gismo · hverhelst · Dec 10, 2024 · Oct 18, 2024 · Oct 20, 2024 · Dec 6, 2024
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -37,4 +37,4 @@ jobs:
       - name: "Run for ${{ matrix.os }}"
         shell: bash
         working-directory: ${{runner.workspace}}
-        run: ctest -S ${{ github.event.repository.name }}/gismo/cmake/ctest_script.cmake -D CTEST_BUILD_NAME="${{ github.event.repository.name }}_actions_$GITHUB_RUN_NUMBER" -D CTEST_SITE="${{ matrix.os }}_[actions]" -D CMAKE_ARGS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE;-DCMAKE_CXX_STANDARD=11;-DGISMO_WITH_XDEBUG=ON;-DGISMO_BUILD_UNITTESTS=ON" -D GISMO_OPTIONAL="${{ github.event.repository.name }}" -Q
+        run: ctest -S ${{ github.event.repository.name }}/gismo/cmake/ctest_script.cmake -D CTEST_BUILD_NAME="${{ github.event.repository.name }}_actions_$GITHUB_RUN_NUMBER" -D CTEST_CONFIGURATION_TYPE=RelWithDebInfo -D LABELS_FOR_SUBPROJECTS="gsElasticity-examples" -D CTEST_SITE="${{ matrix.os }}_[actions]" -D CMAKE_ARGS="-DCMAKE_BUILD_TYPE=$BUILD_TYPE;-DCMAKE_CXX_STANDARD=11;-DGISMO_WITH_XDEBUG=ON;-DGISMO_BUILD_UNITTESTS=ON" -D GISMO_OPTIONAL="${{ github.event.repository.name }}" -Q
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -50,15 +50,22 @@ install(DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}"
   FILES_MATCHING PATTERN "*.h" )
 
 # add filedata folder
-add_definitions(-DELAST_DATA_DIR="${CMAKE_CURRENT_SOURCE_DIR}/filedata/") 
+add_definitions(-DELAST_DATA_DIR="${CMAKE_CURRENT_SOURCE_DIR}/filedata/")
 
 # add example files
-aux_cpp_directory(${CMAKE_CURRENT_SOURCE_DIR}/examples FILES)
-foreach(file ${FILES})
-    add_gismo_executable(${file})
-    get_filename_component(tarname ${file} NAME_WE) # name without extension
-    set_property(TEST ${tarname} PROPERTY LABELS "${PROJECT_NAME}")
-    set_target_properties(${tarname} PROPERTIES FOLDER "${PROJECT_NAME}")
-    # install the example executables (optionally)
-    install(TARGETS ${tarname} DESTINATION "${BIN_INSTALL_DIR}" COMPONENT exe OPTIONAL)
-endforeach(file ${FILES})
+if(GISMO_BUILD_EXAMPLES)
+    add_custom_target(${PROJECT_NAME}-examples)
+    add_subdirectory(examples)
+else()
+    add_subdirectory(examples EXCLUDE_FROM_ALL)
+endif(GISMO_BUILD_EXAMPLES)
+
+# Print the contents of {PROJECT_NAME}-examples
+get_property(dirs TARGET ${PROJECT_NAME}-examples PROPERTY BUILDSYSTEM_TARGETS)
+message(STATUS "dirs: ${dirs}")
+
+
+# # add unittests
+# aux_gs_cpp_directory(${PROJECT_SOURCE_DIR}/unittests unittests_SRCS)
+# set(gismo_UNITTESTS ${gismo_UNITTESTS} ${unittests_SRCS}
+#   CACHE INTERNAL "gismo list of unittests")
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
@@ -0,0 +1,25 @@
+######################################################################
+## CMakeLists.txt --- gsStructuralAnalysis/examples
+## This file is part of the G+Smo library.
+##
+## Author: Angelos Mantzaflaris, Hugo Verhelst
+## Copyright (C) 2023
+######################################################################
+
+# add example files
+aux_cpp_directory(${CMAKE_CURRENT_SOURCE_DIR} FILES)
+foreach(file ${FILES})
+    add_gismo_executable(${file})
+    get_filename_component(tarname ${file} NAME_WE) # name without extension
+    set_property(TEST ${tarname} PROPERTY LABELS "${PROJECT_NAME}-examples")
+    if(GISMO_BUILD_EXAMPLES)
+      set_target_properties(${tarname} PROPERTIES FOLDER "${PROJECT_NAME}")
+    else(GISMO_BUILD_EXAMPLES)
+      set_target_properties(${tarname} PROPERTIES
+      FOLDER "${PROJECT_NAME}"
+      EXCLUDE_FROM_ALL TRUE)
+    endif(GISMO_BUILD_EXAMPLES)
+    add_dependencies(${PROJECT_NAME}-examples ${tarname})
+    # install the example executables (optionally)
+    install(TARGETS ${tarname} DESTINATION "${BIN_INSTALL_DIR}" COMPONENT exe OPTIONAL)
+endforeach(file ${FILES})
diff --git a/examples/aroundCylinder_NS_2D.cpp b/examples/aroundCylinder_NS_2D.cpp
@@ -32,7 +32,7 @@ int main(int argc, char* argv[]){
     real_t meanVelocity = 0.2; // inflow velocity
     real_t density = 1.;
     // space discretization
-    index_t numUniRef = 3;
+    index_t numUniRef = 1; //was 3
     index_t numDegElev = 0;
     index_t numBLRef = 1;
     bool subgridOrTaylorHood = false;

