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 nonlinear 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 gridindependent 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: 

o Download the most current GEOS–Chem source code online.

o Download the most current GEOS–Chem run directories online

o Develop and test their source code additions to GEOS–Chem in their own 

local repository, and

o 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/DIROPTION 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/geoschem/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 GEOSChem. However, we recommend all GEOS-Chem users to build either netCDF4.2 or netCDF CLASSIC with the GEOS-Chem-Libraries installer so that GEOSChem 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-ChemLibraries 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-ChemLibraries 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 netCDF4.2 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 netCDF4.2) 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 GEOSChem-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. ncconfig, 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- Directory where obsolete source code files are placed 
03/obsolete 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- Makefile to build the GEOS–Chem code. Also calls 
03/GeosCore/Makefile 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 SEAC4RS 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 previouslycreated 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-3s

-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 (cm3s

-1

) 

lookup tables.

YIONRATE.txt Text file containing the ionization rate (ion-pairs cm3

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

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.
CAC2008-NH3-

12.geos.1x1

CAC2008-NH3.geos.1x1

CAC2008-NOx.geos.1x1

CAC2008-SOx.geos.1x1

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 activitybased 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. GEOSChem 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.1x

1 

CO/EDGAR.f2000co.generic.1x

1 

CO/EDGAR.f3000co.generic.1x

1 

CO/EDGAR.f4000co.generic.1x

1 

CO/EDGAR.f5100co.generic.1x

1 

CO/EDGAR.f5400co.generic.1x

1 

CO/EDGAR.f5700co.generic.1x

1 

CO/EDGAR.f5800co.generic.1x

1 

CO/EDGAR.f8000co.generic.1x

1 

CO/EDGAR.i1000co.generic.1x

1 

CO/EDGAR.i2000co.generic.1x

1 

CO/EDGAR.i5000co.generic.1x

1 

CO/EDGAR.w4095co.generic.1x

1

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 

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
NOx/EDGAR.f5100nox.generic.

1x1 

NOx/EDGAR.f5400nox.generic.

1x1 

NOx/EDGAR.f5700nox.generic.

1x1 

NOx/EDGAR.f5800nox(IEA).gen

eric.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 

 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 

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 
NOx/EDGAR.NOxScalar-1998-

2000.geos.1x1

NOx/EDGAR.NOxScalar-1997-

2000.geos.1x1

NOx/EDGAR.NOxScalar-1996-

2000.geos.1x1

the given year. 

NOx/anth_NOx_scale.DJF.gene

ric.1x1

NOx/anth_NOx_scale.MAM.gene

ric.1x1

NOx/anth_NOx_scale.JJA.gene

ric.1x1

NOx/anth_NOx_scale.SON.gene

ric.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).gen

eric.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 

Files on the on the GMAO 1° x 1° grid containing 

scale factors for EDGAR SOx emissions for years 

1985-1995.
SOx/EDGAR.SOxScalar-1999-

2000.geos.1x1 

SOx/EDGAR.SOxScalar-1998-

2000.geos.1x1 

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.gene

ric.1x1

SOx/anth_SOx_scale.MAM.gene

ric.1x1

SOx/anth_SOx_scale.JJA.gene

ric.1x1

SOx/anth_SOx_scale.SON.gene

ric.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_EDGAR

2.1x1geos.bpch

C2H2/C2H2_1985_FF_IND_EDGAR

2.1x1geos.bpch

C2H4/C2H4_1985_FF_IND_EDGAR

2.1x1geos.bpch

TOLU/TOLU_1985_FF_IND_EDGAR

2.1x1geos.bpch

XYLE/XYLE_1985_FF_IND_EDGAR

2.1x1geos.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_ga

ses/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/EMEPSeasonalVariation-1.1x1

SeasonalVariation/EMEPSeasonalVariation-2.1x1

SeasonalVariation/EMEPMonthly 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.
SeasonalVariation-3.1x1

SeasonalVariation/EMEPSeasonalVariation-4.1x1

SeasonalVariation/EMEPSeasonalVariation-5.1x1

SeasonalVariation/EMEPSeasonalVariation-6.1x1

SeasonalVariation/EMEPSeasonalVariation-7.1x1

SeasonalVariation/EMEPSeasonalVariation-8.1x1

SeasonalVariation/EMEPSeasonalVariation-9.1x1

SeasonalVariation/EMEPSeasonalVariation-10.1x1

SeasonalVariation/EMEPSeasonalVariation-11.1x1

SeasonalVariation/EMEPSeasonalVariation-12.1x1

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

EPA / NEI99 weekend anthropogenic emissions files 

on the GMAO 1° x 1° grid.
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

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/m2/3hr.

