934      906.342
  7                  0.902031        0.864      913.984
        0.909573                     0.795      921.626
  6                  0.917116        0.726      929.268
        0.924658                     0.657      936.911
  5                  0.932200        0.589      944.553
        0.939743                     0.521      952.195
  4                  0.947285        0.454      959.837
        0.954828                     0.387      967.480
  3                  0.962370        0.320      975.122
        0.969913                     0.254      982.765
  2                  0.977456        0.189      990.408
        0.984999                     0.123      998.051
  1                  0.992500        0.058     1005.650
        1.000000                    -0.006     1013.250

A3.5 MERRA vertical grids
MERRA is not a new data product, but a 30-year reanalysis done with the GMAO GEOS - 5 GCM (version 5.2.0). For more information, please see our MERRA page on the GEOS - Chem wiki.
In the vertical, the MERRA meteorological fields have 72 hybrid eta levels, extending from the surface up to 0.01 hPa. The first 31 levels from the surface upward are pure sigma levels; the rest are fixed pressure levels.
To conserve memory, you have the option of running GEOS - Chem with a reduced vertical resolution of 47 eta levels. GEOS - Chem will combine eta levels above ~80 hPa on-the-fly.

A3.5.1 MERRA native vertical grid
The native vertical resolution of the MERRA meteorological fields is identical to the GEOS - 5 72-layer native grid.

A3.5.2 MERRA reduced vertical grid
The reduced vertical resolution of the MERRA meteorological fields is identical to the GEOS - 5 47-layer reduced grid.

A3.6 GEOS - 5.7.2 vertical grids
GMAO recently released its GEOS - 5.7.2 meteorological data product, which has ultrafine horizontal resolution (0.25° x 0.3125°). For more information, please see our GEOS - 5.7.2 page on the GEOS - Chem wiki.
In the vertical, the GEOS - 5.7.2 meteorological fields have 72 hybrid eta levels, extending from the surface up to 0.01 hPa. The first 31 levels from the surface upward are pure sigma levels; the rest are fixed pressure levels. 
To conserve memory, you have the option of running GEOS - Chem with a reduced vertical resolution of 47 eta levels. GEOS - Chem will combine eta levels above ~80 hPa on-the-fly.

A3.6.1 GEOS5.7.2 native vertical grid
The native vertical resolution of the GEOS - 5.7.2 meteorological fields is identical to the GEOS - 5 72-layer native grid.

A3.6.2 GEOS5.7.2 reduced vertical grid
The reduced vertical resolution of the GEOS - 5.7.2 meteorological fields is identical to the GEOS - 5 47-layer reduced grid.
                                       
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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 4
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 4: GEOS - Chem Meteorological Fields
We compare the meteorological data products that GEOS - Chem reads from disk.
                                       
A4.1 GCAP fields used by GEOS - Chem
NOTES about GCAP met fields:
   1. A3 fields are 3-hour time averages, centered on 01:30 04:30 07:30 ... 22:30 GMT
   2. A6 fields are 6-hour time averages, centered on 00:00 06:00 12:00 18:00 GMT
   3. I6 fields are 6-hour instantaneous fields, centered on 00:00 06:00 12:00 18:00 GMT
   4. Constant fields are time-invariant
   5. Please see the GCAP page on the GEOS-Chem Wiki for more information.
Field
Type
Dimension
Quantity
Units
ALBEDO
A3
2-D
Surface albedo
unitless
PREACC
A3
2-D
Total precipitation
mm H2O/day
PRECON
A3
2-D
Convective precipitation
mm H2O/day
TS
A3
2-D
Surface temprature
K
MOLENGTH
A3
2-D
Monin-Obhukov length
m
USTAR
A3
2-D
Friction velocity
m/s
PBL
A3
2-D
Boundary layer height
m
RADSWG
A3
2-D
Incident radiation at ground
W/m2
SNICE
A3
2-D
Fraction of box covered w/ snow, land, or ocean ice
unitless
OICE
A3
2-D
Ocean or lake ice fraction
unitless
USS
A3
2-D
Zonal wind at 10m above surface
m/s
VSS
A3
2-D
Meridional wind at 10m above the surface
m/s
SOIL
A3
2-D
Volumetric water content
m3/m3
SNOWD
A3
2-D
Snow depth
m
PARDIR
A3
2-D
Direct photosynthetically-active radiation
W/m2
PARDIF
A3
2-D
Diffuse photosynthetically-active radiation
unitless
 
 
 
 
 
T
A6
3-D
Temperature
K
U
A6
3-D
Zonal wind
m/s
V
A6
3-D
Meridional wind
m/s
OPTDEPTH
A6
3-D
Optical depth
unitless
CLDF
A6
3-D
Cloud fraction
unitless
Q
A6
3-D
Specific humidity
kg H2O/kg air
MOISTQ
A6
3-D
Tendency of Q w/r/t precipitation
g H2O/kg air/day
UPDE
A6
3-D
Convective updraft flux
Pa/s
DNDE
A6
3-D
Convective downdraft flux
Pa/s
ENTRAIN
A6
3-D
Convective entrainment
Pa/s
DETRAINE
A6
3-D
Convective detrainment
Pa/s
UPDN
A6
3-D
Convective updraft flux (non-entraining plume)
Pa/s
DNDN
A6
3-D
Convective downdraft flux (non-entraining plume)
Pa/s
DETRAINN
A6
3-D
Convective detrainment (non-entraining plume)
Pa/s
 
 
 
 
 
PS
I6
2-D
Surface pressure
hPa
SLP
I6
2-D
Sea-level pressure
hPa
 
 
 
 
 
PHIS
Constant
2-D
Surface geopotential heights
m2/s2
LWI
Constant
2-D
Land fraction
unitless
                                       
A4.2 GEOS - 4 fields used by GEOS - Chem
NOTES for GEOS - 4 fields:
   1. A-3 fields are 3-hour time-averages, centered on 01:30, 04:30, 07:30, ... 22:30 GMT.
   2. A-6 fields are 6-hour time-averages, centered on 00:00, 06:00, 12:00, and 18:00 GMT.
   3. I-6 fields are 6-hour instantaneous data at 00:00, 06:00, 12:00, and 18:00 GMT.
   4. The air temperature at 2 meters is used as a proxy for the surface air temperature.
   5. Skin temperature is the temperature of the ground (or ocean) surface.
Field
Type
Dimension
Quantity
Units
LWI
I6
2-D
Land-water-ice flags
unitless
PHIS
I6
2-D
Surface geopotential heights
m2/s2
PS
I6
2-D
Surface pressure
mb
SLP
I6
2-D
Sea level pressure
mb
 
 
 
 
 
CLDTOT
A6
3-D
3-D cloud fraction (conv + large scale)
unitless
HKBETA
A6
3-D
Hack overshoot parameter
unitless
HKETA
A6
3-D
Hack convective mass flux
kg/m2/s
MOISTQ
A6
3-D
Tendency in specific humidity
g H2O/kg air/day 
OPTDEPTH
A6
3-D
Grid box optical depth
unitless
Q
A6
3-D
Specific humidity 
g H2O/kg air
T
A6
3-D
Temperature
K
U
A6
3-D
Zonal wind 
m/s
V
A6
3-D
Meridional wind 
m/s
ZMEU
A6
3-D
Zhang-McFarlane updraft entrainment
Pa/s
ZMMD
A6
3-D
Zhang-McFarlane downdraft mass flux
Pa/s
ZMMU
A6
3-D
Zhang-McFarlane updraft mass flux
Pa/s
 
 
 
 
 
ALBEDO
A3
2-D
Surface albedo (visible)
unitless
CLDFRC
A3
2-D
Column cloud fraction at ground
unitless
GWETTOP
A3
2-D
Top soil wetness 
unitless
HFLUX
A3
2-D
Sensible heat flux
W/m2
LAI
A3
2-D
Leaf area indices
%
PARDF
A3
2-D
Photosynthetically active diffuse radiation
W/m2
PARDR
A3
2-D
Photosynthetically active direct radiation
W/m2
PBLH
A3
2-D
Planetary boundary layer depth
m
PREACC
A3
2-D
Total precipitation at ground
mm H2O/day
PRECON
A3
2-D
Convective precipitation at ground
mm H2O/day
RADLWG
A3
2-D
Longwave (IR) radiation emanating from the ground
W/m2
RADSWG
A3
2-D
Solar insolation (shortwave) reaching the ground
W/m2
SNOW
A3
2-D
Snow depth (equivalent water)
mm H2O
T2M
A3
2-D
Air temperature at 2 meter elevation
K
TSKIN
A3
2-D
Skin temperature (ground T or sea surface T)
K
U10M
A3
2-D
UWND at 10 m altitude
m/s
USTAR
A3
2-D
Friction velocity
m/s
V10M
A3
2-D
VWND at 10 m altitude
m/s
Z0M
A3
2-D
Roughness height
m

A4.3 GEOS - 5 fields used by GEOS - Chem
NOTES about GEOS - 5 met fields:
   1. A3 fields are 3-hour time averages, centered on 01:30 04:30 07:30 ... 22:30 GMT
   2. A6 fields are 6-hour time averages, centered on 00:00 06:00 12:00 18:00 GMT
   3. I6 fields are 6-hour instantaneous fields, centered on 00:00 06:00 12:00 18:00 GMT
   4. NOTE: Relative Humidity in the GEOS - 5 "raw data files" is labeled as "percent" but is actually "fraction" (unitless). 
   5. Please see the GEOS-5 page on the GEOS-Chem Wiki for more information.
Field
Type
Dimension
Quantity
Units
ALBEDO
A3
2-D
Surface albedo
unitless
CLDTOT
A3
2-D
Column cloud fraction
unitless
EFLUX
A3
2-D<
Latent heat flux
W/m2
EVAP
A3
2-D
Evapotranspiration flux
unitless
FRLAKE
A3
2-D
Fraction of lake
unitless
FRLAND
A3
2-D
Fraction of land
unitless
FRLANDIC
A3
2-D
Fraction of land ice
unitless
FROCEAN
A3
2-D
Fraction of ocean
unitless
GRN
A3
2-D
Greenness index
unitless
GWETROOT
A3
2-D
Root zone soil moisture
unitless
GWETTOP
A3
2-D
Top soil moisture
unitless
HFLUX
A3
2-D
Sensible heat flux
W/m2
LAI
A3
2-D
Leaf area index
m2/m2
LWGNET
A3
2-D
Net longwave radiation at ground
W/m2
LWTUP
A3
2-D
Outgoing longwave radiation
W/m2
PARDF
A3
2-D
Diffuse photosnythetically-active radiation
W/m2
LWTUP
A3
2-D
Long
 
PARDR
A3
2-D
Direct photosynthetically-active radiation
W/m2
PBLH
A3
2-D
Planetary boundary layer thickness
m
PRECANV
A3
2-D
Anvil precipitation
kg/m2/s
PRECCON
A3
2-D
Total convective precipitation at the ground
kg/m2/s
PRECTOT
A3
2-D
Total precipitation at the ground
kg/m2/s
PRECSNO
A3
2-D
Total snow precipitation at the ground
kg/m2/s
QV2M
A3
2-D
Specific humidity at 2m
kg/kg
SNOMAS
A3
2-D
Snow depth (H2O equivalent)
m
SNODP
A3
2-D
Snow depth (geometric)
m
SWGNET
A3
2-D
Net shortwave radiation at ground
W/m2
T2M
A3
2-D
Temperature at 2m above ground
K
TROPP
A3
2-D
Tropopause pressure
hPa
TSKIN
A3
2-D
Ground (skin) temperature
K
U10M
A3
2-D
Zonal wind at 10m above ground
m/s
USTAR
A3
2-D
Friction velocity
m/s
V10M
A3
2-D
Meridional wind at 10m above ground
m/s
Z0M
A3
2-D
Roughness height
m
 
 
 
 
 
DQRCON
A6
3-D
Precipitation from convective processes
kg/m2/s
DQRLSC
A6
3-D
Precipitation from large-scale processes
kg/m2/s
DTRAIN
A6
3-D
Detrainment mass flux
kg/m2/s
QL
A6
3-D
Water mixing ratio
unitless
QI
A6
3-D
Ice mixing ratio
unitless
OPTDEPTH
A6
3-D
Overall grid-box optical depth
unitless
TAUCLI
A6
3-D
Grid-box optical depth, ice-path
unitless
TAUCLW
A6
3-D
Grid-box optical depth, water-path
unitless
CLOUD
A6
3-D
Cloud fraction
unitless
PV
A6
3-D
Ertel potential vorticity
K*m2/kg/s
OMEGA 
A6 
3-D 
Vertical pressure velocity 
Pa/s 
QV
A6
3-D
Specific humidity
kg/kg
RH
A6
3-D
Relative Humidity
unitless
T 
A6 
3-D 
Temperature 
K 
U
A6
3-D
Zonal wind
m/s
V
A6
3-D
Meridional wind
m/s
DQIDTMST
A6
3-D
Tendency of QV in ice processes
kg/kg/s
DQLDTMST
A6
3-D
Tendency of QV in moist processes
kg/kg/s
DQVDTMST
A6
3-D
Tendency of QV in vapor processes
kg/kg/s
MOISTQ
A6
3-D
Overall tendency of QV
kg/kg/s
CMFMC
A6
3-D
Convective mass flux
kg/m2/s
 
 
 
 
 
LWI
I6
2-D
Land/water/ice flags
m/s
PS
I6
2-D
Surface pressure
hPa
SLP
I6
2-D
Sea-level pressure
hPa
TO3
I6
2-D
Total ozone column
DU
TTO3
I6
2-D
Tropospheric ozone column
DU

A4.4 GEOS - 5.7.2 fields used by GEOS - Chem
Notes about GEOS - 5.7.2 met fields:
   1. A1 fields are 1-hr time-averaged fields with timestamps (i.e. center of averaging period): 00:30, 01:30, 02:30 ... 23:30 GMT
   2. A3 fields are 3-hr time-averaged fields with timestamps (i.e. center of averaging period): 01:30, 04:30, 07:30, 10:30, 13:30, 16:30, 19:30, 22:30 GMT
   3. I3 fields 3-hr instantaneous fields with timestamps: 00:00, 03:00, 06:00, 09:00, 12:00, 15:00, 18:00, 21:00 GMT.
   4. Constant fields are time-invariant.
   5. For more information about the GEOS - 5.7.2 raw data, please see the GEOS - 5.7.2 page on the GEOS - Chem wiki.
   6. For detailed information about how the individual GEOS - 5.7.2 fields were regridded, see the List of GEOS - 5.7.2 met fields page on the GEOS - Chem wiki.
Field
Type
Dimension
Units
Quantity
FRLAKE 
Constant
2-D
Fraction of lake type in grid box 
fraction 
FRLAND 
Constant
2-D
Fraction of land type in grid box 
fraction 
FRLANDIC 
Constant
2-D
Fraction of land ice type in grid box 
fraction 
FROCEAN 
Constant
2-D
Fraction of ocean in grid box 
fraction 
PHIS
Constant
2-D
Surface geopotential 
m[2] s[-2] 
 
 
 
 
 
ALBEDO 
A1
2-D
Surface albedo 
fraction 
CLDTOT 
A1
2-D
Total cloud fraction 
fraction 
EFLUX 
A1
2-D
Latent heat flux (positive upward) 
W m[-2] 
EVAP 
A1
2-D
Surface evaporation 
kg m[-2] s[-2] 
FRSEAICE 
A1
2-D
Fraction of sea ice 
fraction 
FRSNO 
A1
2-D
Fractional snow-covered area 
fraction 
GRN 
A1
2-D
Vegetation greenness fraction 
fraction 
GWETROOT 
A1
2-D
Root zone soil wetness 
fraction 
GWETTOP 
A1
2-D
Root zone soil wetness 
fraction 
HFLUX 
A1
2-D
Sensible heat flux (positive upward) 
W m[-2] 
LAI 
A1
2-D
Leaf area index 
m[2] m[-2] 
LWGNT 
A1
2-D
Surface net downward longwave flux 
W m[-2] 
LWI 
A1
2-D
Land/water/ice flags 
unitless 
LWTUP 
A1
2-D
Upward longwave flux at top of atmosphere (TOA) 
W m[-2] 
PARDF 
A1
2-D
Surface downward PAR diffuse flux 
W m[-2] 
PARDR 
A1
2-D
Surface downward PAR beam flux 
W m[-2] 
PBLH 
A1
2-D
Planetary boundary layer height above surface 
m 
PRECANV 
A1
2-D
Surface precipitation flux from anvils 
kg m[-2] s[-2] 
PRECCON 
A1
2-D
Surface precipitation flux from convection 
kg m[-2] s[-2] 
PRECLSC 
A1
2-D
Surface precipitation flux from large-scale 
kg m[-2] s[-2] 
PRECSNO 
A1
2-D
Surface snowfall flux 
kg m[-2] s[-2] 
PRECTOT 
A1
2-D
Total surface precipitation flux 
kg m[-2] s[-2] 
QV2M 
A1
2-D
Specific humidity at 2 m above the displacement height 
kg kg[-1] 
SEAICE00 
A1
2-D
Fraction of grid box that has < 10% sea ice coverage 
fraction 
SEAICE10 
A1
2-D
Fraction of grid box that has 10-20% sea ice coverage 
fraction 
SEAICE20 
A1
2-D
Fraction of grid box that has 20-30% sea ice coverage 
fraction 
SEAICE30 
A1
2-D
Fraction of grid box that has 30-40% sea ice coverage 
fraction 
SEAICE40 
A1
2-D
Fraction of grid box that has 40-50% sea ice coverage 
fraction 
SEAICE50 
A1
2-D
Fraction of grid box that has 50-60% sea ice coverage 
fraction 
SEAICE60 
A1
2-D
Fraction of grid box that has 60-70% sea ice coverage 
fraction 
SEAICE70 
A1
2-D
Fraction of grid box that has 70-80% sea ice coverage 
fraction 
SEAICE80 
A1
2-D
Fraction of grid box that has 80-90% sea ice coverage 
fraction 
SEAICE90 
A1
2-D
Fraction of grid box that has > 90% sea ice coverage 
fraction 
SLP 
A1
2-D
Sea level pressure 
hPa 
SNODP 
A1
2-D
Snow depth 
m 
SNOMAS 
A1
2-D
Snow mass 
kg m[-2] 
SWGDN 
A1
2-D
Surface incident shortwave flux 
W m[-2] 
SWGNT 
A1
2-D
Net surface downward shortwave flux 
W m[-2] 
TROPPT 
A1
2-D
T based tropopause pressure 
hPa 
TS 
A1
2-D
Surface skin temperature 
K 
T2M 
A1
2-D
Temperature 2 m above displacement height 
K 
U10M 
A1
2-D
Eastward wind 10 m above displacement height 
m s[-1] 
USTAR 
A1
2-D
Friction velocity 
m s[-1] 
V10M 
A1
2-D
Northward wind 10 m above displacement height 
m s[-1] 
Z0M 
A1
2-D
Roughness length, momentum 
m 
 