diff --git a/examples/aroundCylinder_NS_2Dt.cpp b/examples/aroundCylinder_NS_2Dt.cpp
@@ -66,12 +66,12 @@ int main(int argc, char* argv[]){
     real_t meanVelocity = 1; // inflow velocity
     real_t density = 1.0;
     // space discretization
-    index_t numUniRef = 3;
+    index_t numUniRef = 1; //was 3
     index_t numDegElev = 0;
     index_t numBLRef = 1;
     bool subgridOrTaylorHood = false;
     // time integration
-    real_t timeSpan = 10;
+    real_t timeSpan = 0.01; // was 10
     real_t timeStep = 0.01;
     real_t theta = 0.5;
     bool imexOrNewton = false;

diff --git a/examples/biceps_activeMuscle_3D.cpp b/examples/biceps_activeMuscle_3D.cpp
@@ -39,12 +39,12 @@ int main(int argc, char* argv[]){
     gsVector<> fiberDirection(3);
     fiberDirection << 1.,0.,0.;
     // space discretization
-    index_t numUniRefDirX = 2;
+    index_t numUniRefDirX = 0;
     index_t numUniRef = 0;
     index_t numDegElev = 0;
     bool subgridOrTaylorHood = false;
     // output
-    index_t numPlotPoints = 10000;
+    index_t numPlotPoints = 0;
 
     // minimalistic user interface for terminal
     gsCmdLine cmd("This is a simulation of active muscle behavior.");

diff --git a/examples/biceps_activeMuscle_3Dt.cpp b/examples/biceps_activeMuscle_3Dt.cpp
@@ -39,15 +39,15 @@ int main(int argc, char* argv[]){
     gsVector<> fiberDirection(3);
     fiberDirection << 1.,0.,0.;
     // space discretization
-    index_t numUniRefDirX = 2;
+    index_t numUniRefDirX = 0;
     index_t numUniRef = 0;
     index_t numDegElev = 0;
     bool subgridOrTaylorHood = false;
     // time integration
-    real_t timeSpan = 2;
+    real_t timeSpan = 0.1; // was 2.0
     real_t timeStep = 0.1;
     // output
-    index_t numPlotPoints = 100000;
+    index_t numPlotPoints = 0;
 
     // minimalistic user interface for terminal
     gsCmdLine cmd("This is a simulation of active muscle behavior.");

diff --git a/examples/flappingBeam_CFD3_NS_2Dt.cpp b/examples/flappingBeam_CFD3_NS_2Dt.cpp
@@ -81,12 +81,12 @@ int main(int argc, char* argv[]){
     real_t meanVelocity = 2; // inflow velocity
     real_t density = 1.0e3;
     // space discretization
-    index_t numUniRef = 3;
+    index_t numUniRef = 1;// was 3
     index_t numDegElev = 0;
     index_t numBLRef = 1;
     bool subgridOrTaylorHood = false;
     // time integration
-    real_t timeSpan = 10;
+    real_t timeSpan = 0.01; // was 10
     real_t timeStep = 0.01;
     real_t theta = 0.5;
     bool imexOrNewton = false;

diff --git a/examples/flappingBeam_FSI2_coupledFSI_2Dt.cpp b/examples/flappingBeam_FSI2_coupledFSI_2Dt.cpp
@@ -84,7 +84,7 @@ int main(int argc, char* argv[])
     index_t numUniRef = 3;
     // time integration
     real_t timeStep = 0.01;
-    real_t timeSpan = 15.;
+    real_t timeSpan = 0.02; //was 15.
     real_t thetaFluid = 0.5;
     real_t thetaSolid = 1.;
     index_t maxCouplingIter = 10;

