Wu tong

.github/workflows/ci.yml

@@ -213,38 +213,38 @@ jobs:
         id: first-try
         run: |
           cd build 
-          ctest  --output-on-failure
+          ctest  --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the second try for failed cases
         id: second-try
         if: ${{ steps.first-try.outcome == 'failure' }}
         run: |
           cd build 
-          ctest --rerun-failed --output-on-failure
+          ctest --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the third try for failed cases
         id: third-try
         if: ${{ steps.second-try.outcome == 'failure' }}
         run: |
           cd build 
-          ctest --rerun-failed --output-on-failure
+          ctest --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the fourth try for failed cases
         id: fourth-try
         if: ${{ steps.third-try.outcome == 'failure' }}
         run: |
           cd build 
-          ctest --rerun-failed --output-on-failure
+          ctest --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the last try for failed cases
         if: ${{ steps.fourth-try.outcome == 'failure' }}
         run: |
           cd build 
-          ctest --rerun-failed --output-on-failure
+          ctest --rerun-failed --output-on-failure --timeout 1000
 
   ###############################################################################
 
@@ -358,38 +358,38 @@ jobs:
         id: first-try
         run: |
           cd C:\build 
-          ctest.exe --output-on-failure
+          ctest.exe --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the second try for failed cases
         id: second-try
         if: ${{ steps.first-try.outcome == 'failure' }}
         run: |
           cd C:\build 
-          ctest.exe --rerun-failed --output-on-failure
+          ctest.exe --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the third try for failed cases
         id: third-try
         if: ${{ steps.second-try.outcome == 'failure' }}
         run: |
           cd C:\build 
-          ctest.exe --rerun-failed --output-on-failure
+          ctest.exe --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the fourth try for failed cases
         id: fourth-try
         if: ${{ steps.third-try.outcome == 'failure' }}
         run: |
           cd C:\build 
-          ctest.exe --rerun-failed --output-on-failure
+          ctest.exe --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the last try for failed cases
         if: ${{ steps.fourth-try.outcome == 'failure' }}
         run: |
           cd C:\build 
-          ctest.exe --rerun-failed --output-on-failure
+          ctest.exe --rerun-failed --output-on-failure --timeout 1000
 
   ###############################################################################
 
@@ -509,35 +509,35 @@ jobs:
         id: first-try
         run: |
           cd build 
-          ctest  --output-on-failure
+          ctest  --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the second try for failed cases
         id: second-try
         if: ${{ steps.first-try.outcome == 'failure' }}
         run: |
           cd build 
-          ctest --rerun-failed --output-on-failure
+          ctest --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the third try for failed cases
         id: third-try
         if: ${{ steps.second-try.outcome == 'failure' }}
         run: |
           cd build 
-          ctest --rerun-failed --output-on-failure
+          ctest --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the fourth try for failed cases
         id: fourth-try
         if: ${{ steps.third-try.outcome == 'failure' }}
         run: |
           cd build 
-          ctest --rerun-failed --output-on-failure
+          ctest --rerun-failed --output-on-failure --timeout 1000
         continue-on-error: true
 
       - name: Test with the last try for failed cases
         if: ${{ steps.fourth-try.outcome == 'failure' }}
         run: |
           cd build 
-          ctest --rerun-failed --output-on-failure
+          ctest --rerun-failed --output-on-failure --timeout 1000

modules/opencascade/opencascade/relax_dynamics_surface.cpp

@@ -7,12 +7,12 @@
 
 namespace SPH
 {
-//=====================================================================================================//
 namespace relax_dynamics
 {
 //=================================================================================================//
 ShapeSurfaceBounding2::ShapeSurfaceBounding2(RealBody &real_body_)
-    : LocalDynamics(real_body_), RelaxDataDelegateSimple(real_body_), pos_(particles_->pos_)
+    : LocalDynamics(real_body_), DataDelegateSimple(real_body_),
+      pos_(*particles_->getVariableByName<Vecd>("Position"))
 {
     shape_ = &real_body_.getInitialShape();
 }
@@ -52,9 +52,10 @@ void RelaxationStepInnerSecondHalf::exec(Real dt)
 