 
 
 
 
CLOUD 
A3cld
3-D
Total cloud fraction in grid box 
fraction 
QI
A3cld
3-D
Cloud ice mixing ratio
kg kg[-1] 
QIAN 
A3cld
3-D
Cloud ice mixing ratio  -  anvils 
kg kg[-1] 
QILS 
A3cld
3-D
Cloud ice mixing ratio  -  large-scale 
kg kg[-1] 
QL
A3cld
3-D
Cloud liquid water mixing ratio
kg kg[-1] 
QLAN
A3cld
3-D
Cloud liquid water mixing ratio  -  anvil
kg kg[-1] 
QLLS
A3cld
3-D
Cloud liquid water mixing ratio  -  large-scale
kg kg[-1] 
TAUCLI 
A3cld
3-D
In-cloud ice cloud optical thickness (visible band) 
unitless 
TAUCLW 
A3cld
3-D
In-cloud liquid cloud optical thickness (visible band) 
unitless 
OPTDEPTH 
A3cld
3-D
Total in-cloud optical depth (visible band) 
unitless 
 
 
 
 
 
CMFMC 
A3dyn
3-D
Upward moist convective mass flux 
kg m[-2] s[-2] 
DTRAIN 
A3dyn
3-D
Detrainment cloud mass flux 
kg m[-2] s[-2] 
OMEGA 
A3dyn
3-D
Vertical pressure velocity 
Pa s[-1] 
RH 
A3dyn
3-D
Relative humidity 
unitless 
U 
A3dyn
3-D
Eastward component of wind 
m s[-1] 
V 
A3dyn
3-D
Northward component of wind 
m s[-1] 
 
 
 
 
 
DQRCU 
A3mstC
3-D
Precipitation production rate  -  convective 
kg kg[-1] s[-1] 
DQRLSAN 
A3mstC
3-D
Precipitation production rate  -  large-scale + anvil 
kg kg[-1] s[-1] 
REEVAPCN 
A3mstC
3-D
Evaporation of precipitating convective condensate 
kg kg[-1] s[-1] 
REEVAPLS(AN)
A3mstC
3-D
Evaporation of precipitating LS + anvil condensate 
kg kg[-1] s[-1] 
 
 
 
 
 
PFICU 
A3mstE
3-D
Downward flux of ice precipitation  -  convective 
kg m[-2] s[-1] 
PFILSAN 
A3mstE
3-D
Downward flux of ice precip  -  large-scale + anvil 
kg m[-2] s[-1] 
PFLCU 
A3mstE
3-D
Downward flux of liquid precipitation  -  convective 
kg m[-2] s[-1] 
PFLLSAN 
A3mstE
3-D
Downward flux of liquid precip  -  large-scale + anvil 
kg m[-2] s[-1] 
 
 
 
 
 
PS 
I3
2-D
Surface pressure 
Pa 
PV 
I3
3-D
Ertel potential vorticity 
K m[2] kg[-1] s[-1] 
QV 
I3
3-D
Specific humidity 
kg kg[-1] 
T 
I3
3-D
Air temperature 
K 

A4.5 MERRA fields used by GEOS - Chem
Notes about MERRA met fields:
   1. A1 fields are 1-hr time-averaged fields with timestamps (i.e. center of averaging period): 00:30, 01:30, 02:30 ... 23:30 GMT
   2. A3 fields are 3-hr time-averaged fields with timestamps (i.e. center of averaging period): 01:30, 04:30, 07:30, 10:30, 13:30, 16:30, 19:30, 22:30 GMT
   3. I6 fields 6-hr instantaneous fields with timestamps: 00:00, 06:00, 12:00, 18:00 GMT.
   4. Constant fields are time-invariant.
   5. For more information about the MERRA raw data, please see the MERRA post on the GEOS - Chem wiki.
   6. For detailed information about how the individual MERRA fields were regridded, see the List of MERRA met fields post on the GEOS - Chem wiki.
   7. For more information about the native MERRA grids, see the MERRA grid structure post on the GEOS - Chem wiki.
Field
Type
Dimension
Units
Quantity
FRLAKE 
Constant
2-D
Fraction of lake type in grid box 
fraction 
FRLAND 
Constant
2-D
Fraction of land type in grid box 
fraction 
FRLANDIC 
Constant
2-D
Fraction of land ice type in grid box 
fraction 
FROCEAN 
Constant
2-D
Fraction of ocean in grid box 
fraction 
PHIS
Constant
2-D
Surface geopotential 
m[2] s[-2] 
 
 
 
 
 
ALBEDO 
A1
2-D
Surface albedo 
fraction 
CLDTOT 
A1
2-D
Total cloud fraction 
fraction 
EFLUX 
A1
2-D
Latent heat flux (positive upward) 
W m[-2] 
EVAP 
A1
2-D
Surface evaporation 
kg m[-2] s[-2] 
FRSEAICE 
A1
2-D
Fraction of sea ice 
fraction 
FRSNO 
A1
2-D
Fractional snow-covered area 
fraction 
GRN 
A1
2-D
Vegetation greenness fraction 
fraction 
GWETROOT 
A1
2-D
Root zone soil wetness 
fraction 
GWETTOP 
A1
2-D
Root zone soil wetness 
fraction 
HFLUX 
A1
2-D
Sensible heat flux (positive upward) 
W m[-2] 
LAI 
A1
2-D
Leaf area index 
m[2] m[-2] 
LWGNT 
A1
2-D
Surface net downward longwave flux 
W m[-2] 
LWI 
A1
2-D
Land/water/ice flags 
unitless 
LWTUP 
A1
2-D
Upward longwave flux at top of atmosphere (TOA) 
W m[-2] 
PARDF 
A1
2-D
Surface downward PAR diffuse flux 
W m[-2] 
PARDR 
A1
2-D
Surface downward PAR beam flux 
W m[-2] 
PBLH 
A1
2-D
Planetary boundary layer height above surface 
m 
PRECANV 
A1
2-D
Surface precipitation flux from anvils 
kg m[-2] s[-2] 
PRECCON 
A1
2-D
Surface precipitation flux from convection 
kg m[-2] s[-2] 
PRECLSC 
A1
2-D
Surface precipitation flux from large-scale 
kg m[-2] s[-2] 
PRECSNO 
A1
2-D
Surface snowfall flux 
kg m[-2] s[-2] 
PRECTOT 
A1
2-D
Total surface precipitation flux 
kg m[-2] s[-2] 
QV2M 
A1
2-D
Specific humidity at 2 m above the displacement height 
kg kg[-1] 
SEAICE00 
A1
2-D
Fraction of grid box that has < 10% sea ice coverage 
fraction 
SEAICE10 
A1
2-D
Fraction of grid box that has 10-20% sea ice coverage 
fraction 
SEAICE20 
A1
2-D
Fraction of grid box that has 20-30% sea ice coverage 
fraction 
SEAICE30 
A1
2-D
Fraction of grid box that has 30-40% sea ice coverage 
fraction 
SEAICE40 
A1
2-D
Fraction of grid box that has 40-50% sea ice coverage 
fraction 
SEAICE50 
A1
2-D
Fraction of grid box that has 50-60% sea ice coverage 
fraction 
SEAICE60 
A1
2-D
Fraction of grid box that has 60-70% sea ice coverage 
fraction 
SEAICE70 
A1
2-D
Fraction of grid box that has 70-80% sea ice coverage 
fraction 
SEAICE80 
A1
2-D
Fraction of grid box that has 80-90% sea ice coverage 
fraction 
SEAICE90 
A1
2-D
Fraction of grid box that has > 90% sea ice coverage 
fraction 
SLP 
A1
2-D
Sea level pressure 
hPa 
SNODP 
A1
2-D
Snow depth 
m 
SNOMAS 
A1
2-D
Snow mass 
kg m[-2] 
SWGDN 
A1
2-D
Surface incident shortwave flux 
W m[-2] 
SWGNT 
A1
2-D
Net surface downward shortwave flux 
W m[-2] 
TROPPT 
A1
2-D
T based tropopause pressure 
hPa 
TS 
A1
2-D
Surface skin temperature 
K 
T2M 
A1
2-D
Temperature 2 m above displacement height 
K 
U10M 
A1
2-D
Eastward wind 10 m above displacement height 
m s[-1] 
USTAR 
A1
2-D
Friction velocity 
m s[-1] 
V10M 
A1
2-D
Northward wind 10 m above displacement height 
m s[-1] 
Z0M 
A1
2-D
Roughness length, momentum 
m 
 
 
 
 
 
CLOUD 
A3
3-D
Total cloud fraction in grid box 
fraction 
CMFMC 
A3
3-D
Upward moist convective mass flux 
kg m[-2] s[-2] 
DQRCU 
A3
3-D
Precipitation production rate  -  convective 
kg kg[-1] s[-1] 
DQRLSAN 
A3
3-D
Precipitation production rate  -  large-scale + anvil 
kg kg[-1] s[-1] 
DQIDTMST 
A3
3-D
Ice tendency from moist physics 
kg kg[-1] s[-1] 
DQLDTMST 
A3
3-D
Liquid water tendency from moist physics 
kg kg[-1] s[-1] 
DQVDTMST 
A3
3-D
Water vapor tendency from moist physics 
kg kg[-1] s[-1] 
DTRAIN 
A3
3-D
Detrainment cloud mass flux 
kg m[-2] s[-2] 
MOISTQ 
A3
3-D
Overall tendency of QV 
g kg[-1] day[-1] 
OPTDEPTH 
A3
3-D
Total in-cloud optical depth (visible band) 
unitless 
PFICU 
A3
3-D
Downward flux of ice precipitation  -  convective 
kg m[-2] s[-1] 
PFILSAN 
A3
3-D
Downward flux of ice precip  -  large-scale + anvil 
kg m[-2] s[-1] 
PFLCU 
A3
3-D
Downward flux of liquid precipitation  -  convective 
kg m[-2] s[-1] 
PFLLSAN 
A3
3-D
Downward flux of liquid precip  -  large-scale + anvil 
kg m[-2] s[-1] 
QI 
A3
3-D
Cloud ice mixing ratio 
kg kg[-1] 
QL 
A3
3-D
Cloud liquid water mixing ratio 
kg kg[-1] 
QV 
A3
3-D
Specific humidity 
kg kg[-1] 
REEVAPCN 
A3
3-D
Evaporation of precipitating convective condensate 
kg kg[-1] s[-1] 
REEVAPLS 
A3
3-D
Evaporation of precipitating large-scale + anvil condensate 
kg kg[-1] s[-1] 
T 
A3
3-D
Air temperature 
K 
TAUCLI 
A3
3-D
In-cloud ice cloud optical thickness (visible band) 
unitless 
TAUCLW 
A3
3-D
In-cloud liquid cloud optical thickness (visible band) 
unitless 
U 
A3
3-D
Eastward component of wind 
m s[-1] 
V 
A3
3-D
Northward component of wind 
m s[-1] 
 
 
 
 
 
OMEGA 
I6
3-D
Vertical pressure velocity 
Pa s[-1] 
PS 
I6
2-D
Surface pressure 
hPa 
PV 
I6
3-D
Ertel potential vorticity 
K m[2] kg[-1] s[-1] 
RH 
I6
3-D
Relative humidity 
unitless 

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 5
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 5: GEOS - Chem Diagnostics
We list the various diagnostic quantities that you can archive with GEOS - Chem.
                                       
This documentation is also contained in the comments to source code files diag3.F, diag03_mod.F, diag04_mod.F, diag42_mod.F, and diag56_mod.F. For each diagnostic, the following fields are shown:
Flag
Dimension
Quantity
Units
Category
where CATEGORY is the 8-character name used by GAMAP to reference a particular diagnostic field. Information about how to set the different flags in the input.geos file can be found in Chapter 5. DIMENSION is usually 2-D or 3-D, with I,J,L for longitude, latitude and level indices. N as a third or fourth dimension refers to the number of tracers that a diagnostic can carry. 
 
ND01
Dimension
RADON 222 - LEAD 210 - BERYLLIUM 7 SOURCE
Units
Category
1
(I,J,L)
222Rn emissions
[kg/s]
RN-SRCE
2
(I,J,L)
210Pb emissions
[kg/s]
RN-SRCE
3
(I,J,L)
7Be emissions
[kg/s]
RN-SRCE
 
ND02
Dimension
RADON 222 - LEAD 210 - BERYLLIUM 7 DECAY
Units
Category
1
(I,J,L)
222Rn loss
[kg/s]
RN-DECAY
2
(I,J,L)
210Pb loss
[kg/s]
RN-DECAY
3
(I,J,L)
7Be loss
[kg/s]
RN-DECAY
 
ND03
Dimension
MERCURY EMISSIONS, PRODUCTION, LOSS
Units
Category
1
(I,J)
Anthropogenic Hg0 emission
[kg]
HG-SRCE
2
(I,J)
Total mass of oceanic Hg0
[kg]
HG-SRCE
3
(I,J)
Oceanic emission of Hg0
[kg]
HG-SRCE
4
(I,J)
Land reemission of Hg0
[kg]
HG-SRCE
5
(I,J)
Land natural emission of Hg0
[kg]
HG-SRCE
6
(I,J)
Anthropogenic Hg2 emission
[kg]
HG-SRCE
7
(I,J)
Total mass of oceanic Hg2
[kg]
HG-SRCE
8
(I,J)
Mass of Hg2 sunk in the ocean
[kg]
HG-SRCE
9
(I,J)
Anthropogenic HgP emission
[kg]
HG-SRCE
10
(I,J)
Total oceanic mercury
[kg]
HG-SRCE
11
(I,J)
Total mass of oceanic HgP
[kg]
HG-SRCE
12
(I,J)
Mass of organic carbon sunk in ocean
[kg]
HG-SRCE
13
(I,J)
Emissions from biomass burning
[kg]
HG-SRCE
14
(I,J)
Emissions from vegetation
[kg]
HG-SRCE
15
(I,J)
Emissions from soils
[kg]
HG-SRCE
16
(I,J)
Flux-up Hg0 volat from ocean
[kg]
HG-SRCE
17
(I,J)
Flux-down Hg0 dry dep to ocean
[kg]
HG-SRCE
18
(I,J)
Snow emission of Hg
[kg]
HG-SRCE
19
(I,J,L)
Production of Hg2 from Hg0
[kg]
PL-HG2-$
20
(I,J,L)
Production of Hg2 from rxn w/ OH
[kg]
PL-HG2-$
21
(I,J,L)
Production of Hg2 from rxn w/ O3
[kg]
PL-HG2-$
22
(I,J,L)
Loss of Hg2 from rxn w/ sea salt
[kg]
PL-HG2-$
23
(I,J,L)
Loss rate of Hg2 from rxn w/ sea salt
[s-1]
PL-HG2-$
24
(I,J,L)
Production of Hg2 from Br
[kg]
PL-HG2-$
25
(I,J,L)
Br concentration
[kg]
PL-HG2-$
26
(I,J,L)
BrO concentration
[kg]
PL-HG2-$
27
(I,J,L)
Particulate bound mercury
[pptv]
PL-HG2-$
28
(I,J,L)
Reactive gaseous mercury
[pptv]
PL-HG2-$
29
(I,J,L)
+ OCEAN tagged tracers
[kg]
OCEAN-HG
30
(I,J,L)
Total Hg in snowpack
[kg]
SNOW-HG
 
ND04
Dimension
CO2 SOURCES
Units
Category
1
(I,J)
CO2 fossil fuel emiss
[atoms C/cm2/s]
CO2-SRCE
2
(I,J)
CO2 ocean emissions
[atoms C/cm2/s]
CO2-SRCE
3
(I,J)
CO2 balanced biosphere
[atoms C/cm2/s]
CO2-SRCE
4
(I,J)
CO2 biomass burning emiss
[atoms C/cm2/s]
CO2-SRCE
5
(I,J)
CO2 biofuel emission
[atoms C/cm2/s]
CO2-SRCE
6
(I,J)
CO2 net terrestrial exchange
[atoms C/cm2/s]
CO2-SRCE
7
(I,J)
CO2 ship emissions
[atoms C/cm2/s]
CO2-SRCE
8
(I,J,L)
CO2 aircraft emissions
[atoms C/cm2/s]
CO2-SRCE
9
(I,J,L)
CO2 chemical source
[atoms C/cm2/s]
CO2-SRCE
10
(I,J)
CO2 chemical source surface correction
[atoms C/cm2/s]
CO2-SRCE
 
