.. _stretched-grid: ######################### Stretched-Grid Simulation ######################### .. note:: Stretched-grid simulations are described in :cite:`Bindle_et_al._2021`. This paper also discusses related tpics of consideration and offers guidance for choosing appropriate stretching parameters. ======== Overview ======== A stretched-grid is a cubed-sphere grid that is "stretched" to enhance its resolution in a region. To set up a stretched-grid simulation you need to do the following: #. Choose stretching parameters, including stretch factor and target latitude and longitude. #. Create a stretched grid restart file for your simulation using your chosen stretch parameters. #. Configure the GCHP run directory to specify stretched grid parameters in :file:`setCommonRunSettings.sh` and use your stretched grid restart file. Choose stretching parameters ---------------------------- The :term:`target face` is the face of a stretched-grid that shrinks so that the grid resolution is finer. The target face is centered on a target point, and the degree of stretching is controlled by a parameter called the stretch-factor. Relative to a normal cubed-sphere, the resolution of the target face is refined by approximately the stretch-factor. For example, a C60 stretched-grid with a stretch-factor of 3.0 has approximately C180 (~50 km) resolution in the target face. The enhancement-factor is approximate because (1) the stretching gradually changes with distance from the target point, and (2) gnominic cubed-sphere grids are quasi-uniform with grid-boxes at face edges being ~1.5x shorter than at face centers. You can choose a stretch-factor and target point using the interactive figure below. You can reposition the target face by changing the target longitude and target latitude. The domain of refinement can be increased or decreased by changing the stretch-factor. Choose parameters so that the target face roughly covers the refion that you want to refine. .. raw:: html .. note:: The interactive figure above can be a bit fiddly. Refresh the page if the view gets messed up. If the figure above is not showing up properly, please `open an issue `_. Next you need to choose a cubed-sphere size. The cubed-sphere size must be an even integer (e.g., C90, C92, C94, etc.). Remember that the resolution of the target face is enhanced by approximately the stretch-factor. .. _sg_restart_file_regridding: Create a restart file --------------------- A simulation restart file must have the same grid as the simulation. For example, a C180 simulation requires a restart file with a C180 grid. Likewise, a stretched-grid simulation needs a restart file with the same stretched-grid (i.e., an identical cubed-sphere size, stretch-factor, target longitude, and target latitude). You can regrid an existing restart file to a stretched-grid using the GEOS-Chem python package GCPy. See the `Regridding `_ section of the GCPy documentation for instructions. Once you have created a restart file for your simulation, you can move on to updating your simulation's configuration files. .. note:: A stretched grid restart file is available for download if you would like to quickly get set up to run a stretched grid simulation. See the `GEOSCHEM_RESTARTS/GC_14.0.0 `_ directory in the GEOS-Chem data repository. Configure run directory ^^^^^^^^^^^^^^^^^^^^^^^ Modify the section of :file:`setCommonRunSettings.sh` that controls the simulation grid. Turn :envvar:`STRETCH_GRID` to :literal:`ON` and update :envvar:`CS_RES`, :envvar:`STRETCH_FACTOR`, :envvar:`TARGET_LAT`, and :envvar:`TARGET_LON` for your specific grid. .. code-block:: bash #------------------------------------------------ # GRID RESOLUTION #------------------------------------------------ # Integer representing number of grid cells per cubed-sphere face side CS_RES=24 #------------------------------------------------ # STRETCHED GRID #------------------------------------------------ # Turn stretched grid ON/OFF. Follow these rules if ON: # (1) Minimum STRETCH_FACTOR value is 1.0001 # (2) TARGET_LAT and TARGET_LON are floats containing decimal # (3) TARGET_LON in range [0,360) STRETCH_GRID=OFF STRETCH_FACTOR=3.0 TARGET_LAT=40.0 TARGET_LON=260.0 Execute :program:`./setCommonRunSettings.sh` to update your run directory's configuration files. .. code-block:: console $ ./setCommonRunSettings.sh You will also need to configure the run directory to use the stretched grid restart file. #. Update :file:`cap_restart` to match the date of your restart file. This will also be the start date of the run. #. Copy or symbolically link to your restart file in the :literal:`Restarts` subdirectory with the proper filename format. The format includes global resolution but not stretched grid resolution. To avoid confusion about what grid the file contains you can symbolically link to a file with stretched grid parameters in its filename. #. Run :literal:`setRestartLink.sh` to set symbolic link :file:`gchp_restart.nc4` to point to your restart file based on start date in :file:`cap_restart` and global grid resolution in :file:`setCommonRunSettings.sh`. This is also included as pre-run step in all example run scripts provided in :file:`runScriptSamples`. =============================== Tutorial: Eastern United States =============================== This tutorial walks you through setting up and running a stretched-grid simulation for ozone in the eastern United States. The grid parameters for this tutorial are: ===================== ================ Parameter Value ===================== ================ Stretch-factor 3.6 Cubed-sphere size C60 Target latitude 37° N Target longitude 275° E ===================== ================ These parameters are chosen so that the target face covers the eastern United States. Some back-of-the-envelope