Merge pull request #239 from FloatingArrayDesign/dev

Release v2.3.4
FloatingArrayDesign · Aug 7, 2024 · a5e2e7e · a5e2e7e
2 parents 0a9a8aa + 137ef35
commit a5e2e7e
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diff --git a/.github/workflows/mdf_verification.yml b/.github/workflows/mdf_verification.yml
@@ -0,0 +1,75 @@
+name: MoorDynF regression tests
+
+on:
+  push:
+    branches: [ $default-branch, master ]
+  pull_request:
+    branches:
+      - "**"
+
+permissions: write-all
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: Release
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: [ubuntu-22.04]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Setup Python
+      uses: actions/setup-python@v5
+      id: setup-python
+
+    - name: Install Python dependencies
+      run: pip install --upgrade build pytest Bokeh numpy
+
+    - name: Download OpenFAST
+      shell: bash
+      run: |
+        cd ${{github.workspace}}/
+        git clone --recursive https://github.com/OpenFAST/openfast.git
+
+    - name: Compile MoorDynF
+      shell: bash
+      run: |
+        cd ${{github.workspace}}/
+        mkdir -p openfast.build
+        cd openfast.build
+        cmake openfast -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/install -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DBUILD_TESTING=ON ../openfast
+        make moordyn_driver
+        cd ${{github.workspace}}/
+
+    - name: Run MoorDynF regression tests
+      shell: bash
+      run: |
+        cd ${{github.workspace}}/openfast.build
+        ctest -VV -R md_ -LE python
+        cd ${{github.workspace}}/
+
+    - name: Create install folder
+      run: |
+          mkdir -p ${{github.workspace}}/install
+
+    - name: Configure CMake
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/install -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DEXTERNAL_EIGEN:BOOL=OFF -DPYTHON_WRAPPER:BOOL=ON -DFORTRAN_WRAPPER:BOOL=OFF -DRUST_WRAPPER:BOOL=OFF -DUSE_VTK=OFF -DBUILD_TESTING=ON
+
+    - name: Build
+      id: build
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+    - name: Install
+      run: cmake --install ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+    - name: Set env variables for the tests
+      run: |
+        echo "LD_LIBRARY_PATH=${{github.workspace}}/build/source/" >> $GITHUB_ENV
+
+    - name: Run the tests
+      run: python ${{github.workspace}}/tests/.mdf_verification/verify.py ${{github.workspace}}/
diff --git a/.github/workflows/memcheck.yml b/.github/workflows/memcheck.yml
@@ -0,0 +1,39 @@
+name: memcheck
+
+on:
+  pull_request:
+    branches: [ $default-branch, master ]
+
+permissions: write-all
+
+env:
+  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
+  BUILD_TYPE: RelWithDebInfo
+  PROCESSES: 4
+
+jobs:
+  memcheck:
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            os: [ubuntu-22.04]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Install valgrind
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get -qq -y install valgrind
+
+    - name: Configure CMake
+      run: cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DEXTERNAL_EIGEN:BOOL=OFF -DPYTHON_WRAPPER:BOOL=OFF -DRUST_WRAPPER:BOOL=OFF -DUSE_VTK=OFF -DBUILD_TESTING=ON
+
+    - name: Build
+      id: build
+      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}}
+
+    - name: Test
+      working-directory: ${{github.workspace}}/build
+      # We are just testing in Linux
+      run: ctest -C ${{env.BUILD_TYPE}} -T memcheck --output-on-failure -j ${{env.PROCESSES}} -E "(seafloor|time_schemes|wavekin|wilson|lowe_and_langley_2006)"
diff --git a/.github/workflows/python-wheels-manylinux-arch.yml b/.github/workflows/python-wheels-manylinux-arch.yml
@@ -53,7 +53,7 @@ jobs:
           platforms: all
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.1
+        uses: pypa/cibuildwheel@v2.20.0
         with:
             output-dir: dist
         env:

diff --git a/.github/workflows/python-wheels.yml b/.github/workflows/python-wheels.yml
@@ -81,7 +81,7 @@ jobs:
         if: runner.os == 'Linux'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.19.1
+        uses: pypa/cibuildwheel@v2.20.0
         with:
             output-dir: dist
         env:

diff --git a/.github/workflows/python-wrapper.yml b/.github/workflows/python-wrapper.yml
@@ -31,7 +31,7 @@ jobs:
       id: setup-python
 
