Difference between revisions of "GEOS-Chem restart files"

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This page contains information about files produced by GEOS-Chem simulations, including diagnostic data and restart files used for initial conditions.
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__FORCETOC__
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'''''[[GEOS-Chem log files|Previous]] | [[GEOS-Chem diagnostic output files|Next]] | [[Getting Started with GEOS-Chem]]'''''
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#[[Minimum system requirements for GEOS-Chem|Minimum system requirements (and software installation)]]
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#[[Configuring your computational environment]]
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#[[Downloading GEOS-Chem source code|Downloading source code]]
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#[[Downloading GEOS-Chem data directories|Downloading data directories]]
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#[[Creating GEOS-Chem run directories|Creating run directories]]
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#[[GEOS-Chem configuration files|Configuring runs]]
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#[[Compiling GEOS-Chem|Compiling]]
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#[[Running GEOS-Chem|Running]]
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#[[GEOS-Chem output files|Output files]]
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#*[[GEOS-Chem log files|Log files]]
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#*<span style="color:blue">'''Restart files'''</span>
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#*[[GEOS-Chem diagnostic output files|Diagnostic output files]]
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#[[Python tools for use with GEOS-Chem]]
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#[[GEOS-Chem_coding_and_debugging|Coding and debugging]]
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#[[GEOS-Chem_overview#Further_reading|Further reading]]
  
== Overview ==
 
  
GEOS-Chem restart files contain the initial conditions for a GEOS-Chem simulation. There are two restart files for GEOS-Chem:
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This content has been migrated to the [https://geos-chem.readthedocs.io/en/latest/gcc-guide/04-data/restart-files.html '''Restart files''' chapter of <tt>geos-chem.readthedocs.io</tt>].
  
{| border=1 cellspacing=0 cellpadding=5
 
|-bgcolor="#CCCCCC"
 
!width="325px"|File(s)
 
