ww3_gse: merge develop ...

model/bin/ww3_from_ftp.sh

@@ -45,8 +45,8 @@ fi
 
 dir0=$(cd $(dirname $0) > /dev/null && pwd -P)
 ww3dir=$(dirname $(dirname $dir0))
- 
-#Get top level directory of ww3 from user: 
+
+#Get top level directory of ww3 from user:
 echo -e "\n\n This script will download data from the ftp for WAVEWATCH III "
 if [ "$interactive" = "n" ]
 then
@@ -55,19 +55,19 @@ else
 echo -e "Enter the absolute or relative path to the main/top directory, "
 echo -e "this would be '../../' if in the model/bin directory "
 echo -e "or './' if already in the top/main directory:"
-  read ww3dir 
+  read ww3dir
 fi
 
-#Move to top level directory of ww3: 
-cd $ww3dir 
+#Move to top level directory of ww3:
+cd $ww3dir
 
-#Download from ftp and uptar: 
-echo -e "Downloading and untaring file from ftp:" 
+#Download from ftp and uptar:
+echo -e "Downloading and untaring file from ftp:"
 wget --no-check-certificate https://ftp.emc.ncep.noaa.gov/static_files/public/WW3/ww3_from_ftp.${ww3ver}.tar.gz
 tar -xvzf ww3_from_ftp.${ww3ver}.tar.gz
 
 #Move regtest info from data_regtests to regtests:
-echo -e "Moving data from data_regtests to regtests"  
+echo -e "Moving data from data_regtests to regtests"
 cp -r data_regtests/ww3_tp2.18/input/*.nc  regtests/ww3_tp2.18/input/
 cp -r data_regtests/ww3_tp2.15/input/wind.nc  regtests/ww3_tp2.15/input/
 cp -r data_regtests/ww3_tp2.15/input/*.nc  regtests/ww3_tp2.15/input_rho/
@@ -93,7 +93,7 @@ if [ ! -d regtests/ww3_tp2.14/input/oasis3-mct/doc ]
 then
   mkdir regtests/ww3_tp2.14/input/oasis3-mct/doc
 fi
-cp -r data_regtests/ww3_tp2.14/input/oasis3-mct/doc/* regtests/ww3_tp2.14/input/oasis3-mct/doc/ 
+cp -r data_regtests/ww3_tp2.14/input/oasis3-mct/doc/* regtests/ww3_tp2.14/input/oasis3-mct/doc/
 cp -r data_regtests/ww3_tp2.14/input/toy/*.nc.OAS*CM regtests/ww3_tp2.14/input/toy/
 cp -r data_regtests/ww3_tp2.14/input/toy/r-toy.nc.OASACM regtests/ww3_tp2.14/input/toy/r-toy.nc.OASACM2
 cp -r data_regtests/ww3_tp2.14/input/toy/toy_coupled_field.nc.OASACM regtests/ww3_tp2.14/input/toy/toy_coupled_field.nc.OASACM2
@@ -102,13 +102,15 @@ cp -r data_regtests/ww3_tp2.14/input/toy/toy_coupled_field.nc.OASACM regtests/ww
 cp -r data_regtests/ww3_tp2.14/input/toy/toy_coupled_field.nc.OASACM regtests/ww3_tp2.14/input/toy/toy_coupled_field.nc.OASACM6
 cp -r data_regtests/ww3_tp2.14/input/toy/*.nc regtests/ww3_tp2.14/input/toy/
 cp -r data_regtests/ww3_tp2.17/input/*     regtests/ww3_tp2.17/input/
+cp -r data_regtests/ww3_tp2.19/input/*     regtests/ww3_tp2.19/input/
 cp -r data_regtests/ww3_tp2.21/input/*     regtests/ww3_tp2.21/input/
 cp -r data_regtests/mww3_test_09/input/*   regtests/mww3_test_09/input/
 cp -r data_regtests/ww3_ufs1.1/input/*     regtests/ww3_ufs1.1/input/
+cp -r data_regtests/ww3_ufs1.1/input_unstr/*     regtests/ww3_ufs1.1/input_unstr/
 cp -r data_regtests/ww3_ufs1.1/input/*.nc  regtests/ww3_ufs1.2/input/
 cp -r data_regtests/ww3_ufs1.2/input/*     regtests/ww3_ufs1.2/input/
 cp -r data_regtests/ww3_ufs1.3/input/*nc   regtests/ww3_ufs1.3/input/
-#Do you want to clean up (aka delete tar file, delete the data_regtests directory) 
+#Do you want to clean up (aka delete tar file, delete the data_regtests directory)
 echo -e "\n\n Do you want to delete the tar file ww3_from_ftp.${ww3ver}.tar.gz [y|n]: "
 if [ "$interactive" = "n" ]
 then
@@ -118,10 +120,10 @@ else
 fi
 if [ "${keep}" = "N" ] || [ "${keep}" = "n" ]
 then
-  echo -e '\n Deleting tar file ww3_from_ftp.${ww3ver}.tar.gz'
+  echo -e "\n Deleting tar file ww3_from_ftp.${ww3ver}.tar.gz"
   rm ww3_from_ftp.${ww3ver}.tar.gz
 else
-  echo -e ' Not deleting tar file.' 
+  echo -e ' Not deleting tar file.'
 fi
 
