Integer overflow for very large problem output

[Matt Rolchigo]

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