Refactor testcase total aritificial heart for c++ backend and webassembly example

CMakeLists.txt

@@ -39,14 +39,17 @@ if(MSVC)
     add_definitions(-D_USE_MATH_DEFINES)
 else(MSVC)
     add_compile_definitions(__linux__=1)
-    set(CMAKE_CXX_FLAGS "-Wall -std=c++11 -DUNIX -pthread  -Werror=reorder")
+    set(CMAKE_CXX_FLAGS "-Wall -std=c++11 -DUNIX -pthread")
     set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG")
     set(CMAKE_CXX_FLAGS_DEBUG "-g -O0 -ggdb")
     IF(${CMAKE_BUILD_TYPE} MATCHES "Debug")
         set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS}")
     ELSE(${CMAKE_BUILD_TYPE} MATCHES "Debug")
         set(CMAKE_CXX_FLAGS "-fPIC ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
     ENDIF(${CMAKE_BUILD_TYPE} MATCHES "Debug")
+	if(NOT BUILD_WITH_DEPENDENCIES_SOURCE)
+		set(CMAKE_CXX_FLAGS  "${CMAKE_CXX_FLAGS} -Werror=reorder")
+	endif()
 endif(MSVC)
 message("===========================================")
 message("${PROJECT_NAME}, VERSION ${PROJECT_VERSION}")

README.md

@@ -221,7 +221,7 @@ command to run test:
 
 docker run sphinxsys:latest bash scripts/runTest.sh
 
-2. dev.Dockerfile:  development packages are all installed and development. This image is too big and can not be used for github testing. Only for local development purposes. 
+2. dev.Dockerfile:  development packages are all installed and simbody is downloaded and compiled in the image building process. This image is too big and can not be used for github testing. Only for local development purposes. 
 
 command to build:
 
@@ -233,7 +233,6 @@ additional build arguement can be added to the end of the docker build command u
 build_with_dependencies_source=0 : default, builds with preprecompiled dependencies
 build_with_dependencies_source=1 : builds dependencies together with Sphinxsys
 
-
 ### How to run gpuSPHinXsys cases on CUDA enabled GPUs?
 The build process for GPU cases are identical to the CPU cases on all platforms, viz. Linux, Windows and Mac OSX.
 However, the following notes must be considered:

cases_high_level_simulation/high_level_simulation_class/CMakeLists.txt → SPHINXsys/src/for_3D_build/high_level_simulation_class/CMakeLists.txt

@@ -1,7 +1,7 @@
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake) # main (top) cmake dir
-include(Headersearch)
-
-file(GLOB BASE_DIR_HEADERS *.h)
-DIR_INC_HEADER_NAMES("${BASE_DIR_HEADERS}" BASE_DIR_HEADER_NAMES)
-#message("${BASE_DIR_HEADER_NAMES}")
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} ${PROJECT_SOURCE_DIR}/cmake) # main (top) cmake dir
+include(Headersearch)
+
+file(GLOB BASE_DIR_HEADERS *.h)
+DIR_INC_HEADER_NAMES("${BASE_DIR_HEADERS}" BASE_DIR_HEADER_NAMES)
+#message("${BASE_DIR_HEADER_NAMES}")
 INSTALL(FILES ${BASE_DIR_HEADER_NAMES} DESTINATION 3d_code/include)

cases_high_level_simulation/high_level_simulation_class/solid_structural_simulation_class.cpp → SPHINXsys/src/for_3D_build/high_level_simulation_class/solid_structural_simulation_class.cpp

@@ -17,8 +17,8 @@ BodyPartByParticleTriMesh::~BodyPartByParticleTriMesh()
 	delete body_part_shape_;
 }
 
-ImportedModel::ImportedModel(SPHSystem &system, string body_name, TriangleMeshShape* triangle_mesh_shape, Real resolution)
-	: SolidBody(system, body_name, resolution)
+ImportedModel::ImportedModel(SPHSystem &system, string body_name, TriangleMeshShape* triangle_mesh_shape, ParticleAdaptation* particle_adaptation)
+	: SolidBody(system, body_name, particle_adaptation)
 {
 	ComplexShape original_body_shape;
 	original_body_shape.addTriangleMeshShape(triangle_mesh_shape, ShapeBooleanOps::add);
@@ -30,8 +30,8 @@ ImportedModel::~ImportedModel()
 	delete body_shape_;
 }
 
