Regridding

GCPy currently supports regridding of data from:

GEOS-Chem Classic restart files
GEOS-Chem Classic diagnostic files
GCHP restart files
GCHP diagnostic files
HEMCO restart files
HEMCO diagnostic files
As well as any netCDF file adhering to COARDS or CF conventions.

Regridding is supported across any horizontal resolution and any grid type available in GEOS-Chem, including lat/lon (global or non-global), global standard cubed-sphere, and global stretched-grid. GCPy also supports arbitrary vertical regridding across different vertical resolutions.

Regridding with GCPy is currently undergoing an overhaul. As of the current release, regridding is split into two different categories:

Regridding between lat-lon grids using regridding weights computed on the fly by GCPy, and
Regridding either lat-lon or cubed-sphere using regridding weights computed as a preprocessing step.

The latter method may be used for creating GCHP standard grid and stretched grid restart files from either GCHP or GEOS-Chem Classic restart files.

Using Online Regridding Weights

You can regrid existing GEOS-Chem restart or diagnostic files using GCPy function gcpy.file_regrid. This function can called directly from the command line (see the examples below) or from a Python script or interpreter (gcpy.file_regrid.file_regrid())

Note

For regridding to or from GCHP stretched-grid restart files, we recommend using the offline regridding weights method.

The syntax of file_regrid is as follows:

def file_regrid(
        fin,
        fout,
        dim_format_in,
        dim_format_out,
        cs_res_out=0,
        ll_res_out='0x0',
        sg_params_in=None,
        sg_params_out=None,
        vert_params_out=None,
):
    """
    Regrids an input file to a new horizontal grid specification
    and saves it as a new file.
    """

gcpy.file_regrid required arguments:

fin : str: The input filename

fout : str: The output filename (file will be overwritten if it already exists)

dim_format_in : str

Format of the input file’s dimensions. Accepted values are:

classic: For GEOS-Chem Classic restart & diagnostic files
checkpoint : For GCHP checkpoint & restart files
diagnostic: For GCHP diagnostic files

dim_format_out : str

Format of the output file’s dimensions. Accepted values are:

classic: For GEOS-Chem Classic restart & diagnostic files
checkpoint : For GCHP checkpoint & restart files
diagnostic: For GCHP diagnostic files

gcpy.file_regrid optional arguments:

sg_params_in : list of float

Stretching parameters (stretch-factor, target-longitude, target-latitude) for the input grid. Only needed when the data contained in file fin is on a GCHP stretched grid.

Default value: [1.0, 170.0, -90.0]

sg_params_out : list of float

Stretching parameters (stretch-factor, target-longitude, target-latitude) for the output grid. Only needed when the data to be contained in file fout is to be placed on a GCHP stretched grid.

Default value: [1.0, 170.0, -90.0]

cs_res_out : int

Cubed-sphere resolution of the output dataset. Only needed when the data in file fin is on a GCHP cubed-sphere grid.

Default value: 0

ll_res_out : str

The lat/lon resolution of the output dataset. Only needed when the data to be contained in file fout is to be placed on a GEOS-Chem Classic lat-lon grid.

Default value: "0x0".

vert_params_out : list of float

Hybrid grid parameter $A$ (in hPa and $B$ (unitless), returned in list format: [A, B]

Default value: None

Examples

As stated previously, you can call gcpy.file_regrid.file_regrid() from a Python script, or from the command line. Here we shall focus on command-line examples.

Regrid a 4x5 GEOS-Chem Classic restart or diagnostic file to a GEOS-Chem Classic 2x2.5 file:

$ python -m gcpy.file_regrid              \
  --filein         /path/to/file_4x5.nc4  \
  --dim_format_in  classic                \
  --fileout        /path/to/file_2x25.nc4 \
  --ll_res_out     2x2.5                  \
  --dim_format_out classic

Regrid a 4x5 GEOS-Chem Classic restart or diagnostic file to a GCHP C24 restart file:

$ python -m gcpy.file_regrid              \
  --filein         /path/to/file_4x5.nc4  \
  --dim_format_in  classic                \
  --fileout        /path/to/file_c24.nc4  \
  --cs_res_out     24                     \
  --dim_format_out checkpoint