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/m2/3hr

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

Monthly ship emissions for SOx [kg S/month] on the 

GMAO 1° x 1° grid
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

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 Descri

ption

MEGANv2.1_AEF_ALPHA_PINENE.geos.1x1 MEGANv2.1_AEF_BETA_PINENE.geo

s.1x1 MEGANv2.1_AEF_CARENE.geos.1x1 MEGANv2.1_AEF_ISOPRENE

.geos.1x1 MEGANv2.1_AEF_LIMONENE.geos.1x1 MEGANv2.1_AEF_MB

O.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 

Emissi

on 

Factor 

(AEF) 

files for

 I

s

o

p

r

e

n

e

 M

e

t

h

y

l 

B

u

t

e

n

o

l 

(

M

B

O

)

 M

o

n

o

t

e
rpenes(MTP)

Alpha-Pinene

Beta-Pinene

Carene

Limoe
n

e

 M

e

t

h

a

n

o

l

 M

y

r

c

e

n

e

 N

i

t

r

i

c

O

x

i

d

e

 O

c

i

m

e

n

e

 S

a

b

i

n

e

n

e

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

Covera

ge of 

plant 

functio

nal 

types 

based 

on 

MEGA

N v2.0

for:

broadlea

f trees(
BT)

crops(CR)

grasslands(GR)

needlelea

f trees(N
T

)

 s

h

r

u

b

s

(

S

H

)

These 

files will 

be 

needed 

as 

input 

for 

MEGA

N 

emissio

n 

calculat

ions for 

GEOS–

Chem 

v9–01–

03 and 

higher.

Files 

were 

generat

ed in 

binary 

punch 

file 

(bpch) 

file 

format

on the 

GMAO 

1° x 1° 
grid by 

Havala 

Pye 

with 

guidan

ce 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

Anthropogenic emissions of Hg0 (elemental 

mercury), Hg2 (divalent mercury), and HgP 
GEIA_HgP.geos.1x1.2005 (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

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 
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

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-StreetsSeasonalScalar.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.1x

1, 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.1x

1

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.1x

1

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.1

x1

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.1

x1

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

Files for speciated VOC's, taken from 

Inventory 1, for each of the various 
Streets_<VOC>_ind_2006.generic.1x1

Streets_<VOC>_pow_2006.generic.1x1

Streets_<VOC>_tra_2006.generic.1x1

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-YYYY1.1x1

ARP-SeasonalVariation-YYYY2.1x1

ARP-SeasonalVariation-YYYY3.1x1

ARP-SeasonalVariation-YYYY4.1x1

ARP-SeasonalVariation-YYYY5.1x1

ARP-SeasonalVariation-YYYY6.1x1

ARP-SeasonalVariation-YYYY7.1x1

ARP-SeasonalVariation-YYYY8.1x1

ARP-SeasonalVariation-YYYY9.1x1

ARP-SeasonalVariation-YYYY10.1x1

ARP-SeasonalVariation-YYYY11.1x1

ARP-SeasonalVariation-YYYY12.1x1

Ozone seasonal regulation factors on the GMAO 

1° x 1° grid.

