Merge pull request #16 from MatthewMasarik-NOAA/comments/sync-dev/uni…

…fied Langmuir updates: PR to address comments made on NOAA-EMC/WW3 NOAA-EMC#1034
ESCOMP · Dec 14, 2023 · fe15c2a · fe15c2a
2 parents 1effbd7 + 308d7a7
commit fe15c2a
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diff --git a/model/inp/ww3_grid.inp b/model/inp/ww3_grid.inp
@@ -305,25 +305,25 @@ $   limitation and the GSE alleviation.
 $
 $ Unstructured grids ------------------------------------------------ $
 $   UNST parameters       : Namelist UNST
-$                           UGBCCFL    : Turns on/off (TRUE/FALSE) the computation of the CFL number on the physical domain boundary. 
+$                           UGBCCFL    : Turns on/off (TRUE/FALSE) the computation of the CFL number on the physical domain boundary.
 $                                        If FALSE the explicit scheme can be much faster though stability is not guaranteed
 $                                        (default TRUE)
 $                           UGOBCAUTO  : TRUE: OBC points are taken from  type 15 elements (default)
 $                                        FALSE: OBC points must be listed in ww3_grid.inp
 $                           UGOBCDEPTH : Threshold ( < 0) depth (default -10) for OBC points if UGOBCAUTO is TRUE
-$                           UGOBCFILE  : File name of file for reading boudary (default 'unset') 
+$                           UGOBCFILE  : File name of file for reading boudary (default 'unset')
 $
-$                           The following are TRUE/FALSE variables and only one can be TRUE. 
-$                           By default, EXPFSN is TRUE and must be set to false to activate another option  
+$                           The following are TRUE/FALSE variables and only one can be TRUE.
+$                           By default, EXPFSN is TRUE and must be set to false to activate another option
 $                           EXPFSN    : Activation of N scheme (default option)
 $                           EXPFSPSI  : Activation of PSI scheme
 $                           EXPFSFCT  : Activation of FCT scheme
 $                           IMPFSN    : Activation of N implicit scheme
 $                           EXPTOTAL  : Activation of Block explicit N scheme solver
 $                           IMPTOTAL  : Activation of fully implicit scheme, non splitting
-$                             
+$
 $                           The following TRUE/FALSE variables are only for IMPTOTAL=TRUE
-$                           IMPREFRACTION : Turn on implicit freq. shift (default FALSE) 
+$                           IMPREFRACTION : Turn on implicit freq. shift (default FALSE)
 $                           IMPFREQSHIFT  : Turn on implicit freq. shift terms (default FALSE)
 $                           IMPSOURCE     : Turn on implicit source terms (default FALSE)
 $
@@ -332,17 +332,17 @@ $                           JGS_TERMINATE_DIFFERENCE  : Terminate based on the t
 $                           JGS_TERMINATE_NORM  : Terminate based on the norm of the solution (TRUE/FALSE, default FALSE)
 $                           JGS_USE_JACOBI  : Use Jacobi solver family (TRUE/FALSE, default TRUE)
 $                           JGS_BLOCK_GAUSS_SEIDEL  : Use Block Gauss Seidel method for imptotal instead of the conservative jacobi iterator. (TRUE/FALSE, default TRUE)
-$                           JGS_MAXITER  : Max. Number of solver iterations for JGS_TERMINATE_MAXITER (integer, default 100) 
-$                           JGS_PMIN  : % of grid points that do not need to converge during solver iteration (real, default 1) 
+$                           JGS_MAXITER  : Max. Number of solver iterations for JGS_TERMINATE_MAXITER (integer, default 100)
+$                           JGS_PMIN  : % of grid points that do not need to converge during solver iteration (real, default 1)
 $                           JGS_DIFF_THR  : Implicit solver threshold for JGS_TERMINATE_DIFFERENCE (real, default 1.0e-10)
 $                           JGS_NORM_THR  : Norm of the solution for JGS_TERMINATE_NORM (real, default 1.0e-20)
 $                           JGS_LIMITER  : TRUE: Use total (quasi-steady: limits whole equation) instead of local limiter (un-steady: limits only source terms)
-$                                          FALSE: default 
+$                                          FALSE: default
 $                           JGS_LIMITER_FUNC  : 1 - old limiter (default)
 $                                               2 - alternatnive limiter
-$                           SETUP_APPLY_WLV  : Compute wave setup (TRUE/FALSE, default TRUE) 
+$                           SETUP_APPLY_WLV  : Compute wave setup (TRUE/FALSE, default TRUE)
 $                           SOLVERTHR_SETUP  : Solver threshold for setup computations (default 1E-6)
-$                           CRIT_DEP_SETUP  : Critical depth for setup computations (default 0.1) 
+$                           CRIT_DEP_SETUP  : Critical depth for setup computations (default 0.1)
 
