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# GEOS **– Chem v9** 

**– 01** **– 03 Online User's Guide**  **Bob Yantosca, Mic hael Long, Melissa Payer, and Matthew Cooper** 

**Atmospheric Chemistry Modeling Group School of Engineering and Applied Sciences** 

**Harvard University 29 Oxford Street**  **Cambridge, MA 02138** We b Posted 14 Sep 2012 Email: geos - chem - support@as.harvard.eduAlso see our archive of GEOS– Chem User Guides from past releases!

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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. Weexpect that you will ha ve 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, pl ease 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**  Weinvite you to send us a paragraph describing how you and the other members of your research group plan to use GEOS – Chem. Wewill add this to our G EOS – 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 Weexpect you to join t he Wo rking Group that is most relevant to your area of research. The Wo rking Groups foster communication an d 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 W orking 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. W e have also established a general GEOS – Chem email list where we shall make announcements about new model releases, bugs and fixes, and other information p ertient to the entire GEOS – Chem community. Therefore, you should subscribe to the general GEOS – Chem email list and to the email list of your W orking 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 yo ur timing results from the 1 - month benchmark simulation . This will allow us to keep a li st of how the model is performing across several different platform/compiler combinations. Wewill 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 glob al 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 – CT M co de 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 b urning, 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 w ith 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 . W e 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 p roducts 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 Weupdated 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). Se e 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 Histor ical 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 Am os et al. (2012) 2. Primary anthropogenic Hg(p) is emitted as Hg(II)CH4 simulation updates Kevin W echt 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 emission s 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 th e GEOS–Chem full chemistry simulation. See this wiki page for more information Satellite - based NOx emission trends Scaling factors for anthropogenic NO x 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 Wa shout code has been split into three cases: aerosols, HNO3, and soluble gases. This was done to ensure that HNO3 is not affected by the aerosol scavenging updates and is still scavenged according to Eq. 14 from Jacob (2000). Initial source code modification for GEOS– 5.7.2 GEOS – Chem has been modified for compatilibility with the GEOS –5.7.2 meteorological data. Remove support for GEOS –3 meteorology See this wiki page for more information. Updates from the grid independent GEOS – Chem model code Modifications made for the grid - independent GEOS – Chem model include: 1. Fixes to facilitate implementation of grid - independent code2. Preliminary interface to link driving GCM

MAP_A2A regridding package Matt Cooper replace d 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 i n 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**  Wesummarize 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 wikipages entit led 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 res olution 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 (c hances 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 G uide 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 . Weused to disseminate the GEOS – Chem source code and r un 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 submiss ions, 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- ol d 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 s ystem. 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, unle ss you consciously decide to "push" your changes to another repository).  Wh en 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 all ows 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.  Wi th Git, you can "pull" changes from other users directly into your own local source code repository.  Wi th 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 independen tly 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.  Wi th 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 ru n 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** Wehave 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 fil es (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 .  T he 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 lis t 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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## 2. Installation **2.1 What you need to download before you can run GEOS –**  **Chem** Wh en setting up GEOS – Chem on your system, you wil l 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 descri ption 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 Emiss ions 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 fi les from binary punch file format to netCDF format. Weare doing this as part of our Grid - Independent GEOS – Chem project , which seeks to interface GEOS – Che m 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 d escribed 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 prog rams. 

### 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 offic ial 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: W hen you clone, you will always get the most recent state of the repository. (i.e. the latest GEO S– 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 s ee 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. Wehave 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 d ownload the run directories to your local disk space. The command will take the form: git clone git://git.as.harvard.edu/bmy/GEOS - Chem - rundirs/DIR OPTION LOCAL - DIR - NAME LOCAL - DIR - NAME is the name you chose for your local directory to contain GEOS – Chem DIR - OPTION may be one of the following:**DIR_OPTION**

**0.5 x 0.666 GEOS –** **5 simlulations**  **Description** 0.5x0.666/NA/standard 0.5 x 0.666 GEOS– 5 offline nested grid simulation for North America **DIR_OPTION 2 x 2.5 GEOS** **– 4 simlulations**  **Description** 2x2.5/geos4/CO2_run 2 x 2.5 GEOS –4 offline CO2 simulation 2x2.5/geos4/SOA 2 x 2.5 GEOS –4 fullchem w/ SOA simulation 2x2.5/geos4/dicarbonyls 2 x 2.5 GEOS –4 fullchem w/ dicarbonyls option 2x2.5/geos4/isoprene 2 x 2.5 GEOS –4 fullchem w/ Caltech isoprene scheme 2x2.5/geos4/standard 2 x 2.5 GEOS –4 fullchem standard (43 tracers) **DIR_OPTION 2 x 2.5 GEOS** **– 5 simulations**  **Description** 2x2.5/geos5/CO2_run 2 x 2.5 GEOS –5 offline CO2 simulation 2x2.5/geos5/Hg 2 x 2.5 GEOS –5 offline Hg simulation 2x2.5/geos5/SOA 2 x 2.5 GEOS –5 fullchem w/ SOA simulation 2x2.5/geos5/dicarbonyls 2 x 2.5 GEOS –5 fullchem w/ dicarbonyls option 2x2.5/geos5/isoprene 2 x 2.5 GEOS –5 fullchem w/ Caltech isoprene scheme 2x2.5/geos5/standard 2 x 2.5 GEOS –5 fullchem standard (43 tracers) **DIR_OPTION 4 x 5 GEOS**  **– 4 simulations**  **Description**4x5/geos4/SOA 4 x 5 GEOS–4 fullchem w/ SOA simulation 4x5/geos4/dicarbonyls 4 x 5 GEOS–4 fullchem w/ dicarbonyls option 4x5/geos4/isoprene 4 x 5 GEOS–4 fullchem w/ Caltech isoprene scheme 4x5/geos4/standard 4 x 5 GEOS–4 fullchem standard (43 tracers) **DIR_OPTION 4 x 5 GEOS**  **– 5**  **simulations Description**  4x5/geos5/APM 4 x 5 GEOS– 5 fullchem w/ APM aerosol microphysics option 4x5/geos5/Hg 4 x 5 GEOS– 5 offline Hg simulation 4x5/geos5/Hg_GTMM 4 x 5 GEOS– 5 offline Hg simulation with GTMM option 4x5/geos5/SOA 4 x 5 GEOS– 5 fullchem w/ SOA simulation 4x5/geos5/dicarbonyls 4 x 5 GEOS– 5 fullchem w/ dicarbonyls option 4x5/geos5/isoprene 4 x 5 GEOS– 5 fullchem w/ Caltech isoprene scheme 4x5/geos5/standard 4 x 5 GEOS– 5 fullchem standard (43 tracers) **DIR_OPTION 4 x 5 MERRA** 

**simulations Description**  4x5/merra/Hg_GTMM 4 x 5 MERRA offline Hg simulation with GTMM option 4x5/merra/SOA 4 x 5 MERRA fullchem w/ SOA simulation 4x5/merra/dicarbonyls 4 x 5 MERRA fullchem w/ dicarbonyls option 4x5/merra/isoprene 4 x 5 MERRA fullchem w/ Caltech isoprene scheme4x5/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: W e 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 – ChemMailing List if they have a restart file for the particular type of simulation that you

are tryi ng 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 .  Wh en 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 sh**  **ared 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 resea rch 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 s ure 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 G CAP data, please contact Loretta Mickley for more information. 

### 2.4.2 Downloading instructionsWerecommend that you use the GNU wget utili ty to download the GEOS – Chem shared

data directories. W get allows you to download the directories and subdirectories in one fell swoop. The wget commands take the form of: wget - r - nH "ftp://ftp.as.harvard.edu/gcgrid/geos chem/data/DIRECTORY_NAME/" where D IRECTORY_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_1x 1 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. W ith 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 classi c 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 ha ve to install these libraries for GEOS - Chem. 2. Any recent version of netCDF (version 3.0 or higher) may be used with GEOS Chem. However, we recommend all GEOS - Chem users to build either netCDF 4.2 or netCDF CLASSIC with the GEOS - Chem - Libraries installer so t hat GEOS Chem will be able to automatically determine the proper library linking commands . 

### 2.5.1 Downloadi

**ng the GEOS -**  **Chem -** **Libraries installer package** You can use the Git source - code management software to download the GEOS - Chem Libraries installer package onto your system. Type: git clone git://git.as.harvard.edu/bmy/GEOS - Chem - Libraries and then change into the GEOS - Chem - Libraries directory:cd GEOS - Chem - Libraries

In this directory you will find the following files and subdirectories: **File or Directory**  **Description** README File describing the contents of GEOS - Chem Libraries and how to build the netCDF libraries GNUmakefile Main - level makefile. This calls down to the master

GNUmakefile in the src/ sub - directory. opt/ Default directory where libraries will be installed (if

you do not choose an alternate directory) src/ Directory containing netCDF and related library

distrib utions. 

### 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 ha ve the PGI C compilers make COMPILER=pgi PREFIX=root_library_dir GCC=yes # If you don't have the PGI C compilers Makefile options: **Option Description** COMPILER This option is used to pick the compiler that you wish to use to build netCDF -4.2 and the related libraries. At present, you may select either ifort or pgi . If you omit the COMPILER option, the default value of ifort will be selected. PREFIX This option is used to set root_library_dir , which is

the full path name of the directory into which the netCDF 4.2 and related libraries will be installed. If you omit the PREFIX option, then root_library_dir will be automatically set to one of these defa ult 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 a ccess 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 librarie s) 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 . r oot_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 th at 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 CLASS**IC** If you have problems installing the netCDF–4.2 libraries on your system, try installing netCDF classic instead. Follow these instructions: 

### 2.5.3.1 Building netCDF CLASSIC To build the netCDF CLASSIC libraries (which lacks the advanced features of netCDF 4.2) using the Intel Fortran Compiler ( ifort ), type one of the following commands: make CLASSIC=yes PREFIX=root_library_dir # If you have the Intel C compilers make CLASSIC=yes PREFIX=root_library_dir GCC=yes # If you don't have the Intel C compilers To build the netCDF "CLASSIC" libraries for the PGI compiler , type: make CLASSIC=yes COMPILER=pgi PREFIX=root_library_dir # If you have the PGI C compilers: make CLASSIC=yes COMPILER=pgi PREFIX=root_library_dir GCC=yes # If you don't have the PGI C compilers Makefile options: **Option Description**  COMPILER This option is used to pick the compiler that you wish to

use to build netCDF CLASSIC. At present, you mayselect 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_clas sic/ # 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 mi nutes 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 CLASSI C 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 pathsThe 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, ncdu mp, 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 s uccessfully built the netCDF (and related) libraries with the GEOS Chem - Libraries installer, you must tell GEOS - Chem where to find the relevant library, include, and executable files. The easiest way to do this is to set environment variables in your setup files: **Setup file Unix shell**  .cshrc If you use C - shell ( csh ) or T - shell ( tcsh ) .profile If you use Bourne shell ( sh ), or if you use a Macintosh .bashrc If you use Bourne - again shell ( bash ) There are three environment variables that you need to set: **Variable Description**  GC_BIN Specifies the location of the executable files (e.g. nc config , nf - config , ncdump , etc.) GC_INCLUDE Specifies the location of include files ( *.h , *.inc )

and module files ( *.mod ) for the netCDF (and HDF5) libraries GC_LIB Specifies the location of library files ( *.a ) 

### 2.5.4.1 With csh or tcsh If you use C - shell ( csh ) or T - shell ( tcsh ), then add the following lines to your .cshrc file: setenv ROOT_LIBRARY_DIR root_library_dir setenv GC_BIN $(ROOT_LIBRARY_DIR)/bin setenv GC_INCLUDE $(ROOT_LIBRARY_DIR)/include setenv GC_LIB $(ROOT_LIBRARY_DIR)/libwhere 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 ), the n 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 m **ore information** Please see our Installing libraries for GEOS –Chem page on the GEOS – Chem wiki for more detailed information about the GEOS - Chem - Lib raries 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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### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)** 

## 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. in to 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. Wi thout

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 co ntaining parallel copies of GEOS –Chem source code files ( *.F , *.F90 ) that were modified for the TOMAS aerosol microphysics package. Code.v9 - 01 - 03/GeosUt il 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 Directo ry 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 - 0 3/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 w here module ( *.mod ) files will be sent Code.v9 - 01 - Directory where obsolete source code files are placed03/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 com mands 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. W hen 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 calls03/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/Makefi le 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. Weshall 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. W hen you run the executable, it will behave as if Block B had never existed. If yo u 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 "F ortran preprocessor" (FPP). Therefore, even though GEOS – Chem is written in Fortran - 90, we can still incorporate C– preprocesor commands into the source code. Wi th 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' #e lif 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 cod ethat 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 en counter 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 fi elds ( 72 layer , hybrid, 2005– present) GEOS_57 Use G EOS– 5.7.2 met fields ( 72 layer , hybrid, 2011 – present

) MERRA Use MERRA met fields ( 72 laye r, hybrid, 1979 - 2010) **Grids** NESTED_CH Use China/SE Asia nested grid ( GEOS– 5 only) NESTED_NA Use N. American nested - grid ( GEOS – 5 only) NESTED_EU Use European nested grid ( GEOS – 5 only) SEAC4RS Use SEAC4RS nested grid ( GEOS –5.7.2 only).

Note: This grid was developed for the SEAC 4 RS campa ign . 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° gridGRID4x5 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. Wh en 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 , G RID1x125 , 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 compi le 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 M **akefile options** Here is a description of all avail able 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

subdirlibheaders 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 TOMA S aerosol microphy** **sics** 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 Ope nMP 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!)** Wh en 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 ormake 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 wa nt 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 cleanAnd 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. Werecommend updating your compiler to Intel Fortran Compiler (IFORT) Version 11.1.058 or higher versions. Version 11 produces similar results to Version 10 . 3. Wealso 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. Wi th a little effort, you can design a Makefile that can be placed into your GEOS– Chem rundirectory that will create a GEOS– Chem executable and start a simulatio n. 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 developme nt 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 $(GEOSDIR) doccleanhelp: @$(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 = `d ate +%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 n ot 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 – Ch em 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 $(GEOSDIR)/bin/geos . tell GNU Make to call down to the "router" makefile in the GEOS – Chem source code directory /home/bmy/Code.v9 - 01 - 03 . GNU Make will compile GEOS – Chem and create the executab le file /home/bmy/Code.v9 - 01 - 03/bin/geos . This file is then copied to the run directory. The next 3 lines: rm - f log.$(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 manua l  Chapter 6: Running GEOS – Chem

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### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)** 

## 4. GEOS **– Chem Shared Data Directories**  **4.1 Overview** The GEOS – Chem shared data directories contain the various met fields , em issions, 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 directoriesGEOS – 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. W e 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 gri d 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 re solution 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. W alker, D. G. Streets, Q. Zhang, E. J. Dunlea, J. L. J imenez, J. E. Dibb, L. G. Huey, R. We ber, 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. P hys , **8** , 2999 - 3014, 2008. **Files Description**  CO - AnnualScalar.201105 - Fix.geos.1x1 Scale factor files for CO for years 1985 to 2006 on theGMAO 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 ver**

**sions.** 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 update d 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 emissio ns 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 microphysics2. Yu, F., and G. Luo, Sim ulation of particle size distribution with a global aerosol model: Contribution of nucleation to aerosol and C CN 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. Wa ng, S. Wu , Spatial distributions of particle number concentrations in the global troposphere: Sim ulations, ob servations, and im

plications for nucleation mechanisms , J. Geophys. Res. , **115** , D17205, doi:10.1029/2009JD013473, 2010. 4. Yu, F., Ion -me diated nucleation in the atmosphere: Key controlling parameters, im plications, and look - up table , J. Geophy. Res. , **115** , D03 206, 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 nucleati on rate (cm - 3 s - 1 ) lookup tables.

YCK_LT/Yu_CK_1R1.txt YCK_LT/Yu_CK_2D1.txt YCK_LT/Yu_CK_3R2.txt YCK_LT/Yu_CK_4D2.txt YCK_LT/Yu_CK_5T.txt YCK_LT/Yu_CK_6P.txt YCK_LT/Yu_CK_7CK.txt Text files containing coagulation kernel (cm 3 s - 1 ) lookup tables.

YIONRATE.t xt Text file containing the ionization rate (ion - pairs cm 3 s - 1 ) lookup table by magnetic latitude. 

