There is a vertical grid generating routine in the tools/grids subdirectory, in the LANL pop2 distribution; it is not available in the CESM1 distribution. This code is essentially the same code used to generate vertical grids internally in POP, but can be used to generate a vertical grid file off-line which can be edited to suit your simulation. Note that when changing the vertical grid, you will need to re-generate the bottom topography.