Merge in NOAA develop head

.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

@@ -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]
 
@@ -8,34 +13,34 @@ concurrency:
 
 # Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
 env:
-  cache_key: intel7
+  cache_key: intel10-3
   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-latest
 
     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 +56,28 @@ 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-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
         if: steps.cache-env.outputs.cache-hit != 'true'
         run: |
+          sudo mv /usr/local /usr/local_mv
           # 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
-          spack add intel-oneapi-mpi
+          sudo apt install cmake
+          spack external find
+          spack config add "packages:mpi:require:'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 +98,17 @@ 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-latest
 
     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
@@ -112,12 +119,14 @@ jobs:
 
       - name: build-ww3
         run: |
+          sudo mv /usr/local /usr/local_mv
+          sudo apt install cmake
           . /opt/intel/oneapi/setvars.sh
           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

.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 }}-${{ hashFiles('ww3/model/ci/spack_gnu.yaml') }}
+
+      # Build WW3 spack environment
+      - name: install-dependencies-with-spack
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          # Install NetCDF, ESMF, g2, etc using Spack
+          sudo apt install cmake
+          git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
+          source spack/share/spack/setup-env.sh
+          spack env create ww3-gnu ww3/model/ci/spack_gnu.yaml
+          spack env activate ww3-gnu
+          spack compiler find
+          spack external find cmake
+          spack add [email protected]
+          spack concretize
+          spack install --dirty -v
+
+      - name: build-oasis
+        if: steps.cache-env.outputs.cache-hit != 'true'
+        run: |
+          source spack/share/spack/setup-env.sh
+          spack env activate ww3-gnu
+          export WWATCH3_DIR=${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/defs.tex

@@ -94,6 +94,9 @@
 \newcommand{\cR}{{\cal R}}
 \newcommand{\cS}{{\cal S}}
 
+\newcommand{\rd}{{\mathrm d}}
+
+
 \newcommand{\marbox}[1]{\marginpar{\fbox{{\small #1}}}}
 
 \newcommand{\proddefH}[3]{

manual/eqs/ICE4.tex

@@ -52,6 +52,20 @@ \subsubsection{~$S_{ice}$: Empirical/parametric damping by sea ice} \label{sec:I
 
 {\code IC4M7}: This is a formula for dissipation from \cite{art:Dob15}, developed for a mixture of pancake and frazil ice, using data collected in the Weddell Sea (Antarctica). The formula depends on wave frequency and ice thickness:
 \begin{equation}\label{eq:ice7}
-  {\alpha=0.2T^{-2.13}h} \:\:\: .
+  {\alpha=2k_i=0.2h^1f^{2.13}} \:\:\: .
 \end{equation}
 This method is described in \cite{rep:RPLA18}.
+
+{\code IC4M8}: Like {\code IC4M7}, this method is in the general form of 
+\begin{equation}\label{eq:ice8}
+  {k_i=C_{hf}h^mf^n} \:\:\: .
+\end{equation}
+The formula is taken from \cite{Meylan2018}, where it is described as a ``Model with Order 3 Power Law''. It is applied by \cite{Liu2020}, where it is referred to as the ``M2'' model. The model specifies $m=1$ and $n=3$, and $C_{hf}$ is a user-specified calibration coefficient. \cite{Liu2020} provide calibration to two field cases and \cite{rep:RYW2021} provides a calibration to a third field case, \cite{art:RMK2021}. The third calibration is set as the default for {\code IC4M8}, $C_{hf}=0.059$, but can be changed in using the namelist parameter (constant and uniform) {\code IC4CN}, or using the spatially and/or temporally variable parameter  ${C_{ice,2}}$ . Further details on the calibrations are available in the inline documentation in {\file w3sic4md.F90}.  This method is functionally the same as the ``{\code M2}'' model in {\code IC5} (i.e., {\code IC5} with {\code IC5VEMOD=3}) and is redundantly included here as {\code IC4M8} because it is in the same ``family'' as {\code IC4M7} and {\code IC4M9}, being in the form of Eq. (\ref{eq:ice8}). 
+
+For an example of setting the namelist parameter, see {\file /regtests/ww3\_tic1.1/input\_IC4\_M8}.
+
+{\code IC4M9}: This formula is taken from the ``monomial power fit'' given in section 2.2.3 of \cite{rep:RYW2021}. Like {\code IC4M7} and {\code IC4M8}, it is a specific case of the general form of Eq. (\ref{eq:ice8}). The specificity is the constraint that $m=n/2-1$. This constraint is derived by \cite{rep:RYW2021} by invoking the scaling from \cite{art:YRW2019}, which is based on Reynolds number with ice thickness as the relevant length scale. This is also given as equation 2 in \cite{art:YRW2022}. The default namelist settings are $C_{hf}=2.9$ and $n=4.5$, from calibration by \cite{rep:RYW2021} to  \cite{art:RMK2021}. Further details, including alternative calibrations such as \cite{art:Yu2022}, are available in the inline documentation in {\file w3sic4md.F90}. Constant values can be set using namelist parameters, where $C_{hf}$ and $n$ are {\code IC4CN(1)} and {\code IC4CN(2)}, respectively. Spatially and/or temporally versions of the same can be specified as ${C_{ice,2}}$ and ${C_{ice,3}}$, respectively.
+
+The namelist default $C_{hf}$ values in {\code IC4M8} and {\code IC4M9} are consistent with those of identical formulae implemented in \cite{man:SWAN4145A}.
+
+