 echo -e "\n\n Files were copied from the data_regtests to the regtests folder."
@@ -137,9 +139,9 @@ then
   echo -e '\n Deleting the data_regtests folder'
   rm -rf data_regtests
 else
-  echo -e ' Not deleting the data_regtests folder.' 
+  echo -e ' Not deleting the data_regtests folder.'
 fi
 
-#move back to original directory: 
+#move back to original directory:
 cd $curr_dir
 echo -e "End of ww3_from_ftp.sh"

model/ci/spack_gnu.yaml

@@ -13,7 +13,8 @@ spack:
   - g2@3.4.5
   - bacio@2.4.1
   - w3emc@2.9.2
-  - esmf@8.1.1~pio~pnetcdf~xerces
+  - parallelio@2.5.9+fortran~pnetcdf
+  - esmf@8.4.2~debug~xerces+external-parallelio
   view: true
   concretizer:
     unify: when_possible

model/ci/spack_intel.yaml

@@ -5,16 +5,17 @@ spack:
       providers:
         mpi: [intel-oneapi-mpi]
   specs:
+  - netcdf-c@4.7.4~dap
+  - netcdf-fortran@4.5.3
+  - bacio@2.4.1
+  - g2@3.4.5
   - metis@5.1.0~shared
   - parmetis@4.0.3~shared
   - scotch@7.0.1+mpi+metis~shared
-  - netcdf-c@4.7.4~dap
-  - netcdf-fortran@4.5.3
   - jasper@2.0.32
-  - g2@3.4.5
-  - bacio@2.4.1
   - w3emc@2.9.2
-  - esmf@8.1.1~pio~pnetcdf~xerces
+  - parallelio@2.5.9+fortran~pnetcdf
+  - esmf@8.4.2~debug~xerces+external-parallelio
   - intel-oneapi-mpi %intel
   view: true
   concretizer:

model/inp/ww3_gint.inp

@@ -1,9 +1,12 @@
 $ -------------------------------------------------------------------- $
 $ WAVEWATCH III Grid integration input file                            $
 $ -------------------------------------------------------------------- $
-$ Time, time increment and number of outputs
+$ Time, time increment and number of outputs, and optional T/F 
+$ option (default is T) to indicate out_grd (T) or restart (F)
+$ This option for example allows you to create a regional grid from global
+$ Note, there is no interpolation in spectral space only geographic
 $
-  19680606 060000 10800. 1
+  19680606 060000 10800. 1 T
 $
 $ Total number of grids (NGR). The code assumes that the first NGR-1
 $ grids are the input grids and the last grid is the target grid in

