Merge branch 'NOAA-EMC:develop' into init_bugs2

.github/workflows/intel.yml

@@ -1,3 +1,8 @@
+# This is a GitHub actions workflow for WW3.
+#
+# This workflow builds with the Intel compilers.
+#
+# Matt Masarik, Alex Richert, Ed Hartnett
 name: Intel Linux Build
 on: [push, pull_request, workflow_dispatch]
 
@@ -8,7 +13,7 @@ concurrency:
 
 # Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
 env:
-  cache_key: intel10
+  cache_key: intel10-3
   CC: icc
   FC: ifort
   CXX: icpc
@@ -51,7 +56,7 @@ 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-dev-utilities 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-compiler-fortran-2023.2.1 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.1 intel-oneapi-openmp
 
       # Build WW3 spack environment
       - name: install-dependencies-with-spack

.github/workflows/io_gnu_yml.old

@@ -0,0 +1,122 @@
+name: io_gnu
+on: [push, pull_request, workflow_dispatch]
+
+# Cancel in-progress workflows when pushing to a branch
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+env:
+  cache_key: gnu11-1
+  CC: gcc-10
+  FC: gfortran-10
+  CXX: g++-10
+
+
+# Split into a steup step, and a WW3 build step which
+# 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-latest
+
+    steps:
+      - name: checkout-ww3
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        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@v3
+        with:
+          path: |
+            spack
+            ~/.spack
+            work_oasis3-mct
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+
+      # Build WW3 spack environment
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          # Install NetCDF, ESMF, g2, etc using Spack
+          sudo apt install cmake
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create ww3-gnu ww3/model/ci/spack_gnu.yaml
+          spack env activate ww3-gnu
+          spack compiler find
+          spack external find cmake
+          spack add mpich@3.4.2
+          spack concretize
+          spack install --dirty -v
+
+      - name: build-oasis
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate ww3-gnu
+          export WWATCH3_DIR=${GITHUB_WORKSPACE}/ww3/model
+          export OASIS_INPUT_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/oasis3-mct
+          export OASIS_WORK_PATH=${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct
+          cd ww3/regtests/ww3_tp2.14/input/oasis3-mct/util/make_dir
+          cmake .
+          make VERBOSE=1
+          cp -r ${GITHUB_WORKSPACE}/ww3/regtests/ww3_tp2.14/input/work_oasis3-mct ${GITHUB_WORKSPACE}
+
+  io_gnu:
+    needs: setup
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: install-dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install doxygen gcovr valgrind
+
+      - name: checkout-ww3
+        uses: actions/checkout@v3
+        with:
+            path: ww3
+
+      - name: cache-env
+        id: cache-env
+        uses: actions/cache@v3
+        with:
+          path: |
+            spack
+            ~/.spack
+            work_oasis3-mct
+          key: spack-${{ runner.os }}-${{ env.cache_key }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+
+      - name: build-ww3
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate ww3-gnu
+          set -x
+          cd ww3
+          export CC=mpicc
+          export FC=mpif90
+          export OASISDIR=${GITHUB_WORKSPACE}/work_oasis3-mct
+          mkdir build && cd build
+          export LD_LIBRARY_PATH="/home/runner/work/WW3/WW3/spack/var/spack/environments/ww3-gnu/.spack-env/view/:$LD_LIBRARY_PATH"
+          cmake -DSWITCH=${GITHUB_WORKSPACE}/ww3/regtests/unittests/data/switch.io -DCMAKE_BUILD_TYPE=Debug -DCMAKE_Fortran_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -Wall -fno-omit-frame-pointer -fsanitize=address" -DCMAKE_C_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -Wall -fno-omit-frame-pointer -fsanitize=address" ..
+          make -j2 VERBOSE=1
+          ./bin/ww3_grid
+          mv mod_def.ww3 regtests/unittests
+          ctest --verbose --output-on-failure --rerun-failed
+          gcovr --root .. -v  --html-details --exclude ../regtests/unittests --exclude CMakeFiles --print-summary -o test-coverage.html &> /dev/null
+
+      - name: upload-test-coverage
+        uses: actions/upload-artifact@v3
+        with:
+          name: ww3-test-coverage
+          path: |
+            ww3/build/*.html
+            ww3/build/*.css
+
+

