Difference between revisions of "Downloading GEOS-Chem data directories"

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This page describes where you can obtain the GEOS-Chem source code and required data files.
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__FORCETOC__
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'''''[[GEOS-Chem directory structure|Previous]] | [[Creating GEOS-Chem run directories|Next]] | [[Getting Started with GEOS-Chem]]'''''
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#[[Minimum system requirements for GEOS-Chem|Minimum system requirements (and software installation)]]
 +
#[[Configuring your computational environment]]
 +
#[[Downloading GEOS-Chem source code|Downloading source code]]
 +
#<span style="color:blue">'''Downloading data directories'''</span>
 +
#[[Creating GEOS-Chem run directories|Creating run directories]]
 +
#[[GEOS-Chem input files|Configuring runs]]
 +
#[[Compiling GEOS-Chem|Compiling]]
 +
#[[Running GEOS-Chem|Running]]
 +
#[[GEOS-Chem output files|Output files]]
 +
#[[Python tools for use with GEOS-Chem]]
 +
#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
 +
#[[GEOS-Chem_overview#Further_reading|Further reading]]
  
== What you need to download before you can run GEOS-Chem ==
 
  
When setting up GEOS–Chem on your system, you will need install the following components:
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This content has been migrated to the [https://geos-chem.readthedocs.io/en/latest/gcc-guide/04-data/download-data.html '''Download input data''' chapter of <tt>geos-chem.readthedocs.io</tt>].
  
#The '''GEOS–Chem source code directory'''. This is the directory where the Fortran-90 source code files (i.e. <tt>*.F</tt>, <tt>*.F90</tt> files) and <tt>Makefiles</tt> reside. Your Fortran compiler will create an executable (<tt>geos</tt>) from these source code files.
 
#A '''GEOS–Chem run directory'''. Here is where you will run the compiled GEOS–Chem executable <tt>geos</tt>. Each run directory contains:
 
##Various input files that you can modify in order to select different options for your GEOS–Chem simulation
 
##Files that define the GEOS–Chem's chemical and [[Photolysis mechanism|photolysis mechanisms]]
 
##"Restart files" that hold the initial conditions for your GEOS–Chem simulation
 
#The '''GEOS–Chem shared data directories. This is the directory tree where the following types of data are stored:
 
##[[Overview_of_GMAO_met_data_products|Meteorological data]] (a.k.a. the "met fields) used to drive GEOS–Chem
 
##[[HEMCO_data_directories|Emissions inventories]] for the [[HEMCO|HEMCO emissions component]]
 
##Scale factors to used to scale emissions from a base year to a given year
 
##Oxidant (OH, O3) concentrations for both [[GEOS-Chem_chemistry_mechanisms#NOx-Ox-hydrocarbon-aerosol_chemistry_and_variants|full-chemistry]] and [[GEOS-Chem_chemistry_mechanisms#Specialty_simulations|specialty simulations]]
 
##Other GEOS–Chem specific data files.
 
#A '''netCDF library installation'''.  Starting with [[GEOS-Chem v9-01-03]], the model can read data files in netCDF format.  Eventually, we shall replace all of GEOS-Chem's input and output files from binary punch file format to netCDF format. We are doing this as part of our [[Grid-independent GEOS-Chem]] project, which seeks to interface GEOS-Chem with the [http://gmao.gsfc.nasa.gov/systems/geos5/ NASA GEOS&ndash;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 [[Version control with Git|Git version control software]].
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----
 
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'''''[[GEOS-Chem directory structure|Previous]] | [[Creating GEOS-Chem run directories|Next]] | [[Getting Started with GEOS-Chem]]'''''
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 IT staff) 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, [[#Using wget to download files|wget]], or similar file transfer programs. [[Minimum_system_requirements_for_GEOS-Chem#How_much_disk_space_will_I_need_for_GEOS-Chem.3F|''Minimum system requirements for GEOS-Chem]] wiki page]] for more information on  typical disk space requirements for GEOS-Chem.
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+
If your computer system already has a pre-built netCDF library installed, we recommend that you use that.  Check with your IT staff about how to load the netCDF libraries into your Unix environment.  (Usually this is done with the <tt>module</tt> command, if that exists on your system.)  But if you don't have a pre-built netCDF library on your system, you (or your IT staff) can use our [[Installing libraries for GEOS-Chem|<tt>GEOS-Chem-Libraries</tt> netCDF installer]] installer to build the libraries.
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+
For complete downloading instructions, please see:
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+
# GEOS-Chem User's Guide: [http://acmg.seas.harvard.edu/geos/doc/man/chapter_2.html#DownCode Chapter 2.2: Downloading the GEOS-Chem source code]
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# GEOS-Chem wiki: [[Creating_GEOS-Chem_run_directories]]
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# GEOS-Chem wiki: [[#Using_wget_to_download_the_shared_data_directories|Using wget to download the shared data directories]]
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# GEOS-Chem wiki: [[Installing libraries for GEOS-Chem]]
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For more information on the files contained in each of these directories, please see:
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# GEOS-Chem User's Guide: [http://acmg.seas.harvard.edu/geos/doc/man/chapter_3.html Chapter 3: Compiling the GEOS-Chem source code]
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# GEOS-Chem User's Guide: [http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html Chapter 5: GEOS-Chem run directories]
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# GEOS-Chem wiki: [[Downloading_GEOS-Chem_source_code_and_data#Directories_for_met_fields_and_emissions_data|Directories for met fields and emissions data]]
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# GEOS-Chem wiki: [[HEMCO data directories]]
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+
--[[User:Melissa Payer|Melissa Sulprizio]] 16:43, 8 April 2015 (EDT)
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+
== Shared data directory archives ==
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+
There are currently two data archives from which you may download the GEOS–Chem shared data directories:
+
 