Regrid a GCHP C48 restart file to a GCHP stretched grid C48 restart file. The stretch parameters are:

stretch-factor: 5
target-longitude: -72
target-latitude: 41

$ python -m gcpy.file_regrid                 \
  --filein         /path/to/file_c48.nc4     \
  --dim_format_in  checkpoint                \
  --fileout        /path/to/file_c48_sg.nc4  \
  --cs_res_out     48                        \
  --dim_format_out checkpoint                \
  --sg_params_out  5 -72 41

Regrid the GCHP stretched grid C48 restart file from Example 3 above to a GCHP C24 diagnostic file.

$ python -m gcpy.file_regrid                 \
  --filein         /path/to/file_c48_sg.nc4  \
  --sg_params_in   5 -72 41                  \
  --dim_format_in  checkpoint                \
  --fileout        /path/to/file_c24.nc4     \
  --cs_res_out     24                        \
  --dim_format_out diagnostic

Using Offline Regridding Weights

This approach requires generating regridding weights using python packages gridspec and sparselt. Regridding with GCPy, gridspec and sparselt is a three stage process:

Create grid specifications for the source and target grids using gridspec.
Create regridding weights for the transformation using ESMF_RegridWeightGen.
Run the regridding operation using the regrid_restart_file submodule of GCPy.

Note

As of GCPy 1.4.0, the default GCPy environment (aka gcpy_env) now contains gridspec and sparselt packages. You no longer need to use the separate gchp_regridding environment as in prior versions.

gcpy.regrid_restart_file required arguments:

There are three arguments required by the GCPy function regrid_restart_file:

file_to_regrid : str: The GEOS-Chem Classic or GCHP data file to be regridded.

regridding_weights_file : str: Regridding weights to be used in the regridding transformation, generated by ESMF_RegridWeightGen

template_file : str: The GC-Classic or GCHP restart file to use as a template for the regridded restart file. Attributes, dimensions, and variables for the output file will be taken from this template.

gcpy.regrid_restart_file optional arguments:

There are four optional arguments, all of which are for regridded to a stretched cubed-sphere grid.

--stretched-grid : switch: A switch to indicate that the target grid is a stretched cubed-sphere grid.

--stretch-factor : float: The grid stretching factor for the target stretched grid. Only takes effect when --stretched-grid is set. See the GCHP documentation for more information. Make sure this value exactly matches the value you plan to use in GCHP configuration file setCommonRunSettings.sh.

--target-latitude : float: The latitude of the centre point for stretching the target grid. Only takes effect when --stretched-grid is set. See the GCHP documentation for more information. Make sure this value exactly matches the value you plan to use in GCHP configuration file setCommonRunSettings.sh.

--target-longitude : float: The longitude of the centre point for stretching the target grid. Only takes effect when --stretched-grid is set. See the GCHP documentation for more information. Make sure this value exactly matches the value you plan to use in GCHP configuration file setCommonRunSettings.sh.

Example 1: Standard Lat-Lon to Cubed-Sphere Regridding

This example will show regridding a GC-Classic 4x5 restart file to a GCHP c24 restart file.

Activate your GCPy environment.

$ mamba activate gcpy_env  # Or whatever your environment's name is

Create a lat-lon source grid specification using gridspec-create.
```
$ gridspec-create latlon --pole-centered --half-polar 46 72
```
This will produce 1 file: regular_lat_lon_46x72.nc.
Create a target grid specification using gridspec-create.
```
$ gridspec-create gcs 24
```
This will produce 7 files: c24_gridspec.nc and c24.tile[1-6].nc

Create the regridding weights for the regridding transformation (46x72 to C24) using ESMF_RegridWeightGen.