model/inp/ww3_grid.inp

@@ -305,33 +305,44 @@ $   limitation and the GSE alleviation.
 $
 $ Unstructured grids ------------------------------------------------ $
 $   UNST parameters       : Namelist UNST
-$                           UGOBCAUTO  : TRUE: OBC points are taken from  type 15 elements
-$                                       FALSE: OBC points must be listed in ww3_grid.inp
-$                           UGOBCDEPTH : Threshold ( < 0) depth for OBC points if UGOBCAUTO is TRUE
-$                           UGOBCFILE : Reading boundary files from a file
-$                           EXPFSN  : Activation of N scheme (only one of the below 4, True - Active, False - not active)
+$                           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') 
+$
+$                           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 the Block explicit N scheme solver
-$                           IMPTOTAL  : Activation of fully implicit scheme | Non splitting
-$                           IMPREFRACTION : Turn on implicit freq. shift (only with imptotal)
-$                           IMPFREQSHIFT  : Turn on implicit freq. shift terms (only with imptotal)
-$                           IMPSOURCE     : Turn on implicit source terms (only with imptotal)
-$                           JGS_TERMINATE_MAXITER  : max. Number of iterations
-$                           JGS_TERMINATE_DIFFERENCE  : Terminate based on the total change of the unweightet sum of wave action
-$                           JGS_TERMINATE_NORM  : Terminate based on the norm of the solution
-$                           JGS_USE_JACOBI  : Use Jacobi solver family
-$                           JGS_BLOCK_GAUSS_SEIDEL  : Use Block Gauss Seidel method for imptotal instead of the conservative jacobi iterator.
-$                           JGS_MAXITER  : max. Number of solver iterations
-$                           JGS_PMIN  : % of grid points that do not need to converge during solver iteration.
-$                           JGS_DIFF_THR  : implicit solver threshold for JGS_TERMINATE_DIFFERENCE
-$                           JGS_NORM_THR  : terminate based on the norm of the solution
-$                           JGS_LIMITER  : use total (quasi-steady: limits whole equation) instead of local limiter (un-steady: limits only source terms)
-$                           JGS_LIMITER_FUNC  : 1 - old limiter; 2 - alternatnive limiter
-$                           SETUP_APPLY_WLV  : Compute wave setup (experimental)
-$                           SOLVERTHR_SETUP  : Solver threshold for setup computations
-$                           CRIT_DEP_SETUP  : Critical depths for setup computations
+$                           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) 
+$                           IMPFREQSHIFT  : Turn on implicit freq. shift terms (default FALSE)
+$                           IMPSOURCE     : Turn on implicit source terms (default FALSE)
+$
+$                           JGS_TERMINATE_MAXITER  : Terminate based on max number of iterations (TRUE/FALSE, default TRUE)
+$                           JGS_TERMINATE_DIFFERENCE  : Terminate based on the total change of the unweightet sum of wave action (TRUE/FALSE, default TRUE)
+$                           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_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 
+$                           JGS_LIMITER_FUNC  : 1 - old limiter (default)
+$                                               2 - alternatnive limiter
+$                           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) 
 
 $
 $ SMC grid propagation    : Namelist PSMC and default values

model/nml/namelists.nml

@@ -312,10 +312,6 @@ $                           SETUP_APPLY_WLV  : Compute wave setup (experimental)
 $                           SOLVERTHR_SETUP  : Solver threshold for setup computations
 $                           CRIT_DEP_SETUP  : Critical depths for setup computations
 $
-$                           JGS_LGSE = T : Turn off/on GSE correction on unstructured grids
-$                           JGS_GSE_TS = 350000. : Swell age parameter see manual
-$
-$
 $ SMC grid propagation    : Namelist PSMC and default values
 $                           CFLTM  : Maximum CFL no. for propagation, 0.7
 $                           DTIME  : Swell age for diffusion term (s), 0.0