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#[[#Harvard data directory archive|Harvard data directory archive]] (<tt>ftp.as.harvard.edu</tt>)
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#[[#Dalhousie data directory archive|Dalhousie data directory archive]] (<tt>rain.ucis.dal.ca</tt>)
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+
The Dalhousie archive is not as comprehensive as the Harvard archive. However, the Dalhousie archive stores data files for the various nested grids that are not available on the Harvard archive.
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+
--[[User:Bmy|Bob Y.]] 14:19, 16 January 2014 (EST)
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+
=== Harvard data directory archive ===
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You can access the primary GEOS-Chem data download site via anonymous FTP at:
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ftp ftp.as.harvard.edu
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+
We recommend that you use the [[#Using wget to download files|wget utility]] to download these directories instead of anonymous FTP.  Wget allows you to download multiple directories at once, with a command such as this one:
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+
<nowiki>wget -r -nH --cut-dirs=4 "ftp://ftp.as.harvard.edu/DIRECTORY_NAME"</nowiki>
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+
See the [[#Directories for met fields and emissions data|tables below]] for the <tt>DIRECTORY_NAME</tt> options.
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+
==== Downtime ====
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+
The Harvard FTP archive will be unavailable during the weekly maintenance period every Monday between 7-10 AM ET.  Please plan your data downloads accordingly.
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+
==== Directories for met fields and emissions data ====
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+
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; "><strong>
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If you are downloading the GEOS-FP met data, then please note the following:
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#Make sure you only take the files named <tt>GEOSFP*</tt>.  Met field files named <tt>GEOS572*</tt> are obsolete and have been replaced by the <tt>GEOSFP*</tt> files.
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#You will need to download the "CN" (constant) data files for each horizontal grid that you are using.  These are timestamped for 2011/01/01 and are found in these data directories of <tt>ftp.as.harvard.edu</tt>:
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#*<tt>gcgrid/geos-chem/data/GEOS_4x5.d/GEOS_FP/2011/01/GEOSFP.20110101.4x5.nc</tt>
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#*<tt>gcgrid/geos-chem/data/GEOS_2x25.d/GEOS_FP/2011/01/GEOSFP.20110101.2x25.nc</tt>
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#*<tt>gcgrid/geos-chem/data/GEOS_0.25x0.3125_EU.d/GEOS_FP/2011/01/GEOSFP.20110101.0.25x0.3125.NA.nc</tt>
+
 
+
(Bob Yantosca, 05 Feb 2014)
+
</strong></div>
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+
The path <tt>gcgrid/geos-chem/data/ExtData/</tt> (also reachable as <tt>gcgrid/data/ExtData/</tt>) is the root path under which the [http://acmg.seas.harvard.edu/geos/doc/man/chapter_4.html GEOS–Chem shared data directories] reside.  This is where you will find the GEOS-Chem met fields and emissions data.
+
 
