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(I noticed abnormal concentrations at boundaries of the nested region. Is that normal?)
(What should be the resolution of the global boundary conditions data?)
 
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This page contains some basic information pertaining to the GEOS-Chem nested grid simulations.  For more detailed information about met data availability for the various geographic regions, please see our [[Available met data for nested grid simulations]] wiki page.  We also invite you to visit the [[Regional Air Quality Working Group|wiki page of the Regional Air Quality Working Group]], which is responsible for coordinating nested-grid simulations within the GEOS-Chem user community.
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This page contains some basic information pertaining to the GEOS-Chem nested grid simulations.  We also invite you to visit the [[GEOS-Chem Nested Model|''GEOS-Chem Nested Model'' wiki page]] for information current projects.
  
Please also see our [http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf protocol for downloading and processing nested grid met data], which outlines the responsibilities for user groups using GEOS-Chem nested grid simulations.
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== Setting up a nested-grid simulation ==
 +
 
 +
Please see the following wiki pages:
 +
*[[Setting_up_GEOS-Chem_nested_grid_simulations#GEOS-Chem_12.4.0_and_later|Setting up nested grid simulations in GEOS-Chem 12.4.0 and later]]
 +
*[[Setting_up_GEOS-Chem_nested_grid_simulations#GEOS-Chem_12.3.2_and_earlier|Setting up nested grid simulations in GEOS-Chem 12.3.2 and earlier]]
  
 
== Frequently asked questions ==
 
== Frequently asked questions ==
  
=== Can I perform a nested-grid simulation with GEOS-3 meteorology? ===
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===What is involved in running a nested grid simulation?===
  
Yes.  You may perform a [http://acmg.seas.harvard.edu/geos/doc/man/appendix_4.html#A4.2 GEOS-3] nested-grid simulation for one of the following regions:
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Running a nested grid simulation in GEOS-Chem requires the additional step of first running a coarse resolution GEOS-Chem simulation to save out boundary conditions that will be used to initialize species concentrations at the boundaries of your nested grid region.
  
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.1 GEOS-3 1x1, China nested grid]
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=== Is it possible to run nested GEOS-Chem simulations on the AWS cloud? ===
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.2 GEOS-3 1x1, North America nested grid]
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'''''You should be aware that GEOS-3 is now considered to be obsolete.  Also, there is only a limited amount of GEOS-3 met data (2000-2001) available for the nested grid simulations. With the advent of GEOS-5 meteorology, there is really no need for you to use GEOS-3 for your nested grid simulations.'''''
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Yes, you can run the nested grid simulations on AWS cloud. Please see the [https://cloud-gc.readthedocs.io/en/latest/ ''Running GEOS-Chem on AWS cloud'' online tutorial] and contact the [[GEOS-Chem Support Team]] with any questions.
  
=== Can I run a nested grid simulation with GEOS-5 meteorology? ===
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=== If we perform a nested grid simulation, is it possible to save out output in netcdf format? ===
  
Yes!  You can run GEOS-Chem nested grid simulations at the native GEOS-5 horizontal resolution of 0.5° x 0.666° for the following regions:
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Yes, you can output netcdf diagnostics for nested grid runs starting in [[GEOS-Chem 12]] by modifying the settings in [[List_of_diagnostics_archived_to_netCDF_format#Overview|HISTORY.rc]].
  
# [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.1 China/SE Asia region]
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=== What nested grid domains are supported? ===
# [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.2 North America region]
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# [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.3 European region]
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=== Can I run a nested grid simulation with MERRA meteorology? ===
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You can run GEOS-Chem nested grid simulations for the following regions:
  