CMakeLists.txt

@@ -58,3 +58,9 @@ if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$")
 endif()
 
 add_subdirectory(model)
+
+# Turn on unit testing.
+include(CTest)
+if(BUILD_TESTING)
+  add_subdirectory(regtests/unittests)
+endif()

manual/eqs/NL1.tex

@@ -55,37 +55,38 @@ \subsubsection{~$S_{nl}$: Discrete Interaction Approximation (\dia)} \label{sec:
 \sin(\delta_{\theta,3})&=&\sin(\delta_{\theta,2}) (1-\lambda)^2/(1+\lambda)^2.
 \end{eqnarray}
 
- For these quadruplets, each source term value
-$S_{nl}(\bk)$ corresponding to each discrete $(f_r,\theta)$
-we compute the three contributions that correspond to the situation in which $\bk$ takes the role of $\bk$,$\bk_{2,+}$, $\bk_{2,-}$, $\bk_{3,+}$  and $\bk_{3,-}$ in the quadruplet, namely the full source term is 
+Hence for any $\bk$ one quadruplet selects $\bk_{2,+}$ and $\bk_{3,+}$, and the other quadruplet selects its mirror image 
+$\bk_{2,-}$, $\bk_{2,-}$. Because there are 3 different components interacting in the two DIA-selected quadruplets, any discrete spectral component $(f_r,\theta)$ is actually involved in 6 quadruplets and directly exchanges energy with 12 other components $(f_r',\theta')$. Because the values of $f'_r$ and $\theta'$ do not fall exacly on other discrete components, the spectral density is interpolated using a bilinear interpolation, so that each source term value
+$S_{nl}(\bk)$ contains the direct exchange of energy with 48 other discrete components. 
+we compute the three contributions that correspond to the situation in which $\bk$ takes the role of $\bk$,$\bk_{2,+}$, $\bk_{2,-}$, $\bk_{3,+}$  and $\bk_{3,-}$ in the quadruplet, namely the full source term is, without making explicit that bilinear interpolation, 
 \begin{eqnarray} 
-S_{\mathrm{nl}}(\bk) &=& -2  \left[\delta S_{\mathrm{nl}}(\bk,\bk_2,\bk_3,+)+\delta S_{\mathrm{nl}}(\bk,\bk_2,\bk_3,-)\right] \nonumber  \\
- & & + \delta  S_{\mathrm{nl}}(\bk_4,\bk,\bk_5,+) + \delta  S_{\mathrm{nl}}(\bk_6,\bk,\bk_7,-)  \\
-     & &        +   \delta S_{\mathrm{nl}}(\bk_8,\bk_9,\bk, +) + \delta S_{\mathrm{nl}}(\bk_{10},\bk_{11},\bk, -) . \label{eq:diasum}
+S_{\mathrm{nl}}(\bk) &=& -2  \left[\delta S_{\mathrm{nl}}(\bk,\bk_{2,+},\bk_{3,+})+\delta S_{\mathrm{nl}}(\bk,\bk_{2,-},\bk_{3,-})\right] \nonumber  \\
+ & & + \delta  S_{\mathrm{nl}}(\bk_4,\bk,\bk_5) + \delta  S_{\mathrm{nl}}(\bk_6,\bk,\bk_7)  \\
+     & &        +   \delta S_{\mathrm{nl}}(\bk_8,\bk_9,\bk) + \delta S_{\mathrm{nl}}(\bk_{10},\bk_{11},\bk) . \label{eq:diasum}
 \end{eqnarray}
-with elementary contributions given by  
+where the geometry of the quadruplet $(\bk_4,\bk_4,\bk,\bk_5)$ is obtained from that of $(\bk,\bk,\bk_{2,+},\bk_{3,+})$ by a dilation by a factor $(1+\lambda)^2$ and rotation by the angle $\delta_{\theta,2}$;  $(\bk_6,\bk_6,\bk,\bk_7)$ has the same dilation but the opposite rotation; $(\bk_8,\bk_8,\bk_9,\bk)$ is dilated by a factor  $(1-\lambda)^2$ and rotated by the angle $-\delta_{\theta,3}$: and $(\bk_{10},\bk_{10},\bk_{11},\bk)$ is dilated by the same factor and rotated by the opposite angle. 
+
+
+The elementary contributions $\delta  S_{\mathrm{nl}}(\bk_l,\bk_m,\bk_n)$   are given by  
 %----------------------------%
 % Nonlinear interactions DIA %
 %----------------------------%
 % eq:snl_dia
 