$ ESMF_RegridWeightGen                   \
  --source      regular_lat_lon_46x72.nc \
  --destination c24_gridspec.nc          \
  --method      conserve                 \
  --weight      46x72_to_c24_weights.nc

This will produce a log file, PET0.RegridWeightGen.Log, and our regridding weights, 46x72_to_c24_weights.nc

Use the grid weights produced in previous steps to complete the regridding.
```
$ python -m gcpy.regrid_restart_file          \
  GEOSChem.Restart.20190701_0000z.nc4         \
  46x72_to_c24_weights.nc                     \
  GEOSChem.Restart.20190701_0000z.c24_old.nc4
```
The arguments to gcpy.regrid_restart_file are described above. In this example (lat-lon to cubed-sphere) we need to use a GEOS-Chem Classic restart file as the file to be regridded and a GCHP restart file as the template file.

Note

The resolution of the template file does not matter as long as it contains all of the variables and attributes that you wish to include in the regridded restart file.

After running gcpy.regrid_restart_file, a single restart file named new_restart_file.nc will be created. You can rename this file and use it to initialize your GCHP C24 simulation.
Deactivate your GCPy environment when finished.
```
$ mamba deactivate
```

Example 2: Standard Cubed-Sphere to Cubed-Sphere Regridding

We will use the example of regridding the out-of-the-box GEOSChem.Restart.20190701_0000z.c48.nc4 restart file from C48 to C60 to demonstrate the standard cubed-sphere regridding process:

Activate your GCPy environment.

$ mamba activate gcpy_env  # Or whatever your environment's name is

Create a source grid specification using gridspec-create.
```
$ gridspec-create gcs 48
```
This will produce 7 files: c48_gridspec.nc and c48.tile[1-6].nc
Create a target grid specification using gridspec-create.
```
$ gridspec-create gcs 60
```
Again, this will produce 7 files: c60_gridspec.nc and c60.tile[1-6].nc

Create the regridding weights for the regridding transformation (C48 to C60) using ESMF_RegridWeightGen.

$ ESMF_RegridWeightGen               \
  --source      c48_gridspec.nc      \
  --destination c60_gridspec.nc      \
  --method      conserve             \
  --weight      c48_to_c60_weights.nc

This will produce a log file, PET0.RegridWeightGen.Log, and our regridding weights, c48_to_c60_weights.nc

Use the grid weights produced in earlier steps to complete the regridding.
```
$ python -m gcpy.regrid_restart_file      \
  GEOSChem.Restart.20190701_0000z.c48.nc4 \
  c48_to_c60_weights.nc                   \
  GEOSChem.Restart.20190701_0000z.c48.nc4
```
The arguments to gcpy.regrid_restart_file are described above. Because we are regridding from one cubed-sphere grid to another cubed-sphere grid, we can use the file to be regridded as the template file.

After running gcpy.regrid_restart_file, a single restart file named new_restart_file.nc will be created. You can rename this file as you wish and use it for your GCHP C60 simulation.
Deactivate your GCPy environment when you have finished.
```
$ mamba deactivate
```

Example 3: Standard to Stretched Cubed-Sphere Regridding

This example regrids the out-of-the-box c48 restart file (GEOSChem.Restart.20190701_0000z.c48.nc4) from a standard cubed-sphere grid to a stretched grid. The base resolution will remain the same at c48. The regridded file will have a stretch factor of 4.0 over Bermuda which means a regional grid resolution of c196 (4 times 48) in that area.

Activate your GCPy environment:

$ mamba activate gcpy_env  # Or whatever your environment's name is

Create a source grid specification using gridspec-create.
```
$ gridspec-create gcs 48
```
This will produce 7 files: c48_gridspec.nc and c48.tile[1-6].nc
Create a target grid specification using gridspec-create. This will be for the stretched grid.
```
$ gridspec-create sgcs 48 -s 4.0 -t 32.0 -64.0
```
Here, the -s option denotes the stretch factor and the -t option denotes the latitude / longitude of the centre point of the grid stretch.

Again, this will produce 7 files: c48_..._gridspec.nc and c48_..._tile[1-6].nc, where ... denotes randomly generated characters. Be sure to look for these since you will need them in the next step.

Create the regridding weights for the regridding transformation (C48 to C48-stretched) using ESMF_RegridWeightGen, replacing c48_..._gridspec.nc with the actual name of the file created in the previous step. An example is shown below.

