Merge branch 'NOAA-EMC:develop' into feature/pdlib/ufs1.1-unstr

MatthewMasarik-NOAA · Mar 28, 2024 · 7541f84 · 7541f84
2 parents b6c8896 + f66b6d4
commit 7541f84
Show file tree

Hide file tree

Showing 78 changed files with 3,824 additions and 748 deletions.
diff --git a/.github/workflows/intel.yml b/.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
@@ -21,7 +26,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-latest
 
     steps:
 
@@ -51,12 +56,13 @@ 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
         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
           git clone -c feature.manyFiles=true https://github.com/JCSDA/spack.git
@@ -67,7 +73,7 @@ jobs:
           spack compiler find
           sudo apt install cmake
           spack external find
-          spack add intel-oneapi-mpi
+          spack config add "packages:mpi:require:'intel-oneapi-mpi'"
           spack config add "packages:all:require:['%intel']"
           spack concretize
           spack install --dirty -v --fail-fast
@@ -92,7 +98,7 @@ 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
@@ -113,6 +119,8 @@ 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

diff --git a/.github/workflows/io_gnu_yml.old b/.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=${GITHUB_WORKSPACE}/ww3/regtests/unittests/data/switch.io -DCMAKE_BUILD_TYPE=Debug -DCMAKE_Fortran_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -Wall -fno-omit-frame-pointer -fsanitize=address" -DCMAKE_C_FLAGS="-g -fprofile-abs-path -fprofile-arcs -ftest-coverage -O0 -Wall -fno-omit-frame-pointer -fsanitize=address" ..
+          make -j2 VERBOSE=1
+          ./bin/ww3_grid
+          mv mod_def.ww3 regtests/unittests
+          ctest --verbose --output-on-failure --rerun-failed
+          gcovr --root .. -v  --html-details --exclude ../regtests/unittests --exclude CMakeFiles --print-summary -o test-coverage.html &> /dev/null
+
+      - name: upload-test-coverage
+        uses: actions/upload-artifact@v3
+        with:
+          name: ww3-test-coverage
+          path: |
+            ww3/build/*.html
+            ww3/build/*.css
+
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -58,3 +58,9 @@ if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$")
 endif()
 
 add_subdirectory(model)
+
+# Turn on unit testing.
+include(CTest)
+if(BUILD_TESTING)
+  add_subdirectory(regtests/unittests)
+endif()
diff --git a/manual/eqs/ICE4.tex b/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}.
+
+
diff --git a/manual/eqs/ICE5.tex b/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.
diff --git a/manual/eqs/ST3.tex b/manual/eqs/ST3.tex
@@ -57,16 +57,15 @@ \subsubsection{~$S_{in} + S_{ds}$: \wam\ cycle 4 (ECWAM)} \label{sec:ST3}
 waves that travel faster than the wind. This accounts for some gustiness in
 the wind and should possibly be resolution-dependent. For reference, this
 parameter was not properly set in early versions of the SWAN model, as
-discovered by R. Lalbeharry.}.  The roughness $z_1$ is defined as,
-
+discovered by R. Lalbeharry.}.  If the friction velocity $u_\star$ is known, 
+it gives the roughness $z_1$ and the wind speed at altitude $z_u$ (by default $z_u=10$~m),  
 \begin{eqnarray}
-U_{10}&=&\frac{u_\star}{\kappa} \log\left(\frac{z_u}{z_1}\right) \\
-z_1&=&\alpha_0 \frac{\tau}{ \sqrt{1-\tau_w/\tau}},
+z_1&=&\alpha_0 \frac{\tau}{ \sqrt{1-\tau_w/u_\star^2}}, \\
+U(z_u)&=&\frac{u_\star}{\kappa} \log\left(\frac{z_u}{z_1}\right) 
 \end{eqnarray}
 
 \noindent
-where $\tau=u_\star^2$, and $z_u$ is the height at which the wind is
-specified. These two equations provide an implicit functional dependence of
+In practice these two equations provide an implicit functional dependence of
 $u_\star$ on $U_{10}$ and $\tau_w/\tau$. This relationship is then tabulated
 \citep{art:Jan91, rep:Bea07}.
 

