There are at least two aspects to this process:
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create a gridded file in any format representing the geographical features in your domain (states, counties, regular shaped boxes, etc.) which you would like to reference in DESID
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Create an I/O API file containing one REAL variable of fractions between 0 and 1 for each such feature.
There is no ready-made tool for the first step fitting all situations. Depending on their problem, people have used the Spatial Allocator, written custom Fortran code to read information from SMOKE gridding surrogates for their domain and generate gridded files (see the description in the README file for the 12 km grid mask files we posted to the CMAS data warehouse), or used GIS tools to manipulate shapefiles.
For the second step, a number of people have used a combination of tools m3mask and m3merge. For examples, see the discussion in these threads:
What’s the maskdata’s format?
ISAM SA_ACONC output error
How to make ISAM_REGIONS file?