### 4.2.3 The ARCTAS_SHIP_2008 subdirectory NOTES: 1. This dataset is only implemented in ARCTAS - NRT version of GEOS - Chem REFERENCES:1. GEOS - Chem wiki: ARCTAS ship emissions

2. Zhang, Q., D. G. Streets, G. Carmichael, K. He, H. Huo, A. Kannari, Z. Klimont, I. Park, S. Reddy, D. Chen, L. Duan, Y. Lei, L. W ang a nd 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 Bryconcentrations 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: im plications for present and pre -industrial ozone an d 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 strato spheric 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 inventory2. 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.g eos.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 presen t, 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 consum ption 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 consum

ption , Tellus B , accepted, 2011. 4. Baker, D. F., et al., TransCom 3 inversion intercomparison: Im pact 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, 4 650, 2003. 6. Corbett, J. J., and H. W. Koehler, Considering alternative input parameters in an activitybased ship fuel consum ption and emissions model : Reply to comment by Øyvind Endresen et al. on Updated emissions from ocean shipping , J. Geophys. Res. , **1 09**  , 2004. 7. Endresen, O, et al., A historical reconstruction of ships fuel consum ption 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. , Wo rden, J. R., Machida, T., and Matsueda, H.: Modeling global atmospheric CO2 with im proved 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 im portant atmospheric gases and aerosol s, Philosophical Transactions of the Royal Society A , **369** , 20 73 -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_Re gions.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 - 30WLatin 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, onthe GMAO 0.5° x 0.666° grid. biofuel/biofuel_CO2.geos.05x0667 - 1995 CO2 biofuel emissions from Yevich & Log an 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 - 30WLatin 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 regi ons based on Table 16. of Yevich & Logan: 1. 180 - 30WLatin 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 ca**  **n run a GEOS**

**– Chem**  **simulation. Contact Ray**  **Nassar for more**  **information. ALSO NOTE: To obtain**  **these 1° x 1° data, please contact the**  **GEOS**

**– Chem**  **Support Team .**  fossilfuel_andres/monthly_v2010/ff.YYYYMM.geos.1x1 Updated monthly CO2 fossil fuel emissions from the CDIAC inventory (version 2010, by Robert J. Andres), for years YYYY = 1979 to 2009 and MM = 1 .. 12. Data is on the GMAO 1° x 1° grid . **NOTE: The CDIAC inventory goes back to 1950, but we**  **only provide files starting in 1979, since that is the**  **earliest date at which you can run a GEOS** 

**– Chem**  **simulation. Contact Ray**  **Nassar for more**  **information. ALSO NOTE: To obtain**  **these 1° x 1° data, please contact the**  **GEOS**

**– Chem**  **Support Team .** ship_ICOADS/co2_MM.geos.1x1

ship_ICOADS/co2_MM_hp.geos.1x1 Monthly mean CO2 emissions from the ICOADS ship inventory (Corbett et al) on the GEOS 1° x 1° grid, for months MM = 01 .. 12. 

### 4.2.8 The carbon_200909 subdirectory NOTES: 1. The data in this directory is not used in GEOS - Chem, but is left here for reference. GEOS Chem uses the data directly regridded on GMAO 2° x 2.5° or GMAO 4 ° x 5° grids . 

### 4.2.9 The EDGAR_200607 subdirectory REFERENCES: 1. GEOS - Chem wiki: EDGAR anthropogenic and ship emissions **Files Description**  CO/EDGAR.f1000co.generic.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.ge neric.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  W4 0 Wa ste 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. T hese 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/E DGAR.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) TransportNOx/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  W4 0 Wa ste 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 - 19 91 - 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 ye ar 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 toNOx/EDGAR.NOxScalar - 1998 -

2000.geos.1x1 NOx/EDGAR.NOxScalar - 1997 - 2000.geos.1x1 NOx/EDGAR.NOxScalar - 1996 - 2000.geos.1x1 th e 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 )

 WI NTER 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.1 x1 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  W4 0 Wa ste 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_SO x_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_SO x_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, w hich 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 )

 WI NTER 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 b y May Fu. REFERENCE: 1. http://www.mnp.nl/edgar/model/edgar2/precursor_ga ses/edgar_20_nmvoc.jsp 

### 4.2.10 The EMEP_200510 subdirectoryNOTES:

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 We bDab, 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.geo s.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, Swi tzerland. 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_20 0806 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 u pdated 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 - 1 993.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 EME P - SHIP - 2004.geos.1x1 EMEP - SHIP - 2005.geos.1x1 EMEP - SHIP - 2006.geos.1x1 EMEP - SHIP - 2007.geos.1x1 EMEP ship emissions of CO, NH3, NOx, and SOx [molec/cm2/s] for year 1990 to 2007 on the GMAO 1° x 1° grid .

SeasonalVariation/EMEP SeasonalVariation - 1.1x1 SeasonalVariation/EMEP SeasonalVariation - 2.1x1 SeasonalVariation/EMEP Monthly variations. Courtesy of the GENEMIS project coordinated by the Institute of Energy Economics and the Rational Use of Energy (IER) at the University of Stuttgart.SeasonalVariation - 3.1x1

SeasonalVariation/EMEP SeasonalVariation - 4.1x1 SeasonalVariation/EMEP SeasonalVariation - 5.1x1 SeasonalVariation/EMEP SeasonalVariation - 6.1x1 SeasonalVariation/EMEP SeasonalVariation - 7.1x1 SeasonalVariation/EMEP SeasonalVariation - 8.1x1 SeasonalVariation/EMEP SeasonalVariation - 9.1x1 SeasonalVariation/EMEP SeasonalVariation - 10 .1x1 SeasonalVariation/EMEP SeasonalVariation - 11.1x1 SeasonalVariation/EMEP SeasonalVariation - 12.1x1 

### 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 Wi ki . 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.geo s.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_200**806 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 subdirectoryNOTES:

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 versio ns. 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. Th erefore, 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 fir e observations , Atm. Chem. Phys. , **6** , 957 - 974, 2006. 4. G.R. van der We rf, 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** , 342 3 - 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 a lso 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. Werecommend using either the monthly or 8 - day data. 3. The GFED2 emissions in this directory are 3 - hourly data. The "3hr" data are obtained from applying a 3hr diurnal variation to the 8 - day averages. The "synoptic" data distribute the 8 -day average data in their respective 8 days according to the meteorological ISI index, then apply a 3hr diurnal cycle. 4. As of 04/30/2009, there are only 4 months of data available: June, July, August and September 2004. **Files Description**  2004/GFED2.3hr.C_200406.generic.1x1 2004/GFED2.3hr.C_200407.generic.1x1 2004/GFED2.3hr.C_200408.generic.1x1 2004/GFED2.3hr.C_200409.generic.1x1 Files containing 3 - hour carbon fluxes based on GFED2 for June, July, August, and September of 2004. Units are g C/m 2/3hr. 2004/GFED2.synoptic.C_200406.generic.1x1 2004/GFED2.synoptic.C_200407.generic.1x1 2004/GFED2.synoptic.C_200408.generic.1x1 2004/GFED2.synoptic.C_200409.generic.1x1 Files containing synoptic 3 - hour carbon fluxes based on GFED2 for June, July, August, and September of 2004. Units are g C/m 2/3hr 

### 4.2.17 The GFED2_8day_200712 subdirectory NOTES: 1. For GEOS –Chem v9–01 –02 and higher versions, GFED2 emissions data in this subdirectory are superseded by GFED3 emissions data in GFED3_201110 . The emissions data in this subdirectory are kept for compatability with older model versions. 2. The GFED2 emissions in this directory are 8 - day averages. 3. As of 04/30/2009, the GFED2_emission_factors.txt file, the GFED2_emission_factors_73t.txt file and the GFED2_vegmap.generic.1x1 file are the same versions as are found in the GFED2_200601 subdirectory , which contains monthly emissions. At some point we may upgrade to a newer version of the vegetation map file from Prasad Kasibhatla, but that has not been done as of 04/30/2009. 4. GEOS - Chem reads the GFED2 C emissions data on the generic 1x1 grid, then converts to equivalent biomass emissions for e ach 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 We rf, J.T. Randerson, L. Giglio, G.J. Collatz,P.S. Kasi bhatla, 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, OCand 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 curren tly 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 We rf, 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 – 20 09) , Atm. Chem. Phys. , Vol 10, 11707– 11735, 2010. 4. For methodology: Mu, M., J.T. Randerson, G.R. van der We rf, L. Giglio, P. Kasibhatla, D. Morton, G.J. Collatz, R.S. DeFries, E.J. Hyer, E.M. Prins, D. W. T. Griffith, D. W unch, G.C. Toon, V. Sherlock, and P.O . W ennberg, 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 bur nt is a function of the following fire types:

 Agricultural waste  Deforestation  Extratropical forest  Peat  Savanna  Wo odland 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:10.51 94/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. Wa ng, 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.1x 1 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° gridSOx_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 er p e n e s ( M T P )  A l p h a

- P i n e n e  B e t a

- P i n e n e  C a r e n e  L i m o en 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 Thesedata 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:

 b r o a d l e a f t r e e s (B T )  c r o p s ( C R )  g r a s s l a n d s ( G R )  n e e d l e l e a f t r e e s ( NT )  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 - Che m 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 simulation2. 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, Wa sh. 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.g eos.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/es80247 4j, 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. Wi lson, 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 HgPGEIA_HgP.geos.1x1.2005 (particulate mercury) from the GEIA 2005 inventory (cf Pacyna et al., 2010). GEIA 2005 emissions include artisinal mining, whi ch 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 mercur y 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_20 **1205 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)  We st 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 Stree ts 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 NO TES: 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 theOlson 2001 land map.

Olson_2001_Land_Map.025x025.generic.nc NetCDF file containing informatin for Olson 2001 land map, such as Olson land type s 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. W ang, An Im proved In Situ and Satellite SST Analysis for Climate , J. Clim ate , **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 aSST.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_c hem_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 fro m 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. Wa ng, K. He, J. Hao, Y. W u, 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. Wa ng, J - H. Wo o, and K.F. Yarber, An inventory of gaseous and primary aerosol emissions in Asia in the year 2000 , J. Geophys. Res , **108** , D21, doi:10.1029/2002JD003093, 2003.**Files Description** 

China_mask.generic.1x1 China mask file for 2001 emissions of CO, on the generic 1° x 1° grid . This masking file is meant to be used with: Streets_CO_FF_2000.generic.1x1 . NH3 - Streets SeasonalScalar.generic.1x1 Seasonal scale factors used to apply seasonal variation to NH3 following the methodology of Lex Bouwman. SE_Asia_mask.generic.1x1 SE Asia mask for 2000 emissions on the generic 1° x 1° grid . This masking file is meant to be used with the emissions in the files named: Streets_XXX_FF_2000.generic.1x 1 , where XXX = NOx, SO2, NH 3, 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.1 x 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. U nits 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 variousStreets_<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 s pecies 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 columns2. Data: http://acdb - ext.gsfc.nasa.gov/Data_services/merged/

**Files Description**  TOMS_O3col_YYYY.geos.1x1 12 months of TOMS/SBUV data on the GMAO 1° x 1° grid for years YYYY= 1971 ... 2010 

### 4.2.36 The VISTAS_200811 subdirectory NOTES: 1. NOx inventory from Visibility Improvement State and Tribal Association of the Southeast (VISTAS), which "is a collaborative effort of state governments, tribal governments, and various federal agencies established to initiate and coordinate activities associated with the management of regional haze, visibility and other air quality issues in the Southeastern United States." REFERENCES: 1. Data: http://www.vistas - sesarm.org/index.asp **Files Description**  ARP - SeasonalVariation - YYYY 1.1x1 ARP - SeasonalVariation - YYYY 2.1x1 ARP - SeasonalVariation - YYYY 3.1x1 ARP - SeasonalVariation - YYYY 4.1x1 ARP - SeasonalVariation - YYYY 5.1x1 ARP - SeasonalVariation - YYYY 6.1x1 ARP - SeasonalVariation - YYYY 7.1x1 ARP - SeasonalVariation - YYYY 8.1x1 ARP - SeasonalVariation - YYYY 9.1x1 ARP - SeasonalVariation - YYYY 10.1x1 ARP - SeasonalVariation - YYYY 11.1x1 ARP - SeasonalVariation - YYYY 12.1x1 Ozone seasonal regulat ion 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 V istas - Ratio - NOx - 12.1x1 wkday_an_scalar.nei99.geos.1x1 wkend_an_scalar.nei99.geos.1x1 We ekend/weekday factors on the GMAO 1° x 1° grid . 

### 4.2.37 The volcan **o_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 emissionson 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 arestored 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** 

**Ty pe**  **Grid Ty pe**  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 furthe r 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. Wa ng, Y., D.J. Jacob, and J.A. Logan, Global sim ulation of tropospheric O3-NOxhydrocarbon chemistry, 1. Model form ulation , 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 Wa ng et al, 1998) for the GCA P 4° x 5° grid and the GMAO 2° x 2.5° and 4° x 5° grid s. Units are kg NOx/4h. Files are in plain -text format.



### 4.3.2 The biofuel_200202 subdirectoryREFERENCES:

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 Wa ng 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 im plications for natural vi

sibility, 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/mont h]. 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 so lar 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 emi ssions 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 CH 4/cm 2/s.

GWETTOP/GWETTOP.YYYY.geos4.2x25 GWETTOP/GWETTOP.YYYY.geos5.2x25 GWETTOP/GWETTOP.YYYY.geos4.4x5 GWETTOP/GWETTOP.YYYY.geos5.4x5 Monthly and annual mean soil wetness. For GEOS4, the data are for the years YYYY=2000 ... 2006 For GEOS5, the data are for the years YYYY=2004 ... 2009 wetlands/Carbon_litter.geos.2x25 wetlands/Carbon_litter.geos.4x5 Carbon emissions from litter as calculated in a 20th century simulation by the LPJ Vegetation Model wetlands/Carbon_soil.geos.2x25 wetlands/Carbon_soil.geos.4x5 Carbon emissions from soil as calculated in a 20th century simulation by the LPJ Vegetation Model wetlands/Wet_frac.geos.2x25 wetlands/Wet_frac.geos.4x5 We t fraction in each grid cell follows the map in Bergamaschi et. al. 2007wetlands/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, was te, 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 CH 4/cm 2/s. gmi.ch4loss.geos5_47L.2x25.bpch gmi.ch4loss.geos5_47L.4x5.bpch CH4 loss frequencies. These values constitute a linearized stratospheric CH4 chemistry scheme. Loss frequencies from 4° x 5° output are from the GMI model. (Courtesy of Lee Murray) Values are for "generic" year 1985. Units are 1/s. GWETTOP/GWETTOP.geos5.2x25.YYYY.bpch GWETTOP/GWETTOP.geos 5.4x5.YYYY.bpch Monthly and annual mean soil wetness. For GEOS– 5, the data are for the years YYYY=2004 ... 2011wetlands/Carbon_litter.2x25.bpch

wetlands/Carbon_litter.4x5.bpch Carbon emissions from litter as calculated in a 20th century simulation by th e 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 We t 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 su**bdirectory** 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 consum ption 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 consum

ption , Tellus B , accepted, 2011. 4. Baker, D. F., et al., TransCom 3 inversion intercomparison: Im pact 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 consum ption 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 consum ption and emissions , J. Geophys. Res , **112** , D12301, 2007. 8. Nassar, R., Jones, D. B. A., Suntharalingam, P., Ch en, J. M., Andres, R. J., Wecht, K. J., Yantosca, R. M., Kulawik, S. S., Bowman, K. W. , Wo rden, J. R., Machida, T., and Matsueda, H.: Modeling global atmospheric CO2 with im proved emission inventories and CO2 production from

the oxidation of other carbon s pecies , 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., e t al., HIAPER Pole - to -Pole Observations (HIPPO): Fine grained, global scale measurements of climatically im portant atmospheric gases and aerosol s, 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 (ba se 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 - 30WLatin 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] archivedby 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 W echt. 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 W echt. The data is on the GMAO 2° x 2.5° and 4° x 5° grids. fossilfuel_andres/annual/ff.YYYY.geos.2x25 foss ilfuel_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.YY YY.geos.2x25 fossilfuel_andres/annual_v2010/ff.YYYY.geos.4x5 Updated annual CO2 fossil fuel emissions [molec/cm2/s] from the CDIAC inventory (version2010, 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 informati on.**  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 an d 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] fromTakahashi 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 im pact 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_s rc_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 A merican emissions inventory3. 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 wkda y_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 fo r 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 speci es. 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 G CAP 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° gri d . 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 anthropoge nic 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 R EFERENCES: 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 che mistry 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 W ashington) by assimilating observed nutrient distributions in the oc eans (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 simu lation 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: Lig htning 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. Dun can, M. Damon, Im pact 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 parameteri za tions 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 sim ulations , J Geophys Res , **115** , D04301, 2010. 7. Pickering K.E., Y. W ang, 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 sim ple 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 We ather 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 2010OTD - LIS - Local Redist.CTH.v5.geos4.4x5 OTD - LIS - Local Redist.CTH.v5.geos4.4x5 OTD/LIS flash redistribution factors for GEOS –4 meteorology. Data is provided on the global 2° x 2.5° and 4° x 5° grids. OTD - LIS - Local Redist.CTH.v5.geos5.1.0.05x0666.CH OTD - LIS - Local Redist.CTH.v5.geos5.1.0.05x0666.NA OTD - LIS - Local Redist.CTH.v5.geos5.1.0.2x25 OTD - LIS - Local Redist.CTH.v5.geos5.1.0.4x5 OTD/L IS flash redistribution factors for GEOS –5.1.0 meteorology (model dates prior to 01 Sep 2008). Data is provided on the global 2° x 2.5° and 4° x 5° grids, as well as for the 0.5° x 0.666° nested grids ( China and North America ). OTD - LIS - Local Redist.CTH.v5.geos5.2.0.05x0666.CH OTD - LIS - Local Redist.CTH.v5.geos5.2.0.2x25 OTD - LIS - Local Redist.CTH.v5.geos5.2.0.4 x5 OTD/LIS flash redistribution factors for GEOS –5.2.0 meteorology (model dates from 01 Sep 2008 onwards). Data is provided on the global 2° x 2.5° and 4° x 5° grids, as well as for the 0.5° x 0.666° nested China grid. OTD - LIS - Local Redist.CTH.v5.merra.4x5 OTD - LIS - Local Redist.CTH.v5.merra.2x25 OTD/LIS flash redistribution factors for MERRA meteorology. At present, data is provided on the global 2° x 2.5° and 4° x 5° grid. 