+
Starting with [[GEOS-Chem v10-01]], the data directory naming structure has changed since we no longer need to store emissions data on multiple grids. All of the GEOS-Chem data directories are now subdirectories of the '''ExtData''' directory. For more information, please see our [[Setting_up_the_ExtData_directory|''Setting up the ExtData directory'' wiki page]].
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+
{| border=1 cellpadding=5 cellspacing=0
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|-bgcolor="#CCCCCC"
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!width="450px"|Directory
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!width="700px"|Description                               
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|-
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|<tt>gcgrid/geos-chem/data/ExtData/</tt>                             
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|Root Data Directory
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|-                         
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|<tt>gcgrid/geos-chem/data/ExtData/CHEM_INPUTS/</tt>                     
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|Contains non-emissions data for GEOS-Chem chemistry modules
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|-                         
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|<tt>gcgrid/geos-chem/data/ExtData/HEMCO/</tt>                 
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|Contains [[HEMCO_data_directories|emissions data]] for the [[HEMCO|HEMCO emissions component]]
+
|-bgcolor="#CCCCCC"                       
+
!0.25&deg; x 0.3125&deg; Data Directories                 
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!Description
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|-                       
+
|<tt>gcgrid/geos-chem/data/ExtData/GEOS_0.25x0.3125_NA.d/GEOS_FP/YYYY/MM/</tt>         
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|[[GEOS-FP]] met data for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_NA 1/4&deg; x 5/16&deg; North America] nested grid simulations               
+
|-bgcolor="#CCCCCC"                       
+
!0.5&deg; x 0.666&deg; Data Directories                 
+
!Description
+
|-                                                 
+
|<tt>gcgrid/geos-chem/data/ExtData/GEOS_0.5x0.666_CH/GEOS_5/YYYY/MM/</tt>
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|[[GEOS-5]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_CH 1/2&deg; x 2/3&deg; China] nested grid simulations
+
|-                                                 
+
|<tt>gcgrid/geos-chem/data/ExtData/GEOS_0.5x0.666_NA/GEOS_5/YYYY/MM/</tt>         
+
|[[GEOS-5]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_NA 1/2&deg; x 2/3&deg; North America] nested grid simulations 
+
|-bgcolor="#CCCCCC"                       
+
!2&deg; x 2.5&deg; Data Directories               
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!Description
+
|-
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|<tt>gcgrid/geos-chem/data/ExtData/GEOS_2x2.5/GEOS_4_v4/YYYY/MM/</tt> 
+
|[[GEOS-4]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-
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|<tt>gcgrid/geos-chem/data/ExtData/GEOS_2x2.5/GEOS_5/YYYY/MM</tt>
+
|[[GEOS-5]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-
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|<tt>gcgrid/geos-chem/data/ExtData/GEOS_2x2.5/GEOS_FP/YYYY/MM</tt>
+
|[[GEOS-FP]] met data for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-
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|<tt>gcgrid/geos-chem/data/ExtData/GEOS_2x2.5/MERRA/YYYY/MM</tt>
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|[[MERRA]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-bgcolor="#CCCCCC"                       
+
!4&deg; x 5&deg; Data Directories               
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!Description
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|-
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|<tt>gcgrid/geos-chem/data/ExtData/GEOS_4x5/GEOS_4_v4/YYYY/MM/</tt> 
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|[[GEOS-4]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
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|-
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|<tt>gcgrid/geos-chem/data/ExtData/GEOS_4x5/GEOS_5/YYYY/MM/</tt> 
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|[[GEOS-5]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
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|-
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|<tt>gcgrid/geos-chem/data/ExtData/GEOS_4x5/GEOS_FP/YYYY/MM/</tt> 
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|[[GEOS-FP]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
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|-
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|<tt>gcgrid/geos-chem/data/ExtData/GEOS_4x5/MERRA/YYYY/MM/</tt> 
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|[[MERRA]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
+
|}
+
 
+
Please view the [http://acmg.seas.harvard.edu/geos/geos_sim.html catalog of met data at the Harvard archive] to determine if the data period you wish to download is available.
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] 14:48, 8 April 2015 (EDT)
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+
==== Directories for 1-month and 1-year benchmarks ====
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You can find output files and evaluation plots for 1-month and 1-year benchmark simulations in the following directories:
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{| border=1 cellpadding=5 cellspacing=0
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|-bgcolor="#CCCCCC"                       
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!width="450px"|Directory                 
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!width="700px"|Description
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|-
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|<tt>gcgrid/geos-chem/1mo_benchmarks/</tt>
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|Contains the following types of data from the [http://acmg.seas.harvard.edu/geos/geos_benchmark.html 1-month benchmark simulations] that are used to evaluate GEOS-Chem:
+
*Restart files
+
*Model output (bpch and netCDF formats)
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*Log files
+
*Input files
+
*Evaluation plots
+
|-
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|<tt>gcgrid/geos-chem/1yr_benchmarks/</tt>                       
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|Contains the following types of data from the [http://acmg.seas.harvard.edu/geos/geos_1yr_plots.html 1-year benchmarks] used to evaluate GEOS-Chem:
+
*Restart files
+
*Model output (bpch and netCDF formats)
+
*Log files
+
*Input files
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*Evaluation plots
+
|}
+
 
+
--[[User:Bmy|Bob Y.]] 14:22, 16 January 2014 (EST)
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+
==== Data directories to ignore ====
+
 
+
You can ignore the contents of these directories.  Most of these contain obsolete data that are only preserved for archival purposes.
+
 