 //=================================================================================================//
 SurfaceNormalDirection::SurfaceNormalDirection(SPHBody &sph_body)
-    : RelaxDataDelegateSimple(sph_body), LocalDynamics(sph_body),
+    : DataDelegateSimple(sph_body), LocalDynamics(sph_body),
       surface_shape_(DynamicCast<SurfaceShape>(this, &sph_body.getInitialShape())),
-      pos_(particles_->pos_), n_(*particles_->getVariableByName<Vecd>("NormalDirection")) {}
+      pos_(*particles_->getVariableByName<Vecd>("Position")),
+      n_(*particles_->registerSharedVariable<Vecd>("NormalDirection")) {}
 
 //=================================================================================================//
 void SurfaceNormalDirection::update(size_t index_i, Real dt)
@@ -79,18 +80,5 @@ void SurfaceNormalDirection::update(size_t index_i, Real dt)
     n_[index_i] = normal_direction_.normalized();
 }
 //=================================================================================================//
-ConstrainSurfaceBodyRegion::
-    ConstrainSurfaceBodyRegion(BodyPartByParticle &body_part)
-    : BaseLocalDynamics<BodyPartByParticle>(body_part), RelaxDataDelegateSimple(sph_body_),
-      force_(particles_->force_)
-{
-}
-//=================================================================================================//
-void ConstrainSurfaceBodyRegion::update(size_t index_i, Real dt)
-{
-    force_[index_i] = Vecd::Zero();
-}
-//=================================================================================================//
 } // namespace relax_dynamics
-  //=================================================================================================//
 } // namespace SPH

modules/opencascade/opencascade/relax_dynamics_surface.h

@@ -42,7 +42,7 @@ class SurfaceShape;
 namespace relax_dynamics
 {
 class ShapeSurfaceBounding2 : public LocalDynamics,
-                              public RelaxDataDelegateSimple
+                              public DataDelegateSimple
 {
   public:
     ShapeSurfaceBounding2(RealBody &real_body_);
@@ -86,7 +86,7 @@ class RelaxationStepInnerSecondHalf : public BaseDynamics<void>
  * @class SurfaceNormalDirection
  * @brief get the normal direction of surface particles.
  */
-class SurfaceNormalDirection : public RelaxDataDelegateSimple, public LocalDynamics
+class SurfaceNormalDirection : public DataDelegateSimple, public LocalDynamics
 {
   public:
     explicit SurfaceNormalDirection(SPHBody &sph_body);
@@ -98,20 +98,6 @@ class SurfaceNormalDirection : public RelaxDataDelegateSimple, public LocalDynam
     StdLargeVec<Vecd> &pos_, &n_;
 };
 
-/**@class ConstrainSuefaceBodyRegion
- * @brief Fix the position surafce body part.
- */
-class ConstrainSurfaceBodyRegion : public BaseLocalDynamics<BodyPartByParticle>, public RelaxDataDelegateSimple
-{
-  public:
-    ConstrainSurfaceBodyRegion(BodyPartByParticle &body_part);
-    virtual ~ConstrainSurfaceBodyRegion(){};
-    void update(size_t index_i, Real dt = 0.0);
-
-  protected:
-    StdLargeVec<Vecd> &force_;
-};
-
 } // namespace relax_dynamics
 } // namespace SPH
 #endif // RELAX_DYNAMICS_H

modules/opencascade/tests/test_3d_aortic_valve/aortic_valve.cpp

@@ -29,6 +29,9 @@ Vec3d domain_upper_bound(15.0, 15.0, 26.0);
 //	Domain bounds of the system.
 //----------------------------------------------------------------------
 BoundingBox system_domain_bounds(domain_lower_bound, domain_upper_bound);
+
+namespace SPH
+{
 /** Define the boundary geometry. */
 class BoundaryGeometry : public BodyPartByParticle
 {
@@ -51,10 +54,12 @@ class BoundaryGeometry : public BodyPartByParticle
     };
 };
 
-class LeafletParticleGenerator : public ParticleGenerator<Surface>
+class Leaflet;
+template <>
+class ParticleGenerator<Leaflet> : public ParticleGenerator<Surface>
 {
   public:
-    explicit LeafletParticleGenerator(SPHBody &sph_body)
+    explicit ParticleGenerator(SPHBody &sph_body)
         : ParticleGenerator<Surface>(sph_body), sph_body_(sph_body){};
     virtual void initializeGeometricVariables() override
     {
@@ -112,6 +117,7 @@ class LeafletParticleGenerator : public ParticleGenerator<Surface>
     }
     SPHBody &sph_body_;
 };
+} // namespace SPH
 