### 4.3.19 The mercury_201007 subdirectory NOTES: 1. For more information about these files, or about the mercury simulation in general, please contact the Hg and POPs W orking Group . 2. Some other data for the m ercury 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/mercu ry_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. G EOS –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 mo del 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 im pacts 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 im proved global model for air -sea exchange of mercury: High concentrations over the North Atlant ic, Environ. Sci. Technol. , **44** , 8574 - 8580, 2010. **Files Description**  BrOx.GC.geos5.2x25 BrOx.GC.geos5.4x5 Br and BrO mixing ratios from GEOS – Chem using the tropospheric bromine chemistry mechanism (courtesy J. Parrella). The 2° x 2.5° data were regridded from 4° x 5° data for a 2007 simulation. BrOx.GMI.geos5 .2x25 BrOx.GMI.geos4.4x5 BrOx.GMI.geos5.4x5 Br and BrO mixing ratios from GMI combo model. These are regridded from the Aura4 simulations of 2007 (courtesy J. Logan, I. Megretskaia). BrOx.TOMCAT_org.geos5.2x25 BrOx.TOMCAT_org.geos4.4x5 BrOx.TOMCAT_org.geos5.4x5 Br and BrO mixing ratios from University of Cambridge p -TOMCAT model (courtesy Xin Yang). These are from a simulation with only organic Br- y precursors (no sea salt aerosol). Br_3Dglobal.geos4.4x5 Br_3Dglobal.geos5.4x5 Br and BrO mixing ratios from surface through stratosphere. Tropospheric values are from p -TOMCAT (courtesy Xin Yang) and stratospheric values are from GMI combo model (Aura runs, courtesy J. Logan and I. Megretskaia). **NOTE: These files are not used.** Chl_2003.geos. 2x25 Chl_2003.geos.4x5 Mean monthly chlorophyl A concentrations in the ocean. Data is from the MODIS satellite in mg m - 3 for 2003. Obtained from http://oceancolor.gsfc.nasa.gov (cf. Soerenson et al , 2010). MERGE.O3.47L.geos5.2x25 MERGE.O3.47L.geos5.4x5 MERGE.O3.geos4.4x5 O3 mixing ratios for surface through stratosphere. Tropospheric values are from GEOS - Chem v7 full chemistry ( sulfate_sim_200507 ) and stratospheric values are from GMI combo model (Aura runs, courtesy J. Logan and I. Megretskaia).MLD_DReqDT.geos.2x25

MLD_DReqDT.geos.4x5 Mean monthly mixed layer depths of the surface ocean in meters. Data is from de Boyer Montégut et al. (2004). NPP_2003.geos.2x25 NPP_2003.geos.4x5 Mean monthly Net Primary Production from MODIS satellite data in mgC m - 2 d - 1 for 2003 taken from Behrenfeld et al. (1997). OH_3Dglobal.geos5.2x25 OH_3Dglobal.geos4.4x5 OH_3Dglobal.geos5.4x5 OH concentration for surface through stratosphere. Tropospheric values are fro m 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 wh en 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 prelimin ary 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 redu ction rate of Hg(II) in clouds. nasatransp_4x5.*.bpch Monthly mean climatological evapotranspiration fields [Mintz and Wa lker, 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_metf ields/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 W orking 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: Im plementation 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 pre pared by W es 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 222 Rn 210 Pb 7 Be simulations). File is in plain -text format. 

### 4.3.24 The soil_NOx_200203 subdirectory NOTES: 1. Weplan 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. Wa ng, Y., D.J. Jacob, and J.A. Logan, Global sim ulation of tropospheric O3-NOxhydrocarbon chemistry, 1. Model form ulation , J. Geophys. Res. , **103**/D9, 10,713 - 10,726, 1998. [PDF]**Files Description** 

climatprep2x25.dat climatprep4x5.dat Monthly soil precipitation for soil NOx emissions (Wa ng et al, 1998). File is in plain -text format. fert_scale.dat Fertilizer NOx emissions (Wa ng et al, 1998). File is in plain -text format. soiltype.dat Mapping from Olson land type to soil land type (Wa ng 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 stratosph eric 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), Im pact 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 - t ropopause 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, HNO 2, 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, P RPE, 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 com pleteness; 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. W e have regridded these files to the GEOS –4 native vertical grid (55 layers) used by GEOS– Chem . 2. Wecreated 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– Chemwill 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. Wecreated 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.*.geos5.2 x25 and gmi.clim.*.geos5.4x5 files. The MERRA vertical grid is the same as the GEOS –5 native vertical grid (72 layers) . W e 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 Burn ing 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 emission s 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 biofu el burning emissions [kg NH3/month] on the GCAP 4° x 5° , GMAO 2° x 2.5° , and GMAO 4° x 5° grids. FromGEIA.

NH3_natusrce.geos.2x25 NH3_natusrce.geos.4x5 NH3_natusrce.gcap.4x5 Binary punch files containing nat ural - 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 Bin ary 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 aircr aft.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 G CAP 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.g eos.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.ge os5.4x5 Files containing P(H2O2) values ( PORL - L=$ , tracer=5) saved out from 1 -yr benchmark simulations done with GEOS – Chem v7 – 02– 03. Data is saved up to the tropopause only. Units are [molec/cm3/s]. Files are provided for the GEOS –4 , and GEOS – 5 / MERRA / GEOS–5.7.2 vertical grids (reduced resolution) at 2° x 2.5° and 4° x 5° horizontal resolution. For more information about how the individual files were created, contact Bob Yantosca. THNO3.geos4.2x25 THNO3.geos4.4x5 THNO3.geos5.2x25 THNO3.geos5.4x5 Files containing THNO3 (= HNO3 + NIT) values ( IJ AVG - $ , tracer=7) saved out from 1 -yr benchmark simulations done with GEOS – Chem v7 – 02– 03. Files are provided for the GEOS –3 , GEOS–4 , and GEOS –5 vertical grids (reduced resolution) at 2° x 2.5° and 4° x 5° horizontal resolution.For more information about how the individual files were created, contact Bob Yantosca. 

### 4.3.27 The tagged_CO_200106 subdirectory REFERENCES: 1. GEOS - Chem wiki: Tagged CO simulation **Files Description**  acetone.geos.2x25 acetone.geos.4x5 Monthly mean emissions of direct biogenic acetone and acetone from grasslands for the GMAO 2° x 2.5° and 4° x 5° grids . This data was archived from a 1994 GEOS – Chem model simulation (GEOS – 1) ch3oh96.geos.2x25 isop96.geos.2x25 mono96.geos.2x25 ch3oh96.geos.4x5 isop96.geos.4x5 mono96.geos.4x5 Surface concentrations of CH3OH, isoprene, and monoterpenes from 1996 for the GMAO 2° x 2.5° and 4° x 5° grids . tagco_mask.geos.2x25 tagco_mask.geos.4x5 Contains country mask for ICARTT Tagged CO runs for the GMAO 2° x 2.5° and 4° x 5° grids . (1 = USA/Canada, 2 = Mexico, 3 = Europe, 4 = Asia) 

### 4.3.28 The TOMS_201203 subdirectory NOTES: 1. This is an update of the TOMS_200906 subdirectory REFERENCES: 1. GEOS –Chem wiki: Overhead TOMS/SBUV merged O3 columns Data source and version:

------------------------ Data are taken from: http://acdb - ext.gsfc.nasa.gov/Data_services/merged/index.htmlVersion 8 Merged Ozone Data Sets

Total Ozone Revision 05 DATA THROUGH: MAR 2009 LAST MODIFIED: 01 MAY 2009 Resol ution: 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. Wekeep 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 emissionsbiomass_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 Wo rking 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 n ow 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 containedrevisions 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 Am erican 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_20060 5  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 – C hem 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 st ratospheric 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 – Chemvolcano_SO2_200909  Replaced by volcano_SO2_201010

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### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)** 

## 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. Werecommend that you create a unique run directory for ea ch of your GEOS– Chem simulations. Otherwise you risk having important output overwritten by subsequent model runs. Wehave made available for download (via Git) several sample run directories, grouped by simulation , met field type , and hor izontal 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  Wh ich diagnostics to save to disk  Wh ich 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. **dicarbony ls:**  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 mec hanism 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: F or 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 c hecking 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 outpu t options are now defined within this file. An input.geos file ships with each of the GEOS – Chem run directories . W e invite you to download the run directory for the simulation(s) that you are interested in and view the corresponding input.geos file. Wehave 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. Of fline sulfate/carbon/dust/seasalt aerosol simulation 4. H2 and HD simulation Note that the input.geos file is grouped into menus. Each menu controls th e 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 o ptions for both dry deposition and wet deposition . Chemistry Menu Specifies options for chemistry. CO2 Menu Specifies options for the CO2 simulation . Mercury Me nu 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. ND4 8 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 ND20Menu (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 simulati on"). 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 d irectory : /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 timeste p (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 s pecify 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 filename with the appropriate date or time values.

8 Specify DATA_DIR (located in source code file directo ry_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 a nd 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 d irectory_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 onl**

**y 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 fiel d 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 areunzipping met field files on the fly (i.e. if LUNZIP is set to T), then you may also

spec if y if you want GEOS – Chem to wait until the met field fi les are completely unzipped before proceeding. It may be necessary to set LWA IT 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 appropri ate 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 1 9: Tracer #15 : 15 PMN 147.020: 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 3 4: 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 B rNO3 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 simulati on 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 , th en 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 s et 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 ind ividual species which constitute this tracer. In this example, NOx is a family consisting of NO2 + NO + NO3 + HNO2, so you must list these speciesnames after the molecular weight as shown above. These can be separated by spaces (i.e. no commas or semicolo ns 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 plac ing 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) afte r 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 inthe 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 LFI LL 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 Desc**  **ription** 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 LNL PBL 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: %% EMISSION S 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? : T36: => Use lightning NOx? : T

37: => Spat - seas constr?: T 38: => Use soil NOx : T 39: => Use fertilizer NOx : T 40: NOx scaling : 1 41: Us e 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 emissi on 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 i nput to**  **- 1 to let GEOS**  **– Chem**  **automatically**

**scale data to the y ear 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 lo gical_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 S pecify 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 MEG AN 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 dep endency 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 wa nt 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 monthl y- 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 als o 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 W ang, 1998). **NOTE: This switch is now obsolete and is slated to be removed. GEOS –**  **Chem now reads MODIS LAI data from netCDF files. Th**  **e 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 ). Se t LHIST to T to use historical emissions inventories of SO2, NOx, BC, and POA, or to Fotherwise.

51 Specify HISTYR, the emission year for historical emi ssions of SO2, NOx, BC, and POA (located in source code file input_mod.F ). 52 Header line 53 Specify LWAR

WI CK_VSLS (located in source code file logical_mod.F ). Set LWAR WI CK_VSLS to T to use surface CHBr3 emissions from Wa rwick 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 s ource 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 FU TURE_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 carbonaceo us 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 se condary 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, yo u 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 functi on 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 ). Recomm ended 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 otherwi se. 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 Tto turn on dry deposition , or F to turn off dry deposition.

3 Specify LW ETD (located in source code file logical_mod.F ). Set LW ETD 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. W e 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 time step (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, a nd 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.d at) 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 - process or . 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 CO 2 and tagged CO 2 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. We cht, R.M. Yantosca, S.S. Kulawik, K. W. Bowman, J.R. Wo rden, T. Machida, and H. Matsueda, Modeling CO 2 with im

proved emission inventories and CO 2 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 1 8: Net Ter Ex climatology: T19: 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 CO 2 chemical source from oxidation of CO, CH 4 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 co nsistent 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 su b - 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 Ne t 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 CO 2 emissions (annually- averaged) with simplified distribution from EDGAR scaled to scaled to annual values for 1985 - 2006 [Endresen et al. 2007]. 25 International ship CO 2 emissions based on the International Comprehensive Ocean Atmosphere Data Set (ICOADS) with monthly variability [Corbett & Koehler, 2003, 2004; W ang 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 CO 2 valu es for 1985 - 2002 [Sausen & Schumann, 2000; Kim et al., 2005; 2007; Wi lkerson 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 CO 2 sub - header line (select all that apply) 28 Save CO 2 background 29 Tag biosphere regions (28), ocean regions (11) and the Rest of the W orld (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 use r 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 Terrest rial 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 : oc ean.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 LDY NOCEAN (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 cont inuing 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 S pecify LW ETL (located in source code file logical_mod.F ). Set LW ETL 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 outpu t 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 : 30000000 00000000000000000000000 **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 no t 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 rela tive 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 MENULine 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: Cl d 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 all40: 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 ve rtical 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 space s). 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 settin gs. 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/Wtransport mass fluxes) diagnostic settings 27 ND25 (N/S transport mass fluxes) diagn ostic 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 (dicarbony l**  **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 (dicarbony l 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 obsoletenow.