+
{| border=1 cellpadding=5 cellspacing=0
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|-bgcolor="#CCCCCC"
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!width="450px"|Directory         
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!width="700px"|Description
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|-
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|<tt>gcgrid/geos-chem/dao/</tt>
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|Internal use only
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|-
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|<tt>gcgrid/geos-chem/beta_releases</tt> 
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|Contains TARBALL files with source code and run directories for GEOS-Chem beta versions prior to v8-03-01.  We now use Git to manage the GEOS-Chem source code & run directories.
+
|-                         
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|<tt>gcgrid/geos-chem/data/GEOS_0.25x0.3125_NA/</tt>
+
|Emissions etc. files for 1/4&deg; x 5/16&deg; North America nested grid simulations. We now read emission data at its native resolution from the [[HEMCO data directories]].
+
|-
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|<tt>gcgrid/geos-chem/data/GEOS_0.25x0.3125_SEAC4RS</tt>         
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|Emissions etc. data for the 0.25&deg; x 0.3125&deg; simulation on the SE Asia grid.  This was created when the SEAC4RS mission was scheduled to occur over Thailand.  This is now obsolete.
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|-
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|<tt>gcgrid/geos-chem/data/GEOS_0.25x0.3125_SEAC4RS/GEOS_5.7/YYYY/MM</tt>         
+
|Met field data for the 0.25&deg; x 0.3125&deg; simulation on the SE Asia grid.  This was created when the SEAC4RS mission was scheduled to occur over Thailand.  This is now obsolete.
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_0.5x0.666_CH/</tt>
+
|Emissions etc. files for 1/2&deg; x 2/3&deg; China nested grid simulations. We now read emission data at its native resolution from the [[HEMCO data directories]].
+
|-                         
+
|<tt>gcgrid/geos-chem/data/GEOS_0.5x0.666_NA/</tt>
+
|Emissions etc. files for 1/2&deg; x 2/3&deg; North America nested grid simulations. We now read emission data at its native resolution from the [[HEMCO data directories]].
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_1x1_CH/</tt>                 
+
|Emissions etc. data for the China/SE Asia 1&deg; x 1&deg; simulation.  This simulation has been superseded by the GEOS-5 0.5&deg; x 0.666&deg; nested simulation.
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_1x1_CH/GEOS_3/YYYY/MM/</tt>         
+
|GEOS-3 met data for the China/SE Asia 1&deg; x 1&deg; nested grid simulation  This simulation has been superseded by the GEOS-5 0.5&deg; x 0.666&deg; nested simulation.
+
|- 
+
|<tt>gcgrid/geos-chem/data/GEOS_1x1_NA/</tt>     
+
|Emissions etc. data for the North American 1&deg; x 1&deg; nested grid simulation. This simulation has been superseded by the GEOS-5 0.5&deg; x 0.666&deg; nested simulation.
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_1x1_NA/GEOS_3/YYYY/MM/</tt>         
+
|GEOS-3 met data for the North American 1&deg; x 1&deg; nested grid simulation. This simulation has been superseded by the GEOS-5 0.5&deg; x 0.666&deg; nested simulation.
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_2x2.5/</tt>                 
+
|Emissions etc. data for 2&deg; x 2.5&deg; global simulations. We now read emission data at its native resolution from the [[HEMCO data directories]].
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_2x2.5/GEOS_4_flk/YYYY/MM/</tt>
+
|GEOS-4 met data for 2&deg; x 2.5&deg; global simulations (1st-look).  These data were only used for the ITCT/2k2 campaing.  They have been replaced by the data in GEOS_4_v4.
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_4x5/</tt>               
+
|Emissions etc. data for GEOS-chem 4&deg; x 5&deg; global simulations. We now read emission data at its native resolution from the [[HEMCO data directories]].
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_4x5/GEOS_4_flk/YYYY/MM/</tt> 
+
|GEOS-4 met data for 4&deg; x 5&deg; global simulations (1st-look).  These data were only used for the ITCT/2k2 campaing.  They have been replaced by the data in GEOS_4_v4.
+
|-                         
+
|<tt>gcgrid/geos-chem/data/GEOS_MEAN/</tt>                 
+
|Contains P(O3), L(O3) and mean OH data for offline simulations. We now read this data from the [[HEMCO data directories]].
+
|-
+
|<tt>gcgrid/geos-chem/data/GEOS_NATIVE/</tt>
+
|1&deg; x 1&deg; and higher resolution emissions etc. data for use with GEOS-Chem simulations. We now read emission data at its native resolution from the [[HEMCO data directories]].
+
|-                         
+
|<tt>gcgrid/geos-chem/data/aerosol_optics/</tt>                     
+
|Contains versions of the <tt>jv_spec_aod.dat</tt> files which specify the [[Aerosol optical properties|aerosol optical properties]] used for the AOD diagnostics for the [[Photolysis mechanism|FAST-J and FAST-JX photolysis mechanisms]]. We now read this data from <tt>gcgrid/geos-chem/data/ExtData/CHEM_INPUTS/</tt>.
+
|-     
+
|<tt>gcgrid/geos-chem/downloads/</tt>
+
|Formerly used to contain the following code packages:                   
+
*Code to read HDF4 and HDF4-EOS data files
+
*Code to read HDF5 and HDF5-EOS data files
+
*Code to read netCDF data files
+
*Code to process GEOS-5 met data
+
These are now maintained as Git repositories.  Contact [mailto:yantosca@seas.harvard.edu Bob Yantosca] for more information.
+
|-     
+
|<tt>gcgrid/geos-chem/NRT/</tt>                             
+
|Contains some data from the GEOS-Chem near-real-time simulations for ICARTT/ITCT 2k2.  We maintain this directory for archival purposes.  Not all data have been preserved.
+
|-     
+
|<tt>gcgrid/geos-chem/NRT-ARCTAS/</tt>                             
+
|Contains output from the [http://coco.atmos.washington.edu/cgi-bin/ion-p?page=arctas.ion GEOS-Chem Near-Real-Time simulations for ARCTAS].  We maintain this directory for archival purposes.
+
|-
+
|<tt>gcgrid/geos-chem/mean_OH/</tt>
+
|Directory containing 3-D mean OH fields archived from previous GEOS-Chem simulations. We now read this data from the [[HEMCO data directories]].
+
|-
+
|<tt>gcgrid/geos-chem/patches/</tt>
+
|Directory that formerly contained bug-fix software patches (if necessary).  We now use Git to issue GEOS-Chem software patches.
+
|-
+
|<tt>gcgrid/geos-chem/public_releases/</tt>
+
|Contains TARBALL files with source code and run directories for GEOS-Chem public versions prior to v8-03-01.  We now use Git to manage the GEOS-Chem source code & run directories.
+
|}
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] 15:00, 8 April 2015 (EDT)
+
 