     - name: Install Python dependencies
-      run: pip install --upgrade build pytest
+      run: pip install --upgrade build pytest numpy scipy
 
     - name: Install VTK
       run: |

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -0,0 +1,20 @@
+## [](https://github.com/core-marine-dev/MoorDyn/compare/v2.3.3...v) (2024-08-07)
+
+### Features
+
+* **body:** Add centripetal forces for rotating bodies ([f4f816c](https://github.com/core-marine-dev/MoorDyn/commit/f4f816cadb4116f4052f4a3cc36ca2c82f5cabd9))
+
+### Bug Fixes
+
+* accelerations of Coupled/fixed bodies/rods when there are several isntances of them ([1a07a2d](https://github.com/core-marine-dev/MoorDyn/commit/1a07a2d39fe6ffb5f27b6e143830d18ce4f758f2))
+* Add a centripetal force to bodies with a excentric COG ([7a56b7c](https://github.com/core-marine-dev/MoorDyn/commit/7a56b7c941c0bfbddb37fab48423f1ad715270a7))
+* Centripetal force for parallel axes shall be null ([829c837](https://github.com/core-marine-dev/MoorDyn/commit/829c83711a98ed11178cc3b934b76ce515c61f82))
+* Drop the patch to move from extrinsic to intrinsic Euler angles ([6ff56ac](https://github.com/core-marine-dev/MoorDyn/commit/6ff56acc47d756634b1a8238898221ec016c8e0f))
+* EulerXYZ intrinsic angles instead of extrinsic ([1eec2e3](https://github.com/core-marine-dev/MoorDyn/commit/1eec2e3005239c9bd8e19f1ebddd05ead8f2f08f))
+* EulerZYX -> EulerXYZ on moordyn::Euler2Quat() ([5a5f7fd](https://github.com/core-marine-dev/MoorDyn/commit/5a5f7fdfa8bc161cd580c50b3dcedcca394919c6))
+* Freeze when writeLog is not the first option ([d4cce8e](https://github.com/core-marine-dev/MoorDyn/commit/d4cce8ecfb8e5af4819f3877e0f882d59ebb04c8))
+* make rod submergence calcs match what is in MDF (verified code) ([0ac0e92](https://github.com/core-marine-dev/MoorDyn/commit/0ac0e9207eec4c202bf6b85f4a6fbc5178a1fb13))
+* Odd treatment was meant for indexes from 1 to 3, not 0 to 2, and the matrix indexes were transposed ([0bb4ae2](https://github.com/core-marine-dev/MoorDyn/commit/0bb4ae27c8ed307a7a2382f0a53121ef8d73ebb7))
+* Read first the writelog option, and then anything else ([028a567](https://github.com/core-marine-dev/MoorDyn/commit/028a56742226aa27fa900272bf020924eec56b6d))
+* Rebranding to include centripetal forces on getNetForceAndMass ([f20a98a](https://github.com/core-marine-dev/MoorDyn/commit/f20a98aa23a584a0475f6055a33acfda30f39718))
+* The quaternions shall be renormalized to get the rotation matrix ([7256746](https://github.com/core-marine-dev/MoorDyn/commit/7256746793f0c48b6ec4bc8dd97407ad582a9ae2))
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.10)
 set(MOORDYN_MAJOR_VERSION 2)
 set(MOORDYN_MINOR_VERSION 3)
-set(MOORDYN_PATCH_VERSION 3)
+set(MOORDYN_PATCH_VERSION 4)
 set(MOORDYN_VERSION ${MOORDYN_MAJOR_VERSION}.${MOORDYN_MINOR_VERSION})
 project(Moordyn VERSION ${MOORDYN_VERSION})
 