 $
 $ SMC grid propagation    : Namelist PSMC and default values
@@ -457,12 +457,6 @@ $                                    depth (HSL) type.
 $                                     0 : Uniform HSL=10m (default)
 $                                     1 : HSL from coupler
 $
-$   Output parameters :
-$                       USS        : surface Stokes drift
-$                                     USSX/Y  (netCDF: uuss/vuss)
-$                       USSH       : surface layer averaged Stokes drift
-$                                     USSHX/Y (netCDF: uussh/vussh)
-$
 $   For more info on the Langmuir parameterization, see:
 $       Li, Qing, et al. "Langmuir mixing effects on global climate:
 $       WAVEWATCH III in CESM." Ocean Modelling 103 (2016): 145-160.

diff --git a/regtests/bin/matrix_cmake_datarmor b/regtests/bin/matrix_cmake_datarmor
@@ -27,7 +27,7 @@ usage ()
 {
 cat 2>&1 << EOF
 
-Usage: $myname model_dir 
+Usage: $myname model_dir
 Required:
   model_dir : path to model dir of WW3 source
 EOF
@@ -51,7 +51,7 @@ main_dir="`cd $main_dir 1>/dev/null 2>&1 && pwd`"
 
 
 # 1. Set up
-   
+
   export np='28'      #number of mpi tasks
   export npl='28'    #number of mpi tasks for ufs applications and large setups
   export npl1='20'   #number of mpi tasks for ufs/large setups (b4b check)
@@ -151,9 +151,10 @@ main_dir="`cd $main_dir 1>/dev/null 2>&1 && pwd`"
   export      shwtr='y' # shallow water tests
   export      unstr='y' # unstructured grid tests
   export      pdlib='y' # unstr with pdlib for domain decomposition and implicit solver
+  export        lmp='y' # Langmuir mixing parameterization
   export      smcgr='y' # SMC grid test
   export        rtd='y' # Rotated pole test
-  export     mudice='y' # Mud/Ice and wave interaction tests 
+  export     mudice='y' # Mud/Ice and wave interaction tests
   export     infgrv='y' # Second harmonic generation tests
   export       uost='y' # ww3_ts4 Unresolved Obstacles Source Term (UOST)
   export      assim='y' # Restart spectra update
@@ -178,17 +179,17 @@ main_dir="`cd $main_dir 1>/dev/null 2>&1 && pwd`"
   export    nth_b4b='y' # Thread Reproducibility
   export       esmf='n' # ESMF coupling
 # export   filter='PR3 ST2 UQ'
-                      # The filter does a set of consecutive greps on the 
+                      # The filter does a set of consecutive greps on the
                       # command lines generated by filter.base with the above
                       # selected options.
 