$ ESMF_RegridWeightGen                              \
  --source      c48_gridspec.nc                     \
  --destination c48_s4d00_tdtdqp9ktebm5_gridspec.nc \
  --method      conserve                            \
  --weight      c48_to_c48_stretched_weights.nc

This will produce a log file, PET0.RegridWeightGen.Log, and our regridding weights, c48_to_c48_stretched_weights.nc

Use the grid weights produced in earlier steps to complete the regridding.
```
$ python -m gcpy.regrid_restart_file       \
   --stretched-grid                        \
   --stretch-factor 4.0                    \
   --target-latitude 32.0                  \
   --target-longitude -64.0                \
   GEOSChem.Restart.20190701_0000z.c48.nc4 \
   c48_to_c48_stretched_weights.nc         \
   GEOSChem.Restart.20190701_0000z.c48.nc4
```
The arguments to gcpy.regrid_restart_file are described above. Because we are regridding from one cubed-sphere grid to another cubed-sphere grid, we can use the file to be regridded as the template file.

This will produce a single file, new_restart_file.nc, regridded from C48 standard to C48 stretched with a stretch factor of 4.0 over 32.0N, -64.0E, that you can rename and use as you please.
Tip

It is generally a good idea to rename the file to include the grid resolution, stretch factor, and target lat/lon for easy reference. You can copy it somewhere to keep long-term and link to it from the GCHP Restarts subdirectory in the run directory.
```
$ mv new_restart_file.nc GEOSChem.Restart.20190701_0000z.c120.s4_32N_64E.nc
```
You can also easily reference the file’s stretch parameters by looking at the global attributes in the file. When using the file as a restart file in GCHP make sure that you use the exact same parameters in both the file’s global attributes and GCHP configuration file setCommonRunSettings.sh.
Deactivate your GCPy environment when you have finished.
```
$ mamba deactivate
```

Regridding for Plotting in GCPy

When plotting in GCPy (e.g. through gcpy.compare_single_level() or gcpy.compare_zonal_mean()), the vast majority of regridding is handled internally. You can optionally request a specific horizontal comparison resolution in compare_single_level() and compare_zonal_mean(). Note that all regridding in these plotting functions only applies to the comparison panels (not the top two panels which show data directly from each dataset). There are only two scenarios where you will need to pass extra information to GCPy to help it determine grids and to regrid when plotting.

Pass stretched-grid file paths

Stretched-grid parameters cannot currently be automatically determined from grid coordinates. If you are plotting stretched-grid data in gcpy.compare_single_level() or gcpy.compare_zonal_mean() (even if regridding to another format), you need to use the sg_ref_path or sg_dev_path arguments to pass the path of your original stretched-grid restart file to GCPy. If using single_panel(), pass the file path using sg_path. Stretched-grid restart files created using GCPy contain the specified stretch factor, target longitude, and target latitude in their metadata. Currently, output files from stretched-grid runs of GCHP do not contain any metadata that specifies the stretched-grid used.

Pass vertical grid parameters for non-72/47-level grids

GCPy automatically handles regridding between different vertical grids when plotting except when you pass a dataset that is not on the typical 72-level or 47-level vertical grids. If using a different vertical grid, you will need to pass the corresponding grid parameters using the ref_vert_params or dev_vert_params keyword arguments.

Automatic regridding decision process

When you do not specify a horizontal comparison resolution using the cmpres argument in gcpy.compare_single_level() and compare_zonal_mean(), GCPy follows several steps to determine what comparison resolution it should use:

If both input grids are lat/lon, use the highest resolution between them (don’t regrid if they are the same resolution).
Else if one grid is lat/lon and the other is cubed-sphere (standard or stretched-grid), use a 1x1.25 lat/lon grid.
Else if both grids are cubed-sphere and you are plotting zonal means, use a 1x1.25 lat/lon grid.
Else if both grids are standard cubed-sphere, use the highest resolution between them (don’t regrid if they are the same resolution).
Else if one or more grids is a stretched-grid, use the grid of the ref dataset.

For differing vertical grids, the smaller vertical grid is currently used for comparisons.