@@ -141,6 +141,14 @@ if(${MOORDYN_FASTMATH})
     endif()
 endif()
 
+find_program(MEMORYCHECK_COMMAND valgrind)
+if(NOT MEMORYCHECK_COMMAND)
+    message(WARNING "valgrind is not found, you will not be able to run memchecks")
+else(NOT ${MEMORYCHECK_COMMAND})
+    set(MEMORYCHECK_SUPPRESSIONS_FILE "${PROJECT_SOURCE_DIR}/tests/valgrind_suppress.txt")
+endif()
+
+
 # Compile the library
 add_subdirectory(source)
 # And the eventual wrappers

diff --git a/compile/DLL/makefile b/compile/DLL/makefile
@@ -3,7 +3,6 @@
 #
 # Several options can be set:
 #
-#  - USEGL: Enables the OpenGL visualization
 #  - COPTS: Compilation options. For good performance and compatibility use:
 #           COPTS='-msse2 -ffast-math -DMOORDYN_SINGLEPRECISSION'
 #           However, for local-only installations a more aggresive instructions
@@ -24,10 +23,16 @@
 LFLAGS = -shared -static-libgcc -static-libstdc++ -DMoorDyn_EXPORTS -fPIC
 CFLAGS = -c -O3 -g -Wall -Wextra -DMoorDyn_EXPORTS -fPIC -I../../source/
 
-ifdef USEGL
-CFLAGS += -DUSEGL
-LFLAGS += -lopengl32 -lglu32
-endif
+# Automagically collect the library version
+# This should still work fine with mingw, or even in modern Windows with bash
+# I have not tested it anyway
+CMAKEROOT := ../../CMakeLists.txt
+MOORDYN_MAJOR_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_MAJOR_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+MOORDYN_MINOR_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_MINOR_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+MOORDYN_PATCH_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_PATCH_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+CFLAGS += -DMOORDYN_MAJOR_VERSION=$(MOORDYN_MAJOR_VERSION)
+CFLAGS += -DMOORDYN_MINOR_VERSION=$(MOORDYN_MINOR_VERSION)
+CFLAGS += -DMOORDYN_PATCH_VERSION=$(MOORDYN_PATCH_VERSION)
 
 CFLAGS += $(COPTS)
 LFLAGS += $(LOPTS)

diff --git a/compile/DYLIB/makefile b/compile/DYLIB/makefile
@@ -3,7 +3,6 @@
 #
 # Several options can be set:
 #
-#  - USEGL: Enables the OpenGL visualization
 #  - COPTS: Compilation options. For good performance and compatibility use:
 #           COPTS='-msse2 -ffast-math -DMOORDYN_SINGLEPRECISSION'
 #           However, for local-only installations a more aggresive instructions
@@ -29,10 +28,14 @@
 LFLAGS = -shared -DOSX -DMoorDyn_EXPORTS -fPIC
 CFLAGS = -c -O3 -static -g -Wall -Wextra -DOSX -DMoorDyn_EXPORTS -fPIC -I../../source/
 
-ifdef USEGL
-CFLAGS += -DUSEGL
-LFLAGS += -lopengl32 -lglu32
-endif
+# Automagically collect the library version
+CMAKEROOT := ../../CMakeLists.txt
+MOORDYN_MAJOR_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_MAJOR_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+MOORDYN_MINOR_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_MINOR_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+MOORDYN_PATCH_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_PATCH_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+CFLAGS += -DMOORDYN_MAJOR_VERSION=$(MOORDYN_MAJOR_VERSION)
+CFLAGS += -DMOORDYN_MINOR_VERSION=$(MOORDYN_MINOR_VERSION)
+CFLAGS += -DMOORDYN_PATCH_VERSION=$(MOORDYN_PATCH_VERSION)
 