+
=== Dalhousie data directory archive ===
+
 
+
The GEOS-Chem data and meteorological fields used by Dalhousie University are also available via anonymous FTP from:
+
 
+
ftp rain.ucis.dal.ca
+
 
+
We recommend that you use the [[#Using wget to download files|wget utility]] to download these directories instead of anonymous FTP.  Wget allows you to download multiple directories at once.  The Wget command will take the form:
+
 
+
<nowiki>wget -r -nH --cut-dirs=4 "ftp://rain.ucis.dal.ca/DIRECTORY_NAME"</nowiki>
+
 
+
See the [[#Directory structure|table below]] for the <tt>DIRECTORY_NAME</tt> options.
+
 
+
==== Directory structure ====
+
 
+
<div style="color: #aa0000; background: #eeeeee;border: 3px solid red; padding: 1em; margin: auto; width: 90%; "><strong>
+
If you are downloading the GEOS-FP met data, then please note the following:
+
 
+
#Make sure you only take the files named <tt>GEOSFP*</tt>.  Met field files named <tt>GEOS572*</tt> are obsolete and have been replaced by the <tt>GEOSFP*</tt> files.
+
#You will need to download the "CN" (constant) data files for each horizontal grid that you are using.  These are timestamped for 2011/01/01 and are found in these data directories of <tt>rain.ucis.dal.ca</tt>:
+
#*<tt>ctm/GEOS_4x5.d/GEOS_FP/2011/01/GEOSFP.20110101.4x5.nc</tt>
+
#*<tt>ctm/GEOS_2x25.d/GEOS_FP/2011/01/GEOSFP.20110101.2x25.nc</tt>
+
#*<tt>ctm/GEOS_0.25x0.3125_CH.d/GEOS_FP/2011/01/GEOSFP.20110101.0.25x0.3125.CH.nc</tt>
+
#*<tt>ctm/GEOS_0.25x0.3125_EU.d/GEOS_FP/2011/01/GEOSFP.20110101.0.25x0.3125.NA.nc</tt>
+
#*<tt>ctm/GEOS_0.25x0.3125_NA.d/GEOS_FP/2011/01/GEOSFP.20110101.0.25x0.3125.EU.nc</tt>
+
#*<tt>ctm/GEOS_0.25x0.3125_SE.d/GEOS_FP/2011/01/GEOSFP.20110101.0.25x0.3125.SE.nc</tt>
+
 
+
(Bob Yantosca, 05 Feb 2014)
+
</strong></div>
+
 
+
The Dalhousie archive overlaps with many of the above directories from the Harvard site, but it is not as extensive.  This site, however, hosts several nested grid data sets that are not archived at Harvard.
+
 