resolution calculations are: .. math:: \mathrm{average\ resolution\ of\ target\ face = R_{tf} \approx \frac{10000\ km}{N \times S} = 46\ km} .. math:: \mathrm{coarsest\ resolution\ in\ target\ face\ (at\ the\ center) \approx R_{tf} \times 1.2 = 56\ km } .. math:: \mathrm{finest\ resolution\ in\ target\ face\ (at\ the\ edges) \approx R_{tf} \div 1.2 = 39\ km } .. math:: \mathrm{coarsest\ resolution\ globally\ (at\ target\ antipode) \approx R_{tf} \times S^2 \times 1.2 = 720\ km } where :math:`\mathrm{N}` is the cubed-sphere size and :math:`\mathrm{S}` is the stretch-factor. The actual values of these, calculated from the grid-box areas, are 46 km, 51 km, 42 km, and 664 km respectively. .. note:: This tutorial uses a relatively large stretch-factor. A smaller stretch-factor, such as 2.0 rather than 3.6, would have a broader refinement and smaller range resolutions. Requirements ------------ Before continuing with the tutorial check that you have all pre-requisites: * You are able to run global GCHP simulations using MERRA2 data for July 2019 * You have the latest version of GEOS-Chem python package GCPy * You have python package cartopy with version >= 0.19 Create run directory -------------------- Create a standard full chemistry run directory that uses MERRA2 meteorology. The rest of the tutorial assume that your current working directory is your run directory. Create restart file ------------------- You will need to create a restart file with a horizontal resolution that matches your chosen stretched-grid resolution. Unlike other input data, GCHP ingests the restart file with no online regridding. Using a restart file with a horizontal grid that does not match the run grid will result in a run-time error. To create a restart file for a stretched-grid simulation you can regrid a restart file with a uniform grid using GCPy. Follow instructions on how to create a GCHP stretched grid restart file in the `GCPy documentation `_. For this tutorial regrid the c48 fullchem restart file for July 1, 2019 that comes with a GCHP fullchem run directory (:file:`GEOSChem.Restart.20190701_0000z.c48.nc4`). Grid resolution is 60, stretch factor is 3.6, target longitude is 275, and target latitude is 37. Name the output file :file:`initial_GEOSChem_rst.EasternUS_SG_fullchem.c60.s3.6_37N_275E.nc`. Configure run directory ----------------------- Make the following modifications to :file:`setCommonRunSettings.sh`: * Change the simulation's duration to 7 days * Turn on auto-update of diagnostics * Set diagnostic frequency to 24 hours (daily) * Set diagnostic duration to 24 hours (daily) * Update the compute resources as you like. This simulation's computational demands are about 50% more than a C48 or 2°x2.5° simulation. * Change global grid resolution to 60 * Change :literal:`STRETCH_GRID` to :literal:`ON` * Change :literal:`STRETCH_FACTOR` to :literal:`3.6` * Change :literal:`TARGET_LAT` to :literal:`37.0` * Change :literal:`TARGET_LON` to :literal:`275.0` .. note:: In our tests this simulation took approximately 7 hours to run using 30 cores on 1 node. For comparison, it took 2 hours to run using 180 cores across 6 notes. You may choose your compute resources based on how long you are willing to wait for your run to end. Next, execute :file:`setCommonRunSettings.sh` to apply the updates to the various configuration files: .. code-block:: console $ ./setCommonRunSettings.sh Before running GCHP you also need to configure the model to use your stretched-grid restart file. Move or copy your restart file to the :file:`Restarts` subdirectory. Then change the symbolic link :file:`GEOSChem.Restart.20190701_0000z.c48.nc4` to point to your stretched-grid restart file while keeping the name of the link the same. .. code-block:: console $ ln -nsf initial_GEOSChem_rst.EasternUS_SG_fullchem.c60.s3.6_37N_275E.nc GEOSChem.Restart.20190701_0000z.c48.nc4 You could also rename your restart file to this format but this would remove valuable information about the content of the file from the filename. Symbolically linking is a better way to preserve the information to avoid errors. You can check that you did this correctly by running :file:`setRestartLink.sh` in the run directory. Run GCHP -------- To run GCHP you can use the example run script for running interactively located at :file:`runScriptSamples/gchp.local.run` as long as you have enough resources available locally, e.g. 30 cores on 1 node. Copy it to the main level of your run directory and then execute it. If you want to use more resources you can submit as a batch job to your scheduler. .. code-block:: console $ ./gchp.local.run Log output of the run will be sent to log file :file:`gchp.20190701_0000z.log`. Check that your run was successful by inspecting the log and looking for output in the :file:`OutputDir` subdirectory. .. _sg_plotting_example: Plot the output --------------- Plotting stretched grid is simple using Python. Below is an example plotting ozone at model level 22. All libraries are available if using a python environment compatible with GCPy. .. code-block:: python import matplotlib.pyplot as plt import cartopy.crs as ccrs import xarray as xr # Load 24-hr average concentrations for 2019-07-01 ds = xr.open_dataset('GCHP.DefautlCollection.20190701_0000z.nc4') # Get Ozone at level 22 ozone_data = ds['SpeciesConcVV_O3'].isel(time=0, lev=22).squeeze() # Setup axes ax = plt.axes(projection=ccrs.EqualEarth()) ax.set_global() ax.coastlines() # Plot data on each face for face_idx in range(6): x = ds.corner_lons.isel(nf=face_idx) y = ds.corner_lats.isel(nf=face_idx) v = ozone_data.isel(nf=face_idx) pcm = plt.pcolormesh( x, y, v, transform=ccrs.PlateCarree(), vmin=20e-9, vmax=100e-9 ) plt.colorbar(pcm, orientation='horizontal') plt.show() .. image:: /_static/stretched_grid_demo.png :width: 100%