All .gr3 and .prop inputs can be visualized/generated using xmgredit5. For other inputs, you can find some useful pre-proc tools in the src/Utility directory. In general, all FORTRAN scripts have a header that explains its purpose, how to use it (inputs/outputs) and sample compilation command.

## Grid conversion
`2dm2gr3_m2m.pl` and `grd2sms.pl` : These 2 perl scripts are used to convert between .2dm (SMS) and .gr3.

## Interpolation
`interpolate_unstructured.f90`: This efficient script can be used to interpolate depths from .gr3 onto another 
.gr3 quickly. It uses a bucket search algorithm along either x or y direction.

## $LSC^2$ scripts
`gen_vqs.f90` and `plot_VQS.m`: The FORTRAN script can be used as a start for creating a LSC2 grid and you need to use the matlab script to plot out transects to see if the vertical grid makes sense. You may lump multiple transects into 1 transect.bp. If you want to use this type of vgrid, make sure you go through the FORTRAN carefully and understand the details.

## Nudging scripts
`gen_nudge.f90`, `gen_nudge2.f90`: the two scripts generate either a simple elliptic nudging zone or a zone with fixed distance from boundary as *_nudge.gr3. 

`gen_nudge_from_hycom.f90`: This
script generates the actual nudge data for tracers `*_nu.nc` from HYCOM (you may modify this 
for other gridded data sources from other structured-grid models).

## Hotstart
`Gen_Hotstart/change_hotstart4.f90`: This simple script shows you the internal structure of hotstart.nc and how to manipulate it.

`Gen_Hotstart/gen_*_from_hycom.f90`: These scripts show you how to create hotstart.nc and *.th.nc from gridded outputs 
 like HYCOM. It essentially consists of 3D interpolations.

## Sflux_nc
The matlab scripts inside Sflux_nc dir show you the structure of sflux*.nc as well as how to generate your own files.

## METIS for offline domain decomposition
You'll only need to do this if you invoked offline partitioning in compilation (e.g. with `NO_PARMETIS` turned ON in cmake)
 to bypass ParMETIS.
If so, you'll need to prepare an input called `partion.prop` (which is essentially the MPI process # for each element).

Step 1: build METIS v5.1.0 by (`src/metis-5.1.0`) following README inside. You only need gpmetis (for VIMS users, it's in `/sciclone/home10/yinglong/git/schism/src/metis-5.1.0/build/Linux-x86_64/programs/gpmetis`)

Step 2: run a pre-processor for METIS: `src/Utility/Grid_Scripts/metis_prep.f90`, which only requires hgrid.gr3 
   (with B.C. parts) and vgrid.in, to get `graphinfo`;

Step 3: run METIS: `./gpmetis graphinfo <nproc> -ufactor=1.01 -seed=15` 

 where `<nproc>` is # of 
   compute cores excluding scribes. The output is `graphinfo.part.<nproc>`, and then use awk to get `partion.prop`:


   `awk '{print NR,$0}' graphinfo.part.<nproc> > partition.prop`


   (replace `<nproc>` with actual # of cores).