No. At present we are only saving out the [[MERRA|MERRA met data product]] at [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.2 4° x 5°] and [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.3 2° x 2.5°] horizontal resolutions.
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# [[GEOS-Chem_horizontal_grids#0.25_x_0.3125_CH_nested_grid|0.25° x 0.3125° China region]] ([[GEOS-FP]] only)
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# [[GEOS-Chem_horizontal_grids#0.25_x_0.3125_NA_nested_grid|0.25° x 0.3125° North America region]] ([[GEOS-FP]] only)
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# [[GEOS-Chem_horizontal_grids#0.25_x_0.3125_EU_nested_grid|0.25° x 0.3125° European region]]([[GEOS-FP]] only)
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# [[GEOS-Chem_horizontal_grids#0.5_x_0.625_AS_nested_grid|0.5° x 0.625° Asia region]] ([[GEOS-FP]] and [[MERRA-2]])
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# [[GEOS-Chem_horizontal_grids#0.5_x_0.625_NA_nested_grid|0.5° x 0.625° North America region]] ([[GEOS-FP]] and [[MERRA-2]])
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# [[GEOS-Chem_horizontal_grids#0.5_x_0.625_EU_nested_grid|0.5° x 0.625° European region]]([[GEOS-FP]] and [[MERRA-2]])
  
--[[User:Bmy|Bob Y.]] 13:55, 15 November 2010 (EST)
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Starting in [[GEOS-Chem v10-01]] you do not need to use separate emissions files with resolutions matching those of the your nested grid. The [[HEMCO|HEMCO emissions component]] can read the global emissions data and regrid/crop them on-the-fly to the size of the nested grid.
  
=== How can I find which data are available for nested grid simulations? ===
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Starting in [[GEOS-Chem 12#12.4.0|GEOS-Chem 12.4.0]], you can run GEOS-Chem on '''<u>any</u>''' nested-grid region by specifying the boundaries in the [[GEOS-Chem_input_files#Grid_Menu|Grid Menu]] of input.geos. The high-resolution global meteorology fields are read in and regridded/cropped by [[HEMCO|HEMCO]] to the size of your nested grid.  If you are specifying a smaller domain within one of the predefined nested domains listed above, then you can provide the high-resolution met fields for the regional domain instead to avoid having to read in the larger met files. You may also use a coarse resolution restart file (e.g. one from the global simulation used to save out your boundary conditions) to initialize your nested grid simulation. The restart files are also read in and regridded/cropped by HEMCO. As always, we recommend [[GEOS-Chem_basics#Restart_files|spinning up your GEOS-Chem]] to remove the impact of the initial conditions on your results.
  
Please see our [[Available met data for nested grid simulations]] wiki page.  You can download the data from either the Harvard or Dalhousie data archives via FTP (or wget).
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===Can you save out boundary conditions for more than one nested grid in the same global run? ===
  
--[[User:Bmy|Bob Y.]] 14:09, 15 November 2010 (EST)
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Yes, a single global simulation can output boundary conditions for multiple nested grid regions. In GEOS-Chem 12.3.2 and earlier, simply select multiple regions you would like to output boundary conditions for within the Nested Grid Menu of input.geos. In GEOS-Chem 12.4.0 and later, you can choose to either save out global boundary conditions that can be used for any region or you can create additional [[FlexGrid#Save_out_boundary_conditions_in_HISTORY.rc|BoundaryCondition collections in HISTORY.rc]].
  
=== What if I can't find the GEOS-5 met data that I need? ===
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=== How can I find which data are available for nested grid simulations? ===
  
If you cannot find the GEOS-5 nested grid met data for your particular geographic region of interest or time period of interest, then we invite you to download and process the GEOS_5 met data yourself. Please see our  
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Nested grid meteorolgy fields may be downloaded from Harvard, Dalhousie, or Compute Canada. Please see our [[Downloading GEOS-Chem data directories]] wiki page. Starting in [[GEOS-Chem v10-01]] you do not need to use separate emissions files with resolutions matching those of the your nested grid. The [[HEMCO|HEMCO emissions component]] can read the standard recommended emissions data and regrid/crop them on-the-fly to the size of the nested grid. You should ensure you have the necessary [[HEMCO data directories]] on your system.
[http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf GEOS-5 nested grid data protocol document] for more information.
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--[[User:Bmy|Bob Y.]] 14:13, 15 November 2010 (EST)
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=== What if I can't find the meteorology data that I need? ===
  
=== Boundary conditions for 0.5 x 0.667 ===
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If you cannot find the nested grid meteorology data for your particular geographic region of interest or time period of interest, then you have a few options.
 
