Update notes on GOTM5.2

docs/input-output/param.md

@@ -261,13 +261,13 @@ If `itur=3`, then the two-equation closure schemes from the GLS model of Umlauf
 If `itur=4`, GOTM turbulence model is invoked; the user needs to turn on pre-processing flag `USE_GOTM` in makefile 
 and recompile (GOTM5.2 uses cmake, so does not need to be pre-compiled). In this case, the minimum and maximum 
 viscosity/diffusivity are still specified in `diffmin.gr3` 
-and `diffmax.gr3`. In addition, GOTM also requires an input file called `gotmturb.inp` (the file is in NML format. If it is absent in a GOTM run, GOTM will error out with a notice that gotmturb.nml is missing, but SCHISM expects the file to be named .inp). There are some 
-ready-made samples for this input in the source code bundle. An example for the Columbia River 
-(with steady state Richardson number set to ri_st= 0.15) is included in 'sample_inputs/'. If you wish to tune some parameters 
+and `diffmax.gr3`. There are some 
+ready-made samples for this input in the source code bundle. 
+A key parameter is the steady state Richardson number. If you wish to tune some parameters 
 inside, you may consult [gotm.net](https://gotm.net) for more details.
 
 !!! note
-    1. GOTM has only been tested up to v5.2, not newer versions of GOTM. Using `itur=3` generally gave similar results, except in the Columbia River under high flow conditions, where GOTM produces substantially better stratification.
+    1. GOTM has only been tested up to v5.2, not newer versions of GOTM. Using `itur=3` generally gave similar results, but GOTM can produce substantially better stratification in some cases.
 
 ### meth_sink=1 (int)
 Option for sinks. If `meth_sink =1`, the sink value is reset to `0` if an element is dry with 

mk/Make.defs.bora

@@ -80,8 +80,8 @@ include ../mk/include_modules
 
 # Don't comment out the follow ifdef
 ifdef USE_GOTM
-   GTMMOD =  -I/sciclone/home/yinglong/GOTM3.2.5_libs/Bora/modules/IFORT/ #modules
-   GTMLIBS = -L/sciclone/home/yinglong/GOTM3.2.5_libs/Bora/lib/IFORT/ -lturbulence_prod  -lutil_prod
+   GTMMOD =  -I/sciclone/home/yinglong/GOTM5.2_libs/Bora/modules/IFORT/ #modules
+   GTMLIBS = -L/sciclone/home/yinglong/GOTM5.2_libs/Bora/lib/IFORT/ -lturbulence_prod  -lutil_prod
 else
    GTMMOD =
    GTMLIBS =

mk/Make.defs.whirlwind.intel

@@ -82,8 +82,8 @@ include ../mk/include_modules
 
 # Don't comment out the follow ifdef
 ifdef USE_GOTM
-   GTMMOD =  -I/home/yinglong/GOTM/gotm-3.2.5/TSUNAMI/modules/IFORT/ #modules
-   GTMLIBS = -L/home/yinglong/GOTM/gotm-3.2.5/TSUNAMI/lib/IFORT/ -lturbulence_prod  -lutil_prod
+   GTMMOD =  -I/home/yinglong/GOTM/gotm5.2/TSUNAMI/modules/IFORT/ #modules
+   GTMLIBS = -L/home/yinglong/GOTM/gotm5.2/TSUNAMI/lib/IFORT/ -lturbulence_prod  -lutil_prod
 else
    GTMMOD =
    GTMLIBS =

mk/include_modules

@@ -42,7 +42,7 @@
  TVD_LIM = VL
  EXEC := $(EXEC)_$(TVD_LIM)
 
-# GOTM turbulence closure model
+# GOTM turbulence closure model- user needs to compile GOTM5.2 lib first by themselves
 # USE_GOTM = yes
 # EXEC := $(EXEC)_GOTM