 # --------------------------------------------------------------------------- #
 # 2.  Execute matrix.base ...                                                 #
 # --------------------------------------------------------------------------- #
-             
+
   $main_dir/../regtests/bin/matrix.base
 
-  $main_dir/../regtests/bin/matrix_divider_cmake.sh 
+  $main_dir/../regtests/bin/matrix_divider_cmake.sh
 
 # --------------------------------------------------------------------------- #
 # End to the matrix                                                           #

diff --git a/regtests/bin/matrix_cmake_milhydro b/regtests/bin/matrix_cmake_milhydro
@@ -19,10 +19,10 @@
 #                                                                             #
 # --------------------------------------------------------------------------- #
 usage ()
-{ 
+{
   cat 2>&1 << EOF
 
-  Usage: $myname model_dir 
+  Usage: $myname model_dir
   Required:
     model_dir : path to model dir of WW3 source
 EOF
@@ -41,7 +41,7 @@ EOF
 # Convert main_dir to absolute path
   main_dir="`cd $main_dir 1>/dev/null 2>&1 && pwd`"
 
-# Set batchq queue, choose modules and other custom variables to fit system and 
+# Set batchq queue, choose modules and other custom variables to fit system and
 # to define headers etc (default to original version if empty)
 # 1. Set up
 # 1.a Computer/ user dependent set up
@@ -58,7 +58,7 @@ EOF
 echo "  export path_build_root=$(dirname $main_dir)/regtests/buildmatrix" >> matrix.head
   echo '  [[ -d ${path_build_root} ]] && rm -rf ${path_build_root}'         >> matrix.head
 
-  echo ' ' 
+  echo ' '
 
   if [ "$batchq" = 'slurm' ]
   then
@@ -97,9 +97,10 @@ echo "  export path_build_root=$(dirname $main_dir)/regtests/buildmatrix" >> mat
   export      shwtr='y' # shallow water tests
   export      unstr='y' # unstructured grid tests
   export      pdlib='y' # unstr with pdlib for domain decomposition and implicit solver
+  export        lmp='y' # Langmuir mixing parameterization
   export      smcgr='y' # SMC grid test
   export        rtd='y' # Rotated pole test
-  export     mudice='y' # Mud/Ice and wave interaction tests 
+  export     mudice='y' # Mud/Ice and wave interaction tests
   export     infgrv='y' # Second harmonic generation tests
   export       uost='y' # ww3_ts4 Unresolved Obstacles Source Term (UOST)
   export      assim='y' # Restart spectra update
@@ -124,14 +125,14 @@ echo "  export path_build_root=$(dirname $main_dir)/regtests/buildmatrix" >> mat
   export    npl_b4b='n' # MPI task Reproducibility
   export    nth_b4b='n' # Thread Reproducibility
   export       esmf='n' # ESMF coupling
-                      # The filter does a set of consecutinve greps on the 
+                      # The filter does a set of consecutinve greps on the
                       # command lines generated by filter.base with the above
                       # selected options.
 
 # --------------------------------------------------------------------------- #
 # 2.  Execute matrix.base ...                                                 #
 # --------------------------------------------------------------------------- #
-             
+
 
   $main_dir/../regtests/bin/matrix.base
 
@@ -146,7 +147,7 @@ echo "  export path_build_root=$(dirname $main_dir)/regtests/buildmatrix" >> mat
     do
       echo "sbatch < $file"  >> msuball.sh
     done
-  fi 
+  fi
 
 # --------------------------------------------------------------------------- #
 # End to the matrix                                                           #

diff --git a/regtests/bin/matrix_cmake_ukmo_cray b/regtests/bin/matrix_cmake_ukmo_cray
@@ -29,7 +29,7 @@ usage ()
 {
   cat 2>&1 << EOF
 
-  Usage: $myname model_dir 
+  Usage: $myname model_dir
   Required:
     model_dir : path to model dir of WW3 source
 EOF
@@ -139,14 +139,15 @@ fi
   export      shwtr='y' # shallow water tests
   export      unstr='y' # unstructured grid tests
   export      pdlib='y' # unstr with pdlib for domain decomposition and implicit solver
+  export        lmp='y' # Langmuir mixing parameterization
   export      smcgr='y' # SMC grid test
   export        rtd='y' # Rotated pole test
-  export     mudice='y' # Mud/Ice and wave interaction tests 
+  export     mudice='y' # Mud/Ice and wave interaction tests
   export     infgrv='y' # Second harmonic generation tests
   export       uost='y' # ww3_ts4 Unresolved Obstacles Source Term (UOST)
   export      assim='y' # Restart spectra update
   export      oasis='y' # Atmosphere, ocean, and ice coupling using oasis
-  export   calendar='y' # Calendar type 
+  export   calendar='y' # Calendar type
   export   confignc='y' # Configurable netCDF meta data (ww3_ounf)
 
