The [diagnostics] section of a configuration file contains options related to paths containing observations, region-mask files and mapping files used to interpolate MPAS data and observations to common reference grids:

## config options related to observations, mapping files and region files used
## by MPAS-Analysis in diagnostics computations.

# The base path to the diagnostics directory.  Typically, this will be a shared
# directory on each E3SM supported machine (see the example config files for
# its location).  For other machines, this would be the directory pointed to
# when running "download_analysis_data.py" to get the public observations,
# mapping files and region files.
baseDirectory = /path/to/diagnostics

# A second directory where custom diagonstics data such as mapping files and
# regions masks for unsupported grids can be found.  The structure of
# subdirectories in this directory must be the same as baseDirectory
customDirectory = none

# Directory for mapping files (if they have been generated already). If mapping
# files needed by the analysis are not found here, they will be generated and
# placed in the output mappingSubdirectory.  The user can supply an absolute
# path here to point to a path that is not within the baseDirectory above.
mappingSubdirectory = mpas_analysis/maps

# Directory for region mask files. The user can supply an absolute path here to
# point to a path that is not within the baseDirectory above.
regionMaskSubdirectory = mpas_analysis/region_masks

Diagnostics Directories

The baseDirectory is the location where files were downloaded with the download_analysis_data.py. If the user is on an E3SM supported machine, this data has already been downloaded to a shared location (see example config files in the subdirectories of the configs directory in the MPAS-Analysis repository).

The customDirectory, if it is not none is another directory where observations, mapping files and region masks may be stored. This is useful for runs on non-standard grids or for testing out new observations.

The remaining options point to the subdirectories for mapping files (see below) and region masks (see Colormaps), respectively. Typically, there is no reason to change mappingSubdirectory or regionMaskSubdirectory, as these are the standard subdirectories created when these files are downloaded from the E3SM public data repository.

Mapping Files

Mapping files are used in many MPAS-Analysis tasks to remap from either the native MPAS mesh or an observations grid to a comparison grid (see Comparison Grids). By default, these mapping files are generated on the fly as they are needed. This can be a time-consuming process, especially for high resolution meshes, so it is useful to store a cache of these mapping files for reuse. Mapping files at three standard resolutions are avaliable on the E3SM public data repository. The mapping files for the two coarser resolution meshes will be downloaded automatically along with the publicly available observations. (See the Quick Start Guide for details on downloading this data.)

If you notice that MPAS-Analysis is generating mapping files on the fly each time you run, you may wish to copy them from the mapping files output directory (the subdirectory mapping/ inside the output base directory) to your mapping files cache directory.