GEOS-Chem nested grid simulations: Difference between revisions

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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.
This content has been moved to our [https://geos-chem.readthedocs.io/en/latest/supplemental-guides/nested-grid-guide.html '''Run nested grid simulations'''] Supplemental Guide at [https://geos-chem.readthedocs.io <tt>geos-chem.readthedocs.io</tt>].
 
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.
 
== Frequently asked questions ==
 
=== Can I perform a nested-grid simulation with GEOS-3 meteorology? ===
 
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:
 
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.1 GEOS-3 1x1, China nested grid]
* [http://acmg.seas.harvard.edu/geos/doc/man_test/appendix_2.html#A2.5.2 GEOS-3 1x1, North America nested grid]
 
'''''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.'''''
 
=== Can I run a nested grid simulation with GEOS-5 meteorology? ===
 
Yes!  You can run GEOS-Chem nested grid simulations at the native GEOS-5 horizontal resolution of 0.5&deg; x 0.666&deg; for the following regions:
 
# [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.1 China/SE Asia region]
# [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.2 North America region]
# [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.6.3 European region]
 
=== Can I run a nested grid simulation with MERRA meteorology? ===
 
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&deg; x 5&deg;] and [http://acmg.seas.harvard.edu/geos/doc/man/appendix_2.html#A2.3 2&deg; x 2.5&deg;] horizontal resolutions.
 
--[[User:Bmy|Bob Y.]] 13:55, 15 November 2010 (EST)
 
=== How can I find which data are available for nested grid simulations? ===
 
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).
 
--[[User:Bmy|Bob Y.]] 14:09, 15 November 2010 (EST)
 
=== What if I can't find the GEOS-5 met data that I need? ===
 
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
[http://acmg.seas.harvard.edu/geos/wiki_docs/nested_grids/geos_data_downloads.pdf GEOS-5 nested grid data protocol document] for more information.
 
--[[User:Bmy|Bob Y.]] 14:13, 15 November 2010 (EST)
 
=== Boundary conditions for 0.5 x 0.667 ===
 
'''''[mailto:dbm@umn.edu Dylan Millet] wrote:'''''
 
: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?"
 
'''''[mailto:yxw@tsinghua.edu.cn Yuxuan Wang] replied:'''''
: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:
 
:lat = 10S, lon = 70E
:lat = 10S, lon = 150E
:lat = 55N, lon = 70E
:lat = 55N, lon = 150E
 
: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.
 
'''''[mailto:srhb2@cam.ac.uk Steven Barrett] replied:'''''
 
: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.
 
'''''Philippe Le Sager replied:'''''
 
:Those indices are correct. They are default Fortran (starting at one for 1st cell), and correspond to cell within the domain.
 
'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] replied:'''''
 
: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.
 
--[[User:Bmy|Bob Y.]] 16:56, 15 November 2010 (EST)
 
=== Where can I find out more info about nested grid errors? ===
 
Please see the
 
*[[Setting up GEOS-Chem nested grid simulations|Previous issues that are now resolved]] and
*[[Setting up GEOS-Chem nested grid simulations|Outstanding issues that are not yet resolved]]
 
posts on the [[Setting up GEOS-Chem nested grid simulations]] wiki page.
 
--[[User:Bmy|Bob Y.]] 14:22, 15 November 2010 (EST)
 
=== 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 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).
 
'''''Therefore, you should not use the boxes in the “buffer zone” in 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:
#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. 
#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_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>.
#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.
 
== Setting up a 0.5 x 0.667 nested-grid simulation for GEOS-5 ==
 
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.
 
--[[User:Bmy|Bob Y.]] 13:37, 15 November 2010 (EST)
 
== Setting up a 1 x 1 nested grid simulation with GEOS-3 ==
 
'''''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.'''''
 
--[[User:Bmy|Bob Y.]] 14:00, 3 March 2010 (EST)
 
Here is a check list and input.geos file that you need to run the nested-grid China simulation (supplied by Yuxuan Wang):
 
=== define.h ===
 
These are the settings you need to make in the GEOS-Chem <tt>define.h</tt> file:
 
#define GEOS_3      'GEOS_3'
#define GRID1x1    'GRID1x1'
#define NESTED_CH  'NESTED_CH'
#define GRID30LEV  'GRID30LEV'
 
=== input.geos ===
 
These are the settings you need to make in the GEOS-Chem <tt>input.geos</tt> file:
 
=== Saving out 4 x 5 boundary conditions ===
 
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:
 