ND05
Dimension
PROD/LOSS for SULFATE CHEMISTRY QUANTITIES
Units
Category
1
(I,J,L)
P(SO2) from DMS + OH
[kg S]
PL-SUL-$
2
(I,J,L)
P(SO2) from DMS + NO3
[kg S]
PL-SUL-$
3
(I,J,L)
Total P(SO2)
[kg S]
PL-SUL-$
4
(I,J,L)
P(MSA) from DMS
[kg S]
PL-SUL-$
5
(I,J,L)
P(SO4) gas phase
[kg S]
PL-SUL-$
6
(I,J,L)
P(SO4) by cloud H2O2
[kg S]
PL-SUL-$
7
(I,J,L)
P(SO4) by cloud O3
[kg S]
PL-SUL-$
8
(I,J,L)
P(SO4) by seasalt O3
[kg S]
PL-SUL-$
9
(I,J,L)
L(OH) by DMS
[kg OH]
PL-SUL-$
10
(I,J,L)
L(NO3) by DMS
[kg NO3]
PL-SUL-$ 
 
ND06
Dimension
DESERT DUST EMISSIONS
Units
Category
1
(I,J)
DST1 (Dust aerosol, Reff = 0.7 microns)
[kg]
DUSTSRCE
2
(I,J)
DST2 (Dust aerosol, Reff = 1.4 microns)
[kg]
DUSTSRCE
3
(I,J)
DST3 (Dust aerosol, Reff = 2.4 microns)
[kg]
DUSTSRCE
4
(I,J)
DST4 (Dust aerosol, Reff = 4.5 microns)
[kg]
DUSTSRCE
 
ND07
Dimension
SOURCES OF BLACK CARBON & ORGANIC CARBON
(initially developed for offline aerosol simulations)
 
 
1
(I,J)
BLACK CARBON from anthro sources
[kg]
BC-ANTH
2
(I,J)
BLACK CARBON from biomass burning
[kg]
BC-BIOB
3
(I,J)
BLACK CARBON from biofuels
[kg]
BC-BIOF
4
(I,J,L)
Hydrophilic BC from Hydrophobic BC
[kg]
PL-BC=$
5
(I,J)
ORGANIC CARBON from anthro sources
[kg]
OC-ANTH
6
(I,J)
ORGANIC CARBON from biomass burning
[kg]
OC-BIOB
7
(I,J)
ORGANIC CARBON from biofuels
[kg]
OC-BIOF
8
(I,J)
ORGANIC CARBON from biogenic sources
[kg]
OC-BIOG
9
(I,J,L)
Hydrophilic OC from Hydrophobic OC
[kg]
PL-OC=$ 
10
(I,J)
ORGANIC CARBON : a-pinene source
[kg]
OC-ALPH
11
(I,J)
ORGANIC CARBON : limonene source
[kg]
OC-LIMO
12
(I,J)
ORGANIC CARBON : terpene source
[kg]
OC-TERP
13
(I,J)
ORGANIC CARBON : alcohol source
[kg]
OC-ALCO
14
(I,J)
ORGANIC CARBON : sesquiterpene source
[kg]
OC-SESQ
15
(I,J,L)
SOA produced from ALPH + LIMO + TERP tracer
[kg]
PL-OC=$
16
(I,J,L)
SOA produced from ALCO tracer
[kg]
PL-OC=$
17
(I,J,L)
SOA produced from SESQ
[kg]
PL-OC=$
18
(I,J,L)
SOA produced from ISOP
[kg]
PL-OC=$
19
(I,J,L)
SOA produced from Aromatics
[kg]
PL-OC=$
20
(I,J,L)
SOAG production from GLYX in aerosol
[kg]
SOAGM=$
21
(I,J,L)
SOAM production from MGLY in aerosol
[kg] 
SOAGM=$
22
(I,J,L)
SOAG production from GLYX in cloud
[kg] 
SOAGM=$
23
(I,J,L)
SOAM production from MGLY in cloud
[kg] 
SOAGM=$
NOTE: Orange lines indicate output only available for simulations with the secondary organic aerosol (SOA) chemistry mechanism.
 
ND08
Dimension
SEA SALT EMISSIONS
Units
Category
1
(I,J)
Accumulation mode seasalt
[kg]
SALTSRCE
2
(I,J)
Coarse mode seasalt
[kg]
SALTSRCE
 
ND09
Dimension
HCN & CH3CN sources & sinks
Units
Category
1
(I,J,L,N)
Loss of tagged tracer to OH
[kg]
HCN-PL-$
2
(I,J)
HCN from biomass burning
[molec/cm2/s]
HCN-SRCE
3
(I,J)
CH3CN from biomass burning
[molec/cm2/s]
HCN-SRCE
4
(I,J)
HCN from domestic fossil fuel
[molec/cm2/s]
HCN-SRCE
5
(I,J)
CH3CN from domestic fossil fuel
[molec/cm2/s]
HCN-SRCE
6
(I,J)
HCN loss to ocean uptake
[molec/cm2/s]
HCN-SRCE
7
(I,J)
CH3CN loss to ocean uptake
[molec/cm2/s]
HCN-SRCE
 
ND10
Dimension
H2-DEUTERIUM SOURCES (EMISSIONS, PRODUCTION, LOSS)
Units
Category
1
(I,J,L)
Loss of H2 by OH
[molec H2/cm3/s]
PL-H2HD-$
2
(I,J,L)
Production of H2 from Isoprene
[molec H2/cm3/s]
PL-H2HD-$
3
(I,J,L)
Production of H2 from CH4
[molec H2/cm3/s]
PL-H2HD-$
4
(I,J,L)
Production of H2 from CH3OH
[molec H2/cm3/s]
PL-H2HD-$
5
(I,J,L)
Production of H2 from MONO
[molec H2/cm3/s]
PL-H2HD-$
6
(I,J,L)
Production of H2 from ACET
[molec H2/cm3/s]
PL-H2HD-$
7
(I,J,L)
Loss of H2 by stratospheric O1D
[molec H2/cm3/s]
PL-H2HD-$
8
(I,J,L)
Loss of HD by OH
[molec HD/cm3/s]
PL-H2HD-$
9
(I,J,L)
Production of HD from Isoprene
[molec HD/cm3/s]
PL-H2HD-$
10
(I,J,L)
Production of HD from CH4
[molec HD/cm3/s]
PL-H2HD-$
11
(I,J,L)
Production of HD from CH3OH
[molec HD/cm3/s]
PL-H2HD-$
12
(I,J,L)
Production of HD from MONO
[molec HD/cm3/s]
PL-H2HD-$
13
(I,J,L)
Production of HD from ACET
[molec HD/cm3/s]
PL-H2HD-$
14
(I,J,L)
Loss of HD by stratospheric O1D
[molec HD/cm3/s]
PL-H2HD-$
15
(I,J,L)
Ratio of OH k rates kH2/kHD
[unitless]
PL-H2HD-$
16
(I,J)
Fossil Fuel H2 (anthropogenic)
[molec HD/cm2/s]
H2HD-SRC
17
(I,J)
Biomass Burning of H2
[molec HD/cm2/s]
H2HD-SRC
18
(I,J)
Biofuel Burning of H2
[molec HD/cm2/s]
H2HD-SRC
19
(I,J)
Ocean emissions of H2
[molec HD/cm2/s]
H2HD-SRC
20
(I,J)
Ocean emissions of HD
[molec HD/cm2/s]
H2HD-SRC
 
ND11
Dimension
ACETONE SOURCES & SINKS
Units
Category
1
(I,J)
Acetone source from MONOTERPENES
[at C/cm2/s]
ACETSRCE
2
(I,J)
Acetone source from METHYL BUTENOL
[at C/cm2/s]
ACETSRCE
3
(I,J)
Acetone source from DIRECT BIOGENIC EMISSION
[at C/cm2/s]
ACETSRCE
4
(I,J)
Acetone source from OCEANS
[at C/cm2/s]
ACETSRCE
5
(I,J)
Acetone sink from OCEANS
[at C/cm2/s]
ACETSRCE
 
ND12
Dimension
DISTRIBUTION OF SURFACE EMISSIONS IN THE BL
Units
Category
1
(I,J,L)
Fraction of boundary layer occupied by level L
[unitless]
EMDIS-BL
 
ND13
Dimension
TROPOSPHERIC SULFUR EMISSIONS
Units
Category
1
(I,J)
Biogenic DMS
[kg S]
DMS-BIOG
2
(I,J,L)
Aircraft SO2 (1 <= L <= ND13)
[kg S]
SO2-AC-$
3
(I,J,L)
Anthropognic SO2 (1 <= L <= 2 )
[kg S]
SO2-AN-$
4
(I,J)
Biomass SO2
[kg S]
SO2-BIOB
5
(I,J)
Biofuel SO2
[kg S]
SO2-BIOF
6
(I,J,L)
Non-eruptive volcano SO2 (1 <= L <= ND13)
[kg S]
SO2-NV-$
7
(I,J,L)
Eruptive volcano SO2 (1 <= L< = ND13)
[kg S]
SO2-EV-$
8
(I,J)
Ship SO2
[kg S]
SO2-SHIP
9
(I,J,L)
Anthropogenic SO4 (1 <= L <= 2 )
[kg S]
SO4-AN-$
10
(I,J)
Biofuel SO4
[kg S]
SO4-BIOF
11
(I,J)
Natural NH3
[kg S]
NH3-NATU
12
(I,J)
Anthropogenic NH3
[kg]
NH3-AN-$
13
(I,J)
Biomass NH3
[kg]
NH3-BIOB
14
(I,J)
Biofuel NH3
[kg]
NH3-BIOF
 
ND14
Dimension
UPWARD MASS FLUX DUE TO WET CONVECTION
Units
Category
1
(I,J,L,N)
Mass change due to cloud convection
[kg/s]
CV-FLX-$
 
ND15
Dimension
UPWARD MASS FLUX FROM BOUNDARY-LAYER MIXING
Units
Category
1
(I,J,L,N)
Mass change due to boundary-layer mixing
[kg/s]
TURBMC-$
 
ND16
Dimension
AREAL FRACTION OF PRECIP
Units
Category
1
(I,J,L)
Fraction of grid box having rainout + washout (large-scale precip)
[unitless]
WD-FRC-$
2
(I,J,L)
Fraction of grid box having rainout + washout (convectvive precip)
[unitless]
WD-FRC-$
 
ND17
Dimension
RAINOUT FRACTION IN PRECIP
Units
Category
1
(I,J,L,N)
Fraction of soluble tracer lost to rainout (large-scale precip)
[unitless]
WD-LSR-$
2
(I,J,L,N)
Fraction of soluble tracer lost to rainout (convective precip)
[unitless]
WD-CVR-$
 
ND18
Dimension
WASHOUT FRACTION IN PRECIP
Units
Category
1
(I,J,L,N)
Fraction of soluble tracer lost to washout (large-scale precip)
[unitless]
WD-LSW-$
2
(I,J,L,N)
Fraction of soluble tracer lost to washout (convective precip)
[unitless]
WD-CVW-$
 
ND19
Dimension
CH4 LOSS
Units
Category
1
(I,J,L)
CH4 removal by OH
[kg CH4]
CH4-LOSS
 
ND20
Dimension
O3 PROD/LOSS
Units
Category
1
(I,J,L,2)
Save O3 prod/loss rates to disk
[molec/cm3/s]

 
ND21
Dimension
CLOUD OPTICAL DEPTHS AND CLOUD FRACTIONS
Units
Category
1
(I,J,L)
OPTD Cloud Optical Depth
[unitless]
OD-MAP-$
2
(I,J,L)
CLDTOT 3-D Total Cloud fraction (GEOS - 3,GEOS - 4)
unitless]
OD-MAP-$
3
(I,J,L)
CLRO Random Overlap Cloud Fraction
[unitless]
OD-MAP-$
4
(I,J,L)
OPD Mineral Dust Optical Depth (400 nm)
[unitless]
OD-MAP-$
5
(I,J,L)
SD Mineral Dust Surface Area
[cm2/cm3]
OD-MAP-$
6
(I,J,L)
OPSO4 Sulfate Optical Depth (400 nm)
[unitless]
OD-MAP-$
7
(I,J,L)
HGSO4 Hygroscopic growth of SO4
[unitless]
OD-MAP-$
8
(I,J,L)
SSO4 Sulfate Surface Area
[cm2/cm3]
OD-MAP-$
9
(I,J,L)
OPBC Black Carbon Optical Depth (400 nm)
[unitless]
OD-MAP-$
10
(I,J,L)
HGBC Hygroscopic growth of BC
[unitless]
OD-MAP-$
11
(I,J,L)
SBC Black Carbon Surface Area
[cm2/cm3]
OD-MAP-$
12
(I,J,L)
OPOC Organic C Optical Depth (400 nm)
[unitless]
OD-MAP-$
13
(I,J,L)
HGOC Hygroscopic growth of OC
[unitless]
OD-MAP-$
14
(I,J,L)
SOC Organic Carbon Surface Area
[cm2/cm3]
OD-MAP-$
15
(I,J,L)
OPSSa Sea Salt (accum) Opt Depth (400 nm)
[unitless]
OD-MAP-$
16
(I,J,L)
HGSSa Hygroscopic growth of SSa
[unitless]
OD-MAP-$
17
(I,J,L)
SSSa Sea Salt (accum) Surface Area
[cm2/cm3]
OD-MAP-$
18
(I,J,L)
OPSSc Sea Salt (coarse) Opt Depth(400 nm)
[unitless]
OD-MAP-$
19
(I,J,L)
HGSSc Hygroscopic growth of SSc
[unitless]
OD-MAP-$
20
(I,J,L)
SSSc Sea Salt (coarse) Surface Area
[cm2/cm3]
OD-MAP-$
21
(I,J,L)
OPD1 Dust bin 1 AOD (550nm)
[unitless]
OD-MAP-$
22
(I,J,L)
OPD1 Dust bin 2 AOD (550nm)
[unitless]
OD-MAP-$
23
(I,J,L)
OPD1 Dust bin 3 AOD (550nm)
[unitless]
OD-MAP-$
24
(I,J,L)
OPD1 Dust bin 4 AOD (550nm)
[unitless]
OD-MAP-$
25
(I,J,L)
OPD1 Dust bin 5 AOD (550nm)
[unitless]
OD-MAP-$
26
(I,J,L)
OPD1 Dust bin 6 AOD (550nm)
[unitless]
OD-MAP-$
27
(I,J,L)
OPD1 Dust bin 7 AOD (550nm)
[unitless]
OD-MAP-$
 
ND22
Dimension
PHOTOLYSIS RATES (aka J-Values)
Units
Category
1
(I,J,L)
J(NO2)
[1/s]
JV-MAP-$
2
(I,J,L)
J(HNO3)
[1/s]
JV-MAP-$
3
(I,J,L)
J(H2O2)
[1/s]
JV-MAP-$
4
(I,J,L)
J(CH2O)
[1/s]
JV-MAP-$
5
(I,J,L)
J(O3)
[1/s]
JV-MAP-$
6
(I,J,L)
OH source from O3 photolysis
[1/s]
JV-MAP-$
7
(I,J,L)
J(GLYX)
[1/s]
JV-MAP-$
8
(I,J,L)
J(MGLY)
[1/s]
JV-MAP-$
NOTE: Orange lines indicate output only available for simulations with the secondary organic aerosol (SOA) chemistry mechanism.
 