Vistas-NOx-1.1x1 NOx emissions on the GMAO 1° x 1° grid.
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

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-NOxhydrocarbon 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 (rjp snu.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 energyrelated 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/cm2/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/cm2/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 activitybased 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-LocalRedist.CTH.v5.geos4.4x5

OTD-LIS-LocalRedist.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-LocalRedist.CTH.v5.geos5.1.0.05x0666.CH

OTD-LIS-LocalRedist.CTH.v5.geos5.1.0.05x0666.NA

OTD-LIS-LocalRedist.CTH.v5.geos5.1.0.2x25

OTD-LIS-LocalRedist.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-LocalRedist.CTH.v5.geos5.2.0.05x0666.CH

OTD-LIS-LocalRedist.CTH.v5.geos5.2.0.2x25

OTD-LIS-LocalRedist.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-LocalRedist.CTH.v5.merra.4x5

OTD-LIS-LocalRedist.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 seasalt 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 210Pb and 7Be 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 222Rn210Pb7Be 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-NOxhydrocarbon 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/u

sers/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/u

sers/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 (IJAVG-$, 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/ann

ual

 Replaced by 

CO2_201003/fossilfuel_andres/annua

l_v2010

CO2_201003/fossilfuel_andres/mon

thly

 Replaced by 

CO2_201003/fossilfuel_andres/month

ly_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 Specifies options for the ND65 (chemical prod & loss) and ND20 
Menu (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 â€“ 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 â€“ 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 â€“ 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 â€“ 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 â€“ 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 â€“ no net 

annual flux) [Potter et al., 1993; Olsen and Randerson, 2004]

16 CASA model 3-hourly Net Ecosystem Production (balanced â€“ 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 [unitless]
optical depth 

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. Uwind) [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. Uwind) [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. Uwind) [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 timeaveraged between 2 local times. This is useful for comparing model data to sunsynchronous 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. Uwind) [m/s]

98 Meridional wind 

(a.k.a. V-wind) 

[m/s] 

99 Pressure at level [hPa]
edges (PEDGE-$) 

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 fullchemistry 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 fullchemistry 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 fullchemistry 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 fullchemistry 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 fullchemistry 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 fullchemistry 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 timeaveraged 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-Oxhydrocarbon 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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GEOS–Chem v9–01–03 Online User's Guide
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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 = GEOS5.7.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-LeadBeryllium 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-notfound" 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 3rdparty 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 UCIrvine 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 

error_mod.F
trapping routines.

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, endof-year, and end-ofcentury in a consistent 

fashion.)

none

pressure_mod.F Contains variables and 

routines which specify 

the grid box pressures 

for both hybrid or puresigma 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 CMN_GCTM_mod.F
of data from one 

horiziontal resolution 

to another using the 

MAP_A2A regridding 

algorithm.

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-7Be10Be 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 CMN_DIAG_mod.F
and routines used to 

perform a standalone 

simulation for ethane.

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 userdefined 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 

CMN_DIAG_mod.F

CMN_SIZE_mod.F
the ND56 diagnostic --

lightning flash rates.

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 CMN_SIZE_mod.F
routines for returning 

scale factors for IPCC 

A1 & B1 emissions 

scenarios for future 

years such as 2030, 

2050, etc.

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, 

CMN_SIZE_mod.F

bpch2_mod.F

directory_mod.F

error_mod.F

future_emissions_mod.F
ACET, MEK, ALD2, 

PRPE, C3H8, CH2O, 

C2H6, CH4, and CH3I.

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) 

CMN_DIAG_mod.F

CMN_SIZE_mod.F
which perform shallow 

and deep convection 

for the GCAP met 

fields.

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 

CMN_SIZE_mod.F

bpch2_mod.F

dao_mod.F

directory_mod.F

error_mod.F
simulation. 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 CMN_DEP_mod.F
routines used for the 

H2-HD simulation.

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 

CMN_DIAG_mod.F

CMN_SIZE_mod.F
read the GEOS–Chem 

I-6 fields from disk.

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 derivedtype 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 

CMN_GCTM_mod.F

CMN_SIZE_mod.F

a3_read_mod.F
the MEGAN inventory 

of biogenic emissions.

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 

CMN_DEP_mod.F

CMN_SIZE_mod.F
and rebins to the 

proper GEOS–Chem 

LAI arrays.

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 

CMN_DIAG_mod.F

CMN_SIZE_mod.F
depths for GEOS–1, 

GEOS–STRAT, 

GEOS–2, and GEOS–

3 met data sets.

