Merge branch 'develop' into feature/ST4table

.github/workflows/gnu.yml

@@ -7,7 +7,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  cache_key: gnu8
+  cache_key: gnu11
   CC: gcc-10
   FC: gfortran-10
   CXX: g++-10
@@ -24,14 +24,14 @@ jobs:
     steps:
       - name: checkout-ww3
         if: steps.cache-env.outputs.cache-hit != 'true'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
             path: ww3
       # Cache spack, OASIS, and compiler
       # No way to flush Action cache, so key may have # appended
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack
@@ -45,7 +45,7 @@ jobs:
         run: |
           # Install NetCDF, ESMF, g2, etc using Spack
           sudo apt install cmake
-          git clone -c feature.manyFiles=true https://github.com/spack/spack.git
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
           source spack/share/spack/setup-env.sh
           spack env create ww3-gnu ww3/model/ci/spack_gnu.yaml
           spack env activate ww3-gnu
@@ -77,13 +77,13 @@ jobs:
 
     steps:
       - name: checkout-ww3
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
             path: ww3
 
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack

.github/workflows/intel.yml

@@ -8,34 +8,34 @@ concurrency:
 
 # Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
 env:
-  cache_key: intel7
+  cache_key: intel10
   CC: icc
   FC: ifort
   CXX: icpc
   I_MPI_CC: icc
   I_MPI_F90: ifort
 
 # Split into a dependency build step, and a WW3 build step which
-# builds multiple switches in a matrix. The setup is run once and 
+# builds multiple switches in a matrix. The setup is run once and
 # the environment is cached so each build of WW3 can share the dependencies.
 
 jobs:
   setup:
-    runs-on: ubuntu-20.04 
+    runs-on: ubuntu-20.04
 
     steps:
 
       - name: checkout-ww3
         if: steps.cache-env.outputs.cache-hit != 'true'
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
             path: ww3
 
       # Cache spack, OASIS, and compiler
       # No way to flush Action cache, so key may have # appended
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack
@@ -51,26 +51,27 @@ jobs:
           sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
           echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
           sudo apt-get update
-          sudo apt-get install intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
+          sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
 
       # Build WW3 spack environment
       - name: install-dependencies-with-spack
         if: steps.cache-env.outputs.cache-hit != 'true'
         run: |
           # Install NetCDF, ESMF, g2, etc using Spack
           . /opt/intel/oneapi/setvars.sh
-          sudo mv /usr/local /usrlocal_renamed
-          sudo apt install cmake
-          git clone -c feature.manyFiles=true https://github.com/spack/spack.git
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
           source spack/share/spack/setup-env.sh
           ln -s $(realpath $(which gcc)) spack/lib/spack/env/intel/gcc # spack/make bug in ESMF
           spack env create ww3-intel ww3/model/ci/spack_intel.yaml
           spack env activate ww3-intel
           spack compiler find
-          spack external find cmake
+          sudo apt install cmake
+          spack external find
           spack add intel-oneapi-mpi
+          spack config add "packages:all:require:['%intel']"
           spack concretize
           spack install --dirty -v --fail-fast
+          spack clean --all
 
       - name: build-oasis
         if: steps.cache-env.outputs.cache-hit != 'true'
@@ -91,17 +92,17 @@ jobs:
     strategy:
       matrix:
         switch: [Ifremer1, NCEP_st2, NCEP_st4, ite_pdlib, NCEP_st4sbs, NCEP_glwu, OASACM, UKMO, MULTI_ESMF]
-    runs-on: ubuntu-20.04 
+    runs-on: ubuntu-20.04
 
     steps:
       - name: checkout-ww3
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
             path: ww3
 
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack
@@ -116,8 +117,8 @@ jobs:
           source spack/share/spack/setup-env.sh
           spack env activate ww3-intel
           cd ww3
-          export CC=mpicc
-          export FC=mpif90
+          export CC=mpiicc
+          export FC=mpiifort
           export OASISDIR=${GITHUB_WORKSPACE}/work_oasis3-mct
           mkdir build && cd build
           if [[ ${{ matrix.switch }} == "MULTI_ESMF" ]]; then

manual/eqs/output.tex

@@ -12,9 +12,9 @@ \subsection{~Output parameters} \label{sub:outpars}
 in \para\ref{sec:ww3shel}. That input file also provides a list of flags  
 indicating if output parameters are available in different field
 output file types (ASCII, grib, igrads, NetCDF). 
-For any details on how these parameters are computed, the user may read the code of the  {\code w3iogo} routine, in the {\code w3iogomd.ftn} module. 
+For any details on how these parameters are computed, the user may read the code of the  {\code w3iogo} routine, in the {\code w3iogomd.F90} module. 
 