ND23
Dimension
MASS-WEIGHTED OH CONCENTRATION
Units
Category
 
 
Mean OH concentration diagnostic
[10[5] molec/cm3] 
 
 
 
Dimension
MASS TRANSPORT FLUX
Units
Category
ND24 
(I,J,L,N)
East/west mass flux by transport 
[kg/s]
EW-FLX-$
ND25 
(I,J,L,N)
North/south mass flux by transport 
[kg/s]
NS-FLX-$
ND26 
(I,J,L,N)
Up/down mass flux by transport 
[kg/s]
UP-FLX-$
 
ND27
Dimension
STRATOSPHERIC INFLUX (mostly obsolete now)
Units
Category
1
(I,J,3)
NOx, Ox, HNO3 from the stratosphere: if NOx - Ox - HC simulation
[kg/s]
STRT-FL
2
(I,J,2)
H2, HD from the stratosphere: if H2/HD simulation
[kg/s]
STRT-FL
3
(I,J)
Ox from the stratosphere: all other simulations
[kg/s]
STRT-FL
 
ND28
Dimension
BIOMASS BURNING EMISSIONS 
Units
Category
1
(I,J)
NOx biomass emissions
[molec/cm2/s]
BIOBSRCE
4
(I,J)
CO biomass emissions
[molec/cm2/s]
BIOBSRCE
5
(I,J)
ALK4 biomass emissions
[atoms C/cm2/s]
BIOBSRCE
9
(I,J)
ACET biomass emissions
[atoms C/cm2/s]
BIOBSRCE
10
(I,J)
MEK biomass emissions
[atoms C/cm2/s]
BIOBSRCE
11
(I,J)
ALD2 biomass emissions
[atoms C/cm2/s]
BIOBSRCE
18
(I,J)
PRPE (lumped >=C3 alkenes) biomass emissions
[atoms C/cm2/s]
BIOBSRCE
19
(I,J)
C3H8 biomass emissions
[atoms C/cm2/s]
BIOBSRCE
20
(I,J)
CH2O biomass emissions
[molec/cm2/s]
BIOBSRCE
21
(I,J)
C2H6 biomass emissions
[atoms C/cm2/s]
BIOBSRCE
26
(I,J)
SO2 biomass emissions
[molec/cm2/s]
BIOBSRCE
30
(I,J)
NH3 biomass emissions
[molec/cm2/s]
BIOBSRCE
34
(I,J)
BC (black carbon) biomass emissions
[molec/cm2/s]
BIOBSRCE
35
(I,J)
OC (organic carbon) biomass emissions
[molec/cm2/s]
BIOBSRCE
 
ND29
Dimension
TROPOSPHERIC CO EMISSIONS
Units
Category
1
(I,J)
Anthropogenic CO
[molec/cm2/s]
CO--SRCE
2
(I,J)
Biomass Burning CO
[molec/cm2/s]
CO--SRCE
3
(I,J)
Biofuel Burning CO
[molec/cm2/s]
CO--SRCE
4
(I,J)
CO produced from monoterpenes
[molec/cm2/s]
CO--SRCE
5
(I,J)
CO produced from methanol
[molec/cm2/s]
CO--SRCE
 
ND30
Dimension
LAND MAP DIAGNOSTIC
Units
Category
1
(I,J)
GMAO land-water indices
[unitless]
LANDMAP
 
ND31
Dimension
SURFACE PRESSURE DIAGNOSTIC
Units
Category
1
(I,J,L)
Pressure at the bottom of level L (1 <= L <= ND31 )
[hPa]
PEDGE-$
 
ND32
Dimension
TROPOSPHERIC NOx EMISSIONS
Units
Category
1
(I,J,L)
Aircraft NOx
[molec/cm2/s]
NOX-AC-$
2
(I,J,L)
Anthropogenic NOx ( 1 <= L <= NOXEXTENT )
[molec/cm2/s]
NOX-AN-$
3
(I,J)
Biomass Burning NOx
[molec/cm2/s]
NOX-BIOB
4
(I,J)
Biofuel Burning NOx
[molec/cm2/s]
NOX-BIOF
5
(I,J)
Fertilizer NOx
[molec/cm2/s]
NOX-FERT
6
(I,J,L)
Lightning NOx
[molec/cm2/s]
NOX-LI-$
7
(I,J)
Soils NOx
[molec/cm2/s]
NOX-SOIL
8
(I,J)
Stratospheric NOx (upper boundary)
[molec/cm2/s]
NOX-STRT
 
ND33
Dimension
COLUMN TRACER
Units
Category
1
(I,J,N)
Atmospheric column sum of tracer
[kg]
COLUMN-T
 
ND34
Dimension
BIOFUEL BURNING EMISSIONS 
Units
Category
1
(I,J)
NOx biofuel emissions
[molec/cm2/s]
BIOFSRCE
4
(I,J)
CO biofuel emissions
[molec/cm2/s]
BIOFSRCE
5
(I,J)
ALK4 biofuel emissions
[atoms C/cm2/s]
BIOFSRCE
9
(I,J)
ACET biofuel emissions
[atoms C/cm2/s]
BIOFSRCE
10
(I,J)
MEK biofuel emissions
[atoms C/cm2/s]
BIOFSRCE
11
(I,J)
ALD2 biofuel emissions
[atoms C/cm2/s]
BIOFSRCE
18
(I,J)
PRPE (lumped >=C3 alkenes) biofuel emissions
[atoms C/cm2/s]
BIOFSRCE
19
(I,J)
C3H8 biofuel emissions
[atoms C/cm2/s]
BIOFSRCE
20
(I,J)
CH2O biofuel emissions
[molec/cm2/s]
BIOFSRCE
21
(I,J)
C2H6 biofuel emissions
[atoms C/cm2/s]
BIOFSRCE
 
ND35
Dimension
TRACER CONCENTRATION AT 500 mb
Units
Category
1
(I,J,N)
Tracers at 500 mb ( L = 9 ) ( N: selected tracers )
NOTE: this is now obsolete
[v/v]
500-AVRG
 
ND36
Dimension
ANTHROPOGENIC EMISSIONS
Units
Category
1
(I,J)
NOx anthropogenic emissions
[molec/cm2/s]
ANTHSRCE
4
(I,J)
CO anthropogenic emissions
[molec/cm2/s]
ANTHSRCE
5
(I,J)
ALK4 anthropogenic emissions
[atoms C/cm2/s]
ANTHSRCE
9
(I,J)
ACET anthropogenic emissions
[atoms C/cm2/s]
ANTHSRCE
10
(I,J)
MEK anthropogenic emissions
[atoms C/cm2/s]
ANTHSRCE
11
(I,J)
ALD2 anthropogenic emissions
[atoms C/cm2/s]
ANTHSRCE
18
(I,J)
PRPE (lumped >=C3 alkenes) anthropogenic emissions
[atoms C/cm2/s]
ANTHSRCE
19
(I,J)
C3H8 anthropogenic emissions
[atoms C/cm2/s]
ANTHSRCE
20
(I,J)
CH2O anthropogenic emissions
[molec/cm2/s]
ANTHSRCE
21
(I,J)
C2H6 anthropogenic emissions
[atoms C/cm2/s]
ANTHSRCE
 
ND36
Dimension
CH3I EMISSIONS (for simulation type 2)
Units
Category
1
(I,J)
CH3Ioc : Methyl Iodide (oceanic source)
[ng/m2/s]
CH3ISRCE
2
(I,J)
CH3Ibb : Methyl Iodide (biomass burning)
[ng/m2/s]
CH3ISRCE
3
(I,J)
CH3Iwb : Methyl Iodide (wood burning)
[ng/m2/s]
CH3ISRCE
4
(I,J)
CH3Irc : Methyl Iodide (rice paddies)
[ng/m2/s]
CH3ISRCE
5
(I,J)
CH3Iwl : Methyl Iodide (wetlands) 
[ng/m2/s]
CH3ISRCE
 
ND37
Dimension
UDRAFT SCAVENGING FRACTION
Units
Category
1
(I,J,L,N)
Fraction of tracer scavenged by in cloud updrafts in moist convection
[unitless]
MC-FRC-$
 
ND38
Dimension
LOSS OF TRACER IN MOIST CONVECTION
Units
Category
1
(I,J,L,N)
Rainout loss of tracer in convective updrafts
[kg/s]
WETDCV-$
 
ND39
Dimension
LOSS OF TRACER IN AEROSOL WET DEPOSITION
Units
Category
1
(I,J,L,N)
Rainout loss of tracer in large-scale precip
[kg/s]
WETDLS-$
 
ND40
Dimension 
PLANE FLIGHT DIAGNOSTIC
Units 
Category
 
 
Turn on plane flight diagnostic (DO_PF = T). This diagnostic does not save to the bpch file, but rather is output to the specified plane.log file. 
 
 
 
ND41
Dimension
AFTERNOON PBL HEIGHT
Units
Category
1
(I,J)
Afternoon boundary layer heights (1200-1600 local time) 
[m]
PBLDEPTH
 
ND42
Dimension
SOA CONCENTRATIONS
Units
Category
1
(I,J,L)
SOA1
[ug/m3]
IJ-SOA-$
2
(I,J,L)
SOA2
[ug/m3]
IJ-SOA-$
3
(I,J,L)
SOA3
[ug/m3]
IJ-SOA-$
4
(I,J,L)
SOA4
[ug/m3]
IJ-SOA-$
5
(I,J,L
SOA5
[ug/m3]
IJ-SOA-$
6
(I,J,L)
SOA1 + SOA2 + SOA3
[ug/m3]
IJ-SOA-$
7
(I,J,L)
SOA1 + SOA2 + SOA3 + SOA4
[ug/m3]
IJ-SOA-$
8
(I,J,L)
SOA1 + SOA2 + SOA3 + SOA4 + SOA5
[ug/m3]
IJ-SOA-$
9
(I,J,L)
Sum of all Org Aerosols (OC + SOA)
[ug C/m3]
IJ-SOA-$
10
(I,J,L)
Sum of all Org Aerosols (OC+SOA) @ STP
[ug C/m3]
IJ-SOA-$
11
(I,J,L)
Sum of all Org Aerosols (OC+SOA)
[ug/m3]
IJ-SOA-$
12
(I,J,L)
Organic carbon (OCPI + OCPO)
[ug C/m3]
IJ-SOA-$
13
(I,J,L)
Black carbon (BCPI + BCPO)
[ug C/m3]
IJ-SOA-$
14
(I,J,L)
SO4
[ug/m3]
IJ-SOA-$
15
(I,J,L)
NH4
[ug/m3]
IJ-SOA-$
16
(I,J,L)
NIT
[ug/m3] 
IJ-SOA-$
17
(I,J,L)
SAL
[ug/m3]
IJ-SOA-$
18
(I,J,L)
Total aerosol
[ug/m3]
IJ-SOA-$
19
(I,J,L)
SOAG (from GLYX)
[ug/m3] 
IJ-SOA-$
20
(I,J,L)
SOAM (from MGLY)
[ug/m3]
IJ-SOA-$
21
(I,J,L)
SOA1 + SOA2 + SOA3 + SOA4 + SOA5 + SOAG + SOAM
[ug/m3]
IJ-SOA-$
22
(I,J,L)
SOA1 + SOA2 + SOA3 + SOA4 + SOA5 + SOAG + SOAM + OCPO + OCPI
[ug C/m3]
IJ-SOA-$
23
(I,J,L)
SOA1 + SOA2 + SOA3 + SOA4 + SOA5 + SOAG + SOAM @ STP
[ug/m3]
IJ-SOA-$
24
(I,J,L)
SOA1 + SOA2 + SOA3 + SOA4 + SOA5 + SOAG + SOAM + OCPO + OCPI @ STP
[ug C/m3]
IJ-SOA-$
NOTES: 
   1. These output are only available for simulations using the SOA chemistry mechanism.
      
   2. Green lines indicate output only available for simulations using the dicarbonyls chemistry mechanism.
 
ND43
Dimension
CHEMICAL PRODUCTION OF VARIOUS SPECIES
Units
Category
1
(I,J,L)
OH
[molec/cm3]
CHEM-L=$
2
(I,J,L)
NO
[v/v]
CHEM-L=$
3
(I,J,L)
HO2
[v/v]
CHEM-L=$
4
(I,J,L)
NO2
[v/v]
CHEM-L=$
5
(I,J,L)
NO3
[v/v]
CHEM-L=$
 
ND44
Dimension
DRYDEP ( M = NUMber DEP )
Units
Category
1
(I,J,M)
Dry deposition fluxes (M = 1, NUMDEP)
[molec/cm2/s]
DRYD-FLX
2
(I,J,M)
Dry deposition velocities (M = 1, NUMDEP)
[cm/s]
DRYD-VEL
 
ND45
Dimension
TRACER CONCENTRATIONS
Units
Category
1
(I,J,L,N)
Tracer mixing ratio for Levels = 1, LD45, averaged between HR1_OTH and HR2_OTH (time range from input.geos)
[v/v]
IJ-AVG-$
 
ND46
Dimension
BIOGENIC EMISSIONS
Units
Category
1
(I,J)
Isoprene
[atoms C/cm2/s]
BIOGSRCE
2
(I,J)
Acetone
[atoms C/cm2/s]
BIOGSRCE
3
(I,J)
PRPE (Lumped >= C3 alkenes)
[atoms C/cm2/s]
BIOGSRCE
4
(I,J)
Monoterpenes
[atoms C/cm2/s]
BIOGSRCE
5
(I,J)
Methyl Butenol (aka MBO)
[atoms C/cm2/s]
BIOGSRCE
6
(I,J)
Ethene
[atoms C/cm2/s]
BIOGSRCE
7
(I,J)
a-Pinene
[atoms C/cm2/s]
BIOGSRCE
8
(I,J)
b-Pinene
[atoms C/cm2/s]
BIOGSRCE
9
(I,J)
Limonene
[atoms C/cm2/s]
BIOGSRCE
10
(I,J)
Sabinene
[atoms C/cm2/s]
BIOGSRCE
11
(I,J)
Myrcene
[atoms C/cm2/s]
BIOGSRCE
12
(I,J)
3-Carene
[atoms C/cm2/s]
BIOGSRCE
13
(I,J)
Ocimene
[atoms C/cm2/s]
BIOGSRCE
 
ND47
Dimension
24-h AVERAGE TRACER CONCENTRATION
Units
Category
1
(I,J,L,N)
Daily (24-h) average tracer mixing ratio for Levels = L, LD47
[v/v]
IJ-24H-$
 
ND48
Dimension
TIMESERIES AT NL = NUMBER OF LOCATIONS
Units
Category
1-N
(I,J,L)
GEOS - Chem transported tracers
(Tracer # for GAMAP = 1 .. N_TRACERS)
[v/v]
IJ-AVG-$
76
(I,J,L)
OH concentration
(Tracer # for GAMAP = 2)
[molec/cm3]
TIME-SER
77
(I,J,L)
NO2 concentration
(Tracer # for GAMAP = 19)
[v/v]
TIME-SER
78
(I,J,L)
PBL heights
(Tracer # for GAMAP = 1)
[m]
PBLDEPTH
79
(I,J,L)
PBL heights
(Tracer # for GAMAP = 2)
[levels]
PBLDEPTH
80
(I,J,L)
Air density
(Tracer # for GAMAP = 22)
[molec/cm3]
TIME-SER
81
(I,J)
3-D Cloud fractions
(Tracer # for GAMAP = 19)
[unitless]
TIME-SER
82
(I,J)
Column optical depths
(Tracer # for GAMAP = 20)
[unitless]
TIME-SER
83
(I,J)
Cloud top heights
(Tracer # for GAMAP = 21)
[hPa]
TIME-SER
84
(I,J,L)
Sulfate aerosol optical depth
(Tracer # for GAMAP = 6)
[unitless]
OD-MAP-$
85
(I,J,L)
Black carbon aerosol optical depth
(Tracer # for GAMAP = 9)
[unitless]
OD-MAP-$
86
(I,J,L)
Organic carbon aerosol optical depth
(Tracer # for GAMAP = 12)
[unitless]
OD-MAP-$
87
(I,J,L)
Accumulation mode seasalt optical depth
(Tracer # for GAMAP = 15)
[unitless]
OD-MAP-$
88
(I,J,L)
Coarse mode seasalt optical depth
(Tracer # for GAMAP = 18)
[unitless]
OD-MAP_$
89
(I,J,L)
Total dust optical depth
(Tracer # for GAMAP = 4)
[unitless]
OD-MAP-$
90
(I,J,L)
Total seasalt tracer concentration 
(Tracer # for GAMAP = 24)
[unitless]
TIME-SER
91
(I,J,L)
Pure O3 (not Ox) concentration 
(Tracer # for GAMAP = N_TRACERS+1)
[v/v]
IJ-AVG-$
92
(I,J,L)
NO concentration 
(Tracer # for GAMAP = 9)
[v/v]
TIME-SER
93
(I,J,L)
NOy concentration 
(Tracer # for GAMAP = 3)
[v/v]
TIME-SER
94
(I,J,L)
Grid box height
(Tracer # for GAMAP = 1)
[m]
BXHGHT-$
95
(I,J,L)
Relative humidity
(Tracer # for GAMAP = 17)
[%]
TIME-SER
96
(I,J)
Sea level pressure
(Tracer # for GAMAP = 18)
[hPa]
DAO-FLDS
97
(I,J,L)
Zonal wind (a.k.a. U-wind)
(Tracer # for GAMAP = 1)
[m/s]
DAO-3D-$
98
(I,J,L)
Meridional wind (a.k.a. V-wind)
(Tracer # for GAMAP = 2)
[m/s]
DAO-3D-$
99
(I,J)
P(surface) - PTOP
(Tracer # for GAMAP = 1)
[hPa]
PEDGE-$
100
(I,J,L)
Temperature
(Tracer # for GAMAP = 3)
[K]
DAO-3D-$
115-121
(I,J,L)
Size resolved dust optical depth
[unitless]
OD-MAP-$
 
ND49
Dimension
3-D INSTANTANEOUS TRACER TIMESERIES
Units
Category
 
 
Same tracers as ND48 plus:
 
 
101
(I,J)
PARDF (diffuse PAR)
(Tracer # for GAMAP = 20)
[W/m2]
DAO-FLDS
102
(I,J)
PARDR (direct PAR)
(Tracer # for GAMAP = 21)
[W/m2]
DAO-FLDS
103
(I,J)
Daily LAI (leaf area index)
(Tracer # for GAMAP = 32)
[cm2/cm2]
TIME-SER
104
(I,J)
Temperature at 2m (i.e. proxy for surface air temperature)
(Tracer # for GAMAP = 5)
[K]
DAO-FLDS
105
(I,J)
Isoprene emissions
(Tracer # for GAMAP = 1)
[atoms C/cm2]
BIOGSRCE
106
(I,J)
Monoterpene emissions
(Tracer # for GAMAP = 4)
[atoms C/cm2]
BIOGSRCE
107
(I,J)
Methyl Butanol emissions
(Tracer # for GAMAP = 5)
[atoms C/cm2]
BIOGSRCE
108
(I,J)
a-Pinene emissions
(Tracer # for GAMAP = 7)
[atoms C/cm2]
BIOGSRCE
109
(I,J)
b-Pinene emissions
(Tracer # for GAMAP = 8)
[atoms C/cm2]
BIOGSRCE
110
(I,J)
Limonene emissions
(Tracer # for GAMAP = 9)
[atoms C/cm2]
BIOGSRCE
111
(I,J)
Sabinene emissions
(Tracer # for GAMAP = 10)
[atoms C/cm2]
BIOGSRCE
112
(I,J)
Myrcene emissions
(Tracer # for GAMAP = 11)
[atoms C/cm2]
BIOGSRCE
113
(I,J)
3-carene emissions
(Tracer # for GAMAP = 12)
[atoms C/cm2]
BIOGSRCE
114
(I,J)
Ocimene emissions
(Tracer # for GAMAP = 13)
[atoms C/cm2]
BIOGSRCE
115-121
(I,J,L)
Size resolved dust optical depth
[unitless]
OD-MAP-$
 
ND50
Dimension
3-D 24-h AVERAGE TRACER TIMESERIES
Units
Category
 
(I,J,L)
Archives the same diagnostic quantities as ND49 (listed above)
 
 
 
ND51
Dimension
3-D SATELLITE TRACER TIMESERIES
Units
Category
 
(I,J,L,N)
Archives the same diagnostic quantities as ND49 (listed above), averaged between two local times.
 