 //--------------------------------------------------------------------------
 //	Main program starts here.
@@ -128,9 +134,8 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     SolidBody leaflet(sph_system, makeShared<SurfaceShapeSTEP>(full_path_to_geometry, "Leaflet"));
     // here dummy linear elastic solid is use because no solid dynamics in particle relaxation
-    leaflet.defineParticlesAndMaterial<ShellParticles, SaintVenantKirchhoffSolid>(1.0, 1.0, 0.0);
-    LeafletParticleGenerator leaflet_particle_generator(leaflet);
-    leaflet.generateParticles(leaflet_particle_generator);
+    leaflet.defineMaterial<Solid>();
+    leaflet.generateParticles<SurfaceParticles, Leaflet>();
     //----------------------------------------------------------------------
     //	Define simple file input and outputs functions.
     //----------------------------------------------------------------------
@@ -153,7 +158,6 @@ int main(int ac, char *av[])
     RelaxationStepInnerSecondHalf leaflet_relaxation_second_half(leaflet_inner);
     /** Constrain the boundary. */
     BoundaryGeometry boundary_geometry(leaflet, "BoundaryGeometry");
-    SimpleDynamics<ConstrainSurfaceBodyRegion> constrain_holder(boundary_geometry);
     SimpleDynamics<SurfaceNormalDirection> surface_normal_direction(leaflet);
     //----------------------------------------------------------------------
     //	Particle relaxation starts here.
@@ -169,7 +173,6 @@ int main(int ac, char *av[])
     while (ite < relax_step)
     {
         leaflet_relaxation_first_half.exec();
-        constrain_holder.exec();
         leaflet_relaxation_second_half.exec();
         ite += 1;
         if (ite % 100 == 0)

modules/structural_simulation/structural_simulation_class.cpp

@@ -27,8 +27,8 @@ SolidBodyFromMesh::SolidBodyFromMesh(
 {
     defineAdaptationRatios(1.15, system.resolution_ref_ / resolution);
     defineBodyLevelSetShape()->cleanLevelSet();
-    defineParticlesWithMaterial<ElasticSolidParticles>(material_model.get());
-    generateParticles<Lattice>();
+    assignMaterial(material_model.get());
+    generateParticles<BaseParticles, Lattice>();
 }
 
 SolidBodyForSimulation::SolidBodyForSimulation(
@@ -110,8 +110,8 @@ std::tuple<StdLargeVec<Vecd>, StdLargeVec<Real>> generateAndRelaxParticlesFromMe
     SPHSystem system(bb, resolution);
     SolidBody model(system, triangle_mesh_shape);
     model.defineBodyLevelSetShape()->cleanLevelSet();
-    model.defineParticlesAndMaterial<SolidParticles, Solid>();
-    model.generateParticles<Lattice>();
+    model.defineMaterial<Solid>();
+    model.generateParticles<BaseParticles, Lattice>();
 
     if (particle_relaxation)
     {
@@ -120,7 +120,7 @@ std::tuple<StdLargeVec<Vecd>, StdLargeVec<Real>> generateAndRelaxParticlesFromMe
         relaxParticlesSingleResolution(write_particle_relaxation_data, model, inner_relation);
     }
 
-    return std::tuple<StdLargeVec<Vecd>, StdLargeVec<Real>>(model.getBaseParticles().pos_, model.getBaseParticles().Vol_);
+    return std::tuple<StdLargeVec<Vecd>, StdLargeVec<Real>>(model.getBaseParticles().ParticlePositions(), model.getBaseParticles().VolumetricMeasures());
 }
 
 BodyPartByParticle *createBodyPartFromMesh(SPHBody &body, const StlList &stl_list, size_t body_index, SharedPtr<TriangleMeshShape> tmesh)
@@ -215,12 +215,7 @@ StructuralSimulation::StructuralSimulation(const StructuralSimulationInput &inpu
       translation_solid_body_part_tuple_(input.translation_solid_body_part_tuple_),
 