 \begin{equation}
-\delta S_{\mathrm{nl}}(\bk,\bk_2,\bk_3,s) =  \frac{C}{g^4} f_{r,1}^{11} \left [ F^2 \left ( \frac{F_{2,s}}{(1+\lambda_{nl})^4} +
-        \frac{F_{3,s}}{(1-\lambda_{nl})^4} \right ) - \frac{2 F F_{2,s} F_{3,s}}{(1-\lambda_{nl}^2)^4} \right] ,
+\delta S_{\mathrm{nl}}(\bk_l,\bk_m,\bk_n) =  \frac{C}{g^4} f_{r,l}^{11} \left [ F_l^2 \left ( \frac{F_m}{(1+\lambda)^4} +
+        \frac{F_n}{(1-\lambda)^4} \right ) - \frac{2 F_l F_m F_n}{(1-\lambda^2)^4} \right] ,
       \label{eq:snl_dia}
 \end{equation}
-where $s=+$ or $s=-$ is a sign index, and the spectral densities are  $F = F(f_{r} ,\theta)$, $F_{2,+} = F(f_{r,2} ,\theta + \delta_{\theta,2})$, $F_{2,-} = F(f_{r,2} ,\theta - \delta_{\theta,2})$,  etc.
+where the spectral densities are  $F_l = F(f_{r,l} ,\theta_l)$, etc. 
  $C$ is a proportionality constant that was tuned to reproduce the inverse energy cascade.  Default values for different source term packages are presented in Table~\ref{tab:snl_par}.
-As a result, when accounting for the two quadruplet configurations, the source term at $\bk$ includes the interactions with 
-10 other spectral components. Besides, because $f_{r,2}$ and $f_{r,3}$ nor $\theta_{2,\pm} $ and $\theta_{3,\pm} $ fall on discretized frequencies and directions, the spectral densities are bilinearly interpolated, which involves 4 discrete spectral components for each of these 10 components. 
-
 
 
 % tab:snl_par
 
 \begin{table} \begin{center}
  \begin{tabular}{|l|c|c|} \hline
-                    & $\lambda_{nl}$ &     $C$      \\ \hline
+                    & $\lambda$ &     $C$      \\ \hline
 ST6                 &      0.25      & $3.00 \; 10^7$  \\ \hline
 \wam-3              &      0.25      & $2.78 \; 10^7$  \\ \hline
 ST4 (Ardhuin et al.)&      0.25      & $2.50 \; 10^7$  \\ \hline

manual/manual.bib

@@ -3665,6 +3665,17 @@ @article{art:DC23
 	year = {2023}
 }
 
+@ARTICLE{Webb1978,
+   author = "D. J. Webb",
+   title = "Nonlinear transfer between sea waves",
+   journal = DSR,
+   volume = 25,
+   pages = "279--298",
+   year = 1978,
+   where="paper",
+}
+
+
 @ARTICLE{Lavrenov2001,
    author = "Igor V. Lavrenov",
    title = "Effect of wind wave parameter fluctuation on the nonlinear spectrum evolution",

manual/sys/files_w3.tex

@@ -506,11 +506,15 @@ \subsubsection{~Wave model modules} \label{sec:wave_mod}
 \end{flist}
 
 \noindent
-Nonlinear interaction module (\dia) \hfill {\file w3snl1md.ftn}
+Nonlinear interaction module (\dia or GQM) \hfill {\file w3snl1md.ftn}
 
 \begin{flisti}
 \fit{w3snl1}{Calculation of $S_{nl}$.}
 \fit{insnl1}{Initialization for $S_{nl}$.}
+\fit{w3snlgqm}{Calculation of $S_{nl}$.}
+\fit{w3scouple}{Calculation of coupling coefficient.}
+\fit{gauleg}{Calculation of Gauss-Legendre quadrature coefficients.}
+\fit{INSNLGQM}{Initialization for $S_{nl}$ with GQ method.}
 \end{flisti}
 