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#If you are using [[GEOS-Chem 12#12.4.0|GEOS-Chem 12.4.0]] or later, then you can use the high-resolution global met fields as input in your nested grid simulations and HEMCO will automatically regrid/crop them to your region. If you want to reduce the file size on your system, you may also choose to download the high-resolution global met fields and [[Working_with_netCDF_data_files#Cropping_netCDF_files|crop them to your region of interest]] before using in GEOS-Chem.
'''''[mailto:dbm@umn.edu Dylan Millet] wrote:'''''
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#If you are using GEOS-Chem 12.3.2 or earlier, then you may be required to download and process the met data yourself. Please see our
 
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[http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf Nested grid data protocol document] for more information. It is always a good idea to contact the [[Subscribing_to_the_GEOS-Chem_email_lists|GEOS-Chem Nested Model email list]] before processing met fields for a new nested grid domain to ensure no one has done this work already.
:Do you know if the 0.5&deg; x 0.667&deg; nested simulation that's being developed uses a 4&deg; x 5&deg; or a 2&deg; x 2.5&deg; grid outside of the nested domain?"
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'''''[mailto:yxw@tsinghua.edu.cn Yuxuan Wang] replied:'''''
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:The nested simulation uses 4&deg; x 5&deg; simulation results only at the lateral boundaries of the nested domain. For example, the East Asia nested domain covers 10S to 55N and 70E to 150E, one needs to save 4x5 simulation results (tracer concentrations only) for each vertical layer, at a frequency of every 3 hours, at the following four boundaries:
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:lat = 10S, lon = 70E
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:lat = 10S, lon = 150E
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:lat = 55N, lon = 70E
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:lat = 55N, lon = 150E
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:One can easily change the code to have the nested-grid simulation use 2x2.5 simulation as boundary conditions, but the default has been to take 4x5 results since it's much faster to run a 4x5 simulation.
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'''''[mailto:srhb2@cam.ac.uk Steven Barrett] replied:'''''
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:Could you let me know the standard LL box and UR box of the 4x5 region used as boundary conditions for NA nested 1x1 GEOS-Chem simulations?  I think it'll be LL = (9,26) and UR=(29,38), but the upper latitude extent of the NA region falls right on a grid cell boundary, so it's not clear to me which one would be the right one.
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'''''Philippe Le Sager replied:'''''
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:Those indices are correct. They are default Fortran (starting at one for 1st cell), and correspond to cell within the domain.
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'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] replied:'''''
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:With the advent of [[GEOS-Chem v8-03-01]], we recommend that you save out 2&deg; x 2.5&deg; boundary conditions for nested grid simulations.
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--[[User:Bmy|Bob Y.]] 16:56, 15 November 2010 (EST)
+
  
 
=== Where can I find out more info about nested grid errors? ===
 
=== Where can I find out more info about nested grid errors? ===
  
Please see the
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Please see our ''[[Guide to GEOS-Chem error messages]]'' for more information.
 
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*[[Setting up GEOS-Chem nested grid simulations|Previous issues that are now resolved]] and
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*[[Setting up GEOS-Chem nested grid simulations|Outstanding issues that are not yet resolved]]
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posts on the [[Setting up GEOS-Chem nested grid simulations]] wiki page.
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--[[User:Bmy|Bob Y.]] 14:22, 15 November 2010 (EST)
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=== I noticed abnormal concentrations at boundaries of the nested region.  Is that normal? ===
 
=== I noticed abnormal concentrations at boundaries of the nested region.  Is that normal? ===
Line 88: Line 61:
 
For nested grid simulations, we have to leave a “buffer zone” (i.e. typically 3 boxes along each boundary) in which the TPCORE advection is not applied.  However, all other operations (chemistry, wetdep, drydep, convection, PBL mixing) will be applied.  Therefore, in the “buffer zone”, the concentrations will not be realistic because the advection is not allowed to transport the tracer out of these boxes.
 
For nested grid simulations, we have to leave a “buffer zone” (i.e. typically 3 boxes along each boundary) in which the TPCORE advection is not applied.  However, all other operations (chemistry, wetdep, drydep, convection, PBL mixing) will be applied.  Therefore, in the “buffer zone”, the concentrations will not be realistic because the advection is not allowed to transport the tracer out of these boxes.
  