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 o rganic 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 isrecommended 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 se ttings. 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 (We tland 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 Spe cify 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 line2 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 w hich 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 fo llowing 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. U wind) [m/s] 98 Meridional wind

(a.k.a. V-wind) [m/s] 99 Pressure at level

edges (PEDGE - $) [hPa] 100 Temperature [K]


### 5.2.1.18 The ND49 MENU Line numbers are not part of the input.geos file, but have been included for reference.01: %%% ND49 MENU %%% :

02: Turn on ND49 diagnostic : T 03: Inst 3 - D timeser. file : tsYYYYMMDD.bpch 04: Tracers to include : 94 05: Frequency [min] : 120 06: IMIN, IMAX of region : 70 30 07: JMIN, JMAX of region : 23 46 08: LMIN, LMAX of region : 1 20 **Line Description**  1 Header line 2 Set this to T to turn on the ND49 instantaneous 3D timeseries diagnostic. This allows you to archive instantaneous timeseries data for various quantities from a 3D region of the globe. 3 Specify the name of the file which will contain output from the ND49 station time series 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 diagnos tic quantities to save to disk. Separate each number with a space. **# ND49 diagnostic** 

**quantity Units**  1 – N_TRACERS GEOS – Chem

advected tracers [v/v] 76 OH concentration [molec/cm3] 77 NO2 concentration [v/v] 78 PBL heights [m] 79 PBL heights [levels] 80 Air density [molec/cm3] 81 Cloud fractions [unitless] 82 Column optical

depths [unitless] 83 Cloud top heights [hPa] 84 Sulfate aerosol

optical depth [unitless]85 Black carbon aerosol optical depth [unitless] 86 Organic carbon

aerosol optical depth [unitless] 87 Accumulation mode

seasalt optical depth [unitless] 88 Coarse mode seasalt

optical depth [unitless] 89 Total dust optical

depth [unitless] 90 Total seasalt tracer

concentration [unitless] 91 Pure O3 (not Ox)

concentration [v/v] 92 NO concentration [v/v] 93 NOy concentration [v/v] 94 Grid box height [m] 95 Relative humidity [%] 96 Sea level pressure [hPa] 97 Zonal wind (a.k.a. U wind) [m/s] 98 Meridional wind

(a.k.a. V-wind) [m/s] 99 Pressure at level

edges (PEDGE - $) [hPa] 100 Temperature [K] 101 PAR direct [W/m2] 102 PAR diffuse [W/m2] 103 Daily LAI [cm2/cm2] 104 Temperature at 2m [K] 105 Isoprene emissions [atoms C/cm2/s]106 Total Monoterpene emissions [atoms C/cm2/s] 107 Methyl Butenol

emissions [atoms C/cm2/s] 108 Alpha - Pinene

emissions [atoms C/cm2/s] 109 Beta - Pinene

emissions [atoms C/cm2/s] 110 Limonene emissions [atoms C/cm2/s] 111 Sabinene emissions [atoms C/cm2/s] 112 Myrcene emissions [atoms C/cm2/s] 113 3 - Carene emissions [atoms C/cm2/s] 114 Ocimene emissions [atoms C/cm2/s] 115– 121 Size - resolved dust

optical depth (i.e. the 7 FAST - J dust bins) [unitless] 5 Specify the frequency (in minutes) at which ND49 will save data for a 3D region of the globe data to disk. Recommended value: 180 min (3 hours). You may save data at a higher temporal resolution (e.g. every 60 min) but this will create HUGE data files! 6 Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:

 For GCAP 4° x 5° grid : 1 72  For GMAO 4° x 5° grid : 1 72  For GMAO 2° x 2.5° grid : 1 144 Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude. 7 Specify JMIN and JMAX, the indices which determine the latitude extent of the 3Dregion 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 bina ry punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS – Chem will replace these with the appropriate values. 4 To output the ND50 diagnostic quantities in HDF5 format. **Note: HDF5 must be installed on your system for using this option.**  **(The GEOS**

**– Chem support team does not provide help for the installation of this**  **library)** 5 Specify the ND50 diagnostic quantities to save to disk. Separate each number with a space.**# ND50 diagnostic**  **quantity Units**  1 – N_TRACERS GEOS – Chem

advected tracers [v/v] 76 OH concentration [molec/cm3] 77 NO2 concentration [v/v] 78 PBL heights [m] 79 PBL heights [levels] 80 Air density [molec/cm3] 81 Cloud fractions [unitless] 82 Column optical

depths [unitless] 83 Cloud top heights [hPa] 84 Sulfate aerosol

optical depth [unitless] 85 Black carbon aerosol

optical depth [unitless] 86 Organic carbon

aerosol optical depth [unitless] 87 Accumulation mode

seasalt optical depth [unitless] 88 Coarse mode seasalt

optical depth [unitless] 89 Total dust optical

depth [unitless] 90 Total seasalt tracer

concentration [unitless] 91 Pure O3 (not Ox)

concentration [v/v] 92 NO concentration [v/v] 93 NOy concentration [v/v] 94 Grid box height [m]95 Relative humidity [%]

96 Sea level pressure [hPa] 97 Zonal wind (a.k.a. U wind) [m/s] 98 Meridional wind

(a.k.a. V-wind) [m/s] 99 Pressure at level

edges (PEDGE - $) [hPa] 100 Temperature [K] 115– 121 Size - resolved dust

optical depth (i.e. the 7 FAST - J dust bins) [unitless] 6 Specify IMIN and IMAX, the indices which determine the longitude extent of the 3D region of the globe. Note that these are indices and not actual longitude values. To specify all 360 degrees of longitude, type the following:

 For GCAP 4° x 5° grid : 1 72  For GMAO 4° x 5° grid : 1 72  For GMAO 2° x 2.5° grid : 1 14 4 Also, note you can wrap around the date line. In the example shown above, IMIN=70 and IMAX=30. This will create a 3D region (assuming 4x5 grid) which starts at 165° E longitude and extends across the date line to 35° W longitude. 7 Specify JMIN and JMAX, the indices which determine the latitude extent of the 3D region of the globe. Note that these are indices and not actual latitude values. To specify all 180 degrees of latitude, type the following:

 For GCAP 4° x 5° grid : 1 45  For GMAO 4° x 5° grid : 1 46  For GMAO 2° x 2.5° grid : 1 91 8 Specify LMIN and LMAX, the indices which determine the vertical extent of the 3D region of the globe. 

### 5.2.1.20 The ND51 **MENU**Line numbers are not part of the input.geos file, but have been included for

reference. 01: %%% ND51 MENU %%% : 02: Turn on ND51 diagnostic : T 03: LT avg timeseries file : ts_satellite.YYYYMMDD.bpch 04: Output as HDF5? : F 05: Tracers to include : 94 06: GMT Hour for disk write : 0 07: Avg Period [LT hours] : 10 12 08: IMIN, IMAX of region : 1 72 09: JMIN, JMAX of region : 23 46 10: LMIN, LMAX of region : 1 1 **Line Description**  1 Header line 2 Set this to T to turn on the ND51 "satellite" 3D timeseries diagnostic. ND51 allows you to archive 3D data blocks for various quantities which have been time averaged between 2 local times. This is useful for comparing model data to sun synchronous satelli tes such as GOME or MOPITT which have morning overpass times. 3 Specify the name of the file which will contain output from the ND51 station timeseries diagnostic. This file will be in binary punch format and can be read by GAMAP. You may use date & time tokens YYYY, MM, DD, hh, mm, ss as part of the filename and GEOS – Chem will replace these with the appropriate values. 4 To output the ND50 diagnostic quantities in HDF format. **Note: HDF5 must be installed on your system for using this option. (The**  **GEOS**

**– Chem support team does not provide help for the installation of this**  **library)** 5 Specify the ND51 diagnostic quantities to save to disk. Separate each number with a space. **# ND51 diagnostic** 

**quantity Units**  1 – N_TRACERS GEOS – Chem

advected tracers [v/v] 76 OH concentration [molec/cm3] 77 NO2 concentration [v/v] 78 PBL heights [m]79 PBL heights [levels]

80 Air density [molec/cm3] 81 Cloud fractions [unitless] 82 Column optical

depths [unitless] 83 Cloud top heights [hPa] 84 Sulfate aerosol

optical depth [unitless] 85 Black carbon aerosol

optical depth [unitless] 86 Organic carbon

aerosol optical depth [unitless] 87 Accumulation mode

seasalt optical depth [unitless] 88 Coarse mode seasalt

optical depth [unitless] 89 Total dust optical

depth [unitless] 90 Total seasalt tracer

concentration [unitless] 91 Pure O3 (not Ox)

concentration [v/v] 92 NO concentration [v/v] 93 NOy concentration [v/v] 94 Grid box height [m] 95 Relative humidity [%] 96 Sea level pressure [hPa] 97 Zonal wind (a.k.a. U wind) [m/s] 98 Meridional wind

(a.k.a. V-wind) [m/s] 99 Pressure at level [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 thediagnostic 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 (assu ming 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 latitud e 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] : 12006: 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 wil l 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 (assum ing 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. Tospecify 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 SMVGEARdoes not do chemistry in the st ratosphere. 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 producti on and loss families to archive. You must list each family below. 6 Entry for the POx chemical production family (assuming we are performing a full chemistry simulation). The family name comes first and must be followed by a colon. Then you must list the individual species which constitute the POx family. A number in front of a species name is the coefficient by which that species will be multiplied. (You do not have to list the coefficient if it is 1.) Since the family name POx begins with a P, it is inte rpreted to be a chemical production family. 7 Entry for the LOx chemical production family (assuming we are performing a full chemistry simulation). You may proceed as described above. Since the family name LOx begins with an L, it is interpreted to be a chemical loss family. 8 Entry for the PCO chemical production family. 9 Entry for the LCO chemical production family. 10 Entry for the PBrOx chemical production family. 11 Entry for the PBry chemical production family. 12 Entry for the LBry chemical production family. 

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

### 5.2.1.25 The O3 P/L MENU

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

### 5.2.1.26 The NESTED GRID **MENU** NOTE: This menu controls options for the various GEOS – Chem nested grid simulations. This is an optional menu and may be omitted from input.geos if you are not concerned with these simulations. For more information, please see: 1. GEOS – Chem wiki: Nested - grid simulations 2. GEOS – Chem wiki: Setting up nested - grid simulations 3. GEOS – Chem wiki: Available met data for nested - grid simulations Line numbers are not part of th e 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? : F11: 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 LW INDO (located in source code file logical_mod.F ). Set LW INDO 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 Sp ecify LW INDO2x25 (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 LW INDO2x25 to T.  If you are using boundary conditions saved from a 4° x 5° GEOS – Chem simulation, th en set Set LW INDO2x25 to F. 4 Specify LW INDO_NA (located in source code file logical_mod.F ). Set LW INDO_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 LW INDO_EU (located in source code file logical_mod.F ). Set LW INDO_EU to T if you wish to perform a GEOS – Chem nested grid simulation over the Euro pean 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 LW INDO_CH (located in source code file l ogical_mod.F ). Set LW INDO_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 (locate d 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 LW INDO_SE (located in source code file logical_mod.F ). SetLW INDO_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 - g rid simulation. 12 Specify LW INDO_CU (located in source code file logical_mod.F ). Set LW INDO_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 di sk. 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 LOWE R 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 smal ler 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 UN

**IX 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 u nix_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 i nformation**  **.** Sometimes it is necessary to compare GEOS– Chem output against aircraft observations. The plane flight following diagnostic (a.k.a. ND40 diagnostic) allows youto 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 co urse 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 t he 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 l ine) 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 - 20 03 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 42.00 289.00 500.0025: 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, altitudeGMAO_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 lis ted 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 eachfield 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. GE**OS**

**– 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 fil es 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 o f 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 d omain 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 W orking Group . A copy of globchem.dat ships with each of the GEOS– Chem run directories for full chemistry simul ations (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 app ropriate modifications. 

### 5.3.3 The chemga.dat fileThe chemga.dat file defines some aerosol properties for the full - chemistry run with the

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

### 5.4. GEOS

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

**– Chem v9** 

**– 01** **– 03 uses the older**  **FAST –** **J photolysis code . However, we have**  **updated FAST**

**– J so that it uses the same photolysis species as the newer FAST**  **– JX code.**  

### 5.4.1 The rat

**j.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 #. Al so, 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 CH 3 I 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 fileThe jv_atms.dat file contains climatology for O3 and temperature, as used with the

FAST–J photolysis code. You should not modify this file unless you wish to change some parameters for the photolysis. NOTES:

 As of GEOS–Chem v9–01 –03 , the jv_atms.dat file is no longer shipped with the GEOS –Chem run directories, but is now stored in netCDF format in the FastJ_201204 data directory. 

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

### 5.4.4 The jv_spec_aod.dat file The jv_spec_aod.dat file contains the optical properties for aerosols at a single wa velength 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 siz e 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. W e 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 s et 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 timeserie s 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 ND5024 - 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 ( b inary 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 verticall**  **y 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, a**  **nd 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.d**  **at) 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. **N OTE: 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 tim e averaged diagnostic output from GEOS – Chem. Most of the GEOS – Chem diagnostics will place their output in this file. A single file containing multiple data blocks wi ll 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. smv 2.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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## 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. Weprovide below some convenient checklists that you can follow.. 

### 6.1.1 Checklist for NOx **– Ox**  **– Hydrocarbon** **– aerosol ch**  **emistry simulation with SM**  **VGEAR 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 . Wepresent 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

Nu mber 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 mec hanism, increase the number of transported tracers to **59** . A list of the tracer names can be found HERE . To run the dicarbonyls mechanism, increase the number of transported tracers to **75** . A list of the tracer names can be found HERE . To run the Caltech isoprene mechanism, increase the number of transported tracers to **56** . A list of the tracer names can be found HERE . **Aerosol Menu:** Online SULFATE AEROSOLS : T Online CRYST/AQ AEROSOLS: F Online CARBON AEROSOLS : T Online 2dy ORG AEROSOLS : F Online DUST AEROSOLS : T => Use DEAD emissions? : T Online SEASALT AEROSOLS : T => SALA radius bin [um]: 0.01 0.5 => SALC radius bin [um]: 0.5 8.0 Online dicarb. chem. : F If you have included the SOA mechanism, you must toggle the 4th entry: Online 2dy ORG AEROSOLS : T If you have included the dicarbonyls mechanism, you must toggle the 4th and 11th entries: Online 2dy ORG AEROSOLS : T Online dicarb. chem. : T If you switch the other aerosol types (sulfate, carbon, dust, seasalt) to to F (false), GEOS – Chem will attempt to read these from disk as monthly- mean quantities. NOTE: These offline aerosol fields may not be archived for the GEOS5 ( = MERRA = GEOS 5.7.x ) vertical grids. The crystalline sulfur and aqueous aerosols have not been implemented into GEOS – Chem at this point. They will be added into a future version.**Transport Menu:**

Turn on Transport : T => Use Flux Correction?: F => Fill Negative Values : T => IORD, JORD, KORD : 3 3 7 Transport Timestep [min]: 30 Set the transport timestep to 30 min (4° x 5° ), 15 min ( 2° x 2.5° ), or 10 min ( 1° x 1° or higher resolution). Do not use flux correction —that is computationally expensive. **Convection Menu:** Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non - local PBL? : T Convect Timestep (min) : 30 Set the convection timestep to the same value as the transport timestep. Select the non - local PBL mixing option , which performs the boundary layer mixing more accurately. **Chemistry Menu:** Turn on Chemistry? : T Use linear. strat. chem?: T => Use Linoz for O3? : T Chemistry Timestep [min]: 60 Read and save CSPEC_FULL: T USE solver coded by KPP : F Werecommend that you set the chemistry timestep to doub le 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. W e 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 batchqueuing 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). We t depositio n 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 GFE D2 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 Sche dule output for MAR : 3000000000000000000000000000000 Schedule output for APR : 300000000000000000000000000000 Schedule output for MAY : 3000000000000000000000000000000 Schedule output for JUN : 300000000000000000000000000000 Schedule output for JUL : 3000 000000000000000000000000000Schedule output for AUG : 3000000000000000000000000000000

Schedule output for SEP : 300000000000000000000000000000 Schedule output for OCT : 3000000000000000000000000000000 Schedule output for NOV : 30000000000000000000000000000 0 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 tha t 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:** Welist below the most imp ortant diagnostics for the Tagged Ox simulation. W e 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 tim e 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: Trace r 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 . W e 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 fa milies : 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 file s. 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. W e 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**  Wepresent 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 210.0Tracer #3 : 3 Be7 7.0

Specify each tracer and its molecular weight in this menu. **Aerosol Menu:** None of the option s 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 t ransport timestep to 30 min (4° x 5° ), 15 min ( 2° x 2. 5° ), or 10 min ( 1° x 1° or higher resolution). Do not use flux correction —that is computationally expensive. **Convection Menu:** Turn on Cloud Conv? : T Turn on PBL Mixing? : T => Use non - local PBL? : F Convect Timestep (min) : 30 Set the convection timestep to the same value as the transport timestep. At present you cannot use the non - local PBL mixing scheme with the Radon - Lead Beryllium simulation. W e are working to correct this situation. **Chemistry Menu:** Turn on Chemistry? : T Use linear. strat. chem?: F => Use Linoz for O3? : F Che mistry Timestep [min]: 60 Read and save CSPEC_FULL: F USE solver coded by KPP : F Werecommend 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 – Beryl lium 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. W et deposition takes place on every transport timestep. **Emissions Menu:** Turn on emiss ions? : 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:** Welist below the most important diagnostics for the Radon - Lead - Beryllium simulation. Weassume 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 deca y : 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 allND45: 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 Wepresent a checklist of how to customize input.geos for the Tagged Ox simulation. NOTE: W e 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# Nam e 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 Trace rs : 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 48.0Tracer #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 simu lation. 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. Weare 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 Werecommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator spli tting ). Typical chemistry timesteps are 60 min ( 4° x5° ), 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 lin ear stratospheric chemistry and Linoz stratospheric ozone chemistry options. These will ensure that the stratospheric ozone gets computed correct ly. 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. We t depositi on 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:** Welist below the most important diagnostics for the Tagged Ox simulation. W e 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 diagno stic

... 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 TW ICE 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 o n 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 : L OxStrt: 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 f amilies : 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: OxAtlBLProd/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 : POx Init: 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: O xPacBL 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 : LOxSt rat: 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 sp ecify 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** Wepresent 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 Men u:**  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) : 30Set 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 Werecommend 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)?: Fw/ 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 => Iso prene 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:** Schedu le days for diagnostic output as described above in Chapter 6.1.1 . **Diagnostic Menu:** Welist below the most important diagnostics for the Tagged CO simulation. W e assume GEOS - 5 meteorology with the "reduced" g rid (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 a ll 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: CObbafProd/Loss Family #8 : PCObbas: CObbas

Prod/Loss Family #9 : PCObboc: CObboc Prod/Loss Family #10 : PCObb eu: 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: C Omeoh 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**  Wepresent 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 : 2Tracer 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 tim estep. 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 Werecommend 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 hi gher resolution). In all cases, thechemistry 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. We t 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 . **Di agnostic Menu:**  Welist below the most important diagnostics for the H2 - HD simulation. Weassume 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: Bi ofuel emissions : 1 4ND36: 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** Wepresent 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, et c. **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 12.00Tracer #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 aerosol s. 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 CAR BON 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 incl ude 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 => IOR D, 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 tim estep. Select the non - local PBL mixing option , which performs the boundary layer mixing more accurately.**Chemistry Menu:**

Turn on Chemistry? : T Chemistr y Timestep [min]: 60 Werecommend 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). **Dep osition Menu:**  Turn on Dry Deposition? : T Turn on Wet Deposition? : T Dry deposition occurs on every chemistry timestep. W et deposition takes place on every transport timestep. **Emissions Menu:** %%% EMISSIONS MENU %%% : Turn on emissions? : T Emiss tim estep (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 => Iso prene 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 Asi a, 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. **Outp ut Menu:**  Schedule days for diagnostic output as described above in Chapter 6.1.1 . **Diagnostic Menu:**Welist 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 ae r 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 informa tion, refer to Chapter 5.3.2 and Chapter 5.3.3 .  Make s ure 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** T hanks to Eric Sofen (U. W ashington) for compiling this information! NOTE: this assumes a GEOS4 30-level sim ulation. The JH2O2, PH2O2, O3, and NO3 bpch files must extend only up to the tropopause. Wh en you extract the data from the bpch file that is produ ced 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 HN O3+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** Wepresent 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 2 01.0 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 file2. 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 Werecommend 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 Preindustria l sim? : F Ocean Hg restart file : ocean.totHg.YYYYMMDDhh Use GTMM soil model? : F GTMM Hg restart file : GTM.totHg.YYYYMMDDhh Wh enever 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. W et 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 re st 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:** Welist below the most important diagnostics for the mercury simulation. Weassume 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 inform ation about the Prod & Loss Menu, refer to Chapter 5.2.1.22 . 

