Run nested-grid simulations

A nested-grid simulation is a GEOS-Chem Classic simulation running at the native horizontal resolution of the GEOS-FP (0.25° x 0.3125°) or MERRA-2 (0.5° x 0.6125°) meteorology fields over a subset of the globe. Nested-grid simulations use boundary conditions for transport that are archived from a global simulatoin.

Follow these steps to set up a GEOS-Chem Classic nested-grid simulation:

Run a global simulation to create boundary conditions

1. Download the GEOS-Chem source code

Download the GEOS-Chem Classic source code by following these instructions.

2. Create a global simulation run directory

Create a run directory for your global simulation by executing these commands:

$ cd /path/to/GCClassic/run   # or whatever you named the source code directory
$ ./createRunDir.sh

and then follow the prompts.

Tip

A 4° x 5° global simulation should be adequate for producing boundary condition output.

3. Activate the BoundaryConditions diagnostic collection

The BoundaryConditions diagnostic collection is deactivated by default in the HISTORY.rc configuration file that ships with the run directory. Activate this collection by removing the comment character (#) as shown below.

COLLECTIONS: 'Restart',
             'SpeciesConc',
             ... etc ...
             #'BoundaryConditions',    <== Remove the # sign in front
::

The BoundaryConditions collection will save out instantaneous concentrations of advected species every three hours to daily files. You may change those settings by modifying the BoundaryConditions collection section in the HISTORY.rc file.

Tip

If you wish to save disk space, Use the .LON_RANGE and .LAT_RANGE to reduce the size of the region in which the boundary conditions will be saved. The region in which the boundary condition is archived should be a little larger than the nested-grid simulation window.

#==============================================================================
# %%%%% THE BoundaryConditions COLLECTION %%%%%
#
# GEOS-Chem boundary conditions for use in nested grid simulations
#
# Available for all simulations
#==============================================================================
  BoundaryConditions.template:   '%y4%m2%d2_%h2%n2z.nc4',
  BoundaryConditions.format:     'CFIO',
  BoundaryConditions.frequency:  00000000 030000
  BoundaryConditions.duration:   00000001 000000
  BoundaryConditions.mode:       'instantaneous'
  BoundaryConditions.LON_RANGE:  -130.0 -60.0,
  BoundaryConditions.LAT_RANGE:   10.0 60.0,
  BoundaryConditions.fields:     'SpeciesBC_?ADV?             ', 'GIGCchem',
::

4. Configure the global simulation

Configure your global simulation by changing settings in the relevant configuration files. If you do not need the output from your global simulation, you may choose to turn off most of the diagnostic output in HISTORY.rc and HEMCO_Diagn.rc.

Tip

Turn off most diagnostic output in the HISTORY.rc and HEMCO_Diagn.rc files. This will minimize the run time and reduce the size of diagnostic ouptut.

5. Compile GEOS-Chem and run the global simulation

Follow the steps outlined in these sections to compile and run your GEOS-Chem global simulation.

Compile the source code
Download input data (e.g. do a dry-run and download data if necessary)
Run your simulation

Once your global simulation finishes, the boundary conditions files will be placed into the OutputDir subdirectory of your run directory. You should see files named GEOSChem.BoundaryConditions.YYYYMMDD_0000z.nc4 (where YYYYMMDD are replaced by the simulation date) begin to appear in your run directory as your simulation runs. You will need to tell your nested-grid simulation where to find these files.

Set up your nested grid run directory

1. Create a nested-grid simulation run directory

Using the same GEOS-Chem Classic source code directory that we downloaded above follow these steps to create a run directory for your nested-grid simulation.

$ cd /path/to/GCClassic/run   # or whatever you named the source code directory
$ ./createRunDir.sh

Select the native resolution corresponding to your choice of meteorology. You will then be asked to specify which nested region you would like to use.

2. Configure your nested-grid simulation

Check the run-directory configuration files to make sure that you have the same chemistry, emissions, transport, etc. options selected as in the global simulation.

In HEMCO_Config.rc, make sure the GC_BCs option is set to true and update the BC_ entry to point to your boundary condition files.

