Update notes

docs/getting-started/running-model.md

@@ -25,3 +25,6 @@ Some details for using scribed IO mode are following:
 - Each 3D output has its own netcdf output (e.g. `salinity_*.nc`) and all 2D outputs share same output `out2d_*.nc`. Each vector output is split into X,Y components, e.g. `horizontalVel[X,Y]_*.nc`.
 - The outputs `out2d_*.nc` and `zCoordinates_*.nc` are needed for VisIT. 
 - Users must specify # of scribes on cmd line as `mpirun -np NPROC ./pschism <nscribe>`. The specified number can be >= min required based on `param.nml` and explained above. If not you'll get an error. If you specify more than needed, you waste some cores but otherwise fine.
+
+!!!caution "WWM"
+    When running with WWM, make sure to remove fort.* in the directory where hgrid.gr3 is; otherwise the code will try to read in fort.* which may result in NaN error. You can add this into your batch script.

src/Utility/Post-Processing-Fortran/read_output10_xyz.f90

@@ -26,8 +26,8 @@
 !              (1) screen; 
 !              (2) station.bp or station.sta
 !              (3) vgrid.in: in this dir or ../
-!              (4) out2d*.nc
-!              (4) nc outputs for that variable(tri-quad)
+!              (4) out2d*.nc (for forecast, assume hotstart occurs at end of 1st stack of each forecast)
+!              (5) nc outputs for that variable(tri-quad)
 
 !       Outputs: fort.1[89]; fort.21 (magnitude), fort.22 (dir in deg in math convention); fort.20 - local depth for each pt.
 !       For ics=2 (e.g. for lon/lat), use nearest node for output
@@ -87,10 +87,10 @@ program read_out
       print*, 'Is this a hindcast (0) or forecast(1):'
       read(*,*)iforecast
       if(iforecast/=0) then
-        print*, 'Input start and end record # from each forecast:'
+        print*, 'Input start and end record # within each forecast:'
         read(*,*)ifct_rec1,ifct_rec2
         if(ifct_rec1>ifct_rec2) stop 'ifct_rec1>ifct_rec2'
-        print*, 'Input time offset (days) for output start time:'
+        print*, 'Input time offset (days) to be added to output start time:'
         read(*,*)t_offset
       endif