       // iterators
-      iteration_(0),
-
-      // data storage
-      von_mises_stress_max_({}),
-      von_mises_stress_particles_({})
-
+      iteration_(0)
 {
     // scaling of translation and resolution
     scaleTranslationAndResolution();
@@ -906,12 +901,7 @@ void StructuralSimulation::runSimulation(Real end_time)
             runSimulationStep(dt, integration_time);
         }
         TickCount t2 = TickCount::now();
-        // record data for test
-        von_mises_stress_max_.push_back(solid_body_list_[0].get()->getElasticSolidParticles()->getVonMisesStressMax());
-        von_mises_stress_particles_.push_back(solid_body_list_[0].get()->getElasticSolidParticles()->getVonMisesStressVector());
 
-        von_mises_strain_max_.push_back(solid_body_list_[0].get()->getElasticSolidParticles()->getVonMisesStrainMax());
-        von_mises_strain_particles_.push_back(solid_body_list_[0].get()->getElasticSolidParticles()->getVonMisesStrainVector());
         // write data to file
         write_states.writeToFile();
         TickCount t3 = TickCount::now();
@@ -957,12 +947,12 @@ double StructuralSimulation::runSimulationFixedDurationJS(int number_of_steps)
 
 Real StructuralSimulation::getMaxDisplacement(int body_index)
 {
-    StdLargeVec<Vecd> &pos_0 = solid_body_list_[body_index].get()->getElasticSolidParticles()->pos0_;
-    StdLargeVec<Vecd> &pos_n = solid_body_list_[body_index].get()->getElasticSolidParticles()->pos_;
+    StdLargeVec<Vecd> &pos = solid_body_list_[body_index].get()->getElasticSolidParticles()->ParticlePositions();
+    StdLargeVec<Vecd> &pos0 = *solid_body_list_[body_index].get()->getElasticSolidParticles()->registerSharedVariableFrom<Vecd>("InitialPosition", "Position");
     Real displ_max = 0;
-    for (size_t i = 0; i < pos_0.size(); i++)
+    for (size_t i = 0; i < pos0.size(); i++)
     {
-        Real displ = (pos_n[i] - pos_0[i]).norm();
+        Real displ = (pos[i] - pos0[i]).norm();
         if (displ > displ_max)
             displ_max = displ;
     }

modules/structural_simulation/structural_simulation_class.h

@@ -104,7 +104,7 @@ class SolidBodyForSimulation
     ~SolidBodyForSimulation(){};
 
     SolidBodyFromMesh *getSolidBodyFromMesh() { return &solid_body_from_mesh_; };
-    ElasticSolidParticles *getElasticSolidParticles() { return DynamicCast<ElasticSolidParticles>(this, &solid_body_from_mesh_.getBaseParticles()); };
+    BaseParticles *getElasticSolidParticles() { return DynamicCast<BaseParticles>(this, &solid_body_from_mesh_.getBaseParticles()); };
     InnerRelation *getInnerBodyRelation() { return &inner_body_relation_; };
 
     SimpleDynamics<NormalDirectionFromBodyShape> *getInitialNormalDirection() { return &initial_normal_direction_; };
@@ -118,7 +118,7 @@ void expandBoundingBox(BoundingBox *original, BoundingBox *additional);
 
 void relaxParticlesSingleResolution(bool write_particles_to_file,
                                     SolidBodyFromMesh &solid_body_from_mesh,
-                                    ElasticSolidParticles &solid_body_from_mesh_particles,
+                                    BaseParticles &solid_body_from_mesh_particles,
                                     InnerRelation &solid_body_from_mesh_inner);
 
 static inline Real getPhysicalViscosityGeneral(Real rho, Real youngs_modulus, Real length_scale, Real shape_constant = 1.0)
@@ -249,13 +249,6 @@ class StructuralSimulation
     // iterators
     int iteration_;
 
-    // data storage
-    StdVec<Real> von_mises_stress_max_;
-    StdLargeVec<StdLargeVec<Real>> von_mises_stress_particles_;
-
-    StdVec<Real> von_mises_strain_max_;
-    StdLargeVec<StdLargeVec<Real>> von_mises_strain_particles_;
-
     // for constructor, the order is important
     void scaleTranslationAndResolution();
     void setSystemResolutionMax();