+
{| border=1 cellpadding=5 cellspacing=0
+
|-bgcolor="#CCCCCC"
+
!width="450px"|0.25&deg; x 0.3125&deg; Data Directories                         
+
!width="700px"|Description                               
+
|-
+
|<tt>ctm/GEOS_0.25x0.3125_CH.d/GEOS_FP/YYYY/MM</tt>                             
+
|GEOS-FP met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_CH 1/4&deg; x 5/16&deg; China] nested grid simulations
+
|-                         
+
|<tt>ctm/GEOS_0.25x0.3125_EU.d/GEOS_FP/YYYY/MM</tt>                     
+
|GEOS-FP met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_EU 1/4&deg; x 5/16&deg; Europe] nested grid simulations
+
|-
+
|<tt>ctm/GEOS_0.25x0.3125_NA.d/GEOS_FP/YYYY/MM</tt>                             
+
|GEOS-FP met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_NA 1/4&deg; x 5/16&deg; North America] nested grid simulations
+
|-                         
+
|<tt>ctm/GEOS_0.25x0.3125_SE.d/GEOS_FP/YYYY/MM</tt>
+
|GEOS-FP met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_025_SE 1/4&deg; x 5/16&deg; SE Asia] nested grid simulations
+
|- bgcolor="#CCCCCC"
+
! 0.5&deg; x 0.666&deg; Data Directories                         
+
! Description                               
+
|-
+
|<tt>ctm/GEOS_0.5x0.666_CH/</tt>                             
+
|Emissions etc. files for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_CH 1/2&deg; x 2/3&deg; China] nested grid simulations
+
|-                         
+
|<tt>ctm/GEOS_0.5x0.666_CH.d/GEOS_5/YYYY/MM</tt>                     
+
|GEOS-5 met field files for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_CH 1/2&deg; x 2/3&deg; China] nested grid simulations
+
|-
+
|<tt>ctm/GEOS_0.5x0.666_EU/</tt>                             
+
|Emissions etc. files for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_EU 1/2&deg; x 2/3&deg; Europe] nested grid simulations
+
|-                         
+
|<tt>ctm/GEOS_0.5x0.666_EU.d/GEOS_5/YYYY/MM</tt>                     
+
|GEOS-5 met field files for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_EU 1/2&deg; x 2/3&deg; Europe] nested grid simulations
+
|-
+
|<tt>ctm/GEOS_0.5x0.666_NA/</tt>                 
+
|Emissions etc. files for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_NA 1/2&deg; x 2/3&deg; North America] nested grid simulations
+
|-
+
|<tt>ctm/GEOS_0.5x0.666_NA.d/GEOS_5/YYYY/MM</tt>         
+
|GEOS-5 met field files for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_05_NA 1/2&deg; x 2/3&deg; North America] nested grid simulations
+
|-bgcolor="#CCCCCC"
+
!2&deg; x 2.5&deg; Data Directories
+
!Description
+
|- 
+
|<tt>ctm/GEOS_2x2.5/</tt>               
+
|Emissions etc. files for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-
+
| <tt>ctm/GEOS_2x2.5.d/GEOS_4_v4/YYYY/MM/</tt>         
+
|[[GEOS-4]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-
+
|<tt>ctm/GEOS_2x2.5.d/GEOS_5/YYYY/MM</tt>         
+
|[[GEOS-5]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-
+
|<tt>ctm/GEOS_2x2.5.d/GEOS_FP/YYYY/MM</tt>         
+
|[[GEOS-FP]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-
+
|<tt>ctm/GEOS_2x2.5.d/MERRA/YYYY/MM</tt>         
+
|[[MERRA]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GMAO_2x25 2&deg; x 2.5&deg;] global simulations
+
|-bgcolor="#CCCCCC"
+
!4&deg; x 5&deg; Data Directories
+
!Description
+
|- 
+
|<tt>ctm/GEOS_4x5/</tt>               
+
|Emissions etc. files for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
+
|-
+
|<tt>ctm/GEOS_4x5.d/GEOS_4_v4/YYYY/MM</tt>         
+
|[[GEOS-4]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
+
|-
+
|<tt>ctm/GEOS_4x5.d/GEOS_5/YYYY/MM</tt>         
+
|[[GEOS-5]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
+
|-
+
|<tt>ctm/GEOS_4x5.d/GEOS_FP/YYYY/MM</tt>         
+
|[[GEOS-FP]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
+
|-
+
| <tt>ctm/GEOS_4x5.d/MERRA/YYYY/MM</tt>         
+
|[[MERRA]] met fields for [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#GEOS_4x5 4&deg; x 5&deg;] global simulations
+
|}
+
 
+
A catalog of available data may be found [http://fizz.phys.dal.ca/~atmos/martin/?page_id=209 HERE].
+
 
+
--[[User:Lizzie Lundgren|Lizzie Lundgren]] ([[User talk:Lizzie Lundgren|talk]]) 15:48, 16 June 2015 (UTC)
+
 