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 CameronSmith 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 CameronSmith 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 

CMN_GCTM_mod.F

CMN_SIZE_mod.F

CMN_mod.F

error_mod.F

grid_mod.F
GEOS–4/TPCORE 

transport code 

(contained in 

tpcore_fvdas_mod.

F90).

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 

bpch2_mod.F

directory_mod.F

error_mod.F

file_mod.F
global simulation. 

These are needed for 

TPCORE transport for 

nested grid 1° x 1° 

simulations. 

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_mo

d.F90

Contains routines for 

the GEOS–

4/fvDAS transport 

scheme. Original code 

from S-J Lin and Kevin 

Yeh.

none

tpcore_geos57_window_m

od.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 

error_mod.F
related quantities. 

TRACER_MOD also 

contains inquiry 

functions that can be 

used to determine the 

type of GEOS–Chem 

simulation.

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_mo

d.F

tpcore_geos57_window_m

od.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-oferrors 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-patchfile.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 newlyreleased 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 seasalt aerosol62

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-thefly.

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 (nonentraining plume)Pa/s

DNDN A6 3-D Convective downdraft flux (nonentraining plume)Pa/s

DETRAINN A6 3-D Convective detrainment (nonentraining 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-2s

-

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-2s

-

2

PRECCON A1 2-D Surface precipitation flux from 

convection 

kg m-2s

-

2

PRECLSC A1 2-D Surface precipitation flux from 

large-scale 

kg m-2s

-

2

PRECSNO A1 2-D Surface snowfall flux kg m-2s

-

2

PRECTOT A1 2-D Total surface precipitation flux kg m-2s

-

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 – largescale 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-2s

-

2

DTRAIN A3dyn 3-D Detrainment cloud mass flux kg m-2s

-

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-1s

-

1

DQRLSAN A3mstC 3-D Precipitation production rate –

large-scale + anvil 

kg kg-1s

-

1

REEVAPCN A3mstC 3-D Evaporation of precipitating 

convective condensate 

kg kg-1s

-

1

REEVAPLS(AN) A3mstC 3-D Evaporation of precipitating 

LS + anvil condensate 

kg kg-1s

-

1

PFICU A3mstE 3-D Downward flux of ice 

precipitation – convective 

kg m-2s

-

1

PFILSAN A3mstE 3-D Downward flux of ice precip –

large-scale + anvil 

kg m-2s

-

1

PFLCU A3mstE 3-D Downward flux of liquid 

precipitation – convective 

kg m-2s

-

1

PFLLSAN A3mstE 3-D Downward flux of liquid precip 

– large-scale + anvil 

kg m-2s

-

1

PS I3 2-D Surface pressure Pa 

PV I3 3-D Ertel potential vorticity K m2kg1

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-2s

-

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-2s

-

2

PRECCON A1 2-D Surface precipitation flux from 

convection 

kg m-2s

-

2

PRECLSC A1 2-D Surface precipitation flux from 

large-scale 

kg m-2s

-

2

PRECSNO A1 2-D Surface snowfall flux kg m-2s

-

2

PRECTOT A1 2-D Total surface precipitation flux kg m-2s

-

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-2s

-

2

DQRCU A3 3-D Precipitation production rate –

convective 

kg kg-1s

-

1

DQRLSAN A3 3-D Precipitation production rate –

large-scale + anvil 

kg kg-1s

-

1

DQIDTMST A3 3-D Ice tendency from moist physics kg kg-1s

-

1

DQLDTMST A3 3-D Liquid water tendency from moist 

physics 

kg kg-1s

-

1

DQVDTMST A3 3-D Water vapor tendency from moist 

physics 

kg kg-1s

-

1

DTRAIN A3 3-D Detrainment cloud mass flux kg m-2s

-

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-2s

-

1

PFILSAN A3 3-D Downward flux of ice precip –

large-scale + anvil 

kg m-2s

-

1

PFLCU A3 3-D Downward flux of liquid 

precipitation – convective 

kg m-2s

-

1

PFLLSAN A3 3-D Downward flux of liquid precip –

large-scale + anvil 

kg m-2s

-

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-1s

-

1

REEVAPLS A3 3-D Evaporation of precipitating 

large-scale + anvil condensate 

kg kg-1s

-

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 m2kg1

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] RNDECAY

2 (I,J,L) 210Pb loss [kg/s] RNDECAY

3 (I,J,L) 7Be loss [kg/s] RNDECAY

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] OCEANHG
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] HCNSRCE