In any case, the boxes in this “buffer zone” will get overwritten by the 2&deg; x 2.5&deg; or 4&deg; x 5&deg; boundary conditions at the specified time (usually every 3h).
+
In any case, the tracer concentrations in the “buffer zone” will get overwritten by the 2&deg; x 2.5&deg; or 4&deg; x 5&deg; boundary conditions at the specified time (usually every 3h).
  
'''''Therefore, you should not use the boxes in the “buffer zone” in your scientific analysis.'''''
+
'''''Therefore, you should exclude the boxes in the “buffer zone” from your scientific analysis.'''''
  
 
The following diagram illustrates this:
 
The following diagram illustrates this:
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Diagram notes:
 
Diagram notes:
#The outermost box ("GLOBAL REGION") is the global grid size.  This region has <tt>IGLOB</tt> boxes in longitude and <tt>JGLOB</tt> boxes in latitude.  The origin of the "Global Region" is at the south pole, at the lower left-hand corner (point <tt>[1]</tt>).  
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#The outermost box ('''GLOBAL REGION''') is the global grid size.  This region has <tt>IGLOB</tt> boxes in longitude and <tt>JGLOB</tt> boxes in latitude.  The origin of the "Global Region" is at the south pole, at the lower left-hand corner (point <tt>[1]</tt>).  
#The next innermost box ("WINDOW REGION") is the nested-grid window.  This region has <tt>IIPAR</tt> boxes in longitude and </tt>JJPAR</tt> boxes in latitude.  This is the size of the trimmed met fields that will be used for a "nested-grid" simulation.   
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#The next innermost box ('''WINDOW REGION''') is the nested-grid window.  This region has <tt>IIPAR</tt> boxes in longitude and <tt>JJPAR</tt> boxes in latitude.  This is the size of the trimmed met fields that will be used for a "nested-grid" simulation.   
#The innermost region ("TPCORE Region") is the actual area in which TPCORE advection will be performed.  Note that this region is smaller than the "Window Region".  It is set up this way since a cushion of grid boxes is needed TPCORE Region for boundary conditions.
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#The innermost region ('''TPCORE REGION''') is the actual area in which TPCORE advection will be performed.  Note that this region is smaller than the WINDOW REGION.  It is set up this way since a cushion of grid boxes is needed TPCORE Region for boundary conditions.
 
#<tt>I0</tt> is the longitude offset (# of boxes) and <tt>J0</tt> is the latitude offset (# of boxes) which translate between the "Global Region" and the "Window Region".  
 
#<tt>I0</tt> is the longitude offset (# of boxes) and <tt>J0</tt> is the latitude offset (# of boxes) which translate between the "Global Region" and the "Window Region".  
#<tt>I0_W</tt> is the longitude offset (# of boxes), and <tt>J0_W</tt> is the latitude offset (# of boxes) which translate between the "Window Region" and the "TPCORE Region".  These define the thickness of the "buffer zone" mentioned above.
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#<tt>I0_W</tt> is the longitude offset (# of boxes), and <tt>J0_W</tt> is the latitude offset (# of boxes) which translate between the WINDOW REGION and the TPCORE REGION.  These define the thickness of the '''Buffer zone''' mentioned above.
#The lower left-hand corner of the "Window Region" (point <tt>[X]</tt>) has longitude and latitude indices <tt>(I1_W, J1_W)</tt>.  Similarly, the upper right-hand corner (point <tt>[Y]</tt>) has longitude and latitude indices <tt>(I2_W, J2_W)</tt>.
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#The lower left-hand corner of the WINDOW REGION (point <tt>[X]</tt>) has longitude and latitude indices <tt>(I1_W, J1_W)</tt>.  Similarly, the upper right-hand corner (point <tt>[Y]</tt>) has longitude and latitude indices <tt>(I2_W, J2_W)</tt>.
#Note that if <tt>I0=0, J0=0, I0_W=0, J0_W=0, IIPAR=IGLOB, JJPAR=JGLOB</tt> specifies a global simulation.  In this case the "Window Region" totally coincides with the "Global Region".   
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#Note that if <tt>I0=0, J0=0, I0_W=0, J0_W=0, IIPAR=IGLOB, JJPAR=JGLOB</tt> specifies a global simulation.  In this case the WINDOW REGION totally coincides with the "Global Region".   
 