diff --git a/manual/eqs/ST4.tex b/manual/eqs/ST4.tex
@@ -8,10 +8,10 @@ \subsubsection{~$S_{\mathrm{in}} + S_{\mathrm{ds}}$: Saturation-based dissipatio
 This family of parameterizations uses a positive part of the wind input taken
 from WAM cycle 4 with an ad hoc reduction of $u_\star$, implemented in
 order to allow a balance with a saturation-based dissipation that uses different options for 
-a cumulative term. There are three main options for defining the saturation and the cumulative term. Chosing one or the other is done with the  {\F SDSBCHOICE} parameter, with  {\F SDSBCHOICE=1} for \cite{art:Aea10},  {\F SDSBCHOICE=2} for \cite{Filipot&Ardhuin2012}, and {\F SDSBCHOICE=3} for \cite{Romero2019}. That last options uses a saturation that is defined from the local spectral density, and thus gives zero dissipation for directions where the threshold is not reached, leading to much broader directional spectra. Also the stronger bimodality is achieved by having a strong modulation effect as a cumulative term. 
+a cumulative term. There are three main options for defining the saturation and the cumulative term. Chosing one or the other is done with the  {\F SDSBCHOICE} parameter, with  {\F SDSBCHOICE=1} for \cite{art:Aea10},  {\F SDSBCHOICE=2} for \cite{Filipot&Ardhuin2012}, and {\F SDSBCHOICE=3} for \cite{Romero2019} and later adjustments including \cite{art:AA23}. That last option uses a saturation that is defined from the local spectral density, and thus gives zero dissipation for directions where the threshold is not reached, leading to much broader directional spectra. Also the stronger bimodality is achieved by having a strong modulation effect as a cumulative term. 
 
 Many other adjustments can be made by changing the namelist parameters. A few successful combinations 
-are given by tables \ref{tab:ST4_parSIN} and \ref{tab:ST4_parSDS}, with results described by \citep{art:RA13,art:SAG16}. 
+are given by tables \ref{tab:ST4_parSIN} and \ref{tab:ST4_parSDS}, with results described by \citep{art:RA13,art:SAG16,art:AA23}. 
 Further calibration to any particular wind field should be done for best performance. Guidance for this is given by \cite{Stopa2018}. 
 %We also note that the particular 
 %set of parameters T400 corresponds to setting IPHYS=1 in the ECWAM code cycle 45R2, with a few differences 
@@ -216,27 +216,15 @@ \subsubsection{~$S_{\mathrm{in}} + S_{\mathrm{ds}}$: Saturation-based dissipatio
 direction will typically produce less dissipation than a sea state with all
 the energy radiated in the same direction.
 
-Based on recent analysis by \cite{Guimaraes2018} and \cite{Peureux&al.2019}, this saturation is enhanced by a factor $M_L$ that represents 
-the effect of long waves on short waves 
-\begin{equation}
-M_l(k,\theta)=1+M_\theta \sqrt{\mathrm{mss}(k,\theta)} + N_\theta \sqrt{\mathrm{nss}(k,\theta)} \label{defFACSAT}.
-\end{equation}
-where $M_\theta$ is twice the modulation transfer function for short wave steepness, with 
-$M_\theta=8$ when following the simplified theory by \cite{art:LHS60} and using the root mean square enhancement of $B$ over a 
-long wave cycle. $N_\theta$ is an additional straining factor due to the instability of the wave action envelope of short waves 
-propagating in the direction close to that of the long wave \citep{Peureux&al.2019}. The squared slopes $\mathrm{mss}(k,\theta)$ is 
-the mean square slope in direction $\theta$, wheras $\mathrm{nss}(k,\theta)$ is a slope of long waves propagating in a narrow window $\pm \delta_\theta$, 
-around the short wave direction $\theta$.
-
 We finally define our dissipation term as the sum of the saturation-based term
 and a cumulative breaking term $S_{\mathrm{bk,cu}}$,
 \begin{eqnarray}
 \cS_{ds}(k,\theta)& =&  \sigma
  \frac{C_{\mathrm{ds}}^{\mathrm{sat}}}{B^2_r} \left[ \delta_d
-\max\left\{ M_l(k,\theta) B\left(k\right) -
+\max\left\{  B\left(k\right) -
 B_r,0\right\}^2 \right.
 \nonumber \\
-  & & +  \left(1-\delta_d \right) \left. \max\left\{ M_L(k,\theta) B'\left(k,\theta \right)- B_r
+  & & +  \left(1-\delta_d \right) \left. \max\left\{B'\left(k,\theta \right)- B_r
  ,0\right\}^2\right]N(k,\theta)  \nonumber \\
  & & + \cS_{\mathrm{bk,cu}}(k,\theta) + \cS_{\mathrm{turb}}(k,\theta) \label{Sds_all}.
 \end{eqnarray}