Write utility functions to easily convert input files from mpm-benchmarks

`cb-geo/mpm` has multiple benchmarks that we would like to emulate here too but our input format is slightly different for files like `entity_sets.json`, `particles.txt` etc from there. Write some utility functions that can easily convert these input files from https://github.com/cb-geo/mpm-benchmarks into input files used by `diffmpm`.