#In order for the nested-grid to work we must save out concentrations over the WINDOW REGION from a coarse model (e.g. 2&deg; x 2.5&deg; or 4&deg; x 5&deg;) corresponding to the same fine-resolution WINDOW REGION.  These concentrations are copied along the edges of the 1x1 WINDOW REGION and are thus used as boundary conditions for TPCORE.
 
#In order for the nested-grid to work we must save out concentrations over the WINDOW REGION from a coarse model (e.g. 2&deg; x 2.5&deg; or 4&deg; x 5&deg;) corresponding to the same fine-resolution WINDOW REGION.  These concentrations are copied along the edges of the 1x1 WINDOW REGION and are thus used as boundary conditions for TPCORE.
  
== Setting up a 0.5 x 0.667 nested-grid simulation for GEOS-5 ==
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=== What should be the resolution of the global boundary conditions data? ===
 
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Visit our [[Setting up GEOS-Chem nested grid simulations]] wiki page for detailed instructions on how to set up a 0.5&deg; x 0.667&deg; nested grid simulation with GEOS-5 meteorology.
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+
--[[User:Bmy|Bob Y.]] 13:37, 15 November 2010 (EST)
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== Setting up a 1 x 1 nested grid simulation with GEOS-3 ==
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'''''NOTE: With the advent of the GEOS-5 meteorology, the GEOS-3 1x1 nested-grid simulation described below is now obsolete.  We strongly recommend you to use the GEOS-5 meteorology for your nested grid simulation.'''''
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--[[User:Bmy|Bob Y.]] 14:00, 3 March 2010 (EST)
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Here is a check list and input.geos file that you need to run the nested-grid China simulation (supplied by Yuxuan Wang):
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=== define.h ===
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These are the settings you need to make in the GEOS-Chem <tt>define.h</tt> file:
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#define GEOS_3      'GEOS_3'
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#define GRID1x1    'GRID1x1'
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#define NESTED_CH  'NESTED_CH'
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#define GRID30LEV  'GRID30LEV'
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=== input.geos ===
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These are the settings you need to make in the GEOS-Chem <tt>input.geos</tt> file:
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=== Saving out 4 x 5 boundary conditions ===
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You will have to run the global model at 4 x 5 resolution to save out the transport boundary conditions.  Here are the relevant settings in input.geos:
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%%% SIMULATION MENU %%% :
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Start YYYYMMDD, HHMMSS  : 20010101 000000
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End  YYYYMMDD, HHMMSS  : 20020101 000000
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Run directory          : ./
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Input restart file      : restart.YYYYMMDDhh
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Make new restart file?  : F
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Output restart file(s)  : restart.YYYYMMDDhh
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Root data directory    : /data/ctm/GEOS_4x5/
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  => GCAP      subdir  : AGRID/YYYY/MM/
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  => GEOS-3    subdir  : GEOS_3/YYYY/MM/
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  => GEOS-4    subdir  : GEOS_4_v4/YYYY/MM/
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  => GEOS-5    subdir  : GEOS_5/YYYY/MM/
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Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/
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Temporary directory    : TEMP/
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Unzip met fields?       : T
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Wait for met fields?    : T
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Use variable tropopause : N
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Global offsets I0, J0  : 0 0
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  ...
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%%% TRANSPORT MENU %%%  :
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Turn on Transport      : T
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  => Use Flux Correction?: F
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  => Fill Negative Values: T
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  => IORD, JORD, KORD    : 3  3  7
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Transport Timestep [min]: 30 
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Use strat O3/NOy BC's  : T
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+
...
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%%% CONVECTION MENU %%% :
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Turn on Cloud Conv?    : T
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Turn on PBL Mixing?    : T
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Convect Timestep (min)  : 30
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+
...
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%%% NESTED GRID MENU %%%: 
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Save TPCORE 4x5 BC's    : T
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TPCORE 4x5 BC directory : /as/home/ctm/yxw/bc/bc_ozone_std/
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4x5 BC timestep [min]  : 180
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LL box of 4x5 BC region :  51  21
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UR box of 4x5 BC region :  67  37
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1x1 offsets I0_W, J0_W  :  3  3
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=== 1x1 nested grid simulation ===
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+
Then once you have saved out the 4 x 5 boundary conditions you can do the 1 x 1 nested grid simulation.  Here are the appropriate settings in input.geos:
+
 