%%% SIMULATION MENU %%% :
Start YYYYMMDD, HHMMSS  : 20010101 000000
End  YYYYMMDD, HHMMSS  : 20020101 000000
Run directory          : ./
Input restart file      : restart.YYYYMMDDhh
Make new restart file?  : F
Output restart file(s)  : restart.YYYYMMDDhh
Root data directory    : /data/ctm/GEOS_4x5/
  => GCAP      subdir  : AGRID/YYYY/MM/
  => GEOS-3    subdir  : GEOS_3/YYYY/MM/
  => GEOS-4    subdir  : GEOS_4_v4/YYYY/MM/
  => GEOS-5    subdir  : GEOS_5/YYYY/MM/
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/
Temporary directory    : TEMP/
Unzip met fields?      : T
Wait for met fields?    : T
Use variable tropopause : N
Global offsets I0, J0  : 0 0
  ...
%%% TRANSPORT MENU %%%  :
Turn on Transport      : T
  => Use Flux Correction?: F
  => Fill Negative Values: T
  => IORD, JORD, KORD    : 3  3  7
Transport Timestep [min]: 30 
Use strat O3/NOy BC's  : T
...
%%% CONVECTION MENU %%% :
Turn on Cloud Conv?    : T
Turn on PBL Mixing?    : T
Convect Timestep (min)  : 30
...
%%% NESTED GRID MENU %%%: 
Save TPCORE 4x5 BC's    : T
TPCORE 4x5 BC directory : /as/home/ctm/yxw/bc/bc_ozone_std/
4x5 BC timestep [min]  : 180
LL box of 4x5 BC region :  51  21
UR box of 4x5 BC region :  67  37
1x1 offsets I0_W, J0_W  :  3  3
=== 1x1 nested grid simulation ===
 
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 %%% :
Start YYYYMMDD, HHMMSS  : 20010301 000000
End  YYYYMMDD, HHMMSS  : 20010302 000000
Run directory          : ./
Input restart file      : restart.YYYYMMDDhh
Make new restart file?  : F
Output restart file(s)  : restart.YYYYMMDDhh
Root data directory    : /data/geos/GEOS_1x1_CH/
  => GCAP      subdir  : AGRID/YYYY/MM/
  => GEOS-3    subdir  : GEOS_3/YYYY/MM/
  => GEOS-4    subdir  : GEOS_4_v4/YYYY/MM/
  => GEOS-5    subdir  : GEOS_5/YYYY/MM/
Dir w/ 1x1 emissions etc: /data/ctm/GEOS_1x1/
Temporary directory    : TEMP/
Unzip met fields?      : T
Wait for met fields?    : T
Use variable tropopause : F
Global offsets I0, J0  : 250 79      # need to be changed for NA; index refer to 1x1 resolution
  ...
%%% TRANSPORT MENU %%%  :
Turn on Transport      : T
  => Use Flux Correction?: F
  => Fill Negative Values: T
  => IORD, JORD, KORD    : 3  3  7
Transport Timestep [min]: 10 
Use strat O3/NOy BC's  : T
...
%%% CONVECTION MENU %%% :
Turn on Cloud Conv?    : T
Turn on PBL Mixing?    : T
Convect Timestep (min)  : 10
...
%%% NESTED GRID MENU %%%
Save TPCORE 4x5 BC's    : T
TPCORE 4x5 BC directory : /as/home/strat/yxw/bc/  # change to be your own directory
4x5 BC timestep [min]  : 180
LL box of 4x5 BC region :  51  21                # need to be changed for NA; index refer to 4x5 resolution
UR box of 4x5 BC region :  67  37                # need to be changed for NA; index refer to 4x5 resolution
1x1 offsets I0_W, J0_W  :  3  3                # do not change for NA
 
=== NOTES to 1x1 nested-grid simulation for GEOS-3 ===
 
==== General ====
 
# If not NESTED_CH (East Asia window) or NESTED_NA (north America window), need to first obtain
#* The 1x1 meteorological field for the nested domain;
#* Tll the input files (mostly emissions) at 1x1 resolution for the nested domain.  
# There needs to be two run directories: one for the 4x5 global run and one for the 1x1 nested run
# 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
# Run the 4x5 global simulation first. With correct switches in the 4x5 input.geos file, boundary conditions will
#* be saved out automatically into the designated directory and will be read later by the nested run.
#* The code automatically takes care of formatting.
==== Code ====
# Change grid size in define.h
# Change scaling factor in lightning_nox_mod.f (if not Chinese window)
#* search for 1x1 in the file to locate the lines of code where changes should be made
# Change IGLOB, JGLOB in CMN_SIZE (if not Chinese window)
#* IGLOB and JGLOB refers to the size of the nested window measured at 1x1 resolution
# Change PARAMETER( NLAND=2681, NPULSE=3 ) in commsoil.h (if not Chinese window)
#* 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
#* need to create TOMS_O3col_2001.geos file at 1x1 resolution for the nested region
#* 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)

Latest revision as of 16:16, 21 May 2024

This content has been moved to our Run nested grid simulations Supplemental Guide at geos-chem.readthedocs.io.

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