!width="75px"|Format
 
!width="500px"|Description
 
!width="200px"|Notes
 
  
|-valign="top"
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|[[#GEOS-Chem restart files|<tt>GEOSChem.Restart.YYYYMMDD_hhmmz.nc4</tt>]]
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'''''[[GEOS-Chem log files|Previous]] | [[GEOS-Chem diagnostic output files|Next]] | [[Getting Started with GEOS-Chem]]'''''
|netCDF
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|'''The GEOS-Chem restart file.''' Contains species concentrations that are read in at simulation startup. 
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GEOS-Chem writes a restart file at the end of each simulation.  This allows a long simulation to be split into several individal run stages..
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For example, the restart file that was created at 00:00 UTC on August 1, 2016 is named: <tt>GEOSChem.Restart.20160801_0000z.nc4</tt>. The z indicates "Zulu" or "Z" time, which is another name for UTC.
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|-valign="top"
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|<tt>HEMCO_restart.YYYYMMDDhhmm.nc</tt>
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|netCDF
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|'''The HEMCO restart file'''.  The [[HEMCO|HEMCO emissions component]] will save out certain quantities (mostly pertaining to soil NOx and biogenic emissions) in order to facilitate long GEOS-Chem simulations with several run stages. 
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|}
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When you run a GEOS-Chem simulation, it will write new GEOS-Chem restart files at the intervals you specify in <tt>HISTORY.rc</tt>. New HEMCO restart files are written with frequency configured in <tt>HEMCO_Config.rc</tt> if HEMCO is used in your simulation.
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[[Creating_GEOS-Chem_run_directories|GEOS-Chem run directories]] are configured to use initial GEOS-Chem restart files in [[Introduction_to_netCDF|netCDF format]]. These files are available for download at:
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ftp://ftp.as.harvard.edu/gcgrid/data/ExtData/GEOSCHEM_RESTARTS/
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<span style="color:red">'''''CAVEAT: The initial restart files  do not reflect the actual atmospheric state and should only be used to "spin up" the model. In other words, they should be used as initial values in an initialization simulation to generate more accurate initial conditions for your production runs.'''''</span>
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Doing a one year spin up is usually sufficient; however, we recommend ten years for ozone, carbon dioxide, and methane simulations, and four years for radon-lead-beryllium simulations. If you are in doubt about how long your spin up should be for your simulation, we recommend contacting the [http://acmg.seas.harvard.edu/geos/geos_working_groups.html GEOS-Chem Working Group] that specializes in your area of research.
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You may spin up the model starting at any year for which there is met data, but you should always start your simulations at the month and day corresponding to the restart file to more accurately capture seasonal variation. If you want to start your production run at a specific date, we recommend doing a spin up for the appropriate number of years plus the number of days needed to reach your ultimate start date. For example, if you want to do a production simulation starting on 12/1/13, you could spin up the model for one year using the initial GEOS-FP restart file dated 7/1/13 and then use the new restart file to spin up the model for five additional months, from 7/1/13 to 12/1/13. 
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To determine the date of a netCDF restart file, you may use <tt>ncdump</tt> For example:
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ncdump -v time -t initial_GEOSChem_rst.4x5_standard.nc
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The <tt>-t</tt> option will return the time value in human-readable date-time strings rather than numerical values in unit such as "hours since 1985-1-1 00:00:0.0." The date of a binary punch restart file can be determined by opening the file in GAMAP.
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Using a HEMCO restart file for your initial spin up run is optional. The HEMCO restart file contains fields for initializing variables required for [[Soil NOx emissions]], [[MEGAN biogenic emissions]], and the [[UCX chemistry mechanism]]. The HEMCO restart file that comes with a run directory may only be used for the date and time indicated in the filename. HEMCO will automatically recognize when a restart file is not available for the date and time required, and in that case HEMCO will use default values to initialize those fields. You can also force HEMCO to use the default initialization values by setting "HEMCO_RESTART" to false in <tt>HEMCO_Config.rc</tt>. For more information, see the [[The_HEMCO_User's_Guide#Restart_variables|HEMCO User's Guide]].
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 12:25, 16 July 2019 (UTC)
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== Restart files in GEOS-Chem 12 ==
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<span style="color:green">'''''These updates were included in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], which was released on 26 Nov 2018.'''''</span>
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In [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], several restart file updates were introduced. These include:
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=== Restart collection in HISTORY.rc ===
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GEOS-Chem restart files are now saved out via the History component. A new [[List_of_diagnostics_archived_to_netCDF_format#The_Restart_collection|Restart collection]] has been defined in <tt>HISTORY.rc</tt> and fields saved out to the restart file can be modified in that file.
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=== New restart file names ===
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Because we are now [[#Restart collection in HISTORY.rc|using the History component to archive restart files]] in GEOS-Chem 12.1.0 and later versions, GEOS-Chem restart file names now use this nomenclature: <tt>GEOSChem.Restart.YYYYMMDD_hhmmz.nc4</tt>.
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For example, the restart file that was created at 00:00 UTC on August 1, 2016 is named: <tt>GEOSChem.Restart.20160801_0000z.nc4</tt>.  The <tt>z</tt> indicates "Zulu" or "Z" time, which is another name for UTC.