 
 
ND51b
Dimension
3-D SATELLITE TRACER TIMESERIES
Units
Category
 
(I,J,L,N)
Archives the same diagnostic quantities as ND51 (listed above), along a second satellite path.
 
 
 
ND52
Dimension
GAMMA HO2
Units
Category
1
(I,J,L)
Uptake coefficient for HO2 by aerosols
[unitless]
GAMMA
 
ND53
Dimension 
FREE DIAGNOSTIC
Units 
Category
 
ND54
Dimension 
FRACTION OF TIME IN THE TROPOPSPHERE
Units 
Category
1
(I,J,L)
Computes the amount of time that a given grid box spends in the troposphere
[unitless]
TIME-TPS
 
ND55
Dimension
DYNAMIC TROPOPAUSE DIAGNOSTICS
Units
Category
1
(I,J)
Level at which the dynamic tropopause occurs
[unitless]
TR-PAUSE
2
(I,J)
Height of the dynamic tropopause
[km]
TR-PAUSE
3
(I,J)
Pressure of the dynamic tropopause
[mb]
TR-PAUSE
 
ND56
Dimension
LIGHTNING FLASHES
Units
Category
1
(I,J)
Total lightning flash rate
[flashes/min/km2]
LFLASH-$
2
(I,J)
Intra-cloud flash rate
[flashes/min/km2]
LFLASH-$
3
(I,J)
Cloud-ground flash rate
[flashes/min/km2]
LFLASH-$
 
ND57
Dimension 
POTENTIAL TEMPERATURE DIAGNOSTIC
Units 
Category
1
(I,J,L)
Potential temperature
[K]
THETA-$
 
ND58
Dimension
CH4 emissions
Units
CH4-EMIS
1
(I,J)
CH4-TOT: Total emissions
[kg] 
CH4-EMIS
2
(I,J)
CH4-GAO: Gas & Oil emissions
[kg] 
CH4-EMIS
3
(I,J)
CH4-COL: Coal emisisons
[kg] 
CH4-EMIS
4
(I,J)
CH4-LIV: Livestock emissions
[kg] 
CH4-EMIS
5
(I,J)
CH4-WST: Waste emisisons
[kg] 
CH4-EMIS
6
(I,J)
CH4-BFL: Biofuel emissions
[kg] 
CH4-EMIS
7
(I,J)
CH4-RIC: Rice field emissions
[kg] 
CH4-EMIS
8
(I,J)
CH4-OTA: Other anthropic emissions
[kg] 
CH4-EMIS
9
(I,J)
CH4-BBN: Biomass burning emissions
[kg] 
CH4-EMIS
10
(I,J)
CH4-WTL: Wetland emissions
[kg] 
CH4-EMIS
11
(I,J)
CH4-SAB: Soil absorption
[kg] 
CH4-EMIS
12
(I,J)
CH4-OTN: Other natural emissions
[kg] 
CH4-EMIS
 
ND59
Dimension 
FREE DIAGNOSTIC
Units 
Category
 
ND60
Dimension 
WETLAND FRACTION
Units 
Category
1
(I,J)
Wetland fraction
unitless
WET-FRAC
 
ND61
Dimension 
FREE DIAGNOSTIC
Units 
Category
 
ND62
Dimension 
INSTANTANEOUS COLUMN MAPS
Units 
Category
1
(I,J,N)
I-J instantaneous integrated column density for tracers
[molec/cm2] or 
[atoms C/cm2]
INST-MAP
 
ND63
Dimension 
SHIP DIAGNOSTIC
Units 
Category
1
(I,J,N)
Fraction of NOx remaining
unitless
SHIP-$$$
2
(I,J,N)
Integrated Ozone Production Efficiency (OPE)
unitless
SHIP-$$$
3
(I,J,N)
Fraction of NOx remaining * ship emissions
[kg/box/timestep]
SHIP-$$$
4
(I,J,N)
Integrated OPE * ( 1 - fraction of NOx) * ship emissions 
[kg/box/timestep]
SHIP-$$$
5
(I,J,N)
Ship emissions
[kg/box/timestep]
SHIP-$$$
 
ND64
Dimension 
FREE DIAGNOSTIC
Units 
Category
 
ND65
Dimension 
PRODUCTION/LOSS OF SPECIFIED CHEMICAL FAMILIES
Units 
Category
1
(I,J,L,N)
Chemical family P/L rates. Users can define which species/ families to output in input.geos.
[molec/cm3/s]
PORL-L=$
 
ND66
Dimension
GMAO (formerly DAO) 3-D met fields
Units
Category
1
(I,J,L)
UWND : U-winds
[m/s]
DAO-3D-$
2
(I,J,L)
VWND : V-winds
[m/s]
DAO-3D-$
3
(I,J,L)
TMPU : Temperature
[K]
DAO-3D-$
4
(I,J,L)
SPHU : Specific humidity
[g H20/kg air]
DAO-3D-$
5
(I,J,L)
CLDMAS : Convective Mass Flux
[kg/m2/s]
DAO-3D-$
6
(I,J,L)
DTRAIN : Detrainment Flux
[kg/m2/s]
DAO-3D-$
 
ND67
(I,J)
GMAO (formerly DAO) 2-D met fields 
Units
Category
1
(I,J)
HFLUX: sensible heat flux from surface
[W/m2]
DAO-FLDS
2
(I,J)
RADSWG: solar radiation at the ground
For GEOS - 5, this is the net radiation @ ground (SWGNET)
For MERRA, this is the incident radiation @ ground (SWGDN)
[W/m2]
DAO-FLDS
3
(I,J)
PREACC: total precipitation at the ground
For GEOS - 5 and MERRA, this field is named PRECTOT
[mm/day]
DAO-FLDS
4
(I,J)
PRECON: total convective precipitation at the ground
For GEOS - 5 and MERRA, this field is named PRECCON
[mm/day]
DAO-FLDS
5
(I,J)
TS: surface air temperature
NOTE: For GEOS - 4, GEOS - 5, and MERRA, this is really the air temperature at 2 m altitude above the surface.
[K]
DAO-FLDS
6
(I,J)
RADSWT: solar radiation at the top of the atmosphere
[W/m2]
DAO-FLDS
7
(I,J)
USTAR: friction velocity
[m/s]
DAO-FLDS
8
(I,J)
Z0: surface roughness height
[m]
DAO-FLDS
9
(I,J)
PBL (aka PBLM): planetary boundary layer depth
[hPa]
DAO-FLDS
10
(I,J)
CLDFRC: column cloud fraction
[0 - 1]
DAO-FLDS
11
(I,J)
U10M: U-winds at 10 meters altitude
[m/s]
DAO-FLDS
12
(I,J)
V10M: V-winds at 10 meters altitude
[m/s]
DAO-FLDS
13
(I,J)
PS-PBL: Boundary Layer Top Pressure
[hPa]
DAO-FLDS
14
(I,J)
ALBD: Surface Albedo
[unitless]
DAO-FLDS
15
(I,J)
PHIS: Geopotential Heights
[m]
DAO-FLDS
16
(I,J)
CLTOP : Cloud Top Height
[levels]
DAO-FLDS
17
(I,J)
TROPP: Tropopause pressure (read directly from the met fields, without any further processing). For more information see our dynamic tropopause wiki page.
[hPa]
DAO-FLDS
18
(I,J)
SLP: Sea Level pressure (read directly from the met fields)
[hPa]
DAO-FLDS
19
(I,J)
TSKIN : Ground / Sea Surface Temp
[K]
DAO-FLDS
20
(I,J)
PARDF : Photosynthetically active diffuse radiation
[W/m2]
DAO-FLDS
21
(I,J)
PARDR : Photosynthetically active direct radiation
[W/m2]
DAO-FLDS
22
(I,J)
GWETTOP: Top soil wetness
[unitless]
DAO-FLDS
 
ND68
Dimension
GRID BOX QUANTITIES
Units
Category
1
(I,J,L)
BXHEIGHT: Grid box heights
[m]
BXHGHT-$
2
(I,J,L)
AD: Air mass in grid box
[kg]
BXHGHT-$ 
3
(I,J,L)
AVGW : Mixing ratio of water vapor
[v/v]
BXHGHT-$
4
(I,J,L)
N_AIR: Air number density
[molec air/m3]
BXHGHT-$ 
 
ND69
Dimension
GRID BOX SURFACE AREAS
Units
Category
1
(I,J)
DXYP: grid box surface areas
[m2]
DXYP
 
ND70
Dimension
DEBUG OUTPUT
Units
Category
 
 
Turn on debug output statements (LPRT = T)
 
 
                                       
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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 6
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 6: GEOS - Chem List of Chemical Species
In this Appendix, we shall list the chemical species used for the standard GEOS - Chem "full-chemistry" simulation.

See this wiki page for a complete list of chemical species (active + inactive) in the standard GEOS - Chem chemical mechanism file globchem.dat. These species are used in the full chemistry "standard" simulation used by SMVGEAR II and KPP. Many of these species are short-lived, and do not have to be transported as GEOS - Chem tracers. 
NOTE: The following chemistry mechanisms have extra species not listed here. For more information, please consult with the GEOS - Chem Oxidants and Chemistry Working Group.
   1. SOA: 59 advected tracers, with secondary organic aerosols
   2. Dicarbonyls: 75 advected tracers, with dicarbonyl chemistry
   3. Isoprene: 56 advected tracers, with the Caltech isoprene scheme.

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                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 7: GEOS - Chem Style Guide
We provide guidelines for writing clear, concise, and effective Fortran source code.

A7.1 Background
A7.1.1 We have written GEOS - Chem in the Fortran - 90 (F90) language. F90 introduces several new features over its predecessor, Fortran - 77 (F77), including allocatable arrays, modules, derived types, and new programming statements. We invite you to consult the following F90 tutorials:
   * Fortran 90 for the Fortran 77 Programmer
   * User notes on Fortran programming
   * University of Liverpool F90 tutorials and courses
F90 contains all of the features of F77. Legacy code adhering to the F77 standard should build with any F90 compiler. Although we have written GEOS - Chem source code to the F90 standard, you should be aware that many 3rd-party routines included in GEOS - Chem -- such as, SMVGEAR, FAST - J, and ISORROPIA -- were originally written to the F77 standard. In GEOS - Chem v9 - 01 - 03, we have started to replace older F77 code with F90 code, especially to facilitate the Grid Independent GEOS - Chem project.
You should also be aware that several other updates to the Fortran standard (F95, F2000, F2003) have been introduced in recent years. These new Fortran versions contain the same functionality as F90, but generally omit the obsolete F77-style features. Most modern Fortran compilers include support for all of these standards.

A7.1.2 We previously wrote GEOS - Chem source code using fixed-format layout, which has the following requirements:
   * A line continuation character (usually &) is placed in column 6
   * Numeric labels can occupy column 2 through column 5
   * Executable statements begin in column 7 and extend to column 72
We chose the fixed-format layout for compatibility with the F77-style include files that were contained in the Headers/ directory. Starting with GEOS - Chem v9 - 01 - 03, we have now converted all header files (with the exception of define.h) to modules. This allows the use of free-format layout, which does not restrict where you place executable statements. (To continue a free-format statement across several lines of code, you must place an ampersand "&" character at the end of each line.) We recommend that you write all new GEOS - Chem code using the free format layout. 

A7.1.3 Historically, we denote code authors by a 3-letter abbreviation in source code comments (bmy, 5/1/03). However, computer account names grew longer, so did the length of these identifiers, e.g.(mpayer, 7/15/12).

A7.2 Headers, declarations, indentations, and white space
A7.2.1 We generate detailed GEOS - Chem reference documentation with ProTeX. ProTeX is a perl script developed by NASA/GMAO that generates LaTeX files from GEOS - Chem's subroutine, function, and module comment headers. The LaTeX file can then be compiled to produce both PostScript and PDF output.
To use ProTeX, you need to add a standard header at the top of each subroutine, function, and module. The header looks like this:
!------------------------------------------------------------------------------
!            Harvard University Atmospheric Chemistry Modeling Group 
!------------------------------------------------------------------------------
!BOP
!
! !IROUTINE: metero
!
! !DESCRIPTION: Subroutine METERO calculates meteorological constants needed for the
! dry deposition velocity module. (lwh, gmg, djj, 1989, 1994; bmy, 11/21/02)
!
! Arguments as Output:
! ============================================================================
! (1 ) CZ1 (REAL*8) : Midpoint height of first model level [m]
! (2 ) TC0 (REAL*8) : Array for grid box surface temperature [K]
! (3 ) OBK (REAL*8) : Array for the Monin-Obhukov length [m]
!
!\subsection*{Reference}
! (1 ) Wesely, M. L., 1989. 
! (2 ) Jacob, D.J., and S.C. Wofsy, 1990
!
!\\
!\\
! !INTERFACE: 
!
      SUBROUTINE METERO( CZ1, TC0, OBK )
!
! !USES:
! 
      USE DAO_MOD, ONLY : AIRDEN, HFLUX, T, TS, USTAR
      USE PRESSURE_MOD, ONLY : GET_PEDGE 
      
      IMPLICIT NONE

#     include "CMN_SIZE" ! Size parameters
#     include "CMN_GCTM" ! Physical constants
!
! ! OUTPUT PARAMETERS:
!
      REAL*8, INTENT(OUT) :: CZ1(MAXIJ)
      REAL*8, INTENT(OUT) :: TC0(MAXIJ)
      REAL*8, INTENT(OUT) :: OBK(MAXIJ)
!
! !REVISION HISTORY: 
!  (1 ) Now reference GET_PEDGE from "pressure_mod.f". Now reference T from 
!   "dao_mod.f". Removed obsolete code & comments, and added new 
!  documentation header. Now force double precision with "D" 
!  exponents. Now compute OBK here as well. Bundled into F90 module
!  "drydep_mod.f" (bmy, 11/20/02)
!  02 Mar 2011 - J. Fisher - Set aerosol dry deposition velocity to 0.03 cm/s
!                            over snow and ice based on Nilsson & Rannik, 2001
!  02 Mar 2011 - R. Yantosca -  Added ProTeX headers
!EOP
!------------------------------------------------------------------------------
!BOC
!
! ! LOCAL VARIABLES:
!
INTEGER :: I, J, IJLOOP
REAL*8 :: P1, P2, THIK, NUM, DEN

!
! !DEFINED PARAMETERS:
!
REAL*8, PARAMETER :: KAPPA = 0.4d0   ! Von Karman's Constant
REAL*8, PARAMETER :: CP = 1000.0d0  

!
! ! EXTERNAL FUNCTIONS:
!
REAL*8, EXTERNAL :: XLTMMP

!=================================================================
! METERO begins here!
!=================================================================

  ... code goes here ...

END SUBROUTINE METERO
!EOC
Note that the ProTeX header contains the following elements:
   1. Indicators (!BOP, !EOP) as to where ProTeX should look for source code header comments
   2. Indicators (!BOC, !EOC) as to where the source code begins and ends. ProTeX will ignore code between !BOC and !EOC unless you tell it otherwise.
   3. A description of the routine, the original date and most recent
   4. Description of when the routine was last modified (with date & name of the programmers)
   5. A list of input & output arguments
   6. A list of references (if applicable)
   7. References to F90 modules (if any) after the USE keyword followed by the IMPLICIT NONE declaration
   8. Any #include declarations for header files. Since we are using the C-preprocessor with 72-column fixed format, the # character must go in column 1.
   9. Each time the file is modified the REVISION HISTORY section should be updated.
   10. Declarations for local variables
   11. Declarations for Fortran parameters (aka constants)
   12. Declarations for external functions (if necessary)
Fortran 90 allows you to declare an argument to a subroutine or function with one of the following descriptors:
   1. INTENT(IN) (read-only),
   2. INTENT(OUT) (write-only) or
   3. INTENT(INOUT) (read-and-write)
This helps you to prevent overwriting arguments which should not be overwritten.
We recommend that you separate sections of source code with one or more divider comments:
!=================================================================
! 1st level header
!=================================================================

   !--------------------------------------------------------------
   ! 2nd level header
   !--------------------------------------------------------------

      !-----------------------
      ! 3rd-level header
      !----------------------
Line up each header with the the code that follows immediately below it. You can mix and match these styles as you wish. You don't always have to extend the header all the way across the screen.
If you are modifying a fixed-format source code file, end the major section headers at column #72. This will remind your reader where the limits of the allowable source code region occurs. If you are modifying a free-format source code file, feel free to extend the ends of the major section headers to about column 76 or 77.

A7.2.2 We used to write GEOS - Chem source code in ALL CAPITALS. We chose this approach to avoid mistaking similar characters, such as the lowercase l and the number 1, which in some fonts look remarkably alike. You may at your discretion mix capitals and lowercase in variable names and subroutine names, particularly if you want to improve readability or preserve scientific abbreviations ( e.g. Rn_Pb_Be_mod.F).
We still recommend that you write Fortran reserved words in ALL CAPITALS: SUBROUTINE, CALL, IF/THEN/ENDIF, DO/ENDDO, WHERE/ENDWHERE. This distinguishes Fortran language elements from your variable and routine names.
Because GEOS - Chem contains a significant amount of 3rd-party code, you will see many routines where the code is written in all lowercase letters. Feel free to leave this code as-is. Reformatting a fixed-format source code file can be a cumbersome task (and maybe not the best use of your precious time).
Good editors such as emacs and Xemacs can "colorize" the different words in a program (e.g. statements, variables, and quoted text are rendered in different colors), thus making the code infinitely more readable..