### 6.1.8 Checklist for a CH4 offline simulation Wepresent 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 : 9Number of Tracers : 12

Tracer Entri es ------- > : 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 CH 4_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 switch es 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 - lo cal 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 Werecommend that you set the chemistry timestep to double the transpo rt 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 simulati ons (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 Me nu:**  %%% 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 Men u 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:** Welist below the most important diagnostics for the methane simulati on. Weassume 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 N umber 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 Wepresent a checklist of how to customize input.geos for the a typical CO 2 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 CO 2 ; 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 n umber 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 44.0Tracer #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 - CO 2 run is shown below (appropriate selections at the end of the CO 2 menu are also required). Tracers 1 - 11 are as shown above. Tracer 12 is the background including only Fossil Fuel CO 2 . 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 Tr acer #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 Werecommend that you set the chemistry timestep to double the transport timestep (this is known as Strang operator splitting ). Typical chemistry time steps 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 CO 2 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 redun dancy. The rest of the switches in the Emissions Menu do not affect on the CO 2 simulation, so set them all to F (false). **CO 2**  **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 : TTerrestrial 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 Sh ip & 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 Ta g Global Plane CO2 : F The above CO 2 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_l and.dat and Regions_ocean.dat files, which reside in the CO 2 run directory . **Output Menu:** Schedule days for diagnostic output as described above in Chapter 6.1.1 . **Diagnostic Menu:** The CO 2 simulation has its own unique diagnostic ( ND04 ). The CO 2 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** Wedescribe 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 SystemIf 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 # L ists 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 j ob 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 PBCreate 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 th e 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 jobqconf - 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** Weprovide 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 occu rs 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 o ccurred 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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### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)**

## 7. Coding and Debugging

**7.1 Coding: Practice and Style** Weprovide below some guidelines for writing GEOS – Chem source code routines. 

### 7.1.1 GEOS

**– Chem program units**  Wehave 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. W e 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. W e 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 p rogram 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 StyleWehave 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 -- m ajor 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 facilit ate connecting GEOS–Chem to the NASA GEOS –5 GCM .) Wh en 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. W e sought to separate core GEOS– Chem routines from 3rd party code. Here we lis t 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. W e 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. Welist all of the modules and their dependencies below: **Module Name Purpose**  **Other Mo dules Referenced**  **Headers directory**CMN_DEP_mod.F Contains common blocks for dry deposition. CMN_SIZE_mod.F CMN_DIAG_mod.F Contains size parameters and global variables for the GEOS – Chem diagnostic arrays. CMN_SIZE_mod.F

CMN_GCTM_mod.F Contains GEOS – Chem specific physical constraints and derived quantities. none CMN_NOX_mod.F Contains NOx from soils. CMN_SIZE_mod.F CMN_O3_mod.F Contains common blocks for anthropogenic emissions via SMVGEAR. CMN_SIZE_mod.F

CMN_SIZE_mod.F Contains size parameters for GEOS – Chem arrays. none CMN_mod.F Contains global variables (remnant of header file CMN ). CMN_SIZE_mod.F cmn_fj_mod.F Contains parameters and global variables used to interface between Harvard chemistry and UC Irvine FAST - J photolysis programs. CMN_SIZE_mod.F

commsoil_mod.F Contains global variables for the soil NOx emissions routines. CMN_SIZE_mod.F comode_loop_mod.F Contains common blocks and variables for SMVGEAR II. CMN_SIZE_mod.Fjv_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. non e

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.Ftrapping 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 astronomica l Julian date. (This allows GEOS – Chem to handle transitions such as end - of- month, end of-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 pure sigma models. This is necessary for running GEOS – Chem with the fv DAS 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.Fof 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 Co ntains 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 vert ical levels to 30 vertical levels. CMN_SIZE_mod.F error_mod.F

unix_cmds_mod.F Contains Unix command strings which are used for unzipping of meteorological data files. none

**GeosCore directory** RnPbBe_mod.F Contains variables and routines used for the 222Rn - 210Pb - 7Be 10Be simulation. CMN_DEP_mod.F CMN_DIAG_mod.F CMN_SIZE_mod.F dao_mod.F diag_mod.F directory_mod.F file_mod.F grid_mod.F logical_mod.F pressure_mod.F time_mod.F tracer_mod.F tropopause_mod.F a3_read_mod.F Contains routines which unzip, open and read the GEOS– Chem A- 3 fields from disk. CMN_DIAG_mod.F CMN_SIZE_mod.F bpch2_mod.F dao_mod.Fdiag_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 routine s 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.Flogical_mod.F time_mod.F tracer_mod.F tra cerid_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 bio fuel_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_n ei_mod.F error_mod.F future_emissions_mod.Flogical_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.Fand 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_m od.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_e missions_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.Fgfed2_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.Fdao_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 t he 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.Fcomode_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_m od.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.Ftracerid_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 ND4 1diagnostic -- 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.Fcmn_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.Ftracer_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 hd f_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 ti me. 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.Fthe 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_mo d.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 e rror_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.Ftime_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 como de_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 d ust 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.Fdust_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_S IZE_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 f ile_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 simulati on 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.Fcarbon_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 i coads_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 rout ines 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 tra cer_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.Froutines 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 G EOS –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 Conta ins 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.FACET, 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 us ed 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_mo d.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.Fwhich 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 LW I_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 d irectory_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.Ftracer_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 tro popause_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 g rid_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_m od.F bpch2_mod.F dao_mod.F directory_mod.F error_mod.Fsimulation. 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.Froutines 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 th e 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.Fread 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 un ix_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_emissi ons_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 biofue l_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.Fdiag63_mod.F diag_oh_mod.F diag_pl_mod.F d irectory_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 trac erid_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.Ffile_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 trans fer_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 logica l_mod.F Contains all of the logical switches used by GEOS – Chem. none mapping_mod.F90 Contains a derived type object to compute the mapping weight and areal mapping.. CMN_SIZE_mod.F error_mod.F logical_mod.F megan_mod.F Contains variables and routines specifying the algorithms that control CMN_GCTM_mod.F CMN_SIZE_mod.F a3_read_mod.Fthe 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_a 1_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_mercu ry_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.Fvdiff_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 d ata 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_m od.Fand 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_emissio ns_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.Fdepths for GEOS– 1, G EOS –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 dire ctory_mod.F error_mod.F file_mod.F time_mod.F tracer_mod.F tracerid_mod.F pbl_mix_mod.F Contains routines and variables used to compute the planetary boundary layer (PBL) height and to mix tracers underneath the PBL top. CMN_DIAG_mod.F CMN_GCTM_mod.F CMN_SIZE_mod.F dao_mod.F diag_mod.F error_mod.F grid_mod.F logical_mod.F pressure_mod.F time_mod.F tracer_mod.F pjc_pfix_geos5_window_ mod.F Contains routines which implements the Philip Cameron Smith pressure fixer. Specially modified for the GEOS– 5 neste d grid simulation. CMN_GCTM_mod.F CMN_SIZE_mod.F CMN_mod.F error_mod.F grid_mod.F pressure_mod.F pjc_pfix_geos57_window _mod.F Contains routines which implements the Philip Cameron Smith pressure fixer. Specially modified for the GEOS– 5.7.2 nested grid sim ulation. 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.FGEOS –4/TPCORE transport code (contained in tpcore_fvdas_m od. 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 RET RO 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.Ftracer_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 routin es 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.Fssa_bromine_mod.F Contains variables and routines for emi ssions 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 sche me 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.Farctas_ship_emiss_mod. F b iomass_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 tro popause_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.Fdirectory_mod.F error_m od.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 tagge d 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 logic al_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.Fglobal simulation. These are needed for TPCORE transport for nested grid 1° x 1° simu lations. 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 Kevi n 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 pressu re_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 Wa ng. 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.Frelated quantities. TRACER_MOD also contains inquiry functions that can be used to determine the type of GEOS – Chem simulation. tracerid_mod.F Contains variab les 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_fv das_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.Fuvalbedo_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.Fpressure_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 Wh ereas 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.oLooking 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 so urce 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 compiletime. 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. Wi th OpenMP, you can execu te 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, consul t the web site OpenMP.org . 

### 7.2 GEOS

**– Chem Debugging**  The GEOS – Chem model evovles constantly. Our rapidly- increasing user base freq uently submits updates and new features for inclusion into the standard GEOS – Chem repository. As with any software project, mistakes are inevita ble. 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 thes e 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

Westrive 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 GE OSChem version. Clicking on a link will take you to a wiki post which explains the bug (and how it was fixed) in detail. Wh en 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. Weinvite 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 cal l 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 dow n 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 u p 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 arecalling 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. Consi der 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 realcleanmake - 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 ou t- 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 statem ent, 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. Wh en 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 s equence in which individual instructions occur) by specifying the **- O0**  fl ag. 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 parallelizatio n
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### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)** 

## 8. Using Git to manage the GE**OS –**  **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 GE OS – 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. Chan ge 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 A ll 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 com mit.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 lis t 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. Wh enever you need to modify the source code, you should NOT do it on the **master** bra nch. 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. W hen 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 **Bran ch/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 Wi th 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 bran ch. 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. (Werecommend Emacs.) Werecommend 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 M **erging** 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 **CTR L** **– 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 clic k Create.To remove a tag, you can use the git tag command directly:

git tag - d TAG_NAME Wh ere 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 cod es manually. 

### 8.3.1 Creating a patch file to share with others To create a patch file containing the code differences between a branch of your code with your **master** branch, type: git format - patch master..BRANCH_NAME -- stdout > my - patch file.diff where BRANCH_NAME is the name of the branch that you want to compare against the **master** branch. You can also create a patch file for a given number of past commits by typing: git format - patch - 3 -- stdout > my - patch - file.diff If you want the most recent commit the n 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 an d 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 revi sions 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 i f 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 ne w 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 bran ch 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 M **ore 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 u ser. 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 Werecommend that you use the the git clone command to download each newlyrel eased 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 wil l 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 Wh en 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! Wenow 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 **Co de.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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### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)** 

## 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 an d faster sharing of new model features is promoted by users offering co - authorship for recent developments. 

### 9.2.1 Guidelines for offering credit Weinvite 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 developm**  **ent 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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## Appendix 1: GEOS

**– Chem Tracers, by Simulation**  Wi th 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 mech anism. Please consult Appendix 6 for a complete list of chemical species in GEOS – Chem. Wespecify several hydrocarbon tracers (those listed in **BOLD ITALICS** ) as atoms C instead of molecules tracer. W e 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 fol lowing 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 W iki: The "standard" NOx – Ox – Hydrocarbon –aerosol simulation 3. GEOS – Chem W iki: Secondary organic aerosols 4. GEOS – Chem W iki: Dicarbonyls simulation 5. GEOS – Chem W iki: Caltech isoprene mechanism **# Nam**  **e 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 Dicarbony**  **ls 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 W iki: Offline aerosol chemistry simulation 3. GEOS – Chem W iki: Sulfate aerosols 4. GEOS – Chem W iki: Carbonaceous aerosols 5. GEOS – Chem W iki: Secondary organic aerosols 6. GEOS – Chem W iki: Mineral dust aerosols 7. GEOS – Chem W iki: Sea salt aerosols**# Name**  **Description g/mole** 

1 DMS Dimethyl sulfide 62 2 SO2 Sulfur dioxide 64 3 SO4 Sulfate 96 4 SO4s Sulfate on surface of sea salt aerosol 96 5 MSA Methane Sulfionic Acid 96 6 NH3 Ammonia 17 7 NH4 Ammonium 18 8 NIT Inorganic sulfur nitrates 62 9 NITs Inorganic sulfur nitrates on surface of sea salt aerosol 62 10 BCPI Hydrophilic black carbon aerosol 12 11 OCPI Hydrophilic organic carbon aerosol 12 12 BCPO Hydrophobic black carbon aerosol 12 13 OCPO Hydrophobic organic carbon aerosol 12 14 ALPH A- pinene, B - pinene, sabinene, carene,

terpenoid ketones 136.23 15 LIMO Limonene 136.23 16 ALCO Myrcene, terpenoid alcohols, ocimene 142 17 SOG1 Lump of gas products of first 3

(ALPH+LIMO+TERP) hydrocarbon oxidation 150 18 SOG2 Gas product of ALCO oxidation 160 19 SOG3 Gas product of SESQ oxidation 220 20 SOG4 Gas product of ISOP oxidation 130 21 SOG5 Gas product of aromatics oxidation 150 22 SOA1 Lump of aerosol products of first 3

(ALPH+LIMO+TERP) hydrocarbon oxidation 150 23 SOA2 Aerosol product of ALCO oxidation 16024 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 W iki: CO2 simulation **# Name**  **Description g/mole**  1 CO2 Total CO2 44 **If you w ish, y** **ou may add tracers for additional CO2 sources:** 2 CO2ff CO2 from fossil fuel emissions 44 3 CO2oc CO2 from ocean emissions 444 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, y ou can add the following**  **tracers. NOTE: These extra tracers are only**  **v alid 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 W echt updated the CH4 simulation in GEOS – Chem v8–02 –03 . Kevin W echt 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 W iki: 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 164 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 W iki: Mercury simulation 3. GEOS – Chem W iki: 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) 2016 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) 20124 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 W iki: 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 2816 COmeoh CO chemically produced from methanol oxidation 28 17 COacet CO chemically produced from acetone

oxidation 28 

### A1.7 Tagged Ox simulations NOTE: W e 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 W iki: 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 4613 OxUSA Ox produced over the United States (surface

– tropopause) 46


### A1.8 Rn**– Pb** **– Be simulations**  Werecommend 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 W iki: 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

**Previous |**  **Next |**  **Printable View (no frames)** Atmospheric Sciences > GEOS - Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 2



### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)** 

## Appendix 2: GEOS

**– Chem**  **Horizontal Coordinates** Wecompare 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 52.50057.500 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 cente rs:

- 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 :

- 90.0 00 - 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 22.00 0 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 - 1 38.750 - 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 - 6 8.750 - 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

- 160.0 00 - 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 - 90.00 0 - 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

- 20.00 0 - 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 15.00017.500

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 - 33.0 00 - 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 23.0 00 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 79.00 0 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 7 4.375 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 98.12599.375 100.625 101.875 103.125 104.375 105.625 106.875