+
== Using wget to download the shared data directories ==
+
 
+
Probably the simplest way to download the GEOS-Chem emissions and met field data is to use the Unix <tt>wget</tt> utility.  This allows you to download multiple files and directories at a time.
+
 
+
The <tt>wget</tt> utility is free and open-source (published by GNU), and comes standard with pretty much all builds of *nix (Linux, Ubuntu, Fedora, Centos, etc.).  You can check out the [http://www.editcorp.com/Personal/Lars_Appel/wget/wget_1.html user manual] for more information.
+
 
+
=== Syntax ===
+
 
+
Most of the time, the syntax you will use to download multiple directories is as follows:
+
 
+
Downloading data from Harvard:
+
 
+
<nowiki>wget -r -nH "ftp://ftp.as.harvard.edu/DIRECTORY_NAME/"</nowiki>
+
 
+
Downloading data from Dalhousie:
+
 
+
<nowiki>wget -r -nH "ftp://rain.ucis.dal.ca/DIRECTORY_NAME/"</nowiki>
+
 
+
The options to <tt>wget</tt> are as follows:
+
 
+
-r  Specifies recursive directory transfer (i.e. will download all subdirectories)
+
-nH  Will store all directories and subdirectories in <tt>DIRECTORY_NAME</tt>, not <tt>ftp.as.harvard.edu/DIRECTORY_NAME</tt>
+
 
+
If you wish to trim the name of the downloaded directory (i.e., so it downloads as <tt>DIRECTORY_NAME</tt>, not <tt>pub/geos-chem/data/DIRECTORY_NAME</tt>), then use the <tt>--cut-dirs</tt> option:
+
+
<nowiki>wget -r -nH --cut-dirs=X "ftp://ftp.as.harvard.edu/DIRECTORY_NAME/"</nowiki>
+
 
+
where <tt>X</tt> is the number of directories to trim. 
+
 
+
'''''NOTE: The URL must be enclosed in quotes for file transfer to occur. If you omit the quotes then <tt>wget</tt> will just return a directory listing in a file named <tt>index.html</tt> without any files being downloaded.'''''
+
 
+
=== Examples ===
+
 
+
1. Download all available GEOS-Chem 2&deg; x 2.5&deg; met field data files in the <tt>GEOS_2x2.5.d</tt> directory structure:
+
 
+
<nowiki>wget -r -nH "ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_2x2.5.d/" &</nowiki>
+
 
+
Due to the huge volume of data involved, this is not recommended, as the file downloads may swamp your system.  It's better to do download the data smaller chunks. For example:
+
 
+
2. Download all GEOS-5 met data at 2&deg; x 2.5&deg; resolution:
+
 
+
<nowiki>wget -r -nH "ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_2x2.5.d/GEOS_5/" &</nowiki>
+
 
+
It may even be better to download one year at a time.:
+
 
+
3. Download all GEOS-5 met data at 2&deg; x 2.5&deg; resolution for 2008:
+
 
+
<nowiki>wget -r -nH "ftp://ftp.as.harvard.edu/gcgrid/geos-chem/data/GEOS_2x2.5.d/GEOS_5/2008/" &</nowiki>
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] 16:57, 8 April 2015 (EDT)
+
 
+
=== Obtain only updated files ===
+
 
+
'''''[mailto:psk9@duke.edu Prasad Kasibhatla] wrote:'''''
+
:Maybe this is common knowledge, but I just discovered that using the <tt>-N</tt> option in wget ensures that only files with newer timestamps than what resides on my local machines are downloaded - found this very useful to update my shared data directories.
+
 
+
--[[User:Melissa Payer|Melissa Payer]] 10:39, 1 June 2012 (EDT)
+
 
+
 
+
 
+
== Downloading the shared data directories via anonymous FTP ==
+
 
+
You can also download the shared data directories via anonymous FTP:
+
 
+
ftp ftp.as.harvard.edu
+
cd gcgrid/geos-chem/data/ExtData/GCAP_4x5
+
cd gcgrid/geos-chem/data/ExtData/GEOS_0.25x0.3125_CH
+
cd gcgrid/geos-chem/data/ExtData/GEOS_0.25x0.3125_NA
+
cd gcgrid/geos-chem/data/ExtData/GEOS_0.5x0.666_CH
+
cd gcgrid/geos-chem/data/ExtData/GEOS_0.5x0.666_NA
+
cd gcgrid/geos-chem/data/ExtData/GEOS_2x2.5
+
cd gcgrid/geos-chem/data/ExtData/GEOS_4x5
+
cd gcgrid/geos-chem/data/ExtData/GEOS_MEAN
+
cd gcgrid/geos-chem/data/ExtData/GEOS_NATIVE
+
cd gcgrid/geos-chem/data/ExtData/HEMCO
+
cd gcgrid/geos-chem/data/ExtData/CHEM_INPUTS
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] 16:52, 8 April 2015 (EDT)
+
 
