Adding species to CGYRO simulation

[jcandy]

To add a species to an existing CGYRO simulation, you can use the restart_add_species.py tool. The usage is

$ restart_add_species.py -o DIR1 -n DIR2

Here, DIR1 is a directory containing the restart file you want to "expand" to include an added species. It must contain both the original input.cgyro.gen and bin.cgyro.restart files. DIR2 is the new directory. It has an input.cgyro with an added species.

Note that it is necessary to run cgyro -t in DIR2 to also generate input.cgyro.gen which is needed by the script.