108.125 10 9.375 110.625 111.875 113.125 114.375 115.625 116.875 118.125 119.375 120.625 121.875 123.125 124.375 125.625 126.875 128.125 129.375 130.625 131.875 133.125 134.375 135.625 136.875 138.125 139.375 140.625 141.875 143.125 144 .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

- 81.2 50

- 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 - 46.2 50 - 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

- 11.25 0

- 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 23.75 0 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 33.5 00 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 61.5 00 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 89.50 0 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 i s 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° lon gitude 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 - 70.5 00

- 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 - 42.5 00 - 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 - 14.50 0

- 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 13.50 0 14.500 15.500 16.500 17.500 18.50019.500 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 19.00020.000 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 4 2.000 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 7 0.000 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 ed ges:

- 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 20.5 00 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 48.5 00 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 76.50 0 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 - 8 0.000 - 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 60.0 00 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 88.0 00 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 - 1 69.000 - 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 - 15 0.333 - 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 - 13 1.667 - 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 - 38.3 33 - 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 - 19.6 67 - 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 - 1.00 0 - 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 17.66 7 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 95.66796.333

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 1 49.000 149.667 150.333 151.000 151.667 152.333 153.000 153.667 154.333 155.000 155.667 156.333 157.000 157.667 158.333 159.000 159.667 160.333 161.000 161.667 162.333 163.000 163.667 164.333 165.000 165.667 166.333 167.000 1 67.667 168.333 169.000 169.667 170.333 171.000 171.667 172.333 173.000 173.667 174.333 175.000 175.667 176.333 177.000 177.667 178.333 179.000 179.667 0.5° x 0.667° longitude centers:

- 180.000 - 179.333 - 178.667 - 178.000 - 177.333 - 176.6 67 - 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 - 158.0 00 - 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 - 139.33 3 - 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 - 120.66 7 - 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 4 8.000 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 6 6.667 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 99.333 100.000 100.667 101.333 102.000102.667 103.333 104 .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. 333 142.000 142.667 143.333 144.000 144.667 145.333 146.000 146.667 147.333 148.000 148.667 149.333 150.000 150.667 151.333 152.000 152.667 153.333 154.000 154.667 155.333 156.000 156.667 157.333 158.000 158.667 159.333 160.0 00 160.667 161.333 162.000 162.667 163.333 164.000 164.667 165.333 166.000 166.667 167.333 168.000 168.667 169.333 170.000 170.667 171.333 172.000 172.667 173.333 174.000 174.667 175.333 176.000 176.667 177.333 178.000 178.6 67 179.333 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

- 22.7 50

- 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 - 8.7 50 - 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 5.25 0 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 19.25 0 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 33.25033.750 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 - 51.0 00

- 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 - 37.0 00 - 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 - 23.00 0

- 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 - 9.00 0 - 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 33.50034.000 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 90.66791.333 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 16.50 0 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 32.00032.500

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 0.6 **67° 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 - 67.3 33 - 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 - 48.6 67 - 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 16.00 0 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 30.00 0 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 cente rs:

- 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 43.5 00 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 3 0.000 31.000 32.000 33.000 34.000 35.000 36.000 37.000 38.000 39.000 40.000 41.000 42.00043.000

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. 000 143.000 144.000 145.000 146.000 147.000 148.000 149.000 150.000 151.000 152.000 153.000 154.000 155.000 156.000 157.000 158.000 159.000 160.000 161.000 162.000 163.000 164.000 165.000 166.000 167.000 168.000 169.000 170.0 00 171.000 172.000 173.000 174.000 175.000 176.000 177.000 178.000 179.000 180.000 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 - 165.5 00

- 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 - 137.5 00 - 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 21.5 00 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 35.50036.500 37.500 38.500 39.500 40.500 41.500 42.500

43.500 44.500 45.500 46.500 47.500 48.500 4 9.500 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 76.50 0 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 99.500 100.500 101.500 102.500 103.500 104.500 105.500 106.500 107.500 108.500 109.500 110.500 111.500 112.500 113.500 114.500 115.500 116.500 117.500 118.500 119.500 120.500 121.500 122.500 123.500 124.500 125.500 126.500 127.5 00 128.500 129.500 130.500 131.500 132.500 133.500 134.500 135.500 136.500 137.500 138.500 139.500 140.500 141.500 142.500 143.500 144.500 145.500 146.500 147.500 148.500 149.500 150.500 151.500 152.500 153.500 154.500 155.5 00 156.500 157.500 158.500 159.500 160.500 161.500 162.500 163.500> 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:

- 90.0 00 - 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 - 62.00 0 - 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

- 34.00 0 - 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 - 5 3.500 - 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

- 2 5.500 - 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

**Previous |**  **Next |**  **Printable View (no frames)** Atmospheric Sciences > GEOS - Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 3



### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide** **Previous |**  **Next |**  **Printable View (no frames)** 

## Appendix 3: GEOS

**– Chem Vertical Grids**  Wecompare 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 kmGCAP, GEOS –3, GEOS –4, and GEOS –5 vertical levels, up to 32 kmGCAP, 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. Wecomputed 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 0.00223 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 27.3 00 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 0.6 92 933.032 0.000000 0.485 956.321 2 0.000000 0.344 972.365 0.000000 0.206 988.408 1 0.000000 0.099 1000.829 0.000000 - 0.006 1013.250

### A3.3 GEOS **– 4 vertical grids**  The native vertical resolution of GEOS–4 meteorological fields is 55 hybrid eta levels, extending from the surface up to 0.01 hPa. The first 14 levels from the surface upward are pure sigma levels; the rest are fixed pressure levels. To conserve memory, you have the option of running GEOS – Chem a reduced vertical resolution of 30 eta levels . GEOS – Chem will combine eta levels above ~50 hPa on -the fly. Wecomputed 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 66.2 45 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 0.36545 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 47.9 46 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 30.3 83 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 52.0160.055641 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 15.1 98 118.250

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 0.8 57 914.795 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 34.0 24 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 14.1 70 139.115

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 7.700 370.7930.395895 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 0.3 78 968.494 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 ve** **rtical 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 3 1 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. Wecomputed 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 0.0150.000010 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 66.2 45 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 47.9 46 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 9.29348 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 27.1 80 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 15.1 98 118.250

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 6.585 434.2120.447337 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 4.1 32 605.880 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 0.8 64 913.984 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 0.123 998.0511 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 15.7 31 108.663 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 11.578 208.24430 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 5.6 92 491.401 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 1.2 90 868.135

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 0.864 913.9840.909573 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 fiel ds 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 ve rtical 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 i s 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 hP a. 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 r

**educed vertical grid** The reduced vertical resolution of the GEOS –5.7.2 meteorological fields is identical to the GEOS– 5 47 - layer reduced grid . **Previous |**  **Next |**  **Printable View (no frames)** Atmospheric Sciences > GEOS - Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 4



### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)** 

## Appendix 4: GEOS

**– Chem Meteorological Fields**  Wecompare 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 Wi ki for more information. **Field Ty**  **pe 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 RADSW G 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 SNOW D A3 2 - D Snow depth m PARDIR A3 2 - D Direct photosynthetically- active radiation W/m2 PARDIF A3 2 - D Diffuse photosynthetically- active radiation unitlessT A6 3 - D Temperature K

U A6 3 - D Zonal wind m/s V A6 3 - D Meridional wind m/s OPTDEPTH A6 3 - D Optical depth unitless CLDF A6 3 - D Cloud fraction unitless Q A6 3 - D Specific humidity kg H2O/kg air MOISTQ A6 3 - D Tendency of Q w/r/t precipitation g H2O/kg air/day UPDE A6 3 - D Convective updraft flux Pa/s DNDE A6 3 - D Convective downdraft flux Pa/s ENTRAIN A6 3 - D Convective entrainment Pa/s DETRAINE A6 3 - D Convective detrainment Pa/s UPDN A6 3 - D Convective updraft flux (non entraining plume) Pa/s DNDN A6 3 - D Convective downdraft flux (non entraining plume) Pa/s DETRAINN A6 3 - D Convective detrainment (non entraining plume) Pa/s
PS I6 2 - D Surface pressure hPa SLP I6 2 - D Sea - level pressure hPa PHIS Constant 2 - D Surface geopotential heights m2/s2 LW I 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 i s the temperature of the ground (or ocean) surface. **Field Ty**  **pe Dimension**  **Quantity Units**  LW I 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 GW ETTOP A3 2 - D Top soil wetness unitlessHFLUX 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 RADLW G A3 2 - D Longwave (IR) radiation emanating from the ground W/m2 RADSW G 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 UW ND at 10 m altitude m/s USTAR A3 2 - D Friction velocity m/s V10M A3 2 - D VW ND 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 W iki for more information.

**Field Ty**  **pe 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 GW ETROOT A3 2 - D Root zone soil moisture unitless GW ETTOP 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 LW GNET A3 2 - D Net longwave radiation at ground W/m2 LW TUP A3 2 - D Outgoing longwave radiation W/m2 PARDF A3 2 - D Diffuse photosnythetically- active radiation W/m2 LW TUP 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/sQV2M 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 SW GNET 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 Wa ter 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 KU 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 LW I 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, 1 8:00, 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 detaile d 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 Ty**  **pe D**  **imension Units**  **Quantity** FRLAKE Constant 2 - D Fraction of lake type in grid box fractionFRLAND Constant 2 - D Fraction of land type in grid box fraction FRLANDIC Constant 2 - D Fraction of land ice type in grid box fraction FROCEAN Constant 2 - D Fraction of ocean in grid box fraction PHIS Constant 2 - D Surface geopotential m 2 s - 2 ALBEDO A1 2 - D Surface albedo fraction CLDTOT A1 2 - D Total cloud fraction fraction EFLUX A1 2 - D Latent heat flux (positive upward) W m - 2 EVAP A1 2 - D Surface evaporation kg m - 2 s - 2 FRSEAICE A1 2 - D Fraction of sea ice fraction FRSNO A1 2 - D Fractional snow- covered area fraction GRN A1 2 - D Vegetation greenness fraction fraction GW ETROOT A1 2 - D Root zone soil wetness fraction GW ETTOP 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 LW GNT A1 2 - D Surface net downward longwave flux W m - 2 LW I A1 2 - D Land/water/ice flags unitless LW TUP 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 mPRECANV A1 2 - D Surface precipitation flux from anvils kg m - 2 s - 2 PRECCON A1 2 - D Surface precipitation flux from convection kg m - 2 s - 2 PRECLSC A1 2 - D Surface precipitation flux from large - scale kg m - 2 s - 2 PRECSNO A1 2 - D Surface snowfall flux kg m - 2 s - 2 PRECTOT A1 2 - D Total surface precipitation flux kg m - 2 s - 2 QV2M A1 2 - D Specific humidity at 2 m above the displacement height kg kg - 1 SEAICE00 A1 2 - D Fraction of grid box that has < 10% sea ice coverage fraction SEAICE10 A1 2 - D Fraction of grid box that has 10 - 20% sea ice coverage fraction SEAICE20 A1 2 - D Fraction of grid box that has 20 - 30% sea ice coverage fraction SEAICE30 A1 2 - D Fraction of grid box that has 30 -40% sea ice coverage fraction SEAICE40 A1 2 - D Fraction of grid box that has 40 - 50% sea ice coverage fraction SEAICE50 A1 2 - D Fraction of grid box that has 50 - 60% sea ice coverage fraction SEAICE60 A1 2 - D Fraction of grid box that has 60 - 70% sea ice coverage fraction SEAICE70 A1 2 - D Fraction of grid box that has 70 - 80% sea ice coverage fraction SEAICE80 A1 2 - D Fraction of grid box that has 80 - 90% sea ice coverage fraction SEAICE90 A1 2 - D Fraction of grid box that has > 90% sea ice coverage fraction SLP A1 2 - D Sea level pressure hPa SNODP A1 2 - D Snow depth mSNOMAS A1 2 - D Snow mass kg m - 2

SW GDN A1 2 - D Surface incident shortwave flux W m - 2 SW GNT A1 2 - D Net surface downward shortwave flux W m - 2 TROPPT A1 2 - D T based tropopause pressure hPa TS A1 2 - D Surface skin temperature K T2M A1 2 - D Temperature 2 m above displacement height K U10M A1 2 - D Eastward wind 10 m above displacement height m s - 1 USTAR A1 2 - D Friction velocity m s - 1 V10M A1 2 - D Northward wind 10 m above displacement height m s - 1 Z0M A1 2 - D Roughness length, momentum m CLOUD A3cld 3 - D Total cloud fraction in grid box fraction QI A3cld 3 - D Cloud ice mixing ratio kg kg - 1 QIAN A3cld 3 - D Cloud ice mixing ratio – anvils kg kg - 1 QILS A3cld 3 - D Cloud ice mixing ratio – large scale kg kg - 1 QL A3cld 3 - D Cloud liquid water mixing ratio kg kg - 1 QLAN A3cld 3 - D Cloud liquid water mixing ratio

– anvil kg kg - 1 QLLS A3cld 3 - D Cloud liquid water mixing ratio

– large - scale kg kg - 1 TAUCLI A3cld 3 - D In - cloud ice cloud optical thickness (visible band) unitless TAUCLW A3cld 3 - D In - cloud liquid cloud optical thickness (visible band) unitless OPTDEPTH A3cld 3 - D Total in - cloud optical depth (visible band) unitlessCMFMC A3dyn 3 - D Upward moist convective mass flux kg m - 2 s - 2 DTRAIN A3dyn 3 - D Detrainment cloud mass flux kg m - 2 s - 2 OMEGA A3dyn 3 - D Vertical pressure velocity Pa s - 1 RH A3dyn 3 - D Relative humidity unitless U A3dyn 3 - D Eastward component of wind m s - 1 V A3dyn 3 - D Northward component of wind m s - 1 DQRCU A3mstC 3 - D Precipitation production rate – convective kg kg - 1 s - 1 DQRLSAN A3mstC 3 - D Precipitation production rate – large - scale + anvil kg kg - 1 s - 1 REEVAPCN A3mstC 3 - D Evaporation of precipitating convective condensate kg kg - 1 s - 1 REEVAPLS(AN) A3mstC 3 - D Evaporation of precipitating LS + anvil condensate kg kg - 1 s - 1 PFICU A3mstE 3 - D Downward flux of ice precipitation – convective kg m - 2 s - 1 PFILSAN A3mstE 3 - D Downward flux of ice precip – large - scale + anvil kg m - 2 s - 1 PFLCU A3mstE 3 - D Downward flux of liquid precipitation – convective kg m - 2 s - 1 PFLLSAN A3mstE 3 - D Downward flux of liquid precip

– large - scale + anvil kg m - 2 s - 1 PS I3 2 - D Surface pressure Pa PV I3 3 - D Ertel potential vorticity K m 2 kg 1 s - 1 QV I3 3 - D Specific humidity kg kg - 1T 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 s ee 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 Ty**  **pe Dimension**  **Units Quantity**  FRLAKE Constant 2 - D Fraction of lake type in grid box fraction FRLAND Constant 2 - D Fraction of land type in grid box fraction FRLANDIC Constant 2 - D Fraction of land ice type in grid box fraction FROCEAN Constant 2 - D Fraction of ocean in grid box fraction PHIS Constant 2 - D Surface geopotential m 2 s - 2 ALBEDO A1 2 - D Surface albedo fraction CLDTOT A1 2 - D Total cloud fraction fraction EFLUX A1 2 - D Latent heat flux (positive upward) W m - 2 EVAP A1 2 - D Surface evaporation kg m - 2 s - 2 FRSEAICE A1 2 - D Fraction of sea ice fraction FRSNO A1 2 - D Fractional snow- covered area fraction GRN A1 2 - D Vegetation greenness fraction fractionGW ETROOT A1 2 - D Root zone soil wetness fraction