model/src/PDLIB/yownodepool.F90

@@ -77,7 +77,7 @@ module yowNodepool
 
   !> coordinates of the local +  ghost nodes. range [1:npa]
   real(rkind), public, target, allocatable :: x(:), y(:), z(:)
-  real(rkind), public, target, allocatable :: PDLIB_SI(:), PDLIB_TRIA(:), PDLIB_TRIA03(:), PDLIB_IEN(:,:), PDLIB_IEND(:,:,:)
+  real(rkind), public, target, allocatable :: PDLIB_SI(:), PDLIB_TRIA(:), PDLIB_TRIA03(:), PDLIB_IEN(:,:)
   integer, public, target, allocatable :: PDLIB_CCON(:), PDLIB_IA(:), PDLIB_JA(:)
   integer, public, target, allocatable :: PDLIB_IA_P(:), PDLIB_JA_P(:), PDLIB_JA_IE(:,:,:)
   integer, public, target, allocatable :: PDLIB_POS_CELL(:), PDLIB_IE_CELL(:)

model/src/PDLIB/yowpdlibmain.F90

@@ -1306,13 +1306,13 @@ subroutine ComputeTRIA_IEN_SI_CCON
     use yowerr,       only: parallel_abort
     use yowDatapool,    only: myrank
     use yowNodepool,    only: np_global, np, iplg, t_Node, ghostlg, ng, npa
-    use yowNodepool,    only: x, y, z, PDLIB_SI, PDLIB_IEN, PDLIB_IEND, PDLIB_TRIA, PDLIB_CCON, PDLIB_TRIA03
+    use yowNodepool,    only: x, y, z, PDLIB_SI, PDLIB_IEN, PDLIB_TRIA, PDLIB_CCON, PDLIB_TRIA03
 
     integer I1, I2, I3, stat, IE, NI(3)
     real  :: DXP1, DXP2, DXP3, DYP1, DYP2, DYP3, DBLTMP, TRIA03
     logical :: CROSSES_DATELINE
 
-    allocate(PDLIB_SI(npa), PDLIB_CCON(npa), PDLIB_IEN(6,ne), PDLIB_IEND(3,3,ne), PDLIB_TRIA(ne), PDLIB_TRIA03(ne), stat=stat)
+    allocate(PDLIB_SI(npa), PDLIB_CCON(npa), PDLIB_IEN(6,ne), PDLIB_TRIA(ne), PDLIB_TRIA03(ne), stat=stat)
     if(stat/=0) call parallel_abort('SI allocation failure')
 
     PDLIB_SI(:)   = 0.0d0 ! Median Dual Patch Area of each Node
@@ -1350,16 +1350,6 @@ subroutine ComputeTRIA_IEN_SI_CCON
         WRITE(*,*) 'AREA SMALLER ZERO IN PDLIB', IE, NE, PDLIB_TRIA(IE)
         STOP
       ENDIF
-      PDLIB_IEND(1,1,IE) = DOT_PRODUCT(PDLIB_IEN(1:2,IE),PDLIB_IEN(1:2,IE)) ! Tomaich. eq. 3.19 n1 * n1 etc.
-      PDLIB_IEND(1,2,IE) = DOT_PRODUCT(PDLIB_IEN(1:2,IE),PDLIB_IEN(3:4,IE))
-      PDLIB_IEND(1,3,IE) = DOT_PRODUCT(PDLIB_IEN(1:2,IE),PDLIB_IEN(5:6,IE))
-      PDLIB_IEND(2,1,IE) = DOT_PRODUCT(PDLIB_IEN(3:4,IE),PDLIB_IEN(1:2,IE))
-      PDLIB_IEND(2,2,IE) = DOT_PRODUCT(PDLIB_IEN(3:4,IE),PDLIB_IEN(3:4,IE))
-      PDLIB_IEND(2,3,IE) = DOT_PRODUCT(PDLIB_IEN(3:4,IE),PDLIB_IEN(5:6,IE))
-      PDLIB_IEND(3,1,IE) = DOT_PRODUCT(PDLIB_IEN(5:6,IE),PDLIB_IEN(1:2,IE))
-      PDLIB_IEND(3,2,IE) = DOT_PRODUCT(PDLIB_IEN(5:6,IE),PDLIB_IEN(3:4,IE))
-      PDLIB_IEND(3,3,IE) = DOT_PRODUCT(PDLIB_IEN(5:6,IE),PDLIB_IEN(5:6,IE))
-
 