manual/eqs/ICE5.tex

@@ -25,7 +25,7 @@ \subsubsection{~$S_{ice}$: Damping by sea ice (effective medium models)} \label{
 \begin{align}
 k_i^{EFS} &\propto \eta h_i^3 \sigma^{11},\label{eq:fspw}\\ k_i^{RP} &\propto \frac{\eta}{\rho_w g^2} \sigma^3,\label{eq:rppw}
 \end{align}
-whereas previous field measurements \citep[e.g.,][]{Meylan2018, Rogers2021} support a power law $k_i \propto \sigma^n$, with $n$ between 2 and 4. Eqs.~(\ref{eq:fspw}) and (\ref{eq:rppw}) indicate at certain regimes (i.e., $k_r \approx k_0$ and low $k_i$), $k_i$ of the EFS model is too sensitive to wave frequency and $k_i$ of the RP model shows no dependence on ice thickness.
+whereas previous field measurements \citep[e.g.,][]{Meylan2018, RMK21} support a power law $k_i \propto \sigma^n$, with $n$ between 2 and 4. Eqs.~(\ref{eq:fspw}) and (\ref{eq:rppw}) indicate at certain regimes (i.e., $k_r \approx k_0$ and low $k_i$), $k_i$ of the EFS model is too sensitive to wave frequency and $k_i$ of the RP model shows no dependence on ice thickness.
 
 The third model included in the {\code IC5} module is based on the ``Model with Order 3 Power Law'' proposed by \citet[][their section 6.2; hereafter the M2 model]{Meylan2018}, which assumes the loss of wave energy is proportional to the horizontal ice velocity squared times the ice thickness. The attenuation rate is given by
 \begin{equation}
@@ -52,4 +52,4 @@ \subsubsection{~$S_{ice}$: Damping by sea ice (effective medium models)} \label{
 %
 \cit{IC5VEMOD} {the sea ice model to be selected: 1 - {\code EFS}, 2 - {\code RP}, 3 - {\code M2}; Default=3 (i.e., \textbf{the {\code M2} model is chosen}).}
 \end{clist}
-The first 6 parameters were introduced to improve the stability of the numerical solver for the EFS model \citep[the solver may fail for small wave periods in some rare cases, particularly for shallow water depth $d$ and low $G$; see][]{Liu2020}. Nonetheless, since version 7.12, the M2 model becomes the default option and these limiters are therefore not used by default.
+The first 6 parameters were introduced to improve the stability of the numerical solver for the EFS model \citep[the solver may fail for small wave periods in some rare cases, particularly for shallow water depth $d$ and low $G$; see][]{Liu2020}. Nonetheless, since version 7.12, the M2 model becomes the default option and these limiters are therefore not used by default.