+
%%% SIMULATION MENU %%% :
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Start YYYYMMDD, HHMMSS  : 20010301 000000
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End  YYYYMMDD, HHMMSS  : 20010302 000000
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Run directory          : ./
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Input restart file      : restart.YYYYMMDDhh
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Make new restart file?  : F
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Output restart file(s)  : restart.YYYYMMDDhh
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Root data directory    : /data/geos/GEOS_1x1_CH/
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  => GCAP      subdir  : AGRID/YYYY/MM/
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  => GEOS-3    subdir  : GEOS_3/YYYY/MM/
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  => GEOS-4    subdir  : GEOS_4_v4/YYYY/MM/
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  => GEOS-5    subdir  : GEOS_5/YYYY/MM/
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Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/
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Temporary directory    : TEMP/
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Unzip met fields?      : T
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Wait for met fields?    : T
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Use variable tropopause : F
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Global offsets I0, J0  : 250 79      # need to be changed for NA; index refer to 1x1 resolution
+
+
  ...
+
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%%% TRANSPORT MENU %%%  :
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Turn on Transport      : T
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  => Use Flux Correction?: F
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  => Fill Negative Values: T
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  => IORD, JORD, KORD    : 3  3  7
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Transport Timestep [min]: 10 
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Use strat O3/NOy BC's  : T
+
+
...
+
+
%%% CONVECTION MENU %%% :
+
Turn on Cloud Conv?    : T
+
Turn on PBL Mixing?    : T
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Convect Timestep (min)  : 10
+
+
...
+
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%%% NESTED GRID MENU %%%
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Save TPCORE 4x5 BC's    : T
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TPCORE 4x5 BC directory : /as/home/strat/yxw/bc/  # change to be your own directory
+
4x5 BC timestep [min]  : 180
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LL box of 4x5 BC region :  51  21                # need to be changed for NA; index refer to 4x5 resolution
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UR box of 4x5 BC region :  67  37                # need to be changed for NA; index refer to 4x5 resolution
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1x1 offsets I0_W, J0_W  :  3  3                # do not change for NA
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=== NOTES to 1x1 nested-grid simulation for GEOS-3 ===
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==== General ====
+
 
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# If not NESTED_CH (East Asia window) or NESTED_NA (north America window), need to first obtain
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#* The 1x1 meteorological field for the nested domain;
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#* Tll the input files (mostly emissions) at 1x1 resolution for the nested domain.
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# There needs to be two run directories: one for the 4x5 global run and one for the 1x1 nested run
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# Only one code directory is necessary. Code version v7-01-02 and higher can be compiled for both the global run and the nested run
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# Run the 4x5 global simulation first. With correct switches in the 4x5 input.geos file, boundary conditions will
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#* be saved out automatically into the designated directory and will be read later by the nested run.
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#* The code automatically takes care of formatting.
+
+
==== Code ====
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# Change grid size in define.h
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# Change scaling factor in lightning_nox_mod.f (if not Chinese window)
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#* search for 1x1 in the file to locate the lines of code where changes should be made
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# Change IGLOB, JGLOB in CMN_SIZE (if not Chinese window)
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#* IGLOB and JGLOB refers to the size of the nested window measured at 1x1 resolution
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# Change PARAMETER( NLAND=2681, NPULSE=3 ) in commsoil.h (if not Chinese window)
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#* changes are already made in the code; just uncomment the NA part
+
# Change datadir for O3 column in toms_mod.f --- if not CHINA or NA windows
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#* need to create TOMS_O3col_2001.geos file at 1x1 resolution for the nested region
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#* use the IDL code: regrid_4to1_O3_column.pro  (note that line 33 and 34 needs to be modified for NA)
+
  
--[[User:Bmy|Bob Y.]] 13:42, 15 November 2010 (EST)
+
[[Setting_up_GEOS-Chem_nested_grid_simulations#GEOS-Chem_12.4.0_and_later|Please see this section]].