   export    multi01='y' # mww3_test_01 (wetting and drying)
@@ -166,14 +167,14 @@ fi
   export    nth_b4b='y' # Thread Reproducibility
   export       esmf='n' # ESMF coupling
 # export   filter='PR3 ST2 UQ'
-                      # The filter does a set of consecutinve greps on the 
+                      # The filter does a set of consecutinve greps on the
                       # command lines generated by filter.base with the above
                       # selected options.
 
 # --------------------------------------------------------------------------- #
 # 2.  Execute matrix.base ...                                                 #
 # --------------------------------------------------------------------------- #
-             
+
   $main_dir/../regtests/bin/matrix.base
 
   $main_dir/../regtests/bin/matrix_divider_cmake.sh

diff --git a/regtests/ww3_tp2.22/input/ww3_ounf.inp b/regtests/ww3_tp2.22/input/ww3_ounf.inp
@@ -13,15 +13,15 @@ $ file for a full documentation of field output options. Namelist type
 $ selection is used here (for alternative F/T flags, see ww3_shel.inp).
 $
  N
- HS T01 DIR SPR USS USSH
+ HS EF T01 DIR SPR USS USSH
 $
 $--------------------------------------------------------------------- $
 $ netCDF version [3,4]
 $        and variable type 4 [2 = SHORT, 3 = it depends , 4 = REAL]
 $ swell partitions [0 1 2 3 4 5]
 $ variables in same file [T] or not [F]
 $
- 3 4
+ 4 4
  0 1 2
  T
 $

diff --git a/regtests/ww3_tp2.22/input/ww3_ounp.inp b/regtests/ww3_tp2.22/input/ww3_ounp.inp
@@ -1,14 +1,14 @@
 $ -------------------------------------------------------------------- $
 $ WAVEWATCH III NETCDF Point output post-processing                    $
 $--------------------------------------------------------------------- $
-$ First output time (yyyymmdd hhmmss), increment of output (s), 
+$ First output time (yyyymmdd hhmmss), increment of output (s),
 $ and number of output times.
 $
   19680606 000000 21600.  1000
 $
 $ Points requested --------------------------------------------------- $
 $
-$ Define points index for which output is to be generated. 
+$ Define points index for which output is to be generated.
 $ If no one defined, all points are selected
 $ One index number per line, negative number identifies end of list.
  1
@@ -21,16 +21,16 @@ $--------------------------------------------------------------------- $
 $ file prefix
 $ number of characters in date [4(yearly),6(monthly),8(daily),10(hourly)]
 $ netCDF version [3,4]
-$ points in same file [T] or not [F] 
+$ points in same file [T] or not [F]
 $                    and max number of points to be processed in one pass
 $ output type ITYPE [0,1,2,3]
 $ flag for global attributes WW3 [0] or variable version [1-2-3-4]
 $ flag for dimensions order time,station [T] or station,time [F]
 $
  ww3.
  6
- 3
- T 150 
+ 4
+ T 150
  1
  0
  T
@@ -72,7 +72,7 @@ $                              2 : Mean wave pars.
 $                              3 : Nondimensional pars. (U*)
 $                              4 : Nondimensional pars. (U10)
 $                              5 : 'Validation table'
-$                              6 : WMO standard output 
+$                              6 : WMO standard output
 $  4
 $
 $ -------------------------------------------------------------------- $

diff --git a/regtests/ww3_tp2.22/input/ww3_outf.inp b/regtests/ww3_tp2.22/input/ww3_outf.inp
@@ -3,7 +3,7 @@ $ -----------------------------------------
   19680606 000000 3600. 12
 $
   N
-  HS T01 DIR SPR USS USSH
+  HS EF T01 DIR SPR USS USSH
 $
   1 0
 $