-Selection of field outputs in  {\code ww3\_shel.inp} is most easily performed by providing a list of the 
+Selection of field outputs in {\code ww3\_shel.nml} or {\code ww3\_shel.inp} is most easily performed by providing a list of the 
 requested parameters, for example, {\textbf HS DIR SPR}  will request the calculation of significant wave height, mean direction and directional spread. These will thus be stored in the {\code out\_grd.XX} file and can be post-processed, for example in NetCDF using   {\code ww3\_ouf}. Examples are given in \para\ref{sec:ww3multi} and
 \para\ref{sec:ww3ounf}. The names for these namelists are the bold names below, for 
 example \textbf{HS}. 
@@ -26,6 +26,9 @@ \subsection{~Output parameters} \label{sub:outpars}
 file extensions, NetCDF variable names and namelist-based selection (see 
 also \para\ref{sec:ww3ounf}), and the long parameter name/definition.
 
+When the result is not overly sensitive to the contribution of the unresolved part of the spectrum (for $f<f_{NK}$), the contribution of the tail is parameterized assuming a power law decay of the spectrum, by default $E(f,\theta) = E(f_{NK},\theta) (f_{NK}/f)^{-5}$, for some parameters this is either unnecessary or misleading, and the integrals are computed only up to $f_{NK}$. 
+
+
 Finally we note that in all definitions the frequency is the \emph{relative} frequency. Thus, in the presence of currents, these can only be compared to drifting measurement data or data obtained in wavenumber and converted to frequency. Comparison to fixed instrument data requires the use of the full spectrum and proper conversion to the fixed reference frame.
 
 \begin{list}{\Roman{outgrps})\hfill}
@@ -300,8 +303,12 @@ \subsection{~Output parameters} \label{sub:outpars}
 \item \textbf{MSD} Direction of the maximum slope variance mss$_u$
 \item \textbf{MCD} Spectral tail direction
 \item \textbf{QP}  Peakedness parameter \citep{art:G70}
-      \begin{equation} Q_p = \frac{2}{E^2} \int_0^{2\pi} \int_0^\infty
-      \sigma\:F(\sigma,\theta)^2\:d\sigma\:d\theta \: \label{eq:qp}
+      \begin{equation} Q_p = \frac{2}{E^2} \int_0^{f_{NK}} f \left( \int_0^{2\pi} 
+      F(f,\theta) \:\rd \theta \right)^2 \: \rd  f \: \label{eq:qp}
+      \end{equation}
+\item \textbf{QKK}  wavenumber peakedness \citep{art:DC23}
+      \begin{equation} Q_{kk} = \frac{1}{E^2} \int_0^{f_{NK}} \int_0^{2\pi} 
+      0.5 \left[ A(k,\theta)+ A(k,\theta+\pi)\right]^2 \frac{\sigma^2}{k C_g} \:\rd \theta  \: \rd  \sigma \: \label{eq:qkk}
       \end{equation}
 \end{list}
 

manual/manual.bib

@@ -3654,3 +3654,13 @@ @article{vanVledder2006
 	volume = {53},
 	year = {2006}
 }
+
+@article{art:DC23,
+	author = {De Carlo, Marine and Fabrice Ardhuin and Annabelle Ollivier and Adrien Nigou },
+	journal = {Journal of Geophysical Research - Oceans},
+	keywords = {wave groups,altimetry},
+	pages = {},
+	title = {Wave groups and small scale variability of wave heights observed by altimeters},
+	volume = {},
+	year = {2023}
+}

model/ci/spack_gnu.yaml

@@ -13,7 +13,8 @@ spack:
   - [email protected]
   - [email protected]
   - [email protected]
-  - [email protected]~pio~pnetcdf~xerces
+  - [email protected]+fortran~pnetcdf
+  - [email protected]~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:
+  - [email protected]~dap
+  - [email protected]
+  - [email protected]
+  - [email protected]
   - [email protected]~shared
   - [email protected]~shared
   - [email protected]+mpi+metis~shared
-  - [email protected]~dap
-  - [email protected]
   - [email protected]
-  - [email protected]
-  - [email protected]
   - [email protected]
-  - [email protected]~pio~pnetcdf~xerces
+  - [email protected]+fortran~pnetcdf
+  - [email protected]~debug~xerces+external-parallelio
   - intel-oneapi-mpi %intel
   view: true
   concretizer:

model/inp/ww3_shel.inp

@@ -139,6 +139,7 @@ $  T  T  2    15   HMAXD      SDMH  St Dev of MXC (STE)
 $  T  T  2    16   HCMAXD     SDMHC St Dev of MXHC (STE)
 $  F  T  2    17   WBT        WBT   Dominant wave breaking probability bT
 $  F  F  2    18   FP0        TP    Peak period (from peak freq)
+$  F  F  2    19   WNMEAN     WNM   Mean wavenumber
 $   -------------------------------------------------
 $        3                          Spectral Parameters (first 5)
 $   -------------------------------------------------
@@ -211,10 +212,10 @@ $        8                          Spectrum parameters
 $   -------------------------------------------------
 $  F  F  8     1   MSS[X,Y]   MSS   Mean square slopes
 $  F  F  8     2   MSC[X,Y]   MSC   Spectral level at high frequency tail
-$  F  F  8     3   WL02[X,Y]  WL02  East/X North/Y mean wavelength compon
-$  F  F  8     4   ALPXT      AXT   Correl sea surface gradients (x,t)
-$  F  F  8     5   ALPYT      AYT   Correl sea surface gradients (y,t)
-$  F  F  8     6   ALPXY      AXY   Correl sea surface gradients (x,y)
+!  F  F  8     3   MSSD       MSD   Slope direction
+!  F  F  8     4   MSCD       MCD   Tail slope direction
+!  F  F  8     5   QP         QP    Goda peakedness parameter
+!  F  F  8     6   QKK        QKK   Wavenumber peakedness
 $   -------------------------------------------------
 $        9                          Numerical diagnostics
 $   -------------------------------------------------

model/nml/ww3_multi.nml

@@ -195,13 +195,13 @@
 !
 ! * the detailed list of field names is given in model/nml/ww3_shel.nml :
 !  DPT CUR WND AST WLV ICE IBG TAU RHO D50 IC1 IC5
-!  HS LM T02 T0M1 T01 FP DIR SPR DP HIG
+!  HS LM T02 T0M1 T01 FP DIR SPR DP HIG MXE MXES MXH MXHC SDMH SDMHC WBT TP WNM
 !  EF TH1M STH1M TH2M STH2M WN
 !  PHS PTP PLP PDIR PSPR PWS PDP PQP PPE PGW PSW PTM10 PT01 PT02 PEP TWS PNR
 !  UST CHA CGE FAW TAW TWA WCC WCF WCH WCM FWS
 !  SXY TWO BHD FOC TUS USS P2S USF P2L TWI FIC USP TOC
 !  ABR UBR BED FBB TBB
-!  MSS MSC WL02 AXT AYT AXY
+!  MSS MSC MSD MCD QP QKK
 !  DTD FC CFX CFD CFK
 !  U1 U2
 !

model/nml/ww3_shel.nml

@@ -129,6 +129,7 @@
 !  T  T  2    16   HCMAXD     SDMHC St Dev of MXHC (STE)
 !  F  T  2    17   WBT        WBT   Dominant wave breaking probability bT
 !  F  F  2    18   FP0        TP    Peak period (from peak freq)
+!  F  F  2    19   WNMEAN     WNM   Mean wavenumber
 !   -------------------------------------------------
 !        3                          Spectral Parameters (first 5)
 !   -------------------------------------------------
@@ -201,10 +202,10 @@
 !   -------------------------------------------------
 !  F  F  8     1   MSS[X,Y]   MSS   Mean square slopes
 !  F  F  8     2   MSC[X,Y]   MSC   Spectral level at high frequency tail
-!  F  F  8     3   WL02[X,Y]  WL02  East/X North/Y mean wavelength compon
-!  F  F  8     4   ALPXT      AXT   Correl sea surface gradients (x,t)
-!  F  F  8     5   ALPYT      AYT   Correl sea surface gradients (y,t)
-!  F  F  8     6   ALPXY      AXY   Correl sea surface gradients (x,y)
+!  F  F  8     3   MSSD       MSD   Slope direction
+!  F  F  8     4   MSCD       MCD   Tail slope direction
+!  F  F  8     5   QP         QP    Goda peakedness parameter
+!  F  F  8     6   QKK        QKK   Wavenumber peakedness
 !   -------------------------------------------------
 !        9                          Numerical diagnostics
 !   -------------------------------------------------

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
     !/
     !/                  +-----------------------------------+