Latest revision as of 19:04, 13 July 2020

This page contains some basic information pertaining to the GEOS-Chem nested grid simulations. We also invite you to visit the GEOS-Chem Nested Model wiki page for information current projects.

Setting up a nested-grid simulation

Please see the following wiki pages:

Frequently asked questions

What is involved in running a nested grid simulation?

Running a nested grid simulation in GEOS-Chem requires the additional step of first running a coarse resolution GEOS-Chem simulation to save out boundary conditions that will be used to initialize species concentrations at the boundaries of your nested grid region.

Is it possible to run nested GEOS-Chem simulations on the AWS cloud?

Yes, you can run the nested grid simulations on AWS cloud. Please see the Running GEOS-Chem on AWS cloud online tutorial and contact the GEOS-Chem Support Team with any questions.

If we perform a nested grid simulation, is it possible to save out output in netcdf format?

Yes, you can output netcdf diagnostics for nested grid runs starting in GEOS-Chem 12 by modifying the settings in HISTORY.rc.

What nested grid domains are supported?

You can run GEOS-Chem nested grid simulations for the following regions:

  1. 0.25° x 0.3125° China region (GEOS-FP only)
  2. 0.25° x 0.3125° North America region (GEOS-FP only)
  3. 0.25° x 0.3125° European region(GEOS-FP only)
  4. 0.5° x 0.625° Asia region (GEOS-FP and MERRA-2)
  5. 0.5° x 0.625° North America region (GEOS-FP and MERRA-2)
  6. 0.5° x 0.625° European region(GEOS-FP and MERRA-2)

Starting in GEOS-Chem v10-01 you do not need to use separate emissions files with resolutions matching those of the your nested grid. The HEMCO emissions component can read the global emissions data and regrid/crop them on-the-fly to the size of the nested grid.

Starting in GEOS-Chem 12.4.0, you can run GEOS-Chem on any nested-grid region by specifying the boundaries in the Grid Menu of input.geos. The high-resolution global meteorology fields are read in and regridded/cropped by HEMCO to the size of your nested grid. If you are specifying a smaller domain within one of the predefined nested domains listed above, then you can provide the high-resolution met fields for the regional domain instead to avoid having to read in the larger met files. You may also use a coarse resolution restart file (e.g. one from the global simulation used to save out your boundary conditions) to initialize your nested grid simulation. The restart files are also read in and regridded/cropped by HEMCO. As always, we recommend spinning up your GEOS-Chem to remove the impact of the initial conditions on your results.

Can you save out boundary conditions for more than one nested grid in the same global run?

Yes, a single global simulation can output boundary conditions for multiple nested grid regions. In GEOS-Chem 12.3.2 and earlier, simply select multiple regions you would like to output boundary conditions for within the Nested Grid Menu of input.geos. In GEOS-Chem 12.4.0 and later, you can choose to either save out global boundary conditions that can be used for any region or you can create additional BoundaryCondition collections in HISTORY.rc.

How can I find which data are available for nested grid simulations?

Nested grid meteorolgy fields may be downloaded from Harvard, Dalhousie, or Compute Canada. Please see our Downloading GEOS-Chem data directories wiki page. Starting in GEOS-Chem v10-01 you do not need to use separate emissions files with resolutions matching those of the your nested grid. The HEMCO emissions component can read the standard recommended emissions data and regrid/crop them on-the-fly to the size of the nested grid. You should ensure you have the necessary HEMCO data directories on your system.

What if I can't find the meteorology data that I need?

If you cannot find the nested grid meteorology data for your particular geographic region of interest or time period of interest, then you have a few options.

  1. If you are using GEOS-Chem 12.4.0 or later, then you can use the high-resolution global met fields as input in your nested grid simulations and HEMCO will automatically regrid/crop them to your region. If you want to reduce the file size on your system, you may also choose to download the high-resolution global met fields and crop them to your region of interest before using in GEOS-Chem.
  2. If you are using GEOS-Chem 12.3.2 or earlier, then you may be required to download and process the met data yourself. Please see our

Nested grid data protocol document for more information. It is always a good idea to contact the GEOS-Chem Nested Model email list before processing met fields for a new nested grid domain to ensure no one has done this work already.