A7.2.3 Indent each new block of code 3 columns deeper than the last block: 
         1         2         3         4
1234567890123456789012345678901234567890
      IF ( X == 0 ) THEN
         PRINT*, 'Hello, X is 0!'

         IF ( Y == 0 ) THEN
            PRINT*, 'Hello, X is 0 and Y is also 0!'
         ENDIF
      ENDIF
A good editor such as emacs will indent for you automatically. You can specify the level of indent in your editor setup file (e.g. .emacs).

A7.2.4 Omit indentation for each line of a multiple DO loop. Use this syntax:
DO N = 1, NNPAR
DO L = 1, LLPAR
DO J = 1, JJPAR
DO I = 1, IIPAR
   A(I,J,L,N) = A(I,J,L,N) / 2.0d0
ENDDO
ENDDO
ENDDO
ENDDO
instead of letting the DO loops "creep" unneccessarily across the screen:
DO N = 1, NNPAR
   DO L = 1, LLPAR
      DO J = 1, JJPAR
         DO I = 1, IIPAR
            A(I,J,L,N) = A(I,J,L,N) / 2.0d0
         ENDDO
      ENDDO
   ENDDO
ENDDO

A7.2.5 Use LOTS of white space to separate code. For example instead of
IF(X.eq.0)CALL DOLOOP(X,Y,Z,A,B,C,1,2,3)
type:
IF ( X == 0 ) CALL DOLOOP( X, Y, Z, A, B, C, 1, 2, 3 )
This makes the code much more readable, which prevents bugs.. If you can't read what you've written, you will never find your mistake! Don't be afraid to continue the statement to the next line if necessary.
In the above example, we also have used the new F90 equality test operator == (see below for more information). 

A7.2.6 Always line up quantities in assignment statements. Instead of:
A=1
THISLOOP=2
C=3
D=THISLOOP*C - A
add white space so that all of the equals signs fall in the same column.
A        = 1
THISLOOP = 2
C        = 3 
D        = ( THISLOOP * C ) - A
Your eyes can make more sense out of text that is lined up into vertical columns.
Group multiple terms of an equation with parentheses (as we have done for the D equation above). The compiler evaluates evaluate expressions in the order the parentheses are placed, from innermost to outermost.

A7.2.7 Do not leave white space between array indices: 
A = X(I,J,L)
Leave white space between arguments of functions and WRITE statements:
A = MYFUNCTION( I, J, L )
WRITE( 6, '(a)' ) A

A7.2.8 Line up arguments in subroutine or function calls. If there are an even number of arguments, break them up symmetrically:
 CALL MYSUB( THIS_A, THIS_B, THIS_C,
&            THIS_D, THIS_E, THIS_F )
or
 X = MYFUNCTION( THIS_A, THIS_B, THIS_C,
&                THIS_D, THIS_E, THIS_F )

A7.3 Numeric and character data types
A7.3.1 GEOS - Chem uses the following data types:
LOGICAL            --> TRUE or FALSE switch
INTEGER            --> 32 byte integer value
REAL*4             --> 32 byte floating-point value
REAL*8             --> 64 byte floating-point value
CHARACTER(LEN=255) --> string w/ 255 characters (the max limit)
where
INTEGER can express numbers from -2e9   to +2e9
REAL*4  can express numbers from -1e38  to +1e38
REAL*8  can express numbers from -1e312 to +1e312
Use REAL*8 as your default floating-point type. This will prevent round off and precision truncation errors. 
However, you should use REAL*4 data type instead of REAL*8 in the following instances:
   * Diagnostic arrays: GEOS - Chem diagnostic values rarely exceed 10[38], since they are usually in units such as kg, v/v, ppbv, or molecules/cm[2]/s.
   * Arrays and scalars required for binary or netCDF file I/O: Declaring these types of variables REAL*4 will help to keep file sizes as small as possible, thus saving disk space.
Some third-party routines used by GEOS - Chem (such as TPCORE) use the REAL datatype. Most compilers (but not all) interpret REAL as REAL*4. If you want to force the compiler to interpret REAL as REAL*8, you must use a special compiler switch (usually -r8, but check your compiler manual to be sure). The GEOS - Chem Makefiles already take care of this for you..
NOTE: See the GEOS - Chem wiki page on floating point math issues for more information. 

A7.3.2 Use D (double-precision) exponents when assigning a value to a REAL*8 variable:
REAL*8 :: PI
PI = 3.14159265358979323d0
instead of this syntax:
REAL*8 :: PI
PI = 3.14159265359e0
In F90, the E (single-precision) exponent only yields about 7 decimal places of precision, whereas the D exponent yields 15 or 16 decimal places of precision. Using D exponents prevents roundoff errors.

A7.3.3 Declare strings with 255 characters, even if you don't know a priori how long the string will be. Use the TRIM statement to strip excess white space. For example:
CHARACTER(LEN=255) :: STR

STR = 'I am the very model of a modern major general...'

WRITE( 6, '(a)' ) TRIM( STR )

A7.4 Converting from number to character (and vice versa)
A7.4.1 Several GEOS - Chem routines convert a numeric variable to a character variable (and vice-versa). This usually happens when a number representing a date or time has to be incorporated into a file path. 
Use a Fortran internal write statement to convert from from INTEGER to CHARACTER. This looks like a regular WRITE statement, only that the unit number is replaced by a character variable. Think of it as "writing" your number into a character variable instead of to a file.
For example, the following code creates a string containing the date 20110701:
! Declare variables
CHARACTER(LEN=8) :: DATE_STR
INTEGER          :: DATE = 20110701

! FORTRAN internal write -- converts number to string
WRITE( DATE_STR, '(i8.8)' ) DATE
You can incorporate DATE_STR into a directory or file path. The format '(i8.8)' tells the WRITE command to make the string 8 characters long, and to change any spaces (if they exist) into preceding zeroes.
Caveat: Some versions of the PGI compiler did not allow internal WRITE statements. You can use the ENCODE function instead:
! Declare variables
CHARACTER(LEN=8) :: DATE_STR
INTEGER :: DATE = 20010701

! Writes value from DATE into DATE_STR
ENCODE( 8, '(i8.8)', DATE_STR ) DATE
You must specify the length of the character variable (in this case, 8), the format string, and the character variable when calling ENCODE.

A7.4.2 Use a Fortran internal read to extract numbers from a character string. This is the reverse of the Fortran internal write described above:
! Declare variables
CHARACTER(LEN=8) :: DATE_STR = '20010101'
INTEGER :: DATE

! FORTRAN internal read -- converts string to number
READ( DATE_STR, '(i8.8)' ) DATE
Caveat: Some versions of the PGI compiler did not allow Fortran internal reads. You can use the DECODE function instead:
! Declare variables
CHARACTER(LEN=8) :: DATE_STR = '20010101'
INTEGER :: DATE

! Reads string value from DATE_STR into DATE
DECODE( 8, '(i8.8)', DATE_STR ) DATE
As with ENCODE, you must specify the length of the character variable (in this case, 8), the format string, and the character variable in the call to DECODE.

A7.4.3 When writing GEOS - Chem code, you may have to use both the internal read / internal write and ENCODE / DECODE methods simultaneously, separated by the appropriate C - preprocessor compiler flags.
! Declare variables
CHARACTER(LEN=8) :: DATE_STR
INTEGER :: DATE = 20010701
 
# include "define.h" ! C-preprocessor flags
 
#if defined( LINUX_PGI )
   ! Write numeric value from DATE into DATE_STR for PGI Linux
   ENCODE( 8, '(i8)', DATE_STR ) DATE
#else
   ! FORTRAN Internal Write for other platforms
   WRITE( DATE_STR, '(i8)' ) DATE
#endif

A7.5 New language features of Fortran 90
A7.5.1 Use the new F90-style operators instead of the older F77-style operators:
== instead of .EQ.
/= instead of .NE.
>  instead of .GT.
>= instead of .GE.
<  instead of .LT.
>= instead of .LE.
The new operators take up only one or two spaces (instead of four spaces) and are easier to read.
Some operators (.AND., .OR., and .NOT.) are the same in F90 as in F77. This is also true of the boolean values (.TRUE. and .FALSE.).

A7.5.2 Use the F90 ! comment character. This replaces the F77 comment character (a C placed in the first column of fixed-format code). You can can create very legible comments by lining up the ! with your source code.

A7.5.3 To continue an instruction from one line to the next, place an ampersand (&) at the end of the line (for free-format layout).
If you are working with a source code file that has not yet been converted to free-format, place an ampersand in column 6 of each continued line of code.

A7.5.4 Use the F90 array assignment functionality to assign a value to all elements of an array without using array indices. For example:
INTEGER :: ARRAY(10,10)
ARRAY(:,:) = 0
You can also leave off the default array mask (:,:), so
ARRAY = 0
is also acceptable. 

A7.5.5 Initialize PARAMETER constants on the same line where they are declared:
REAL*8, PARAMETER :: PI = 3.14159265358979323d0
Avoid using obsolete F77 syntax:
REAL*8 PI
PARAMETER( PI = 3.14159265358979323 )

A7.5.6 Use F90 direct assignment statements to assign values to arrays:
REAL*8 :: A(2) = (/ 1.0d0, 2.0d0 /)
Avoid using obsolete F77 syntax:
REAL*8 A(2)
DATA A / 1.0, 2.0 /

A7.5.7 Include the SAVE attribute on the same line where the variable is declared:
LOGICAL, SAVE :: FIRSTTIME = .TRUE.
Avoid using obsolete F77 syntax:
LOGICAL FIRSTTIME 
SAVE FIRSTTIME
DATA FIRSTTIME / .TRUE. /
Note: SAVEd variables within a subroutine or function keep their values from one call to the next. This allows you to do some initialization only on the first call to a subroutine, for example: 
LOGICAL, SAVE :: FIRSTTIME = .TRUE. 

IF ( FIRSTTIME ) THEN
   PRINT*, 'This is the first time this routine is called!'
   FIRSTTIME = .FALSE.
ENDIF
Since the value of FIRSTTIME is saved between calls, the sentence above will only be printed out on the first call to the subroutine.

A7.5.8 Include the EXTERNAL attribute on the same line where a function's type is declared. Use this syntax:
INTEGER, EXTERNAL :: MYFUNC
Avoid using obsolete F77 syntax:
INTEGER MYFUNC
EXTERNAL MYFUNC
NOTE: If you are referencing functions contained within a module file, then you do not need to declare it with EXTERNAL. The EXTERNAL statement is a hangover from F77.

A7.5.9 Use the F90 SELECT CASE statement to pick from a list of options. In F77 you would have had to write:
IF ( X .EQ. 1 ) THEN
   CALL MYSUB( X1 )
ELSE IF ( X .EQ. 2 ) THEN 
   CALL MYSUB( X2 )
ELSE
   CALL MYSUB( X0 )
ENDIF
but with F90, you can write this instead:
SELECT CASE ( X )
   CASE( 1 )
      CALL MYSUB( X1 )
   CASE( 2 ) 
      CALL MYSUB( X2 )
   CASE DEFAULT
      CALL MYSUB( X0 )
END SELECT
SELECT CASE also works with character constants:
SELECT CASE ( TRIM( TRACERNAME ) )
   CASE( 'NOx' )
      CALL MYSUB( 1 )
   CASE( 'Ox' )
      CALL MYSUB( 2 )
   CASE DEFAULT
      CALL MYSUB( 3 )
END SELECT
A note of warning: You cannot specify CASE( X ) where X is a variable, or else the compiler will balk. Then you must resort to the IF - ELSE IF block structure as shown above.

A7.5.10 Use the F90 intrinsic functions LOG( X ) and LOG10( X ) to take the natural and common logarithms of X. Here X may be declared either as REAL*4 or REAL*8.
Avoid using the F77 intrinsic functions ALOG( X ) and ALOG10( X ). Some compilers do not support these functions.

A7.5.11 Use F90's keyword argument capability to clarify subroutine calls. You can replace this:
 SUBROUTINE READ_A1( NYMD,     NHMS, 
&                    ALBEDO,   CLDTOT,   EFLUX,    EVAP,    
&                    ... etc ...                         )
with this:
      CALL READ_A1( NYMD     = NYMD, 
     &              NHMS     = NHMS,
     &              ALBEDO   = ALBD,
     &              CLDTOT   = CLDTOT
     &              EFLUX    = EFLUX
     &              EVAP     = EVAP
                    ... etc ...      )
In the call above, you see several pairs of variable names separated by an equals sign:
ALBEDO   = ALBD,
The name on the left of the equals sign is the name of the argument as defined in the subroutine (i.e. ALBEDO). This is often called the "dummy argument" because it is just a name for the memory that is getting passed to it from outside of the subroutine.
The name on the right of the equals sign is the name of the variable that we are passing down to the subroutine. Here we are using the ALBD variable (from GEOS - Chem module dao_mod.F and passing that down to READ_A1 as the ALBEDO argument. 

A7.6 Math optimizations
A7.6.1 Logarithms and exponentiation are the most computationally expensive mathematical functions. Avoid using the traditional formulation:
 Y = A0 + A1*X + A2*X**2 + A3*X**3 + A4*X**4 + A5*X**5 
but instead use parentheses to group the polynomial terms.
 Y = A0 + X* ( A1 + X* ( A2 + X* ( A3 + X* ( A4 + X* ( A5 )))))
This modified polynomial expression replaces the costly exponentiations with more efficient multiplication operations. A Nth order polynomial will now only require N multiplications.

A7.6.2 Although it is tempting to replace EXP(  - x ) with the first-order approximation 1  -  x, this can result in negative values for certain values of x. This can cause negative tracer concentrations.

A7.7 DO loops
A7.7.1 Always use the CYCLE statement to skip to the next iteration in a DO-loop. Use this syntax:
DO I = 1, 1000

   ! Skip to next iteration
   IF ( X(I) == 0 ) CYCLE
 
   ! Print
   PRINT*, X(I)
ENDDO
instead of this obsolete F77 syntax:
DO 100 I = 1, 1000
   IF ( X(I) .EQ. 0 ) GOTO 100
   PRINT*, X(I)
100 CONTINUE
Notice that the F90 ENDDO statement replaces the labeled CONTINUE statement. This results in cleaner code.

A7.7.2 Always use the EXIT statement to completely exit from a DO loop. Use this syntax:
DO I = 1, 1000
 
   ! Break out of this loop if X==0!
   IF ( X(I) == 0 ) EXIT
 
   ! Print info if we have not exited
   WRITE( 6, '(''Iteration: '', i5, f13.6)' ) I, X(I)
ENDDO 

PRINT*, 'outside loop'
instead of this obsolete F77 syntax:
C Do-loop
DO 100 I = 1, 1000
   IF ( X(I) .EQ. 0 ) GOTO 200
   PRINT*, 'inside loop'
100 CONTINUE

C Continue outside loop
200 CONTINUE
PRINT*, 'outside loop'

A7.7.3 Structure your DO loops so that they access memory in the most optimal manner. Fortran is a column-major language, which means that arrays are stored in memory by columns first, then by rows. If you have declared an array such as:
INTEGER :: I, J, L, N
REAL*8  :: ARRAY(IIPAR,JJPAR,LLPAR,NNPAR)
then for optimal efficiency, the leftmost dimension (I) needs to vary the fastest, and needs to be accessed by the innermost DO-loop. Then the next leftmost dimension (J) should be accessed by the next innermost DO-loop, and so on. 
Therefore, the proper way to loop over this array is:
DO N = 1, NNPAR
DO L = 1, LLPAR
DO J = 1, JJPAR
DO I = 1, IIPAR
   ARRAY(I,J,L,N) = ARRAY(I,J,L,N) * 2.0d0
ENDDO
ENDDO
ENDDO
ENDDO 
Note that the I index is varying most often, since it is the innermost DO-loop, then J, L, and N. This is opposite to how a car's odometer reads.
If you loop through an array in this fashion, with leftmost indicies varying fastest, then the code minimizes the number of times it has to load subsections of the array into cache memory. In this optimal manner of execution, all of the array elements sitting in the cache memory are read in the proper order before the next array subsection needs to be loaded into the cache. But if you step through array elements in the wrong order, the number of cache loads is proportionally increased. Because it takes a finite amount of time to reload array elements into cache memory, the more times you have to access the cache, the longer it will take the code to execute. This can slow down the code dramatically.

A7.7.4 Use "infinite" DO loops in situations where you need to iterate for an unknown number of iterations before some exit criterion is reached. This is most often used to read data from a file whose length you do not know a priori. 
Here is an example of an infinite DO loop used to read data from disk:
INTEGER :: I, IOS, IUNIT
REAL*8 :: A(10000) 

! Open file
OPEN( IUNIT, FILE='myfile.txt', IOSTAT=IOS )

! Quit if we can't open the file
IF ( IOS /= 0 ) THEN
   PRINT*, 'Error opening the file!'
   STOP
ENDIF

! Infinite DO loop for reading data from "myfile.txt"
DO

   ! Read I and A(I) from the file
   READ( IUNIT, '(i3,f11.3)', IOSTAT=IOS ) I, A(I)
 
   ! IOS < 0 is end-of-file, so we exit the loop
   IF ( IOS < 0 ) EXIT
	
   ! If IOS < 0, then this is an I/O error,
   ! so we print an error msg and quit
   IF ( IOS > 0 ) THEN
      PRINT*, 'I/O error reading from file!
      STOP
   ENDIF
ENDDO
 
! Close the file after we exit the loop
CLOSE( IUNIT )
In this example, the DO loop wants to execute forever, but it is stopped by an external criterion -- the end of the file. The OPEN, READ, and CLOSE functions can return the I/O status to a variable if you specify via the IOSTAT keyword. If the I/O status variable (in this case, named IOS) is negative, then this is a normal end-of-file condition, and so we can just exit the loop and close the file. However, if IOS is a nonzero, positive number, then this means that we have encountered a real error condition.

