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Connectivity files

Introduction

The horizontal grids used by E3SM's atmosphere component EAM—and sometimes the land component ELM—are cubed spheres. Since these are unstructured grids, our tools need to know how to map the data to the globe. Therefore, for each simulation data file, a "connectivity file" is needed for the visualization.

In EAM version 1, both the dynamical core (dycore) and the physics parameterizations used the same grid consisting of Gauss-Lobatto-Legendre (GLL) nodes. From version 2 onwards, the default is to calculate the parameterizations on on a "physics grid" (also referred to as the "physgrid", "FV grid", or "control volume mesh"). The naming convention is ne*np4 for the dycore grids and ne*pg2 for the physics grids, with * being numbers like 4, 30, 120, 256, 1024, etc.

Starting in QuickView version 2.10.1, both grid types are supported. Variables on the dycore grids are handled as point data while those on the physics grids are handled as cell data.

Connectivity file download

Collections of connectivity files can be found on Zenodo for quasi-uniform meshes and regionally refined meshes. These collections are continually updated as more users inform us about the grids they use.

Generating pg2 grid files

Users can generate connectivity files for the physics grids through TempestRemap (Ullrich and Taylor, 2015; Ullrich et al., 2016) using this script shared by Mark A. Taylor at Sandia National Laboratories.

Tip: Paths in Mark's script

Before using Mark's script, please set exepath therein to where TempestRemap is installed and change wdir to the location where the newly generated connectivity files should be written to.

Tip: TempestRemap

TempestRemap is available as a part of the E3SM-Unified conda environment. It can also be installed following the instructions provided in its repo.

Quasi-uniform pg2 grids

Using Mark's script, the command

./makeSE.sh 30

will generate several different files for the ne30pg2 grid, including, e.g.,

  • TEMEPST_NE30pg2.g (Exodus format),
  • TEMPEST_ne30pg2.scrip.nc (SCRIP format).

The QuickView family uses the SCRIP format.

Regionally refined pg2 grids

Each configuration of the E3SM Regionally Refined Model (RRM, see, e.g., Tang et al., 2023) has a corresponding grid file in the Exodus format (a .g file). The .g file can be used to generate the SCRIP-format pg2 grid file needed by the QuickView family.

For example, a pg2 grid file for the NARRM grid described in Tang et al., 2023 can be generated using Mark's script via the following command, assuming the paths in the script have been adapted as needed and the grid file northamericax4v1.g is available in the current directory:

./makeSE.sh northamericax4v1.g

Generating np4 grid files

These grids are generated by compiling and running homme_tool included in the E3SM source code. A sample script for Perlmutter at NERSC will be provided soon.