3 (I,J) CH3CN from biomass burning [molec/cm2/s] HCNSRCE

4 (I,J) HCN from domestic fossil fuel [molec/cm2/s] HCNSRCE

5 (I,J) CH3CN from domestic fossil fuel [molec/cm2/s] HCNSRCE

6 (I,J) HCN loss to ocean uptake [molec/cm2/s] HCNSRCE

7 (I,J) CH3CN loss to ocean uptake [molec/cm2/s] HCNSRCE

ND10 Dimension H2-DEUTERIUM SOURCES 

(EMISSIONS, PRODUCTION, LOSS)

Units Category

1 (I,J,L) Loss of H2 by OH [molec 

H2/cm3/s]

PLH2HD-$

2 (I,J,L) Production of H2 from Isoprene [molec 

H2/cm3/s]

PLH2HD-$

3 (I,J,L) Production of H2 from CH4 [molec 

H2/cm3/s]

PLH2HD-$

4 (I,J,L) Production of H2 from CH3OH [molec 

H2/cm3/s]

PLH2HD-$

5 (I,J,L) Production of H2 from MONO [molec 

H2/cm3/s]

PLH2HD-$
6 (I,J,L) Production of H2 from ACET [molec 

H2/cm3/s]

PLH2HD-$

7 (I,J,L) Loss of H2 by stratospheric O1D [molec 

H2/cm3/s]

PLH2HD-$

8 (I,J,L) Loss of HD by OH [molec 

HD/cm3/s]

PLH2HD-$

9 (I,J,L) Production of HD from Isoprene [molec 

HD/cm3/s]

PLH2HD-$

10 (I,J,L) Production of HD from CH4 [molec 

HD/cm3/s]

PLH2HD-$

11 (I,J,L) Production of HD from CH3OH [molec 

HD/cm3/s]

PLH2HD-$

12 (I,J,L) Production of HD from MONO [molec 

HD/cm3/s]

PLH2HD-$

13 (I,J,L) Production of HD from ACET [molec 

HD/cm3/s]

PLH2HD-$

14 (I,J,L) Loss of HD by stratospheric O1D [molec 

HD/cm3/s]

PLH2HD-$

15 (I,J,L) Ratio of OH k rates kH2/kHD [unitless] PLH2HD-$

16 (I,J) Fossil Fuel H2 (anthropogenic) [molec 

HD/cm2/s]

H2HDSRC

17 (I,J) Biomass Burning of H2 [molec 

HD/cm2/s]

H2HDSRC

18 (I,J) Biofuel Burning of H2 [molec 

HD/cm2/s]

H2HDSRC

19 (I,J) Ocean emissions of H2 [molec 

HD/cm2/s]

H2HDSRC

20 (I,J) Ocean emissions of HD [molec 

HD/cm2/s]

H2HDSRC

ND11 Dimension ACETONE SOURCES & SINKS Units Category

1 (I,J) Acetone source from [at ACETSRCE
MONOTERPENES C/cm2/s]

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] EMDISBL

ND13 Dimension TROPOSPHERIC SULFUR 

EMISSIONS

Units Category

1 (I,J) Biogenic DMS [kg S] DMSBIOG

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 [unitless] OD-MAP-
nm) $

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 [105

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] NOXBIOB

4 (I,J) Biofuel Burning NOx [molec/cm2/s] NOXBIOF

5 (I,J) Fertilizer NOx [molec/cm2/s] NOXFERT

6 (I,J,L) Lightning NOx [molec/cm2/s] NOX-LI-

$

7 (I,J) Soils NOx [molec/cm2/s] NOXSOIL

8 (I,J) Stratospheric NOx (upper 

boundary)