A7.7.5 Reserve the following variable names for DO-loop and array indices:
   * Use I for the longitude index
   * Use J for the latitude index
   * Use L for the altitude index
   * Use N for the quantity index (tracer, species, etc.) 
Therefore, you can assume that any DO-loop that uses I, J, and L is looping over grid box longitude, latitude, and altitude dimensions, and that any DO-loop which uses N is looping over tracer, species, or some other quantity. These special indices should NOT be used to refer other quantities. In this way, if you should get an error message such as:
 Error at grid box (I,J) = (23,34)!
you will immediately understand (I,J) are the longitude and latitude indices of the box where the error happened.
NOTE: In some 3rd-party routines, you will see K used instead of L to denote the altitude index. We recommend leaving these as-is, so as to avoid having to rewrite entire sections of 3rd-party code. However, you should use L for the altitude index in any new GEOS - Chem code that you write.

A7.8 Fortran-90 modules
A7.8.1 Place all of your new GEOS - Chem code into Fortran 90 modules, if possible. These allow you to save both and routines and variables within a single program unit.
An example module is shown below.
!------------------------------------------------------------------------------
!          Harvard University Atmospheric Chemistry Modeling Group            !
!------------------------------------------------------------------------------
!BOP
!
! !MODULE: MY\_MODULE
!
! !DESCRIPTION: \subsection*{Overview}
! Module MY\_MODULE contains variables and routines to do something.
! (bmy, 5/1/03)
!\\
!\\
!
! !INTERFACE
       MODULE MY_MODULE
!
! !USES:
! 
      IMPLICIT NONE

 ! Make everything private...
      PRIVATE
 !
 ! !PUBLIC MEMBER FUNCTIONS: 
 !
      PUBLIC :: DRIVER
      PUBLIC :: INIT_MY_MODULE
      PUBLIC :: CLEANUP_MY_MODULE
 !
 ! !REVISION HISTORY:
 !  (1 ) Bug fix in MY_SUBROUTINE (bmy, 5/1/03)
 !EOP
 !------------------------------------------------------------------------------
 !
 ! !PRIVATE DATA MEMBERS:
 !
      ! Argument to the SIN function
      REAL*8, ALLOCATABLE :: B(:)

      CONTAINS

!------------------------------------------------------------------------------
!          Harvard University Atmospheric Chemistry Modeling Group            !
!------------------------------------------------------------------------------
!BOP
!
! !IROUTINE: DRIVER
!
! !DESCRIPTION: \subsection*{Overview}
! Subroutine DRIVER is the driver routine for MY_MODULE. (bmy, 5/1/03)
!\\
!\\
!
! !INTERFACE:
      SUBROUTINE DRIVER
!
! !REVISION HISTORY:
!
!EOP
!------------------------------------------------------------------------------
!BOC
!
! !LOCAL VARIABLES:
!
      LOGICAL, SAVE :: FIRST = .TRUE.
      INTEGER, :: I
      REAL*8 :: X, Y1, Y2
      REAL*8, PARAMETER :: PI180 = 180d0 / 3.14159265358979323d0
 
      !=================================================================
      ! DRIVER begins here!
      !=================================================================
 
      ! Initialize 
      IF ( FIRST ) THEN
         CALL INIT_MY_MODULE
      ENDIF
 
      !=================================================================
      ! Loop over degrees
      !=================================================================
      DO I = 1, 360
 
         ! Convert to radians
         B = DBLE( I ) / PI180
 
         ! Call subroutine
         CALL MY_SUBROUTINE( B(I), Y1 )
 
         ! Call function
         Y2 = MY_FUNCTION( B(I) )
 
         ! Write output
         WRITE( 6, '(i3, 1x, 3(f13.6,1x))' ) I, B(I), Y1, Y2
      ENDDO 
 
      ! Return to calling program
      END SUBROUTINE DRIVER
!EOC
!-----------------------------------------------------------------------------
!          Harvard University Atmospheric Chemistry Modeling Group            !
!------------------------------------------------------------------------------
!BOP
!
! !IROUTINE: MY\_SUBROUTINE
!
! !DESCRIPTION: \subsection*{Overview}
! Function MY_SUBROUTINE returns the sine of a number. (bmy, 5/1/03)
!\\
!\\
!
! !INTERFACE:

      SUBROUTINE MY_SUBROUTINE( X, Y )
!
! !INPUT PARAMETERS: 
!
      ! Argument for the sine function
      REAL*8, INTENT(IN) :: X
!
! !RETURN VALUE:
!     
      REAL*8, INTENT(OUT) :: Y 
!
! !REVISION HISTORY:
! (1 ) Corrected typographic error (bmy, 5/1/03)
!EOP
!------------------------------------------------------------------------------
!BOC
 
      !=================================================================
      ! MY_SUBROUTINE begins here!
      !=================================================================
      Y = SIN( X )
 
      ! Return to calling program
      END SUBROUTINE MY_SUBROUTINE
!EOC
!-----------------------------------------------------------------------------
!          Harvard University Atmospheric Chemistry Modeling Group            !
!------------------------------------------------------------------------------
!BOP
!
! !IROUTINE: MY\_FUNCTION
!
! !DESCRIPTION: \subsection*{Overview}
! Function MY_FUNCTION returns the sine of a number. (bmy, 5/1/03)
!\\
!\\
!
! !INTERFACE:

      FUNCTION MY_FUNCTION( X ) RESULT( Y )
!
! !INPUT PARAMETERS: 
!
      ! Argument for the sine function
      REAL*8, INTENT(IN) :: X
!
! !RETURN VALUE:
!     
      REAL*8, INTENT(OUT) :: Y 
!
! !REVISION HISTORY:
!
!EOP
!------------------------------------------------------------------------------
!BOC
 
      !=================================================================
      ! MY_FUNCTION begins here!
      !=================================================================
      Y = SIN( X )
 
      ! Return to calling program
      END FUNCTION MY_FUNCTION
!EOC
!------------------------------------------------------------------------------
!!          Harvard University Atmospheric Chemistry Modeling Group            !
!------------------------------------------------------------------------------
!BOP
!
! !IROUTINE: INIT\_MY\_MODULE
!
! !DESCRIPTION: \subsection*{Overview}
! Subroutine INIT\_MY\_MODULE allocates and zeroes the B array. (bmy, 5/1/03)
!\\
!\\
!
! !INTERFACE:
      SUBROUTINE INIT_MY_MODULE
!
! !USES
!
      USE ERROR_MOD, ONLY : ALLOC_ERR
!
! !REVISION HISTORY:
!
!EOP
!------------------------------------------------------------------------------
!BOC
!
! !LOCAL VARIABLES
      INTEGER :: AS
 
      !=================================================================
      ! INIT_MY_MODULE begins here!
      !=================================================================
 
      ! Allocate B, check status
      ALLOCATE( B(360), STAT=AS )
 
      ! Error check
      IF ( AS /= 0 ) CALL ALLOC_ERR( 'B' )
 
      ! Zero B
      B(:) = 0d0
 
      ! Return to calling program
      END SUBROUTINE INIT_MY_MODULE
!EOC
!-----------------------------------------------------------------------------
!!          Harvard University Atmospheric Chemistry Modeling Group            !
!------------------------------------------------------------------------------
!BOP
!
! !IROUTINE: CLEANUP\_MY\_MODULE
!
! !DESCRIPTION: \subsection*{Overview}
! Subroutine CLEANUP_MY_MODULE deallocates all module arrays. (bmy, 5/1/03)
!\\
!\\
!
! !INTERFACE:
      SUBROUTINE CLEANUP_MY_MODULE 
!
! !REVISION HISTORY:
!
!EOP
!------------------------------------------------------------------------------
!BOC

      !=================================================================
      ! CLEANUP_MY_MODULE begins here!
      !=================================================================
      IF ( ALLOCATED( B ) ) DEALLOCATE( B )

      ! Return to calling program
      END SUBROUTINE CLEANUP_MY_MODULE
!EOC
 END MODULE MY_MODULE
Fortran 90 modules written for GEOS - Chem contain the following features:
   1. Module header: This is similar to the subroutine header. Contains a list of all module variables, routines, and modification notes, in ProTeX style.
   2. PRIVATE declarations: You can "hide" certain routines or variables within a F90 module from other routines or modules. Ideally your module will be like a "black box" with only a few routines or variables that are publicly accessible. By convention, in GEOS - Chem, we declare everything PRIVATE first then indicate the public routines.
   3. IMPLICIT NONE: If you declare IMPLICIT NONE once at the top of the module, then you don't have to declare it in the individual subroutines; the declaration "carries through" below.
   4. Module variables and arrays: Any variables declared above the CONTAINS statement are as if they were stored in F77 common blocks; that is, they are preserved between calls to the various module routines. Also, you should declare module arrays as ALLOCATABLE whenever possible. This allows you to only set aside memory for that array if a certain routine is called. This results in more efficient memory management.
   5. CONTAINS statement: All module variables and PRIVATE declarations go above the CONTAINS statement. Module routines and functions go below the CONTAINS statement.
   6. Subroutines and functions: Your module will contain various subroutines and functions depending on the particular needs at hand.
   7. An INIT routine: Your module should have a subroutine named INIT_modulename, which initializes and allocates all module arrays.
   8. A CLEANUP routine: Your module should have a subroutine named CLEANUP_modulename, which deallocates module arrays. (You only need this if you have allocatable arrays).
F90 modules are very similar to classes in Java and C++; they allow you to group data and the routines which work on the data in a single package.
Theoretically, each GEOS - Chem routine and/or variable should belong to a module. In practice, this is not true, as we do have common blocks and separate subroutine and function files from some of the older routines which were written by 3rd party sources. However, you should write all new GEOS - Chem code in module form.
Also, it is OK for modules to reference other modules. If Module B references Module A, all that you have to do is to make sure that Module B declaration in the Makefile refers to Module A. The GEOS - Chem Makefiles have been prepared for you by the GEOS - Chem Support Team, so in most instances, you will not have to concern yourself with this.

A7.8.2 We used to refer to variables in modules by means of the USE statement, such as:
! Reference variables from dao_mod.F
USE DAO_MOD, ONLY : UWND, VWND, T
While many routines in GEOS - Chem still use this syntax, we are abandoning this approach. Instead of referring to module variables with USE, we shall (wherever expedient) use derived type objects to contain variables and arrays, which then can be passed from one routine to another via the argument list. We are doing this to facilitate our Grid Independent GEOS - Chem project, which seeks to embed GEOS - Chem within the NASA GEOS - 5 GCM.
Eventually, the only things that you should obtain from modules via the USE statement will be:
   1. Subroutines
   2. Functions
   3. Derived type definitions
such as:
! Refer to derived type definition from gc_type_mod.F
USE GC_TYPE_MOD, ONLY : GC_MET_LOCAL

! Refer to subroutines from dao_mod.F
USE DAO_MOD, ONLY: AIRQNT, COSSZA
For more information about derived types, please see Appendix 8.

A7.9 Programming techniques to facilitate grid-independence
A7.9.1 When GEOS - Chem connects to an external GCM -- such as NASA's GEOS - 5 GCM -- it will utilize MPI parallelization. Each CPU will perform all of GEOS - Chem's operations, but on a much smaller geographical domain (i.e. on a single vertical column or several vertical columns). This also means that each CPU will print informational messages to the screen (or log file, if you redirect screen output there) simultaneously. All of these I/O operations can seriously impact performance.
We have now started the process of bracketing WRITE and PRINT statements with IF blocks. In GEOS - Chem v9 - 01 - 03 and higher versions, you will see code like this:
      IF ( am_I_Root ) THEN 
         WRITE( 6, '(a  )' ) REPEAT( '=', 79 )           
         WRITE( 6, '(a,/)' ) 'G E O S - C H E M   U S E R   I N P U T'
         WRITE( 6, 100   ) TRIM( FILENAME )
 100     FORMAT( 'READ_INPUT_FILE: Reading ', a )        
      ENDIF
When we use MPI parallelization, the am_I_Root variable, which is passed as an argument to subroutines and functions, determines if we are on the root CPU. This will restrict the printing of informational messages to just the root CPU. We encourage you to use this approach as you write new GEOS - Chem code.
For more information, please see this post on our Grid-Independent GEOS - Chem wiki page. 

A7.9.2 GEOS - Chem v9 - 01 - 02 and prior versions used fixed parameters (stored in module GeosUtil/file_mod.F) for Fortran logical unit numbers. Logical unit numbers, or LUN's, are numeric values that are used in Fortran OPEN, WRITE, READ, and CLOSE statements. A typical GEOS - Chem file read operation looks like this:
      USE FILE_MOD, ONLY : IU_FILE
      ...
      
      ! Open file
      OPEN( UNIT=IU_FILE, FILE=TRIM( FILENAME ) ... )
      
      ! Read data
      READ( IU_FILE, IOSTAT=IOS ) ...
      
      ! Close file
      CLOSE( IU_FILE )
But when we connect GEOS - Chem to an external GCM, we can no longer rely on pre-defined LUNs. The GCM may have already assigned the LUN that we are trying to use to a different file. Therefore, starting in GEOS - Chem v9 - 01 - 03, all LUNs will be determined dynamically. We now call a function (inquireMod/findFreeLUN) to return the next unused LUN. You will now see code that looks like this:
      USE inquireMod, ONLY : findFreeLUN
      ...
      
      INTEGER :: IU_FILE
      ...

      ! Find a free file LUN
      IU_FILE = findFreeLUN()
    
      ! Open file
      OPEN( UNIT=IU_FILE, FILE=TRIM( FILENAME ) ... )
      
      ! Read data
      READ( IU_FILE, IOSTAT=IOS ) ...
      
      ! Close file
      CLOSE( IU_FILE )
For more information, please see this post on our Grid-Independent GEOS - Chem wiki page.

A7.9.3 As mentioned in Chapter A7.8.2, we are now moving away from referring to module variables via USE statements. Please see this wiki post on our Grid Independent GEOS-Chem wiki page for more information about how we are passing data between subroutines via derived type objects.

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 8
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 8: Modifications to facilitate Grid-Independence in GEOS - Chem
GEOS - Chem will form the core of a fully-coupled system that will connect to the NASA GEOS - 5/GCM. Before this can happen, the GEOS - Chem standard model must become compliant with the Earth System Model Framework (ESMF). This will allow us to take advantage of Message Passing Interface (MPI) parallelization via ESMF, which has been a long-term goal of the GEOS-Chem development community. MPI parallelization will facilitate GEOS - Chem simulations at extremely fine horizontal resolution, running on hundreds or thousands of CPUs.
To achieve this coupling between GEOS - Chem and the NASA GEOS - 5 GCM, we have introduced the concept of grid-independence. We no longer shall assume a preset horizontal grid, but instead shall allow the GCM to dictate the size of the grid, and how many grid boxes will be processed by each CPU. This lets us to keep the all calls to ESMF library routines completely outside of GEOS - Chem.
We have made it a priority to implement necesary structural changes into GEOS - Chem without disrupting ongoing GEOS - Chem research projects. We have already removed several legacy code routines that prevented GEOS - Chem from connecting to the NASA GCM. We have added new source code instructions into many GEOS - Chem routines, set apart by C-preprocessor switches. Eventually, the new code will replace the old code, but during the transition phase we must keep both new and old code side-by-side.
We describe below the structural changes that we made to facilitate Grid-Independence in GEOS - Chem. Please also see our Grid-Independent GEOS - Chem wiki page for the latest information.

A8.1 Initial preparations
Our initial preparations involved replacing F77-style legacy code with modern F90 code:
   1. Removal of global parameters
   2. Renaming file extensions from *.f and *.f90 to *.F and *.F90
   3. Elmination of COMMON blocks
   4. Removal of the hardwired grid

A8.2 Construction of the Chemistry Component
We began by attempting to interface GEOS - Chem's chemistry solver, photolysis, and dry deposition routines into a "Chemistry Component" that could be plugged into the GEOS - 5 GCM. An initial test (using the Beijing Climate Center's GCM as a proxy) revealed several bottlenecks that we had to rectify immediately:
   1. We modified all functions in in grid_mod.F (as well as routine GET_LOCALTIME in time_mod.F) to accept longitude, latitude, and altitude indices as inputs. In other words, functions such as GET_XMID( I ) now look like GET_XMID( I, J, L ), etc.
   2. We moved computation of the overhead ozone columns (and interpolation to TOMS/SBUV, where that data exists) outside of FAST - J. FAST - J now accepts this as an input argument.
   3. We introduced netCDF I/O capability into GEOS - Chem and converted several ASCII data files to netCDF. We shall continue to migrate all of GEOS - Chem's data files to netCDF, but this will be a gradual transiton.
   4. We created a new module to read and regrid Olson land map data from its native resolution. This module can be used with both the older (1992, 0.5° x 0.5°) and newer (2001, 0.25° x 0.25°) Olson map products. This removed legacy code that relied on ASCII data input.
   5. We created a new module to read and regrid MODIS leaf-area-index data from its native resolution (either 0.5° x 0.5° or 0.25° x 0.25°). This removed legacy code that relied on ASCII data input.
We corrected all of these issues prior to the release of v9 - 01 - 03. Please see our GEOS - Chem v9 - 01 - 03 wiki page for more details about each of these improvements.
For better compatibility with the Earth System Model Framework -- which controls the flow of data between components of the GEOS - 5 GCM -- we have added the following structural changes into the standard GEOS - Chem code:
   1. We have introduced new derived type objects into GEOS - Chem. These objects will render referencing data arrays via USE statements obsolete. 
   2. We have set derived type objects (as well as other structural modifications) apart from existing source code with C-preprocessor switches.
   3. We now pass an argument named am_I_Root from main.F to lower level subroutines. This will allow us to restrict printing to the root CPU when we connect GEOS - Chem to the GEOS - 5 GCM.
   4. We now determine available Fortran logical unit numbers while GEOS - Chem is running rather than using fixed, pre-defined values.