+
== Downloading the HEMCO data directories ==
+
 
+
The [[GEOS-Chem Support Team]] has created a package called '''hemco_data_download'''.  With this package, you can download the various emissions inventories and related data files for HEMCO to your own disk server.  For complete instructions, please see our [[HEMCO_data_directories#Downloading_the_HEMCO_data_directories|''HEMCO data directories'' wiki page]]
+
 
+
--[[User:Melissa Payer|Melissa Sulprizio]] 16:52, 8 April 2015 (EDT)
+
 
+
== For more information ==
+
 
+
=== For GCAP users ===
+
 
+
For those users who wish to run GEOS-Chem with the [http://acmg.seas.harvard.edu/gcap/ GISS/GCAP] met fields, please contact [mailto:mickley@fas.harvard.edu Loretta Mickley].
+
 
+
--[[User:Bmy|Bob Y.]] 09:52, 8 March 2010 (EST)
+
 
+
=== Question about directory structure ===
+
 
+
'''''Shanna Shaked wrote:'''''
+
 
+
:We are working again on trying to run GEOS-Chem.  However, we are encountering some errors that may be due to the directory structure.  We find a discrepancy between the directory structure described in the GEOS-Chem manual and that available on the ftp site.
+
 
+
:The GEOS-Chem manual describes a directory structure of:
+
+
    data/GEOS_4x5/GEOS_5/YYYY/MM
+
 
+
:However, on the ftp site, we find a directory structure with an extra '.d':
+
 
+
    data/GEOS_4x5.d/GEOS_5/YYYY/MM
+
 
+
:(the <tt>GEOS_5</tt> folder is in <tt>GEOS_4x5.d</tt> rather than <tt>GEOS_4x5</tt>).  There does exist a  <tt>GEOS_4x5</tt> that contains many of the emissions data, but does not contain <tt>GEOS_5</tt>.
+
 
+
:If we leave the structure as is, and enter <tt>../data/GEOS_4x5/</tt> as our root data directory in <tt>input.geos</tt>, we get a file not found error when it looks for <tt>GEOS_5</tt> within this directory (obviously).
+
 
+
:If we instead enter <tt>../data/GEOS_4x5.d</tt> as our root data directory, we get a file not found error when the program looks for emissions within this directory (lightning NOx emissions, in this case).
+
 
+
:QUESTION: To solve this problem, we have moved the <tt>GEOS_5</tt> folder into the <tt>GEOS_4x5</tt> directory.  [Is this] okay?
+
 
+
'''''[[User:Bmy|Bob Yantosca]] replied:'''''
+
 
+
:The only difference on our system between e.g. <tt>GEOS_4x5</tt> and <tt>GEOS_4x5.d</tt> is that our sysadmin (Jack Yatteau) set up the ".d" directories separately so that they only contain met data (which is much larger than the emissions etc. data).  That way he could separate the disks that just had met data from the disk that have the emissions data to facilitate our configuration here.  There are symbolic links from <tt>GEOS_4x5</tt> to <tt>GEOS_4x5.d</tt> etc. (i.e. the directory <tt>GEOS_4x5/GEOS_5</tt> is actually a symbolic link to the corresponding directory in <tt>GEOS_4x5.d/GEOS_5/</tt> and etc. for the other met field resolutions & directories). 
+
 
+
:You don't necessarily have to do this on your end, but this is what we did here.  You can just make the <tt>GEOS_4x5/GEOS_5</tt> etc. real subdirectories and not symbolic links and store the data there.  The solution you picked above is OK.
+
 
+
:Also to facilitate FTP file transfer, you could do the following:
+
:* Write a script or an FTP macro
+
:* Use a 3rd-party GUI program like FireFTP in Mozilla Firefox.
+
:* Or even better yet, use the Unix <tt>wget</tt> utility (see below)
+
 
+
:Each user is responsible for their own file transfers.
+
 
+
--[[User:Bmy|Bob Y.]] 11:04, 5 February 2009 (EST)
+

Latest revision as of 14:56, 4 August 2022

Previous | Next | Getting Started with GEOS-Chem

  1. Minimum system requirements (and software installation)
  2. Configuring your computational environment
  3. Downloading source code
  4. Downloading data directories
  5. Creating run directories
  6. Configuring runs
  7. Compiling
  8. Running
  9. Output files
  10. Python tools for use with GEOS-Chem
  11. Coding and debugging
  12. Further reading


This content has been migrated to the Download input data chapter of geos-chem.readthedocs.io.



Previous | Next | Getting Started with GEOS-Chem