       PDLIB_CCON(I1) = PDLIB_CCON(I1) + 1
       PDLIB_CCON(I2) = PDLIB_CCON(I2) + 1

model/src/gx_outf.F90

@@ -1,5 +1,37 @@
+!> @file
+!> @brief Generate GrADS input files from raw WAVEWATCH data file.
+!>
+!> @author H. L. Tolman
+!> @author A. Chawla
+!> @author J.H.G.M. Alves
+!> @date   22-Mar-2021
+!>
 #include "w3macros.h"
+
 !/ ------------------------------------------------------------------- /
+!>
+!> @brief Generate GrADS input files from raw WAVEWATCH data file.
+!>
+!> @details
+!>  Data is read from the grid output file out_grd.ww3 (raw data)
+!>  and from the file gx_outf.inp ( NDSI, output requests ).
+!>  Model definition and raw data files are read using WAVEWATCH III
+!>  subroutines.
+!>
+!>  Output files are ww3.ctl and ww3.grads. The output files
+!>  contains a land-sea map, followed by requested fields. See the
+!>  control file for the names of the fields.
+!>
+!> @author H. L. Tolman
+!> @author A. Chawla
+!> @author J.H.G.M. Alves
+!> @date   22-Mar-2021
+!>
+!> @copyright Copyright 2009-2022 National Weather Service (NWS),
+!>       National Oceanic and Atmospheric Administration.  All rights
+!>       reserved.  WAVEWATCH III is a trademark of the NWS.
+!>       No unauthorized use without permission.
+!>
 PROGRAM GXOUTF
   !/
   !/                  +-----------------------------------+
@@ -740,6 +772,16 @@ PROGRAM GXOUTF
   !/
 CONTAINS
   !/ ------------------------------------------------------------------- /
+  !>
+  !> @brief Perform actual output for GrADS postprocessing.
+  !>
+  !> @param[in] NX    Grid dimensions.
+  !> @param[in] NY    Grid dimensions.
+  !> @param[in] NSEA  Number of sea points.
+  !>
+  !> @author H. L. Tolman
+  !> @date   22-Mar-2021
+  !>
   SUBROUTINE GXEXGO ( NX, NY, NSEA )
     !/
     !/                  +-----------------------------------+

model/src/gx_outp.F90

@@ -1,5 +1,27 @@
+!> @file
+!> @brief Post-processing of point output for GrADS post-processing.
+!>
+!> @author H. L. Tolman
+!> @author J.H. Alves
+!> @author F. Ardhuin
+!> @date   27-Aug-2015
+!>
+
 #include "w3macros.h"
 !/ ------------------------------------------------------------------- /
+!>
+!> @brief Post-processing of point output for GrADS post-processing.
+!>
+!> @author H. L. Tolman
+!> @author J.H. Alves
+!> @author F. Ardhuin
+!> @date   27-Aug-2015
+!>
+!> @copyright Copyright 2009-2022 National Weather Service (NWS),
+!>       National Oceanic and Atmospheric Administration.  All rights
+!>       reserved.  WAVEWATCH III is a trademark of the NWS.
+!>       No unauthorized use without permission.
+!>
 PROGRAM GXOUTP
   !/
   !/                  +-----------------------------------+
@@ -539,6 +561,12 @@ PROGRAM GXOUTP
   !/
 CONTAINS
   !/ ------------------------------------------------------------------- /
+  !>
+  !> @brief Perform actual point output.
+  !>
+  !> @author H. L. Tolman
+  !> @date   16-Jul-2012
+  !>
   SUBROUTINE GXEXPO
     !/
     !/                  +-----------------------------------+