diff --git a/examples/muscleBeam_activeMuscle_3Dt.cpp b/examples/muscleBeam_activeMuscle_3Dt.cpp
@@ -88,8 +88,8 @@ int main(int argc, char* argv[]){
     for (size_t p = 0; p < geometry.nPatches(); ++p)
         for (index_t i = 0; i < numUniRefDirX; ++i)
         {
-            static_cast<gsTensorNurbsBasis<3,real_t> &>(basisDisplacement.basis(p)).knots(0).uniformRefine();
-            static_cast<gsTensorNurbsBasis<3,real_t> &>(basisPressure.basis(p)).knots(0).uniformRefine();
+            basisDisplacement.basis(p).uniformRefine(1,1,0);
+            basisPressure.basis(p).uniformRefine(1,1,0);
         }
     // additional displacement refinement for stable mixed FEM
     if (!subgridOrTaylorHood) // subgrid
@@ -105,7 +105,7 @@ int main(int argc, char* argv[]){
     gsConstantFunction<> prestressRight(prestress,0.,0.,3);
 
     // boundary conditions
-    gsBoundaryConditions<> bcInfo; 
+    gsBoundaryConditions<> bcInfo;
     for (size_t p = 0; p < geometry.nPatches(); ++p)
     {
         bcInfo.addCondition(p,boundary::west,condition_type::neumann,&prestressLeft);

diff --git a/examples/muscleBeam_mixedNonLinElast_3D.cpp b/examples/muscleBeam_mixedNonLinElast_3D.cpp
@@ -65,8 +65,8 @@ int main(int argc, char* argv[]){
     for (size_t p = 0; p < geometry.nPatches(); ++p)
         for (index_t i = 0; i < numUniRefDirX; ++i)
         {
-            static_cast<gsTensorNurbsBasis<3,real_t> &>(basisDisplacement.basis(p)).knots(0).uniformRefine();
-            static_cast<gsTensorNurbsBasis<3,real_t> &>(basisPressure.basis(p   )).knots(0).uniformRefine();
+            basisDisplacement.basis(p).uniformRefine(1,1,0);
+            basisPressure.basis(p).uniformRefine(1,1,0);
         }
     // additional displacement refinement for stable mixed FEM
     if (!subgridOrTaylorHood) // subgrid
@@ -97,6 +97,8 @@ int main(int argc, char* argv[]){
     gsElasticityAssembler<real_t> assembler(geometry,basisDisplacement,basisPressure,bcInfo,gravity);
     assembler.options().setReal("YoungsModulus",youngsModulus);
     assembler.options().setReal("PoissonsRatio",poissonsRatio);
+    assembler.options().setInt("MaterialLaw",material_law::mixed_neo_hooke_ln);
+
     gsInfo << "Initialized system with " << assembler.numDofs() << " dofs.\n";
 
     // setting Newton's method

diff --git a/examples/muscleBeam_mixedNonLinElast_3Dt.cpp b/examples/muscleBeam_mixedNonLinElast_3Dt.cpp
@@ -31,7 +31,7 @@ int main(int argc, char* argv[]){
     index_t numDegElev = 0;
     bool subgridOrTaylorHood = false;
     // time integration
-    real_t timeSpan = 1;
+    real_t timeSpan = 0.01; // was 1.0
     real_t timeStep = 0.01;
     // output
     index_t numPlotPoints = 1000;
@@ -72,8 +72,8 @@ int main(int argc, char* argv[]){
     for (size_t p = 0; p < geometry.nPatches(); ++p)
         for (index_t i = 0; i < numUniRefDirX; ++i)
         {
-            static_cast<gsTensorNurbsBasis<3,real_t> &>(basisDisplacement.basis(p)).knots(0).uniformRefine();
-            static_cast<gsTensorNurbsBasis<3,real_t> &>(basisPressure.basis(p)).knots(0).uniformRefine();
+            basisDisplacement.basis(p).uniformRefine(1,1,0);
+            basisPressure.basis(p).uniformRefine(1,1,0);
         }
     // additional displacement refinement for stable mixed FEM
     if (!subgridOrTaylorHood) // subgrid
@@ -104,6 +104,7 @@ int main(int argc, char* argv[]){
     gsElasticityAssembler<real_t> assembler(geometry,basisDisplacement,basisPressure,bcInfo,gravity);
     assembler.options().setReal("YoungsModulus",youngsModulus);
     assembler.options().setReal("PoissonsRatio",poissonsRatio);
+    assembler.options().setInt("MaterialLaw",material_law::mixed_neo_hooke_ln);
     gsInfo << "Initialized system with " << assembler.numDofs() << " dofs.\n";
 
