Regridding¶

This page describes the regridding capabilities of GCPy. GCPy currently supports regridding of data from GEOS-Chem restarts and output NetCDF files. 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 GEOS-Chem Classic format files (lat/lon), and regridding GCHP format files (standard cubed-sphere, stretched cubed-sphere).

Regridding Files - GEOS-Chem Classic¶

You can regrid existing GEOS-Chem Classic restart or output diagnostic files between lat/lon resolutions using gcpy.file_regrid. gcpy.file_regrid can either be called directly from the command line using python -m gcpy.file_regrid or as a function (gcpy.file_regrid.file_regrid()) from a Python script or interpreter. The syntax of file_regrid is as follows:

def file_regrid(fin, fout, dim_format_in, dim_format_out, ll_res_out='0x0'):
"""
Regrids an input file to a new horizontal grid specification and saves it
as a new file.
"""

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 (set this to ‘classic’ - denoting a GEOS-Chem Classic file with a lat/lon grid)

dim_format_out : str¶: Format of the output file’s dimensions (set this to ‘classic’ - denoting a GEOS-Chem Classic file with a lat/lon grid)

Optional arguments:¶

ll_res_out : str¶

The lat/lon resolution of the output dataset.

Default value: ‘0x0’

There is now only one grid format supported for regridding files using the gcpy.file_regrid method: classic. You must specify classic as the value of both dim_format_in and dim_format_out, as well as specifying a resolution as the value of ll_res_out.

As stated previously, you can either call file_regrid.file_regrid() directly or call it from the command line using python -m gcpy.file_regrid ARGS. An example command line call (separated by line for readability) for regridding a 2x2.5 lat/lon restart file to a 4x5 lat/lon grid looks like:

python -m gcpy.file_regrid                     \
      --filein initial_GEOSChem_rst.2x2.5.nc   \
      --dim_format_in classic                  \
      --fileout GEOSChem_rst.4x5.nc            \
      --ll_res_out 4x5                         \
      --dim_format_out classic

Regridding Files - GCHP¶

GCHP regridding is where the first steps of the overhaul in GCPy regridding have happened. We are moving towards an integrated approach for all GEOS-Chem grid types using gridspec and sparselt. For now, this is only supported for GCHP grid formats, but in a later GCPy this will be the single method for regridding all GEOS-Chem grid formats.

Currently, this method is only available from the command line. The syntax of regrid_restart_file is as follows:

Required Arguments:¶

file_to_regrid : str¶: The GCHP restart 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 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. Typically this will be the same file as the file you are regridding!

Optional arguments:¶

--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

--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

--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

First Time Setup¶

Until GCPy contains a complete regridding implementation that works for all GEOS-Chem grid formats, we recommend that you create a small conda environment in which to carry out your GCHP regridding.

The following conda environment file will get you set up with an environment for regridding with gridspec and sparselt:

name: gchp_regridding
channels:
  - conda-forge
dependencies:
  - python=3.9
  - esmf
  - gridspec
  - numpy
  - requests
  - sparselt
  - xarray
  - xesmf

Tip

For your convenience, we have placed a copy of the above environment file at the path docs/environment/gchp_regridding.yml.

After installing and switching to this new conda environment, you should have the gridspec commands available to you at the command line.

Regridding¶

Regridding with 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 new regrid_restart_file submodule of GCPy

Standard 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:

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 and c60.tile[1-6].nc

Create the regridding weights for the regridding transformation 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

Finally, use the grid weights produced in step 3 to complete the regridding. You will need to activate your GCPy python environment for this step.
```
$ python -m gcpy.regrid_restart_file        \
    GEOSChem.Restart.20190701_0000z.c48.nc4 \
    c48_to_c60_weights.nc                   \
    GEOSChem.Restart.20190701_0000z.c48.nc4
```
This will produce a single file, new_restart_file.nc, regridded from C48 to C60, that you can rename and use as you please.

Stretched 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 a C120 base resolution stretched grid with a stretch factor of 4.0 over Bermuda to demonstrate the stretched cubed-sphere regridding process:

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 sgcs 120 -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 - c120_..._gridspec.nc and c120_..._tile[1-6].nc, where ... denotes randomly generated characters.
Create the regridding weights for the regridding transformation using ESMF_RegridWeightGen, replacing c120_..._gridspec.nc with the actual name of the file created in the previous step.
```
$ ESMF_RegridWeightGen                 \
    --source c48_gridspec.nc           \
    --destination c120_..._gridspec.nc \
    --method conserve                  \
    --weight c48_to_c120_stretched_weights.nc
```
This will produce a log file, PET0.RegridWeightGen.Log, and our regridding weights, c48_to_c120_stretched_weights.nc

Finally, use the grid weights produced in step 3 to complete the regridding. You will need to switch to your GCPy python environment for this step.

$ 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_c120_stretched_weights.nc        \
    GEOSChem.Restart.20190701_0000z.c48.nc4

This will produce a single file, new_restart_file.nc, regridded from C48 to C120, with a stretch factor of 4.0 over 32.0N, -64.0E, that you can rename and use as you please. It is generally a good idea to rename the file to include the grid resolution, stretch factor, and target lat/lon for easy reference.

$ mv new_restart_file.nc GEOSChem.Restart.20190701_0000z.c120.s4_32N_64E.nc

Regridding for Plotting in GCPy¶

When plotting in GCPy (e.g. through compare_single_level() or 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 compare_single_level() or 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 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.