Where can I find out more info about nested grid errors?

Please see our Guide to GEOS-Chem error messages for more information.

I noticed abnormal concentrations at boundaries of the nested region. Is that normal?

If you see high tracer concentrations right at the boundary of your nested grid region, then this may be normal.

For nested grid simulations, we have to leave a “buffer zone” (i.e. typically 3 boxes along each boundary) in which the TPCORE advection is not applied. However, all other operations (chemistry, wetdep, drydep, convection, PBL mixing) will be applied. Therefore, in the “buffer zone”, the concentrations will not be realistic because the advection is not allowed to transport the tracer out of these boxes.

In any case, the tracer concentrations in the “buffer zone” will get overwritten by the 2° x 2.5° or 4° x 5° boundary conditions at the specified time (usually every 3h).

Therefore, you should exclude the boxes in the “buffer zone” from your scientific analysis.

The following diagram illustrates this:

 <-------------------------------------- IGLOB ---------------------->

 +-------------------------------------------------------------------+   ^
 | GLOBAL REGION                                                     |   |
 |                                                                   |   |
 |                       <-------------- IIPAR ------------->        |   |
 |                                                                   |   |
 |                       +=================================[Y]  ^    |   |
 |                       |  WINDOW REGION (met field size)  |   |    |   |
 |                       |                                  |   |    |   |
 |                       |      <------- IM_W ------->      |   |    |   |
 |                       |      +--------------------+  ^   |   |    |   |
 |                       |      |  TPCORE REGION     |  |   |   |    |   |
 |                       |      |  (advection is     |  |   |   |    |   |
 |<------- I0 ---------->|<---->|   done in this     | JM_W | JJPAR  | JGLOB
 |                       | I0_W |   window!!!)       |  |   |   |    |   |
 |                       |      |                    |  |   |   |    |   |
 |                       |      +--------------------+  V   |   |    |   |
 |                       |        ^                         |   |    |   |
 |                       |        | J0_W                    |   |    |   |
 |                       |        V                         |   |    |   |
 |                      [X]=================================+   V    |   |
 |                                ^                                  |   |
 |                                | J0                               |   |
 |                                V                                  |   |
[1]------------------------------------------------------------------+   V

Diagram notes:

  1. The outermost box (GLOBAL REGION) is the global grid size. This region has IGLOB boxes in longitude and JGLOB boxes in latitude. The origin of the "Global Region" is at the south pole, at the lower left-hand corner (point [1]).
  2. The next innermost box (WINDOW REGION) is the nested-grid window. This region has IIPAR boxes in longitude and JJPAR boxes in latitude. This is the size of the trimmed met fields that will be used for a "nested-grid" simulation.
  3. The innermost region (TPCORE REGION) is the actual area in which TPCORE advection will be performed. Note that this region is smaller than the WINDOW REGION. It is set up this way since a cushion of grid boxes is needed TPCORE Region for boundary conditions.
  4. I0 is the longitude offset (# of boxes) and J0 is the latitude offset (# of boxes) which translate between the "Global Region" and the "Window Region".
  5. I0_W is the longitude offset (# of boxes), and J0_W is the latitude offset (# of boxes) which translate between the WINDOW REGION and the TPCORE REGION. These define the thickness of the Buffer zone mentioned above.
  6. The lower left-hand corner of the WINDOW REGION (point [X]) has longitude and latitude indices (I1_W, J1_W). Similarly, the upper right-hand corner (point [Y]) has longitude and latitude indices (I2_W, J2_W).
  7. Note that if I0=0, J0=0, I0_W=0, J0_W=0, IIPAR=IGLOB, JJPAR=JGLOB specifies a global simulation. In this case the WINDOW REGION totally coincides with the "Global Region".
  8. In order for the nested-grid to work we must save out concentrations over the WINDOW REGION from a coarse model (e.g. 2° x 2.5° or 4° x 5°) corresponding to the same fine-resolution WINDOW REGION. These concentrations are copied along the edges of the 1x1 WINDOW REGION and are thus used as boundary conditions for TPCORE.

What should be the resolution of the global boundary conditions data?

Please see this section.