     // creating mass assembler

diff --git a/examples/spring_nonLinElast_3D.cpp b/examples/spring_nonLinElast_3D.cpp
@@ -55,7 +55,7 @@ int main(int argc, char* argv[])
         basis.uniformRefine();
     for (index_t i = 0; i < numUniRefX; ++i)
         for (size_t p = 0; p < geometry.nPatches(); ++p)
-            static_cast<gsTensorBSplineBasis<3,real_t> &>(basis.basis(p)).knots(2).uniformRefine();
+        basis.basis(p).uniformRefine(1,1,2);
 
     //=============================================//
         // Setting loads and boundary conditions //

diff --git a/gsBaseAssembler.h b/gsBaseAssembler.h
@@ -36,9 +36,9 @@ class gsBaseAssembler : public gsAssembler<T>
                           const std::vector<gsMatrix<T> > & fixedDDoFs) = 0;
 
     /// assembly procedure for linear problems
-    virtual void assemble(bool saveEliminationMatrix) {};
-    virtual void assemble() {};
-    virtual void assemble(const gsMultiPatch<T> & curSolution)
+    virtual void assemble(bool /* saveEliminationMatrix */) {};
+    virtual void assemble() { assemble(false); };
+    virtual void assemble(const gsMultiPatch<T> & /* curSolution */)
     {GISMO_NO_IMPLEMENTATION}
 
     /// Returns number of free degrees of freedom
@@ -50,17 +50,17 @@ class gsBaseAssembler : public gsAssembler<T>
                                    gsMultiPatch<T> & result,
                                    const gsVector<index_t> & unknowns) const;
 
-    virtual void constructSolution(const gsMatrix<T>& solVector,
-                                   gsMultiPatch<T>& result, short_t unk = 0) const
+    virtual void constructSolution(const gsMatrix<T>& /* solVector */,
+                                   gsMultiPatch<T>& /* result */, short_t /* unk */ = 0) const
     {GISMO_NO_IMPLEMENTATION}
-    virtual void constructSolution(const gsMatrix<T>& solVector,
-                                   gsMultiPatch<T>& result,
-                                   const gsVector<index_t>  & unknowns) const
+    virtual void constructSolution(const gsMatrix<T>& /* solVector */,
+                                   gsMultiPatch<T>& /* result */,
+                                   const gsVector<index_t>  & /* unknowns */) const
     {GISMO_NO_IMPLEMENTATION}
 
-    virtual void constructSolution(const gsMatrix<T> & solVector,
-                                   const std::vector<gsMatrix<T> > & fixedDDofs,
-                                   gsMultiPatch<T> & result) const {};
+    virtual void constructSolution(const gsMatrix<T> & /* solVector */,
+                                   const std::vector<gsMatrix<T> > & /* fixedDDofs */,
+                                   gsMultiPatch<T> & /* result */) const {};
 
     //--------------------- DIRICHLET BC SHENANIGANS ----------------------------------//
 

diff --git a/gsBiharmonicAssembler.h b/gsBiharmonicAssembler.h
@@ -38,11 +38,16 @@ class gsBiharmonicAssembler : public gsBaseAssembler<T>
     virtual void refresh();
 
     /// @brief Assembles the matrix
-    virtual void assemble(bool saveEliminationMatrix = false);
+    /// @{
+    virtual void assemble(bool saveEliminationMatrix);
 
-    virtual bool assemble(const gsMatrix<T> & solutionVector,
-                          const std::vector<gsMatrix<T> > & fixedDDoFs)
+    virtual void assemble() { assemble(false); };
+
+    using Base::assemble;
+    virtual bool assemble(const gsMatrix<T> & /* solutionVector */,
+                          const std::vector<gsMatrix<T> > & /* fixedDDoFs */)
     {assemble(); return true;}
+    /// @}
 
     //--------------------- SOLUTION CONSTRUCTION ----------------------------------//
 

diff --git a/gsBiharmonicAssembler.hpp b/gsBiharmonicAssembler.hpp
@@ -17,7 +17,7 @@
 #include <gsElasticity/gsBiharmonicAssembler.h>
 