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=== New variable names ===
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Prior to [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]], species names in restart files began with the <tt>SPC_</tt> prefix:
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  SPC_NO          # Initial concentration of NO
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  SPC_O3          # Initial concentration of O3
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  SPC_CO          # Initial concentration of CO
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  SPC_CH4          # Initial concentration of CH4
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  ...etc...
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In [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]] and later versions, the species names now begin with the prefix <tt>SpeciesRst_</tt> prefix:
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  SpeciesRst_NO    # Initial concentration of NO
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  SpeciesRst_O3    # Initial concentration of O3
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  SpeciesRst_CO    # Initial concentration of CO
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  SpeciesRst_CH4  # Initial concentration of CH4
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  ...etc...
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:16, 30 November 2018 (UTC)
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=== New fields added to the GEOS-Chem restart file ===
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Several new fields have been added to the GEOS-Chem output restart file in an attempt to remove differences between single and multi-segmented GEOS-Chem simulations.
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{| border=1 cellpadding=5 cellspacing=0
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|-valign="top"
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!width="50px"  bgcolor="#CCCCCC"|Item
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!width="950px" bgcolor="#CCCCCC"|Description
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|-valign="top"
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|1
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|Module-level variables <tt>H2O2s</tt> and <tt>SO2s</tt> from <tt>wetscav_mod.F</tt> have been added to State_Chm (as <tt>State_Chm%H2O2AfterChem, StateChm%SO2AfterChem</tt>). These fields will be output to the GEOS-Chem restart file and then initialized to the values saved in the restart file at the start of the next simulation. Prior to this update, both H2O2s and SO2s were initialized to the H2O2 and SO2 tracer concentrations at the start of every simulation. '''''This change will impact multi-segmented runs only'''''.
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|-valign="top"
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|2
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|Module-level variables <tt>DRY_TOTN</tt> and <tt>WET_TOTN</tt> from <tt>get_ndep_mod.F</tt> have been added to State_Chm (as <tt>State_Chm%DryDepNitrogen, StateChm%WetDepNitrogen</tt>). These fields will be output to the GEOS-Chem restart file and then initialized to the values saved in the restart file at the start of the next simulation. Prior to this update, both variables were initialized to zero at the start of every simulation. Storing them in the restart file may improve accuracy of soil NOx emissions over multi-segmented runs. '''''This change will impact multi-segmented runs only'''''.
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|-valign="top"
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|3
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|Move <tt>State_PSC</tt> from the HEMCO restart file to the GEOS-Chem restart file.
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|-valign="top"
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|4
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|Save out instantaneous met fields <tt>TMPU1, SPHU1, PS1DRY, PS1WET, DELPDRY</tt> to the GEOS-Chem restart file. These will be used to initialize the met fields at the start of the timestep, otherwise they will be set to the values of those fields at the end of the timestep.
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|}
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While this update was added to GEOS-Chem Classic in [[GEOS-Chem_12#12.1.0|12.1.0]], it will be added to GCHP in 12.2.0.
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=== Read restart file via HEMCO ===
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GEOS-Chem restart files are now read in via HEMCO. The entries listed below have been added to <tt>HEMCO_Config.rc</tt> (and may vary slightly for different simulation types). These fields are obtained from HEMCO and copied to the appropriate <tt>State_Chm</tt> and <tt>State_Met</tt> fields in the new routine <tt>Get_GC_Restart</tt> (found in <tt>GeosCore/hcoi_gc_main_mod.F90</tt>).
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  #==============================================================================
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  # --- GEOS-Chem restart file ---
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  #
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  # PSC state only needed for UCX
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  #==============================================================================
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  (((GC_RESTART
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  * SPC_          ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesRst_?ALL?    $YYYY/$MM/$DD/$HH CS xyz 1 * - 1 1
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  * TMPU1          ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_TMPU1          $YYYY/$MM/$DD/$HH E  xyz 1 * - 1 1
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  * SPHU1          ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_SPHU1          $YYYY/$MM/$DD/$HH E  xyz 1 * - 1 1
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  * PS1DRY        ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_PS1DRY          $YYYY/$MM/$DD/$HH E  xy  1 * - 1 1
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  * PS1WET        ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_PS1WET          $YYYY/$MM/$DD/$HH E  xy  1 * - 1 1
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  * DELPDRY        ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Met_DELPDRY        $YYYY/$MM/$DD/$HH E  xyz 1 * - 1 1
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  * KPP_HVALUE    ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_KPPHvalue      $YYYY/$MM/$DD/$HH E  xyz 1 * - 1 1
