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:
Download the GEOS-Chem Classic source code by following these
instructions <get-code-steps>
.
Create a run directory <rundir>
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.
The BoundaryConditions
diagnostic collection is deactivated by default in the cfg-hist
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 cfg-hist
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',
::
Configure your global simulation by changing settings in the
relevant configuration files <cfg>
. 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 cfg-hist
and cfg-hco-diagn
files. This will minimize the run time and reduce the size of diagnostic ouptut.
Follow the steps outlined in these sections to compile and run your GEOS-Chem global simulation.
compile
data
(e.g. do a dry-run and download data if necessary)run
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.
Using the same GEOS-Chem Classic source code directory that we
downloaded above <nestgrid-global-sim>
follow these steps to create a run directory <rundir>
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.
Check the run-directory configuration files <cfg>
to make sure that you have the same chemistry, emissions, transport, etc. options selected as in the global simulation.
In cfg-hco-cfg
, 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:
cfg-hist
cfg-hco-diagn
Planeflight.dat.YYYYMMDD <planeflight-diagnostic>
The ObsPack menu of geoschem_config.yml <gc-yml-xdiag-obspack>
You do not have to recompile GEOS-Chem Classic when changing grids. Therefore, you can copy the gcclassic
executable from your global simulation <nestgrid-global-sim>
run directory to your nested-grid run directory.
Follow the steps outlined in these sections to run your nested-grid simulation.
data
(e.g. do a dry-run and download data if necessary)run
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.
We recommend that you generate boundary conditions
<nestgrid-global-sim>
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.
You will download meteorology and emissions data from one of the GEOS-Chem data portals <input-overview>
. You can browse the WashU data portal (http://geoschemdata.wustl.edu/ExtData) to see if the data you need are available.
Please see the following Supplemental Guides:
errguide
debug-guide
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 hasNX global grid
boxes in longitude andNY global grid
boxes in latitude. The origin of theGLOBAL 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 hasNX nested grid
boxes in longitude andNY 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 whichTPCORE
advection will be performed. Note that this region is smaller ehan theNESTED 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) andJ0
is the latitude offset (# of boxes) which translate between theGLOBAL REGION
and theNESTED GRID WINDOW REGION
.I0_W
is the longitude offset (# of boxes), andJ0_W
is the latitude offset (# of boxes) which translate between theNESTED GRID WINDOW REGION
and theTPCORE 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 theNESTED GRID WINDOW REGION
totally coincides with theGLOBAL 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 theNESTED GRID WINDOW REGION
and are thus used as boundary conditions forTPCORE
.