 #include <gsPde/gsPoissonPde.h>
-#include <gsElasticity/gsVisitorBiharmonic.h>
+#include <gsElasticity/gsVisitorBiharmonicMixed.h>
 
 namespace gismo
 {
@@ -89,8 +89,8 @@ void gsBiharmonicAssembler<T>::assemble(bool saveEliminationMatrix)
         eliminationMatrix.reservePerColumn(m_system.numColNz(m_bases[0],m_options));
     }
 
-    gsVisitorBiharmonic<T> visitor(*m_pde_ptr, saveEliminationMatrix ? &eliminationMatrix : nullptr);
-    Base::template push<gsVisitorBiharmonic<T> >(visitor);
+    gsVisitorBiharmonicMixed<T> visitor(*m_pde_ptr, saveEliminationMatrix ? &eliminationMatrix : nullptr);
+    Base::template push<gsVisitorBiharmonicMixed<T> >(visitor);
 
     m_system.matrix().makeCompressed();
 

diff --git a/gsElPoissonAssembler.h b/gsElPoissonAssembler.h
@@ -37,12 +37,18 @@ class gsElPoissonAssembler : public gsBaseAssembler<T>
     virtual void refresh();
 
     /// @brief Assembles the mass matrix
-    virtual void assemble(bool saveEliminationMatrix = false);
+    /// @{
+    virtual void assemble(bool saveEliminationMatrix);
 
-    virtual bool assemble(const gsMatrix<T> & solutionVector,
-                          const std::vector<gsMatrix<T> > & fixedDDoFs)
+    virtual void assemble() { assemble(false); };
+
+    using Base::assemble;
+    virtual bool assemble(const gsMatrix<T> & /* solutionVector */,
+                          const std::vector<gsMatrix<T> > & /* fixedDDoFs */)
     {assemble(); return true;}
+    /// @}
 
+    using Base::constructSolution;
     virtual void constructSolution(const gsMatrix<T> & solVector,
                                    const std::vector<gsMatrix<T> > & fixedDoFs,
                                    gsMultiPatch<T> & displacement) const;

diff --git a/gsElTimeIntegrator.h b/gsElTimeIntegrator.h
@@ -16,15 +16,12 @@
 
 #include <gsElasticity/gsBaseAssembler.h>
 #include <gsElasticity/gsBaseUtils.h>
+#include <gsElasticity/gsElasticityAssembler.h>
+#include <gsElasticity/gsMassAssembler.h>
 
 namespace gismo
 {
 
-template <class T>
-class gsElasticityAssembler;
-template <class T>
-class gsMassAssembler;
-
 /** @brief Time integation for equations of dynamic elasticity with implicit schemes
 */
 template <class T>
@@ -63,6 +60,7 @@ class gsElTimeIntegrator : public gsBaseAssembler<T>
     void makeTimeStep(T timeStep);
 
     /// assemble the linear system for the nonlinear solver
+    using Base::assemble;
     virtual bool assemble(const gsMatrix<T> & solutionVector,
                           const std::vector<gsMatrix<T> > & fixedDoFs);
 
@@ -91,6 +89,7 @@ class gsElTimeIntegrator : public gsBaseAssembler<T>
     void constructSolution(gsMultiPatch<T> & displacement) const;
 
     /// construct displacement and pressure (if applicable) using the stiffness assembler
+    using Base::constructSolution;
     void constructSolution(gsMultiPatch<T> & displacement, gsMultiPatch<T> & pressure) const;
 
     /// assemblers' accessors

diff --git a/gsElasticityAssembler.h b/gsElasticityAssembler.h
@@ -54,12 +54,14 @@ class gsElasticityAssembler : public gsBaseAssembler<T>
 
     //--------------------- SYSTEM ASSEMBLY ----------------------------------//
 
-    virtual void assemble() { assemble(false); }
-
     /// @brief Assembles the stiffness matrix and the RHS for the LINEAR ELASTICITY
     /// set *assembleMatrix* to false to only assemble the RHS;
+    /// @{
     virtual void assemble(bool saveEliminationMatrix);
 
+    virtual void assemble() { assemble(false); };
+    /// @}
+
     /// Assembles the tangential linear system for Newton's method given the current solution
     /// in the form of free and fixed/Dirichelt degrees of freedom.
     /// Checks if the current solution is valid (Newton's solver can exit safely if invalid).