Integer overflow for very large problem output

[MattRolchigo]

As the current code collects data from all cells on rank 0 to print to files, if the total number of cells across all ranks is larger than INT_MAX, this will fail. Will require updating int variables to long int in any subroutines where the total number of cells across all ranks is calculated or used

~Similarly an issue in placing nuclei, since global number of cells is also used~