A8.3 Construction of the Emissions Component
Initally, we focused on delivering the GEOS - Chem "Chemistry Component" (chemistry, photolysis, dry deposition) to NASA/GSFC for inclusion into the GEOS - 5 GCM. We achieved this in June 2011.With the help of our colleagues at GSFC, we are continuing to refine the performance of the GEOS-Chem within the GEOS - 5 GCM.
We also are re-engineering GEOS - Chem's emissions routines into an "Emissions Component". We have the following goals in mind:
   1. We wish to achieve a total separation between emissions routines and chemistry routines
   2. We wish to implement "top-down" data flow (i.e. all data enters/leaves each subroutine via the argument list, contained in derived type objects)
   3. We wish to segregate all file I/O operations from routines in which computations are performed. This will prevent bottlenecks to parallelization.
   4. We wish to have a flexible data structure to which we can attach emissions data, scale factors, or geographical masks.
Christoph Keller (Harvard) is currently working on this task. He has created a new emissions data structure (a "linked list") that will form the backbone of the GEOS - Chem Emissions Component. The work is ongoing.

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 9
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 9: Addenda to GEOS - Chem Online User's Guide
In this Appendix, we shall post additions and corrections to the GEOS - Chem Online User's Guide.

9.1 Addenda
At this time there are no addenda for GEOS - Chem v9 - 01 - 03.

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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 10
                 GEOS - Chem v9 - 01 - 03 Online User's Guide
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Appendix 10: GEOS - Chem Version History
On this page we shall preserve the list of "What's new" in each GEOS - Chem public release.
Please also see our archive of past GEOS - Chem User's Guides page.

A10.1 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

A10.2 What's new in GEOS - Chem v9 - 01 - 02
The following features were introduced into GEOS - Chem public release v9 - 01 - 02:
                                    Feature
                                  Description
                                Science updates
Updated dry deposition velocities for aerosols over ice and snow
Modeled aerosol dry deposition velocities over snow and ice surfaces in the Arctic were much higher than estimated from measured values (e.g., Ibrahim et al. [1983]; Duan et al. [1988]; Nilsson and Rannik [2001]). In v9 - 01 - 02, a dry deposition velocity of 0.03 cm/s is imposed for all aerosols over snow and ice surfaces.
Imposed seasonality on the NH3 emissions from David Streets 2000 inventory
The Streets 2000 inventory for anthropogenic ammonia (NH3) does not include any seasonal cycle. This has been corrected by using the annual total from Streets 2000 superimposed with monthly scale factors from a global inventory compiled by Marcel Meinders and Lex Bouwman. 
RETRO anthropogenic VOC emissions
Monthly RETRO anthropogenic VOC emissions have been added as an optional inventory.
For more information, please see this document:
   * W. Reinhart and D. Millet, Implementation of the RETRO Anthropogenic Emission Inventory into the GEOS - Chem model, May 2011.
APM aerosol microphysics
Fangqun Yu and Gan Luo developed the Advanced Particle Microphysics (APM) package for implementation into GEOS - Chem. APM is now one of two microphysics packages in GEOS - Chem, the other being TOMAS.
GFED3 biomass burning emissions
Monthly mean GFED3 biomass burning emissions have been added to v9-01-02. The GFED3 emissions inventory will eventually replace GFED2.
GEIA 2005 Hg emissions
Bess Corbit prepared the GEIA 2005 emission inventory for anthropogenic Hg. 
                              Structural updates
Modifications for compatability with ESMF
Modifications were made to GEOS - Chem source code to enable compatability with the Earth System Model Framework (ESMF). These changes were were aimed at cleaning up legacy code and making specific portions of the code FORTRAN 90/95 compliant. For more information, please see the following links:
   1. Source code cleanup and initial ESMF prep
   2. Elimination of COMMON blocks
MERRA SEAICExx fields added to the planeflight diagnostic
The MERRA SEAICExx fields are now saved to the plane flight diagnostic.
Overhaul of AOD diagnostics
Patrick Kim discovered some inconsistencies in the way aerosol optical depth diagnostics were being computed in v9 - 01 - 01 and prior versions. See this wiki page for more information.
Archive MERRA SWGDN field in the ND67 diagnostic
MERRA "incident shortwave radiation at the ground" (SWGDN) is now archived to ND67, not "net longwave radiation at the ground" (LWGNT).
Centralized chemistry time step
The time at which chemistry, emissions, photolysis, and drydep operations are performed has been moved to the midpoint of the chemistry time step. See this wiki page for more information.
                                   Bug fixes
Bug fixes for the offline Hg simulation 
The following issues were discovered in the offline Hg simulation shortly after the release of v9-01-01 and have been fixed in v9-01-02:
   * De-hardwire file path BR_DIR in global_br_mod.F
   * Negative concentrations of aquatic mercury
   * VEGEMIS bug fix for GCAP simulation
   * Division by zero error
   * Bug fixes for ND03 mercury diagnostics
Various other bug fixes
The following updates were made to fix several bugs:
   * Corrected mis-indexing error in partition.F caused by the dynamic tropopause
   * Corrected out-of-bounds error in readchem.F
   * Fix for mis-indexing issue in CSPEC restart file
   * Bug fixes for leap years when using GCAP met fields
   * Minor bug fixes for emissions routines affecting offline simulations
   * Fixes for minor issues affecting nested-grid simulations
   * Bug fixes for compatibility with the PGI compiler
   * Washout fix for non-aerosol species
   * Fix for GEIA emissions scaling factor over Botswana
   * Fixed minor issues in MERRA cloud convection routine
   * Fix for vertical regridding of offline OH for offline simulations
   * Further fixes for nested-grid simulations 
   * Fix for partitioning chemical species
   * Bug fix for Streets biofuel emissions
   * Bug fix in EDGAR ship emissions code
   * Bug fix in ship NOx emissions

A10.3 What's new in GEOS - Chem v9 - 01 - 01
The following features were introduced into GEOS - Chem public release v9 - 01 - 01:
                                    Feature
                                  Description
Capability to run with GMAO MERRA meteorological fields
GEOS - Chem v9 - 01 - 01 is the first version to be compatible with the MERRA met data product from GMAO. MERRA is a 30-year reanalysis data set which spans the years 1979-2010.
Bug fix for lightning NOx emissions
In GEOS - Chem v9 - 01 - 01, the following updates were made that impact the emissions of lightning NOx:
   1. Bug fix for incorrect cloud-top-height determination
   2. Addition of updated vertical release profiles (cf. Ott et al 2010)
   3. Removal of obsolete options from the source code (lightning_nox_mod.f)
For detailed information about these updates, please see this document:
   * L.T. Murray, Changes affecting lightning NOx emissions in GEOS - Chem v9-01-01, January 2011
Improvements to the wet deposition and convective updraft scavenging algorithms
Helen Amos and Bess Corbitt have updated the wet deposition and convective updraft scavenging algorithms, particularly for the new MERRA met fields. Also, following upon the work of Qiaoqiao Wang, we now allow both rainout and washout to happen simultaneously in a grid box where new precipitation is forming.
Updated volcanic SO2 emissions from Aerocom
The latest volcanic SO2 emissions update from Thomas Diehl have been applied to GEOS - Chem v9 - 01 - 01.
Important bug fixes for ship emissions
Geert Vinken has submitted a couple of important fixes for ship emissions. These have been added to v9-01-01. For more information, please see the following links: 
   * Bug fix for ship emissions in emfossil.f
   * Updated mask for EMEP ship emissions
EPA/NEI05 biofuel bug fix
A bug in the EPA/NEI05 emissions code was found prior to the release of GEOS - Chem v9 - 01 - 01. Long story short: when the EPA/NEI05 option is selected, the wrong biofuel emissions inventory is used over the continental USA.
For a complete description of this bug, please see this post on our EPA/NEI05 wiki page.
Various technical improvements
The following updates were made to fix several technical issues:
   * All bug fix patches from v8 - 03 - 02 have now been standardized in v9 - 01 - 01
   * Simulations may be started at times other than 0h GMT
   * Modifications were made to the non-local PBL mixing scheme to improve efficiency
   * The main loop in the LINOZ stratospheric chemistry scheme was parallelized
   * Duplicate printout of certain diagnostics was corrected
   * A fix was added to prevent div-by-zero in sulfate_mod.f
   * Erroneous ND15 diagnostic behavior in the non-local PBL scheme was corrected
   * The PEDGE-$ diagnostic category is archived to timeseries diagnostics
   * Offline simulations can now run on the GEOS-5/MERRA full-vertical grid

A10.4 What's new in GEOS - Chem v8 - 03 - 01 and v8 - 03 - 02
The following features were introduced into GEOS - Chem public release v8 - 03 - 01:
                                    Feature
                                  Description
Caltech isoprene chemistry mechanism
A new isoprene chemistry was introduced as an option to solve an over-estimation in isoprene in previous GEOSChem versions.
LINOZ stratospheric ozone chemistry
Implementation of LINOZ which provides a linear chemistry for ozone in the stratosphere.
ISORROPIA II
ISORROPIA II is now used to calculate the aerosol thermodynamic equilibrium instead of RPMARES.
Updated aerosol optical properties for FAST-J photolysis
The GEOS - Chem Aerosols Working Group has created an updated list of aerosol optical properties (i.e. quantum yields, cross-sections) for input into the FAST - J photolysis mechanism. 
Option to use chemical solver from KPP software
The KPP chemical solver now contains 3 mechanisms to choose from: 
   * Standard simulation without secondary organic aerosols
   * Standard simulation with secondary organic aerosols
   * Simulation with new isoprene chemistry scheme
Emissions modifications
Various modifications to existing emissions inventories, including: 
   * Extension of annual anthropogenic scale factors to 2006
   * EMEP emissions extended to 2007 and Seasonality extended to SOx, CO, and NH3
   * BOND inventory for BC and OC with monthly variations
   * Implementation of MEGAN v2.1 biogenic emissions
   * Implementation of ICOADS ship emissions
   * Volcanic SO2 emissions from AeroCom
   * EPA/NEI 2005 inventory for North America 
New non-local planetary boundary layer scheme
Jintai Lin has implemented a new boundary layer mixing scheme option into GEOS - Chem. It is a non-local scheme formulated by Holtslag and Boville (1993).
Modifications to SOA formation
Several modifications were applied to the secondary organic aerosol scheme:
   * SOA no longer depends on inorganic concentrations
   * SOA formation now includes formation by aromatics
   * We now use the speciated emissions from MEGAN v2.1
Updates for sea salt aerosols
Lyatt Jaeglé and Becky Alexander have updated the sea salt emissions scheme in GEOS - Chem.
TOMAS aerosol microphysics option
The Carnegie-Mellon group has interfaced the TOMAS aerosol microphysics scheme into GEOS - Chem.
Global 1° x 1.25° simulation capability
Lok Lamsal from Dalhousie University has added the capability to run GEOS - Chem at the GEOS - 4 native resolution of 1° x 1.25°.
Modifications to / Creation of the GEOS-5 0.5° x 0.667° N. American and European Nested Grid simulation
Several modifications were made to GEOS - Chem's nested grid simulation capability, including:
   * Standardization of North America 0.5° x 0.667° nested grid (GEOS - 5) 
   * Introduction of Europe 0.5° x 0.667° nested grid (GEOS - 5) 
   * Ability to keep boundary conditions for different grids in different directories
   * HDF5 output has been added to selected timeseries diagnostics. 
Updated CH4 simulation
Christopher Pickett-Heaps and Kevin Wecht have updated the CH4 simulation in GEOS - Chem, following earlier work by Jerome Drevet. 
The following features were introduced into GEOS - Chem beta release v8 - 03 - 02:
                                    Feature
                                  Description
Terrestrial and deep ocean mercury
The Global Terrestrial Mercury Model (cf. Nicole Smith-Downey) can now be selected as an option in the standard mercury simulation. Many features of the mercury simulation have also been improved (cf. E. Sunderland, C. Holmes).
Updated CO2 simulation
Ray Nassar has updated the CO2 simulation with new inventories and fluxes. For a full description, see our CO2 simulation wiki page.
Obtain liquid water content from GEOS - 5 met fields
Jenny Fisher modified the existing SO2 chemistry scheme such that it will obtain the cloud fraction and liquid water content directly from the GEOS - 5 meteorlogy.

A10.5 What's new in GEOS - Chem v8 - 02 - 01
The following features were introduced into GEOS - Chem public release v8 - 02 - 01:
                                    Feature
                                  Description
Updated chemical reactions
Chemical relations and relation rates are updated mainly from JPL06 and IUPAC06. Photolysis quantum yields are updated from FAST - JX version 6.4 data. See HERE for detailed changes compared to v8 - 01 - 04. The pressure-dependency sheme for acetone photolysis is now updated to FAST - JX version 6.4.
The format of jv_spec.dat file has slightly changed. The new format is explained in Chapter 5: GEOS - Chem run directories.
Updated dust scattering
 
Updated emissions
Several emission inventories are updated or newly implemented. All details concerning emissions are in Chapter 4: GEOS - Chem data directories.
Improved stratospheric exchange
GEOS - Chem uses now the transport routine and pressure fixer from GMI. This ensures to have a reasonable troposphere-stratosphere exchange.

A10.6 What's new in GEOS - Chem v8 - 01 - 01
The following features were introduced into GEOS - Chem public release v8 - 01 - 01:
                                    Feature
                                  Description
Compatibility with GEOS - 5 meteorological fields
GEOS - Chem v8 - 01 - 01 is now fully compatible with the GMAO GEOS - 5 operational data product (e.g. GEOS-5.0.1 and GEOS-5.1.0). You must upgrade to GEOS - Chem v8 - 01 - 01 if you wish to drive GEOS - Chem with the GEOS - 5 meteorology.
Please see the GEOS - Chem wiki for a more complete account of some of the issues that were encountered during GEOS - 5 implementation.
GEOS - 1 and GEOS - STRAT meteorology is no longer supported
With the availability of several years of GMAO's GEOS - 4 and GEOS - 5 meteorological data products, it is no longer necessary to use the older GEOS - 1 and GEOS - STRAT products. Therefore, GEOS - Chem v8 - 01 - 01 no longer supports these data sets.
NOTE: GMAO's GEOS - 3 meteorological data product is still supported in GEOS - Chem v8 - 01 - 01, and will continue to be supported indefinitely. 
Dynamic tropopause
GEOS - Chem now has the capability to perform chemistry with SMVGEAR up to the location of the actual tropopause, as diagnosed by the tropopause pressure (TROPP) meteorological field. This results in a more accurate representation of the tropopause, and causes more grid boxes in the tropics to be sent to the SMVGEAR solver. In prior versions, SMVGEAR chemistry was only done up to the location of the annual mean tropopause. 
Updated lightning with OTD/LIS local redistribution 
The lightning NOx emissions algorithm in GEOS - Chem v8 - 01 - 01 has been substantially rewritten to try to better match the observational distribution of lightning flashes. The location of lightning flashes now follows the patterns observed by the OTD/LIS satellite instruments. 
Updated global and regional anthropogenic emissions
In GEOS - Chem v8 - 01 - 01, the default GEIA/Piccot anthropogenic emissions can now be overwritten with a combination of global and regional anthropogenic emissions inventories, including:
   * EDGAR (global) 
   * EMEP (Europe)
   * BRAVO (Mexico) 
   * Updated EPA-NEI99 (USA)
   * David Streets (SE Asia)
Click HERE to view a table with more detailed information about each of these inventories. 
NOTE: In afuture version of GEOS - Chem, we will be introducing an improved algorithm to scale fossil fuel emissions from the baseline year of 2000 to the present year (cf. Aaron van Donkelaar).
GFED2 biomass burning emissions
In GEOS - Chem v8 - 01 - 01, you may select either the default Duncan et al (2001) biomass burning emissions, or the GFED2 biomass burning emissions. 
NOTE: At present only the GFED2 monthly mean emissions have been implemented. The 8-day-averaged GFED2 emissions will be introduced into a future version of GEOS - Chem (cf. Ray Nassar). 
Safer floating-point operations 
GEOS - Chem v8 - 01 - 01 includes some extra floating point error traps (e.g. safe division, avoiding division by zero, etc.) in order to prevent NaN and infinity values from propagating throughout the code. Also, a bug fix was implemented into SMVGEAR in order to better screen out negative values. 
Aerosol Thermodynamic Equilibrium with RPMARES
It was recently discovered that the version of ISORROPIA that ships with GEOS - Chem can give bad values when computing the aerosol thermodynamical equilibrium for grid boxes where relative humidity is below 30%. Therefore, until further notice we have reverted back to the RPMARES code for computing aerosol thermodynamical equilibrium until further notice.
Compatibility with SunStudio 11/12 and Intel Fortran Compiler 10
GEOS - Chem v8 - 01 - 01 now ships with Makefiles for compiling with the newest Sun or Intel Fortran compilers. Options for using the TotalView Debugger are also now included in the makefiles. 

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