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  * WETDEP_N      ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_WetDepNitrogen $YYYY/$MM/$DD/$HH E  xy  1 * - 1 1
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  * DRYDEP_N      ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_DryDepNitrogen $YYYY/$MM/$DD/$HH E  xy  1 * - 1 1
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  * SO2_AFTERCHEM  ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_SO2AfterChem  $YYYY/$MM/$DD/$HH E  xyz 1 * - 1 1
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  * H2O2_AFTERCHEM ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_H2O2AfterChem  $YYYY/$MM/$DD/$HH E  xyz 1 * - 1 1
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  (((+STATE_PSC+
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  * STATE_PSC      ./GEOSChem.Restart.$YYYY$MM$DD_$HH$MNz.nc4 Chem_StatePSC      $YYYY/$MM/$DD/$HH E  xyz count      * - 1 1
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  )))+STATE_PSC+
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  )))GC_RESTART
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The <tt>CS</tt> cycle flag was added as an option to HEMCO in [[GEOS-Chem 12#12.1.0|GEOS-Chem 12.1.0]] to tell HEMCO to skip fields that aren't found in the provided file. This is useful when certain species aren't found in the restart file and, in that case, GEOS-Chem will initialize that species to the background concentrations specified in the species database.
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--[[User:Melissa Payer|Melissa Sulprizio]] ([[User talk:Melissa Payer|talk]]) 16:30, 7 November 2018 (UTC)
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== Viewing and manipulating restart files ==
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For information on viewing and manipulating GEOS-Chem restart files in netCDF format, please see the following sections of [[Working with netCDF data files|our ''Working with netCDF data files'' wiki page]]:
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# [[Working_with_netCDF_data_files#Viewing and manipulating netCDF files|Resources for viewing and manipulating netCDF files]]
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# [[Working_with_netCDF_data_files#Regridding_netCDF_files|Regridding netCDF files]]
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# [[Working_with_netCDF_data_files#Adding_a_new_variable_to_a_netCDF_file|Adding a new species to a restart file]]
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# [[Working_with_netCDF_data_files#Cropping_netCDF_files|Cropping restart files to a subset of the globe]]
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# [[Working_with_netCDF_data_files#Chunking_and_deflating_a_netCDF_file_to_improve_I.2FO|Chunking and deflating restart files]]
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 15:19, 30 November 2018 (UTC)
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== Previous issues that are now resolved ==
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=== GAMAP can now read GEOS-Chem restart files in netCDF format ===
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<span style="color:green">'''''This update was included in [[GEOS-Chem v11-01#v11-01 public release|GEOS-Chem v11-01 public release]]'''''</span>
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Starting in [[GEOS-Chem v11-01]], all restart files are now saved in [[Preparing_data_files_for_use_with_HEMCO#The_COARDS_netCDF_standard|COARDS-compliant netCDF format]].  We have had to make some minor modifications to both GEOS-Chem and GAMAP in order to allow GAMAP to read these files.  The table below gives a summary of these modifications.
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{| border=1 cellspacing=0 cellpadding=5
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|-valign="top" bgcolor="#CCCCCC"
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!width="100px"|GEOS-Chem or GAMAP?
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!width="250px"|File
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!width="650px"|Modification
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|-valign="top"
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|GEOS-Chem
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|<tt>GeosCore/gamap_mod.F</tt>
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|In routine <tt>INIT_TRACERINFO</tt>, we now write metadata for all species (advected or not) to the tracerinfo.dat file under the ND45 tracer concentration diagnostic section.  Because the netCDF restart file contains concentrations for both advected and non-advected species, we need to make sure that the <tt>tracerinfo.dat</tt> file created by GEOS-Chem contains metadata for all species.
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|-valign="top"
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|GAMAP
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|<tt>internals/ctm_open_file.pro</tt>
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|The prior algorithm always assumed that a netCDF file would end in either <tt>.nc</tt> or <tt>.nc4</tt>.  We now have removed this restriction.  We now split the filename string on <tt>.</tt> and then examine the substrings for <tt>nc</tt> or <tt>nc4</tt> (case-insensitive).
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|-valign="top"
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|GAMAP
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|<tt>internals/ctm_read_coards.pro</tt>
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|Added some minor modifications to read netCDF restart files:
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#Determine vertical grid from the number of layers (if the <tt>Model</tt> global attribute is not specified).
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#Assign category <tt>DXYP</tt> to variable <tt>AREA</tt>, which is included in the netCDF restart file.
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#Assign category <tt>IJ-AVG-$</tt> to variables beginning with either <tt>SPC_</tt> or <tt>TRC_</tt>.  Also remove the <tt>SPC_</tt> and <tt>TRC_</tt> from the variable name internally so that the variable name will match the metadata in <tt>tracerinfo.dat</tt>.
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|}
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--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 19:29, 23 January 2017 (UTC)
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Latest revision as of 15:26, 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 Restart files chapter of geos-chem.readthedocs.io.



Previous | Next | Getting Started with GEOS-Chem