 CFLAGS += $(COPTS)
 LFLAGS += $(LOPTS)

diff --git a/compile/SO/makefile b/compile/SO/makefile
@@ -3,7 +3,6 @@
 #
 # Several options can be set:
 #
-#  - USEGL: Enables the OpenGL visualization
 #  - COPTS: Compilation options. For good performance and compatibility use:
 #           COPTS='-msse2 -ffast-math -DMOORDYN_SINGLEPRECISSION'
 #           However, for local-only installations a more aggresive instructions
@@ -25,10 +24,14 @@
 LFLAGS = -shared -static-libgcc -static-libstdc++ -DLINUX -DMoorDyn_EXPORTS -fPIC
 CFLAGS = -c -O3 -g -Wall -Wextra -DLINUX -DMoorDyn_EXPORTS -fPIC -I../../source/
 
-ifdef USEGL
-CFLAGS += -DUSEGL
-LFLAGS += -lopengl32 -lglu32
-endif
+# Automagically collect the library version
+CMAKEROOT := ../../CMakeLists.txt
+MOORDYN_MAJOR_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_MAJOR_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+MOORDYN_MINOR_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_MINOR_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+MOORDYN_PATCH_VERSION=$(shell cat ${CMAKEROOT} | grep "set(MOORDYN_PATCH_VERSION" | cut -d " " -f 2 | cut -d ")" -f 1)
+CFLAGS += -DMOORDYN_MAJOR_VERSION=$(MOORDYN_MAJOR_VERSION)
+CFLAGS += -DMOORDYN_MINOR_VERSION=$(MOORDYN_MINOR_VERSION)
+CFLAGS += -DMOORDYN_PATCH_VERSION=$(MOORDYN_PATCH_VERSION)
 
 CFLAGS += $(COPTS)
 LFLAGS += $(LOPTS)
@@ -47,12 +50,16 @@ DIRGUARD = @mkdir -p $(@D)
 
 all: libmoordyn.so
 
-libmoordyn.so: libmoordyn.so.2.0.0
+libmoordyn.so: libmoordyn.so.$(MOORDYN_MAJOR_VERSION).$(MOORDYN_MINOR_VERSION)
 	rm -f libmoordyn.so
-	ln -s libmoordyn.so.2.0.0 libmoordyn.so
+	ln -s libmoordyn.so.$(MOORDYN_MAJOR_VERSION).$(MOORDYN_MINOR_VERSION) libmoordyn.so
 
-libmoordyn.so.2.0.0: $(OBJECTS)
-	$(CXX) $(LFLAGS) -o libmoordyn.so.2.0.0 $(OBJECTS)
+libmoordyn.so.$(MOORDYN_MAJOR_VERSION).$(MOORDYN_MINOR_VERSION): libmoordyn.so.$(MOORDYN_MAJOR_VERSION).$(MOORDYN_MINOR_VERSION).$(MOORDYN_PATCH_VERSION)
+	rm -f libmoordyn.so
+	ln -s libmoordyn.so.$(MOORDYN_MAJOR_VERSION).$(MOORDYN_MINOR_VERSION).$(MOORDYN_PATCH_VERSION) libmoordyn.so.$(MOORDYN_MAJOR_VERSION).$(MOORDYN_MINOR_VERSION)
+
+libmoordyn.so.$(MOORDYN_MAJOR_VERSION).$(MOORDYN_MINOR_VERSION).$(MOORDYN_PATCH_VERSION): $(OBJECTS)
+	$(CXX) $(LFLAGS) -o libmoordyn.so.$(MOORDYN_MAJOR_VERSION).$(MOORDYN_MINOR_VERSION).$(MOORDYN_PATCH_VERSION) $(OBJECTS)
 
 %.o: ../../source/%.cpp $(HEADERS)
 	${CXX} $(CPPFLAGS) -o $@ $<