GW ETTOP 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 LW GNT A1 2 - D Surface net downward longwave flux W m - 2 LW I A1 2 - D Land/water/ice flags unitless LW TUP A1 2 - D Upward longwave flux at top of atmosphere (TOA) W m - 2 PARDF A1 2 - D Surface downward PAR diffuse flux W m - 2 PARDR A1 2 - D Surface downward PAR beam flux W m - 2 PBLH A1 2 - D Planetary boundary layer height above surface m PRECANV A1 2 - D Surface precipitation flux from anvils kg m - 2 s - 2 PRECCON A1 2 - D Surface precipitation flux from convection kg m - 2 s - 2 PRECLSC A1 2 - D Surface precipitation flux from large - scale kg m - 2 s - 2 PRECSNO A1 2 - D Surface snowfall flux kg m - 2 s - 2 PRECTOT A1 2 - D Total surface precipitation flux kg m - 2 s - 2 QV2M A1 2 - D Specific humidity at 2 m above the displacement height kg kg - 1 SEAICE00 A1 2 - D Fraction of grid box that has < 10% sea ice coverage fraction SEAICE10 A1 2 - D Fraction of grid box that has 10 - 20% sea ice coverage fraction SEAICE20 A1 2 - D Fraction of grid box that has 20 - 30% sea ice coverage fractionSEAICE30 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 SW GDN A1 2 - D Surface incident shortwave flux W m - 2 SW GNT 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 fractionCMFMC A3 3 - D Upward moist convective mass flux kg m - 2 s - 2 DQRCU A3 3 - D Precipitation production rate – convective kg kg - 1 s - 1 DQRLSAN A3 3 - D Precipitation production rate – large - scale + anvil kg kg - 1 s - 1 DQIDTMST A3 3 - D Ice tendency from moist physics kg kg - 1 s - 1 DQLDTMST A3 3 - D Liquid water tendency from moist physics kg kg - 1 s - 1 DQVDTMST A3 3 - D Wa ter vapor tendency from moist physics kg kg - 1 s - 1 DTRAIN A3 3 - D Detrainment cloud mass flux kg m - 2 s - 2 MOISTQ A3 3 - D Overall tendency of QV g kg - 1 day- 1 OPTDEPTH A3 3 - D Total in - cloud optical depth (visible band) unitless PFICU A3 3 - D Downward flux of ice precipitation

– convective kg m - 2 s - 1 PFILSAN A3 3 - D Downward flux of ice precip – large - scale + anvil kg m - 2 s - 1 PFLCU A3 3 - D Downward flux of liquid precipitation – convective kg m - 2 s - 1 PFLLSAN A3 3 - D Downward flux of liquid precip – large - scale + anvil kg m - 2 s - 1 QI A3 3 - D Cloud ice mixing ratio kg kg - 1 QL A3 3 - D Cloud liquid water mixing ratio kg kg - 1 QV A3 3 - D Specific humidity kg kg - 1 REEVAPCN A3 3 - D Evaporation of precipitating convective condensate kg kg - 1 s - 1 REEVAPLS A3 3 - D Evaporation of precipitating large - scale + anvil condensate kg kg - 1 s - 1 T A3 3 - D Air temperature KTAUCLI A3 3 - D In - cloud ice cloud optical thickness (visible band) unitless TAUCLW A3 3 - D In - cloud liquid cloud optical thickness (visible band) unitless U A3 3 - D Eastward component of wind m s - 1 V A3 3 - D Northward component of wind m s - 1 OMEGA I6 3 - D Vertical pressure velocity Pa s - 1 PS I6 2 - D Surface pressure hPa PV I6 3 - D Ertel potential vorticity K m 2 kg 1 s - 1 RH I6 3 - D Relative humidity unitless

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### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide**  **Previous |**  **Next |**  **Printable View (no frames)** 

## Appendix 5: GEOS

**– Chem Diagn**  **ostics** Welist 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 fol lowing 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 filecan be found in Chapter 5 . DIMENSION i s 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**  **RA DON 222**  **- LEA** **D 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**  **RA DON 222**  **- LEA** **D 210 -**  **BERYLLIUM**

**7 DECA Y**  **Units Category**  1 (I,J,L) 222Rn loss [kg/s] RN DECAY 2 (I,J,L) 210Pb loss [kg/s] RN DECAY 3 (I,J,L) 7Be loss [kg/s] RN DECAY

**ND03 Dimension**  **MERCURY EMISSIONS,**

**PRODUCTION, LOSS Units**  **Category** 1 (I,J) Anthropogenic Hg0 emission [kg] HG - SRCE 2 (I,J) Total mass of oceanic Hg0 [kg] HG - SRCE 3 (I,J) Oceanic emission of Hg0 [kg] HG - SRCE 4 (I,J) Land reemission of Hg0 [kg] HG - SRCE 5 (I,J) Land natural emission of Hg0 [kg] HG - SRCE 6 (I,J) Anthropogenic Hg2 emission [kg] HG - SRCE 7 (I,J) Total mass of oceanic Hg2 [kg] HG - SRCE 8 (I,J) Mass of Hg2 sunk in the ocean [kg] HG - SRCE9 (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- dow n Hg0 dry dep to ocean [kg] HG - SRCE 18 (I,J) Snow emission of Hg [kg] HG - SRCE 19 (I,J,L) Production of Hg2 from Hg0 [kg] PL - HG2 - $ 20 (I,J,L) Production of Hg2 from rxn w/ OH [kg] PL - HG2 - $ 21 (I,J,L) Production of Hg2 from rxn w/ O3 [kg] PL - HG2 - $ 22 (I,J,L) Loss of Hg2 from rxn w/ sea salt [kg] PL - HG2 - $ 23 (I,J,L) Loss rate of Hg2 from rxn w/ sea salt [s - 1] PL - HG2 - $ 24 (I,J,L) Production of Hg2 from Br [kg] PL - HG2 - $ 25 (I,J,L) Br concentration [kg] PL - HG2 - $ 26 (I,J,L) BrO concentration [kg] PL - HG2 - $ 27 (I,J,L) Particulate bound mercury [pptv] PL - HG2 - $ 28 (I,J,L) Reactive gaseous mercury [pptv] PL - HG2 - $ 29 (I,J,L) + OCEAN tagged tracers [kg] OCEAN HG30 (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 SULFA TE** 

**CHEMISTRY QUA NTITIES**  **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 BLA CK CA**  **RBON &**

**ORGA NIC CA**  **RBON (initially**  **dev eloped 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 - BIOF4 (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 S**  **AL T EMISSIONS**  **Units Category** 1 (I,J) Accumulation mode seasalt [kg] SALTSRCE

2 (I,J) Coarse mode seasalt [kg] SALTSRCE

**ND09 Dimension**  **HCN & CH3CN sources & sinks Units**  **Category** 1 (I,J,L,N) Loss of tagged tracer to OH [kg] HCN - PL - $ 2 (I,J) HCN from biomass burning [molec/cm2/s] HCN SRCE 3 (I,J) CH3CN from biomass burning [molec/cm2/s] HCN SRCE 4 (I,J) HCN from domestic fossil fuel [molec/cm2/s] HCN SRCE 5 (I,J) CH3CN from domestic fossil fuel [molec/cm2/s] HCN SRCE 6 (I,J) HCN loss to ocean uptake [molec/cm2/s] HCN SRCE 7 (I,J) CH3CN loss to ocean uptake [molec/cm2/s] HCN SRCE

**ND10 Dimension**  **H2 -**  **DEUTERIUM SOURCES**

**(EMISSIONS, PRODUCTION, LOSS) Units**  **Category** 1 (I,J,L) Loss of H2 by OH [molec H2/cm3/s] PL H2HD - $ 2 (I,J,L) Production of H2 from Isoprene [molec H2/cm3/s] PL H2HD - $ 3 (I,J,L) Production of H2 from CH4 [molec H2/cm3/s] PL H2HD - $ 4 (I,J,L) Production of H2 from CH3OH [molec H2/cm3/s] PL H2HD - $ 5 (I,J,L) Production of H2 from MONO [molec H2/cm3/s] PL H2HD - $6 (I,J,L) Production of H2 from ACET [molec H2/cm3/s] PL H2HD - $ 7 (I,J,L) Loss of H2 by stratospheric O1D [molec H2/cm3/s] PL H2HD - $ 8 (I,J,L) Loss of HD by OH [molec HD/cm3/s] PL H2HD - $ 9 (I,J,L) Production of HD from Isoprene [molec HD/cm3/s] PL H2HD - $ 10 (I,J,L) Production of HD from CH4 [molec HD/cm3/s] PL H2HD - $ 11 (I,J,L) Production of HD from CH3OH [molec HD/cm3/s] PL H2HD - $ 12 (I,J,L) Production of HD from MONO [molec HD/cm3/s] PL H2HD - $ 13 (I,J,L) Production of HD from ACET [molec HD/cm3/s] PL H2HD - $ 14 (I,J,L) Loss of HD by stratospheric O1D [molec HD/cm3/s] PL H2HD - $ 15 (I,J,L) Ratio of OH k rates kH2/kHD [unitless] PL H2HD - $ 16 (I,J) Fossil Fuel H2 (anthropogenic) [molec HD/cm2/s] H2HD SRC 17 (I,J) Biomass Burning of H2 [molec HD/cm2/s] H2HD SRC 18 (I,J) Biofuel Burning of H2 [molec HD/cm2/s] H2HD SRC 19 (I,J) Ocean emissions of H2 [molec HD/cm2/s] H2HD SRC 20 (I,J) Ocean emissions of HD [molec HD/cm2/s] H2HD SRC

**ND11 Dimension**  **AC ETONE SOURCES & SINKS**  **Units Category**  1 (I,J) Acetone source from [at ACETSRCEMONOTERPENES 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 SURFA CE** 

**EMISSIONS IN THE BL Units**  **Category** 1 (I,J,L) Fraction of boundary layer occupied by

level L [unitless] EMDIS BL

**ND13 Dimension**  **TROPOSPHERIC SULFUR**

**EMISSIONS Units**  **Category** 1 (I,J) Biogenic DMS [kg S] DMS BIOG 2 (I,J,L) Aircraft SO2 (1 <= L <= ND13) [kg S] SO2 - AC - $ 3 (I,J,L) Anthropognic SO2 (1 <= L <= 2 ) [kg S] SO2 - AN - $ 4 (I,J) Biomass SO2 [kg S] SO2 - BIOB 5 (I,J) Biofuel SO2 [kg S] SO2 - BIOF 6 (I,J,L) Non - eruptive volcano SO2 (1 <= L <=

ND13) [kg S] SO2 - NV - $ 7 (I,J,L) Eruptive volcano SO2 (1 <= L< = ND13) [kg S] SO2 - EV - $ 8 (I,J) Ship SO2 [kg S] SO2 -SHIP

9 (I,J,L) Anthropogenic SO4 (1 <= L <= 2 ) [kg S] SO4 - AN - $ 10 (I,J) Biofuel SO4 [kg S] SO4 - BIOF 11 (I,J) Natural NH3 [kg S] NH3 - NATU 12 (I,J) Anthropogenic NH3 [kg] NH3 - AN - $ 13 (I,J) Biomass NH3 [kg] NH3 - BIOB 14 (I,J) Biofuel NH3 [kg] NH3 - BIOF

**ND14 Dimension**  **UPWA RD MA** **SS FLUX DUE TO WET**

**CONVECTION Units**  **Category** 1 (I,J,L,N) Mass change due to cloud convection [kg/s] CV - FLX - $

**ND15 Dimension**  **UPWA RD MA** **SS FLUX FROM**

**BOUNDA RY**  **- LA** 

**YER MIXING Units**  **Category** 1 (I,J,L,N) Mass change due to boundary- layer

mixing [kg/s] TURBMC - $

**ND16 Dimension**  **AR EA**  **L FRA CTION 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**  **RA INOUT FRA** **CTION 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**  **WA SHOUT FRA** **CTION 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 OPTICA L DEPTHS A**  **ND**

**CLOUD FRA CTIONS**  **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 RA TES (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**  **MA SS**  **- WEIGHTED OH**  **CONCENTRA TION**  **Units Category**  Mean OH concentration diagnostic [10 5 molec/cm3]

**Dimension MA** **SS TRA**  **NSPORT 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**  **STRA TOSPHERIC 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**  **BIOMA SS 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] BIOBSRCE10 (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**  **LA ND MA**  **P DI AG**  **NOSTIC Units**  **Category**1 (I,J) GMAO land -water indices [unitless] LANDMAP

**ND31 Dimension**  **SURFA CE PRESSURE DIA** **GNOSTIC Units**  **Category** 1 (I,J,L) Pressure at the bottom of level L (1 <= L

<= ND31 ) [hPa] PEDGE - $

**ND32 Dimension**  **TROPOSPHERIC NOx**

**EMISSIONS Units**  **Category** 1 (I,J,L) Aircraft NOx [molec/cm2/s] NOX - AC - $ 2 (I,J,L) Anthropogenic NOx ( 1 <= L <=

NOXEXTENT ) [molec/cm2/s] NOX - AN - $ 3 (I,J) Biomass Burning NOx [molec/cm2/s] NOX BIOB 4 (I,J) Biofuel Burning NOx [molec/cm2/s] NOX BIOF 5 (I,J) Fertilizer NOx [molec/cm2/s] NOX FERT 6 (I,J,L) Lightning NOx [molec/cm2/s] NOX - LI - $ 7 (I,J) Soils NOx [molec/cm2/s] NOX SOIL 8 (I,J) Stratospheric NOx (upper

boundary) [molec/cm2/s] NOX STRT

**ND33 Dimension**  **COLUMN TRA** **CER Units**  **Category** 1 (I,J,N) Atmospheric column sum of tracer [kg] COLUMN T**ND34 Dimension**  **BIOFUEL BURNING EMISSIONS Units**  **Category**

1 (I,J) NOx biofuel emissions [molec/cm2/s] BIOFSRCE 4 (I,J) CO biofuel emissions [molec/cm2/s] BIOFSRCE 5 (I,J) ALK4 biofuel emissions [atoms C/cm2/s] BIOFSRCE 9 (I,J) ACET biofuel emissions [atoms C/cm2/s] BIOFSRCE 10 (I,J) MEK biofuel emissions [atoms C/cm2/s] BIOFSRCE 11 (I,J) ALD2 biofuel emissions [atoms C/cm2/s] BIOFSRCE 18 (I,J) PRPE (lumped >=C3 alkenes)

biofuel emissions [atoms C/cm2/s] BIOFSRCE 19 (I,J) C3H8 biofuel emissions [atoms C/cm2/s] BIOFSRCE 20 (I,J) CH2O biofuel emissions [molec/cm2/s] BIOFSRCE 21 (I,J) C2H6 biofuel emissions [atoms C/cm2/s] BIOFSRCE

**ND35 Dimension**  **TRA CER**  **CONCENTRA TION A** **T 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**  **AN THROPOGENIC 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] ANTHSRCE9 (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**

**ty pe 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**  **UDRA FT SCA**  **VENGING FRA CTION**  **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 TRA CER IN MOIST** 

**CONVECTION Units**  **Category**1 (I,J,L,N) Rainout loss of tracer in convective updrafts [kg/s] WETDCV - $

**ND39 Dimension**  **LOSS OF TRA CER IN A**  **EROSOL WET**

**DEPOSITION Units**  **Category** 1 (I,J,L,N) Rainout loss of tracer in large - scale

precip [kg/s] WETDLS - $

**ND40 Dimension**  **PLA NE FLIGHT DI**  **AG NOSTIC**  **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**  **AF TERNOON PBL HEIGHT**  **Units Category**  1 (I,J) Afternoon boundary layer heights

(1200 - 1600 local time) [m] PBLDEPTH

**ND42 Dimension**  **SOA CONCENTRA** **TIONS 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**  **CHEMICA L PRODUCTION OF** 

**VA RIOUS SPECIES**  **Units Category**  1 (I,J,L) OH [molec/cm3] CHEM L=$ 2 (I,J,L) NO [v/v] CHEM L=$ 3 (I,J,L) HO2 [v/v] CHEM L=$ 4 (I,J,L) NO2 [v/v] CHEM L=$ 5 (I,J,L) NO3 [v/v] CHEM L=$

**ND44 Dimension**  **DRYDEP ( M = NUMber DEP ) Units**  **Category** 1 (I,J,M) Dry deposition fluxes (M = 1,

NUMDEP) [molec/cm2/s] DRYD FLX 2 (I,J,M) Dry deposition velocities (M = 1,

NUMDEP) [cm/s] DRYD VEL**ND45 Dimension**  **TRA CER CONCENTRA** **TIONS 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 A VERA** **GE TRACER CONCENTRA** **TION 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 A T NL = NUMBER** 

**OF LOCA TIONS**  **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 INSTA NT** **ANEOUS TRA CER** 

**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 A VERA** **GE TRA CER**  **TIMESERIES Units**  **Category**(I,J,L) Archives the same diagnostic quantities as ND49 (listed above)

**ND51 Dimension**  **3 -**  **D SA TELLITE 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 SA TELLITE TRACER** 

**TIMESERIES Units**  **Category** (I,J,L,N) Archives the same diagnostic quantities

as ND51 (listed above), along a second satellite path.

