You can find some useful post-processing tools in the src/Utility directory. 

## Combining scripts
`combine_output11.f90` is used to combine process-specific netcdf to global netcdf. 
`autocombine_MPI_elfe.pl` is a simple perl wrapper script that automatically combines 
all available outputs during or after the run. Use these if you invoked OLDIO.

`combine_hotstart7.f90` is used combine process-specific hotstart outputs (`outputs/hotstart_0*.nc`)
 into `hotstart.nc`. This is required even if you used scribed I/O (as hotstart outputs are still be emitted per MPI
 process).

`combine_gr3.f90` is used to combine process-specific `maxelev_*` and `maxdahv_*` (ASCII) into `maxelev.gr3` or `maxdahv.gr3`.

## Extraction
`read_output*.f90`: This group of scripts read multiple nc4 outputs and extract time series of a point, 
a slab, a transect etc. They share similar code structure and can be used to understand the nc4 output 
format as well as how to do your own processing. You may start from `read_output*_xyz.f90`. 
After you are familiar with these scripts, you can easily customize them for your own purpose.

Note that you'll need to use different extraction scripts depending on whether you use scribe I/O or not.
 E.g., if you use scribe I/O, the FORTRAN extraction scripts are `read_output10*.f90`.

## One-way nesting
`OneWayNestScripts/interpolate_variables7.f90`: The purpose of this script is to generate `elev2D.th.nc`, 
`SAL_3D.th.nc`, `TEM_3D.th.nc` and/or `uv3D.th.nc` from a large-domain run to be used in a small-domain run. 
This is of limited utility now because `uv3D.th.nc` for the sub-tidal component 
can be generated using e.g. HYCOM.

To prepare for the nesting, first do a 2D barotropic run for a larger or same grid, with only elevation b.c. Note that 2D model is inherently more stable than 3D model, and to further enhance stability, make sure you use `indvel=1 (ishapiro=ihorcon=0)`, `thetai=1`, and also use a large Manning’s $n$ (e.g., 0.025 or larger) near the boundary. Once this is done

1. use interpolate_variables7.f90 to generate *[23]D.th.nc for the small-domain run;
2. use the new *[23]D.th.nc as inputs for the small-domain run.

Note that `interpolate_variables.in` in the directory are sample inputs for the script. A common mistake is that the parent elements of some open boundary nodes in `fg.gr3` (i.e. ‘small-domain’ hgrid) become dry and the script then fails to find a wet element to interpolate from. So make sure all open boundary nodes in `fg.gr3` are located in wet region of `bg.gr3`; this is especially important for those nodes near the coast. You can use xmgredit5 to ascertain this. If necessary, modify `fg.gr3` by moving some nodes to deeper depths.