# ExtNr ExtName                on/off  Species
0       Base                   : on    *
# ----- RESTART FIELDS ----------------------
    --> GC_RESTART             :       true
    --> GC_BCs                 :       true    <== make sure this is true
    --> HEMCO_RESTART          :       true
...
#==============================================================================
# --- GEOS-Chem boundary condition file ---
#==============================================================================
(((GC_BCs
* BC_  /path/to/your/GEOSChem.BoundaryConditions.$YYYY$MM$DD_$HH$MNz.nc4 SpeciesBC_?ADV?  1980-2023/1-12/1-31/0-23 RFY xyz 1 * - 1 1
)))GC_BCs

Activate your preferred diagnostics by changing the relevant settings in these configuration files:

3. Copy the executable to the nested-grid run directory

You do not have to recompile GEOS-Chem Classic when changing grids. Therefore, you can copy the gcclassic executable from your global simulation run directory to your nested-grid run directory.

4. Run the nested-grid simulation

Follow the steps outlined in these sections to run your nested-grid simulation.

Download input data (e.g. do a dry-run and download data if necessary)
Run your simulation

Frequently asked questions

Can I 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.

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

We recommend that you generate boundary conditions over the entire global domain (at 4° x 5° or 2° x 2.5°). Then these boundary conditions can be used as input to simulations on different nested domains.

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

You will download meteorology and emissions data from one of the GEOS-Chem data portals. You can browse the WashU data portal (http://geoschemdata.wustl.edu/ExtData) to see if the data you need are available.

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

Please see the following Supplemental Guides:

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).

Attention

You should exclude the boxes in the “buffer zone” from your scientific analysis.

The following diagram illustrates this:

 <----------------------------NX global grid------------------------->

 +-------------------------------------------------------------------+   ^
 | GLOBAL REGION                                                     |   |
 |                                                                   |   |
 |                       <----------NX nested grid--------->         |   |
 |                                                                   |   |
 |                       +=================================[Y]  ^    |   |
 |                       |     NESTED GRID WINDOW REGION    |   |    |   |
 |                       |                                  |   |    |   |
 |                       |      <------- IM_W ------->      |   |    |   |
 |                       |      +--------------------+  ^   |   |    |   |
 |                       |      |  TPCORE REGION     |  |   |   |    |   |
 |                       |      |  (advection is     |  |   |  NY    |  NY
 |<------- I0 ---------->|<---->|   done in this     | JM_W | nested | global
 |                       | I0_W |   window!!!)       |  |   |  grid  | grid
 |                       |      |                    |  |   |   |    |   |
 |                       |      +--------------------+  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 NX global grid boxes in longitude and NY global grid boxes in latitude. The origin of the GLOBAL REGION” is at the south pole, at the lower left-hand corner (point [1]).
The next innermost box (NESTED GRID WINDOW REGION) is the nested-grid window. This region has NX nested grid boxes in longitude and NY nested grid 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 ehan the NESTED GRID WINDOW REGION. It is set up this way since a cushion of grid boxes is needed for boundary conditions.
I0 is the longitude offset (# of boxes) and J0 is the latitude offset (# of boxes) which translate between the GLOBAL REGION and the NESTED GRID WINDOW REGION.
I0_W is the longitude offset (# of boxes), and J0_W is the latitude offset (# of boxes) which translate between the NESTED GRID WINDOW REGION and the TPCORE REGION. These define the thickness of the buffer zone mentioned above.
The lower left-hand corner of the NESTED GRID 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).
Note that if I0=0, J0=0, I0_W=0, J0_W=0, NX nested grid = NX global grid, NY nested grid = NY global grid specifies a global simulation. In this case the NESTED GRID WINDOW REGION totally coincides with the GLOBAL REGION.
In order for the nested-grid simulation to work we must save out concentrations over the NESTED GRID WINDOW REGION from a coarse model (e.g. 2° x 2.5° or 4° x 5°). These concentrations are copied along the edges of the NESTED GRID WINDOW REGION and are thus used as boundary conditions for TPCORE.