**ND52 Dimension**  **GA MMA**  **HO2 Units**  **Category** 1 (I,J,L) Uptake coefficient for HO2 by aerosols [unitless] GAMMA

**ND53 Dimension**  **FREE DIA GNOSTIC**  **Units Category** 

**ND54 Dimension**  **FRA CTION OF TIME IN THE** 

**TROPOPSPHERE Units**  **Category** 1 (I,J,L) Computes the amount of time that a

given grid box spends in the troposphere [unitless] TIME TPS**ND55 Dimension**  **DYN AMI**  **C TROPOPAUSE DIA** **GNOSTICS Units**  **Category** 1 (I,J) Level at which the dynamic tropopause

occurs [unitless] TR PAUSE 2 (I,J) Height of the dynamic tropopause [km] TR PAUSE 3 (I,J) Pressure of the dynamic tropopause [mb] TR PAUSE

**ND56 Dimension**  **LIGHTNING FLA SHES**  **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**  **POTENTIA L TEMPERA** **TURE**

**DIA GNOSTIC**  **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 -WS T: W aste 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 -WT L: We tland 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 DIA GNOSTIC**  **Units Category** 

**ND60 Dimension**  **WETLA ND FRA** **CTION Units**  **Category** 1 (I,J) We tland fraction unitless WET FRAC

**ND61 Dimension**  **FREE DIA GNOSTIC**  **Units Category** 

**ND62 Dimension**  **INSTA NT** **ANEOUS COLUMN MA PS**  **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 DIA GNOSTIC**  **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 DIA GNOSTIC**  **Units Category** 

**ND65 Dimension**  **PRODUCTION/LOSS OF**

**SPECIFIED CHEMICA**  **L FA MILIES**  **Units Category**  1 (I,J,L,N) Chemical family P/L rates. Users

can define which species/ families to output in input.geos . [molec/cm3/s] PORL L=$

**ND66 Dimension**  **GMA O (formerly**  **DA O) 3**  **- D met fields**  **Units Category**  1 (I,J,L) UW ND : U -winds [m/s] DAO - 3D - $ 2 (I,J,L) VW ND : 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)**  **GMA O (formerly**  **DA O) 2**  **- D met fields**  **Units Category**  1 (I,J) HFLUX: sensible heat flux from surface [W/m2] DAO FLDS 2 (I,J) RADSW G: solar radiation at the ground

For GEOS

– 5, this is the net radiation @ ground (SWGNET) For MERRA , this is the incident radiation @ ground (SWGDN) [W/m2] DAO FLDS 3 (I,J) PREACC: total precipitation at the ground

For GEOS

– 5 and MERRA, this field is named PRECTOT [mm/day] DAO FLDS 4 (I,J) PRECON: total convective precipitation at

the ground For GEOS

– 5 and MERRA, this field is named PRECCON [mm/day] DAO FLDS 5 (I,J) TS: surface air temperature

NOTE: For GEOS

–4, GEOS

– 5, and MERRA, this is really the air tem perature at 2 m

altitude above the surface. [K] DAO FLDS 6 (I,J) RADSW T: solar radiation at the top of the

atmosphere [W/m2] DAO FLDS 7 (I,J) USTAR: friction velocity [m/s] DAO FLDS 8 (I,J) Z0: surface roughness height [m] DAO FLDS 9 (I,J) PBL (aka PBLM): planetary boundary

layer depth [hPa] DAO FLDS10 (I,J) CLDFRC: column cloud fraction [0 - 1] DAO FLDS 11 (I,J) U10M: U -winds at 10 meters altitude [m/s] DAO FLDS 12 (I,J) V10M: V-winds at 10 meters altitude [m/s] DAO FLDS 13 (I,J) PS - PBL: Boundary Layer Top Pressure [hPa] DAO FLDS 14 (I,J) ALBD: Surface Albedo [unitless] DAO FLDS 15 (I,J) PHIS: Geopotential Heights [m] DAO FLDS 16 (I,J) CLTOP : Cloud Top Height [levels] DAO FLDS 17 (I,J) TROPP: Tropopause pressure (read

directly from the met fields, without any further processing). For more information see our dynamic tropopause wiki page . [hPa] DAO FLDS 18 (I,J) SLP: Sea Level pressure (read directly

from the met fields) [hPa] DAO FLDS 19 (I,J) TSKIN : Ground / Sea Surface Temp [K] DAO FLDS 20 (I,J) PARDF : Photosynthetically active diffuse

radiation [W/m2] DAO FLDS 21 (I,J) PARDR : Photosynthetically active direct

radiation [W/m2] DAO FLDS 22 (I,J) GW ETTOP: Top soil wetness [unitless] DAO FLDS

**ND68 Dimension**  **GRID BOX QUA NTITIES**  **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) AVG W : 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 SURFA CE A**  **RE AS**  **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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## 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 glo bchem.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 Wo rking Group . 1. **SOA :**  59 advected tracers, with secondary organic aerosols 2. **Dicarbony ls:**  75 advected tracers, with dicarbonyl chemistry 3. **Isoprene:** 56 advected tracers, with the Caltech isoprene scheme . **Previous |**  **Next |**  **Printable View (no frames)** Atmospheric Sciences > GEOS - Chem Model > Manuals > Archive > Man.v9 01 03 > Appendix 7



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## Appendix 7: GEOS

**– Chem Style**  **Guide** Weprovide guidelines for writing clear, concise, and effective Fortran source code . 

### A7.1 Background **A7.1.1** Wehave 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. W e invite you to consult the foll owing 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 s ource 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 versionscontain 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** Wepreviously wrote GEOS – Chem source code using **fixed -** **format lay out**  , 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 Wechose 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 lay out**  , 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.) W e 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** Wegenerate 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: S ubroutine 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 hea ders !EOP ! -------------------------------------------------------------------------

-----!BOC

! ! ! LOCAL VARIABLES: ! INTEGER :: I, J, IJLOOP REAL*8 :: P1, P2, THIK, NUM, DEN ! ! !DEFINED PARAMETERS: ! REAL*8, PARAMETER :: KAPPA = 0.4d0 ! Von Karman's Constant REAL*8, PARAMETER :: CP = 1000.0d0 ! ! ! EXTERNAL FUNCTIONS: ! REAL*8, EXTERNAL :: XLTMMP !================================================================= ! METERO begins here! !============================================================== === ... code goes here ... END SUBROUTINE METERO !EOC Note that the ProTeX header contains the following elements: 1. Indicators ( !BOP , !EOP ) as to where ProTeX should look for source code header comments 2. Indicators ( !BOC , !EOC ) as to where the source code begins and ends. ProTeX will ignore code between !BOC and !EOC unless you tell it otherwise. 3. A description of the routine, the original date and most recent 4. Description of when the routine was last modified (with date & name of the programmers) 5. A list of input & output arguments 6. A list of references (if applicable) 7. References to F90 modules (if any) after the USE keyword followed by the IMPLICIT NONE declaration 8. Any #include declarations for header files. Since we are using the C preprocessor with 72 - column fixed format, the # character must go in column 1. 9. Each time the file is modified the REVISION HISTORY section should be updated. 10. Declarations for local variables 11. Declarations for Fortran parameters (aka constants) 12. Declarations for external functions (if necessary)Fortran 90 allows you to declare an argument to a subroutine or function with one of the

following descriptors: 1. INTENT(IN) (read - only), 2. INTENT(OUT) (write - only) or 3. INTENT(INOUT) (read - and -write) This helps you to prevent overwriting arguments which should not be overwritten. Werecommend 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 s tyles as you wish. You don't always have to extend the header all the wa y 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 s ource 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** Weused to write GEOS – Chem source code in ALL CAPITALS. W e 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 readabi lity or preserve scientific abbreviations ( e.g. Rn_Pb_Be_mod.F ). Westill 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 va riable 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 thiscode 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 ENDDOENDDO

ENDDO ENDDO **A7.2.5** Use LOTS of white space to separate code. For example instea d 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 afrai d 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 column s. 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 WR ITE 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 char acters (the max limit) where INTEGER can express numbers from - 2e9 to +2e9 REAL*4 can express numbers from - 1e38 to +1e38 REAL*8 can express numbers from - 1e312 to +1e312 Use REAL*8 as your default floating - point type. This will prevent round off and precision truncation errors. However, you should use REAL*4 data type instead of REAL*8 in the following instances:

 **Diagnostic arrays:** GEOS – Chem diagnostic values rarely exceed 10 38 , si nce they are usually in units such as kg, v/v, ppbv, or molecules/cm 2/s. **Arrays and scalars required for binary or netCDF file I/O:** Declaring these

types of variables REAL*4 will help to keep file sizes as small as possible, thus saving disk space. Some th ird - 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 chec k 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 i**  **ssues 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 kn ow 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 interna l 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 in ternal 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)' ) DATECaveat: Some versions of the PGI compiler did not allow Fort ran 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** Wh en writing GEOS – Chem code, you may have to use both the internal read / internal write and ENCODE / D ECODE 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 ar ray 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: LOGI CAL, SAVE :: FIRSTTIME = .TRUE. Avoid using obsolete F77 syntax: LOGICAL FIRSTTIME SAVE FIRSTTIME DATA FIRSTTIME / .TRUE. / Note: SAVE d 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 t he same line where a function's type is declared. Use this syntax: INTEGER, EXTERNAL :: MYFUNC Avoid using obsolete F77 syntax: INTEGER MYFUNC EXTERNAL MYFUNCNOTE: If you are referencing functions contained within a module file, then you do not

need to de clare 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 ALBE DO 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 o nly 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, 1 000 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 sy ntax: 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 sitt ing 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 fi nite 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 nee d 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 jus t 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  U se 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. W e 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 routi ne 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 retur ns 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_SUBROUTI NE begins here! !================================================================= Y = SIN( X ) ! Return to calling program END SUBROUTINE MY_SUBROUTINE !EOC ! -------------------------------------------------------------------------

---- ! Harvard University Atmospheric Chemistry Modeling Group ! ! -------------------------------------------------------------------------

----- !BOP ! ! !IROUTIN E: 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 functio n 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 Grou p ! ! -------------------------------------------------------------------------

----- !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 com mon 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 resu lts 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 subrout ine 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 pa ckage. 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 so urces. **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 Modu le 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** Weused 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 Wh ile 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. W e 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** Wh en GEOS –Chem connects to an external GCM —such as NASA's GEOS –5 GCM — it will utilize MPI parallelizati on. 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 informationalmessages to the screen (or log file, i f you redirect screen output there) simultaneously.

All of these I/O operations can seriously impact performance. Wehave 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 Wh en 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. W e 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=T RIM( FILENAME ) ... ) ! Read data READ( IU_FILE, IOSTAT=IOS ) ... ! Close file CLOSE( IU_FILE ) But when we connect GEOS – Chem to an external GCM, we can no longer rely on pre defined LUNs. The GCM may have already assi gned 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. W e 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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## Appendix 8: Modifications t**o facilitate Grid****** **Independence in GEOS –**  **Chem** GEOS – Chem will form the core of a fully- coupled system that will connect to the NASA GEOS –5/GCM. Before this can happen, the GEOS – Chem standard model must become compliant with the Earth System Model Framework (ESMF) . This will allow usto 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 thou sands of CPUs. To achieve this coupling between GEOS – Chem and the NASA GEOS – 5 GCM, we have introduced the concept of **grid -**  **independence** . W e 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. Wehave made it a priority to implement necesary structural changes into GEOS – Chem without disrupting ongoing G EOS– Chem research projects. Wehave already removed several legacy code routines that prevented GEOS – Chem from connecting to the NASA GCM. W e 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. Wedescribe 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 cod e: 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 Webegan 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. Wemodified 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. Wemoved 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. Weintroduced netCDF I/O capa bility into GEOS – Chem and converted several ASCII data files to netCDF. W e shall continue to migrate all of GEOS – Chem's data files to netCDF, but this will be a gradual transiton. 4. Wecreated 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 relie d on ASCII data input. 5. Wecreated a new module to read and regrid MODIS leaf- area - index data from its native resoluti on (either 0.5° x 0.5° or 0.25° x 0.25°). This removed legacy code that relied on ASCII data input. Wecorrected 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. Wehave introduced new derived type objects into GEOS– Chem. These objects will render referencing data arrays via USE statements obsolete. 2. Wehave set derived type objects (as well as other structural modifications) apart from existing source code with C - preprocessor switches. 3. Wenow 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. Wenow determine available Fortran logical unit numbers while GEOS – Chem is runn ing 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. Wi th the help of our colleagues at GSFC, we are continuing to refine the performance of the GEOS - Chem within the GEOS –5 GCM. W e also are re - engineering GEOS – Chem's emissions routines into an "Emissions Component". Wehave the following goals in mind:1. Wewish to achieve a total separation between emissions routines and chemistry

routines 2. Wewish to implement "top - down" data flow ( i.e. all data enters/leaves each subroutine via the argument list, contained in derived type obj ects ) 3. Wewish to segregate all file I/O operations from routines in which computations are performed. This will prevent bottlenecks to parallelization. 4. Wewish 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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## 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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### GEOS **– Chem v9** **– 01**  **– 03 Online User's Guide** **Previous |**  **Next |**  **Printable View (no frames)** 

## Appendix 10: GEOS

**– Chem Vers** **ion 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 pag e. 

### 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 informat ion. 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 partit ioning 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 Histor ical 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 W echt 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. **Stru ctural 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 Wa shout code has been split into three cases: aerosols, HNO3, and soluble gases. This was done to ensure that HNO3 is not affected by the aerosol scavenging updates and is still scavenged according to Eq. 14 from Jacob (2000). Initial source code modification for GEOS– 5.7.2 GEOS – Chem has been modified for compatilibility with the GEOS –5.7.2 meteorological data. Remove support for GEOS –3 meteorology See this wiki page for more information. Updates from the grid independent GEOS – Chem model code Modifications made for the grid - independent GEOS – Chem model include: 1. Fixes to facilitate i mplementation 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 (devel oped 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 w iki 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 inGEOS – 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 a erosols 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 an thropogenic 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 Bes s 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 specifi c 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 SW GDN field in the ND67 diagnostic MERRA "incident shortwave radiation at the ground" (SW GDN) is now archived to ND67, not "net longwave radiation at the ground" (LW GNT). Centralized chemistry The time at which chemistry, emissions, photolysis, andtime 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  Wa shout 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 S treets 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 emissi ons 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 W ang, 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 stratosph eric 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 PEDG E - $ diagnostic category is archived to timeseries diagnostics  Offline simulations can now run on the GEOS 5/MERRA full -vertical grid


### A10.4 What's new in GEOS **– Chem v8** 

**– 03**  **– 01 and v8** 

**– 03**  **– 02**  The following features were introduced into GEOS – Chem public release v8– 03– 01 : **Feature Description**  Caltech isoprene chemistry mechanism A new isoprene chemistry was introduced as an option to solve an over- estimation in isoprene in prev ious 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 W orking 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 form ulated 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  Wenow 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 i nterfaced 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 an d Kevin W echt have updated the CH4 simulation in GEOS – Chem , following earlier work by Jerome Drevet. The following features were introduced into GEOS – Chem beta re lease v8– 03 –02: **Feature Description**  Terrestrial and deep ocean mercury The Global Terrestrial Mercury Model (cf. Nicole Smith Downey) can now be selected as an option in the standard mercury simulation. Many features of the mercury simulation have also been improved (cf. E. Sunderland, C. Holmes). Updated CO2 simulation Ray Nassar has updated the CO2 simulation with new inventories and fluxes. For a full description, see our CO2 simulation wiki page . Obtain liquid water content from GEOS– 5 met fields Jenny Fisher modified the existing SO2 chemistry scheme such that it will obtain the clo ud fraction and liquid water content directly from the GEOS – 5 meteorlogy. 

### A10.5 What's new in GEOS **– Chem v8** 

**– 02**  **– 01**  The following features were introduced into GEOS – Chem public release v8– 02– 01 : **Feature Description** Updated chemical

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

### A10.6 What's new in GEOS **– Chem v8** 

**– 01** **– 01**  The following features were introduced into GEOS – Chem public release v8– 01 – 01 : **Feature Description**  Compatibility with GEOS –5 meteorological fields GEOS – Chem v8–01 –01 is now fully compatible with the GMAO GEOS – 5 operational data product (e.g. GEOS - 5.0.1 and GEOS - 5.1.0). You must upgrade to GEOS – Chem v8– 01 –01 if you wish to drive GEOS – Chem with the GEOS –5 meteorology. Please see the GEOS– Chem wiki for a more complete account of some of the issues that were encountered during GEOS –5 implementation . GEOS – 1 and GEOS– STRAT meteorology is no longer supported Wi th 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 t he 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 fol lows 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 a nthropogenic 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. Aar on 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 fo r 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 u sing the TotalView Debugger are also now included in the makefiles.

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