[molec/cm2/s] NOXSTRT

ND33 Dimension COLUMN TRACER Units Category

1 (I,J,N) Atmospheric column sum of tracer [kg] COLUMNT
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 [ug/m3] IJ-SOA-
+ SOAG + SOAM @ STP $

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] CHEML=$

2 (I,J,L) NO [v/v] CHEML=$

3 (I,J,L) HO2 [v/v] CHEML=$

4 (I,J,L) NO2 [v/v] CHEML=$

5 (I,J,L) NO3 [v/v] CHEML=$

ND44 Dimension DRYDEP ( M = NUMber DEP ) Units Category

1 (I,J,M) Dry deposition fluxes (M = 1, 

NUMDEP)

[molec/cm2/s] DRYDFLX

2 (I,J,M) Dry deposition velocities (M = 1, 

NUMDEP)

[cm/s] DRYDVEL
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] TIMETPS
ND55 Dimension DYNAMIC TROPOPAUSE 

DIAGNOSTICS

Units Category

1 (I,J) Level at which the dynamic tropopause

occurs

[unitless] TRPAUSE

2 (I,J) Height of the dynamic tropopause [km] TRPAUSE

3 (I,J) Pressure of the dynamic tropopause [mb] TRPAUSE

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 WETFRAC

ND61 Dimension FREE DIAGNOSTIC Units Category

ND62 Dimension INSTANTANEOUS COLUMN MAPS Units Category

1 (I,J,N) I-J instantaneous integrated column [molec/cm2] INST-
density for tracers or 

[atoms 

C/cm2]

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] PORLL=$

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] DAOFLDS

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] DAOFLDS

3 (I,J) PREACC: total precipitation at the ground

For GEOS–5 and MERRA, this field is named 

PRECTOT

[mm/day] DAOFLDS

4 (I,J) PRECON: total convective precipitation at 

the ground

For GEOS–5 and MERRA, this field is named 

PRECCON

[mm/day] DAOFLDS

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] DAOFLDS

6 (I,J) RADSWT: solar radiation at the top of the 

atmosphere

[W/m2] DAOFLDS

7 (I,J) USTAR: friction velocity [m/s] DAOFLDS

8 (I,J) Z0: surface roughness height [m] DAOFLDS

9 (I,J) PBL (aka PBLM): planetary boundary 

layer depth

[hPa] DAOFLDS
10 (I,J) CLDFRC: column cloud fraction [0 - 1] DAOFLDS

11 (I,J) U10M: U-winds at 10 meters altitude [m/s] DAOFLDS

12 (I,J) V10M: V-winds at 10 meters altitude [m/s] DAOFLDS

13 (I,J) PS-PBL: Boundary Layer Top Pressure [hPa] DAOFLDS

14 (I,J) ALBD: Surface Albedo [unitless] DAOFLDS

15 (I,J) PHIS: Geopotential Heights [m] DAOFLDS

16 (I,J) CLTOP : Cloud Top Height [levels] DAOFLDS

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] DAOFLDS

18 (I,J) SLP: Sea Level pressure (read directly 

from the met fields)

[hPa] DAOFLDS

19 (I,J) TSKIN : Ground / Sea Surface Temp [K] DAOFLDS

20 (I,J) PARDF : Photosynthetically active diffuse 

radiation

[W/m2] DAOFLDS

21 (I,J) PARDR : Photosynthetically active direct 

radiation

[W/m2] DAOFLDS

22 (I,J) GWETTOP: Top soil wetness [unitless] DAOFLDS

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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Atmospheric Sciences > GEOS-Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 7

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 Cpreprocessor 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 1038, since 

they are usually in units such as kg, v/v, ppbv, or molecules/cm2/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 predefined 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 GridIndependence 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 An updated linearized stratospheric chemistry scheme has 

been implemented into GEOS–Chem v9–01–03. See the 
(monthly climatology) 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 gridindependent 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 The time at which chemistry, emissions, photolysis, and 
time step 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 GEOS5/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 

The GEOS–Chem Aerosols Working Group has created an 

updated list of aerosol optical properties (i.e. quantum yields, 
photolysis 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 SmithDowney) 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 pressuredependency 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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