Restructure reading of simulation input

[jcurtis2]

Addressing #184 by moving input file reading and setting of run_part_opt options into run_part.F90.

[mwest1066]

I wonder whether this code would be better outside of spec_file_read_run_part()? It doesn't really seem to be strictly related to reading the spec file. In particular, I don't like having RNG initialization hidden inside a spec-file-reading function because a caller might not expect to have their RNG state reset just because they read a spec file.

[jcurtis2]

Yep, i can see this. This RNG is purely for the creation of a UUID (which has more to do with the starting of a simulation and not necessarily reading a main spec file). Would it make sense to move the UUID generation outside the spec file reading but before the MPI calls/new suggested broadcast call? To borrow the code suggestion from above:

if (pmc_mpi_rank() == 0) then
    call spec_file_read_run_part()
    call uuid_generate()
end if
call spec_file_broadcast_run_part()

[mwest1066]

Yep, I think that structure is a good idea, with a call to pmc_srand() above that code block (or maybe immediately before uuid_generate()) with a comment saying that we are initializing it for UUID generation.

One thing that was a bit unclear with the previous code was that it would generate a UUID on all processes, but then overwrite them all by broadcasting from process 0. Your new structure above makes this clearer 🎉