 \noindent

model/src/w3iopomd.F90

@@ -1023,17 +1023,81 @@ SUBROUTINE W3IOPE ( A )
     !/ End of W3IOPE ----------------------------------------------------- /
     !/
   END SUBROUTINE W3IOPE
-  !/ ------------------------------------------------------------------- /
+
+  !> Read or write point output.
   !>
-  !> @brief Read/write point output.
+  !> This subroutine can either read or write the point output file,
+  !> depending on the value of the first parameter.
   !>
-  !> @param[in]  INXOUT  Test string for read/write.
-  !> @param[in]  NDSOP   File unit number.
-  !> @param[out] IOTST   Test indictor for reading.
-  !> @param[in]  IMOD    Model number for W3GDAT etc.
+  !> When reading, the entire file is read with one call to this
+  !> subroutine.
   !>
-  !> @author H. L. Tolman  @date 25-Jul-2006
+  !> When writing, this subroutine can either write one timestep or
+  !> the whole model run. This is an option in the input file. If the
+  !> entire model run is to be written, then OFILES(2) is 0. If only
+  !> one timestep is to be written, then OFILES(2) is 1.
+  !>
+  !> If OFILES(2) is 0, the output file is names out_pnt.ww3. If
+  !> OFILES(2) is 1, the output file is named TIMETAG.out_pnt.ww3.
+  !>
+  !> The format of the point output file is:
+  !> Size (bytes) | Type | Variable | Meaning
+  !> -------------|------|----------|--------
+  !> 40 | character*40 | IDTST | ID string
+  !> 4 | integer | VERTST | Model definition file version number
+  !> 4 | integer | NK | Dimension of frequency
+  !> 4 | integer | MTH | Directionality of the frequency
+  !> 4 | integer | NOPTS | Number of output points.
+  !> 8*NOPTS | integer(2,NOPTS) | PTLOC | Point locations
+  !> 7*NOPTS | character*7 | PTNME | Point names
+  !> 8 | integer(2) | TIME | Time
+  !> reclen*NOPTS | * | * | records
+  !>
+  !> Each record contains:
+  !> Size (bytes) | Type | Variable | Meaning
+  !> -------------|------|----------|--------
+  !> 4 | integer | IW | Number of water points in interpolation box for output point.
+  !> 4 | integer | II | Number of ice points in interpolation box for output point.
+  !> 4 | integer | IL | Number of land points in interpolation box for output point.
+  !> 4 | real | DPO | Interpolated depths.
+  !> 4 | real | WAO | Interpolated wind speeds.
+  !> 4 | real | WDO | Interpolated wind directions.
+  !> 4 | real | TAUAO | (W3_FLX5 only) Interpolated atmospheric stresses.
+  !> 4 | real | TAUDO | (W3_FLX5 only) Interpolated atmospheric stress directions.
+  !> 4 | real | DAIRO | (W3_FLX5 only) Interpolated rho atmosphere.
+  !> 4 | real | ZET_SETO | (W3_SETUP only) Used for wave setup.
+  !> 4 | real | ASO | Interpolated air-sea temperature difference
+  !> 4 | real | CAO | Interpolated current speeds.
+  !> 4 | real | CDO | Interpolated current directions.
+  !> 4 | real | ICEO | Interpolated ice concentration.
+  !> 4 | real | ICEHO | Interpolated ice thickness.
+  !> 4 | real | ICEFO | Interpolated ice floe.
+  !> 13 | char | GRDID | Originating grid ID
+  !> 4 | real | SPCO(J,I),J=1,NSPEC | Output spectra
   !>
+  !> In the event of error, EXTCDE() will be called with the following exit codes:
+  !> - 1 INXOUT must be 'READ' or 'WRITE'.
+  !> - 2 Unexpectedly changed from WRITE to READ in subsequent call.
+  !> - 10 Unexpected IDSTR
+  !> - 11 Unexpected VEROPT
+  !> - 12 Unexpected MK or MTH
+  !> - 20 Error opening file.
+  !> - 21 Unexpected end of file during read.
+  !> - 22 Error reading file.
+  !> - 23 Unexpected end of file during read.
+  !>
+  !> @param[in] INXOUT String indicating read/write. Must be 'READ' or
+  !> 'WRITE'.
+  !> @param[in] NDSOP File unit number.
+  !> @param[out] IOTST Error code:
+  !> - 0 No error.
+  !> - -1 Unexpected end of file when reading.
+  !> @param[in] IMOD Model number for W3GDAT etc.
+#ifdef W3_ASCII
+  !> @param[in] NDSOA File unit number for ASCII output.
+#endif
+  !>
+  !> @author H. L. Tolman  @date 25-Jul-2006
   SUBROUTINE W3IOPO ( INXOUT, NDSOP, IOTST, IMOD &
 #ifdef W3_ASCII
       ,NDSOA &