-SolidBodyForSimulation::SolidBodyForSimulation(SPHSystem &system, string body_name, TriangleMeshShape& triangle_mesh_shape, Real resolution, Real physical_viscosity, LinearElasticSolid& material_model):
-	imported_model_(ImportedModel(system, body_name, &triangle_mesh_shape, resolution)),
+SolidBodyForSimulation::SolidBodyForSimulation(SPHSystem &system, string body_name, TriangleMeshShape& triangle_mesh_shape, ParticleAdaptation& particle_adaptation, Real physical_viscosity, LinearElasticSolid& material_model):
+	imported_model_(ImportedModel(system, body_name, &triangle_mesh_shape, &particle_adaptation)),
 	//material_model_(material_model),
 	elastic_solid_particles_(ElasticSolidParticles(&imported_model_, &material_model)),
 	inner_body_relation_(InnerBodyRelation(&imported_model_)),
@@ -115,7 +115,7 @@ StructuralSimulationInput::StructuralSimulationInput(
 	vector<Real> resolution_list,
 	vector<LinearElasticSolid> material_model_list,
 	Real physical_viscosity,
-	vector<IndexPair> contacting_bodies_list
+	vector<array<int, 2>> contacting_bodies_list
 	):
 	relative_input_path_(relative_input_path),
 	imported_stl_list_(imported_stl_list),
@@ -143,7 +143,7 @@ StructuralSimulation::StructuralSimulation(StructuralSimulationInput* input):
 	imported_stl_list_(input->imported_stl_list_),
 	scale_stl_(input->scale_stl_),
 	translation_list_(input->translation_list_),
-	default_resolution_(input->resolution_list_[0]),
+	default_resolution_(0.0),
 	resolution_list_(input->resolution_list_),
 	material_model_list_(input->material_model_list_),
 	physical_viscosity_(input->physical_viscosity_),
@@ -161,8 +161,12 @@ StructuralSimulation::StructuralSimulation(StructuralSimulationInput* input):
 {
 	// scaling of translation and resolution
 	ScaleTranslationAndResolution();
-	// creating body mesh list for triangular mesh shapes storage
+	// set the default resolution to the max in the resolution list
+	SetDefaultSystemResolutionMax();
+	// create the body mesh list for triangular mesh shapes storage
 	CreateBodyMeshList();
+	// create the particle adaptions for the bodies
+	CreateParticleAdaptationList();
 	// set up the system
 	CalculateSystemBoundaries();
 	system_.run_particle_relaxation_ = true;
@@ -176,6 +180,9 @@ StructuralSimulation::StructuralSimulation(StructuralSimulationInput* input):
 	InitializeAccelerationForBodyPartInBoundingBox();
 	InitializeSpringDamperConstraintParticleWise();
 	InitializeConstrainSolidBodyRegion();
+
+	// initialize simulation
+	InitSimulation();
 }
 
 StructuralSimulation::~StructuralSimulation()
@@ -230,6 +237,19 @@ void StructuralSimulation::ScaleTranslationAndResolution()
 	}
 }
 
+void StructuralSimulation::SetDefaultSystemResolutionMax()
+{
+	default_resolution_ = 0.0;
+	for (unsigned int i = 0; i < resolution_list_.size(); i++)
+	{
+		if (default_resolution_ < resolution_list_[i])
+		{
+			default_resolution_ = resolution_list_[i];
+		}
+	}
+	system_.resolution_ref_ = default_resolution_;
+}
+
 void StructuralSimulation::CalculateSystemBoundaries()
 {	
 	for (unsigned int i = 0; i < body_mesh_list_.size(); i++)
@@ -249,12 +269,22 @@ void StructuralSimulation::CreateBodyMeshList()
 	}
 }
 
+void StructuralSimulation::CreateParticleAdaptationList()
+{
+	particle_adaptation_list_ = {};
+	for (unsigned int i = 0; i < resolution_list_.size(); i++)
+	{
+		Real h_spacing_ratio = resolution_list_[i] / default_resolution_;
+		particle_adaptation_list_.push_back(ParticleAdaptation(h_spacing_ratio, 0));
+	}
+}
+
 void StructuralSimulation::InitializeElasticSolidBodies(bool particle_relaxation)
 {
 	solid_body_list_ = {};
 	for (unsigned int i = 0; i < body_mesh_list_.size(); i++)
 	{
-		SolidBodyForSimulation* sb = new SolidBodyForSimulation(system_, imported_stl_list_[i], body_mesh_list_[i], resolution_list_[i], physical_viscosity_, material_model_list_[i]);
+		SolidBodyForSimulation* sb = new SolidBodyForSimulation(system_, imported_stl_list_[i], body_mesh_list_[i], particle_adaptation_list_[i], physical_viscosity_, material_model_list_[i]);
 		solid_body_list_.push_back(sb);
 		if (particle_relaxation)
 		{
@@ -286,7 +316,7 @@ void StructuralSimulation::InitializeAllContacts()
 	contact_force_list_ = {};
 	for (unsigned int i = 0; i < contacting_bodies_list_.size(); i++)
 	{
-		InitializeContactBetweenTwoBodies(contacting_bodies_list_[i].first, contacting_bodies_list_[i].second);
+		InitializeContactBetweenTwoBodies(contacting_bodies_list_[i][0], contacting_bodies_list_[i][1]);
 	}
 }
 
@@ -477,14 +507,14 @@ void StructuralSimulation::RunSimulation(Real end_time)
 {
 	WriteBodyStatesToVtu write_states(in_output_, system_.real_bodies_);
 	GlobalStaticVariables::physical_time_ = 0.0;
-	
+
 	/** INITIALALIZE SYSTEM */
 	system_.initializeSystemCellLinkedLists();
 	system_.initializeSystemConfigurations();
 
 	/** INITIAL CONDITION */
-	ExecuteCorrectConfiguration();
-	
+	ExecuteCorrectConfiguration();	
+
 	/** Statistics for computing time. */
 	write_states.WriteToFile(GlobalStaticVariables::physical_time_);
 	int ite = 0;
@@ -510,3 +540,46 @@ void StructuralSimulation::RunSimulation(Real end_time)
 	tt = t4 - t1 - interval;
 	cout << "Total wall time for computation: " << tt.seconds() << " seconds." << endl;
 }
+
+void StructuralSimulation::InitSimulation()
+{	
+	/** INITIALALIZE SYSTEM */
+	system_.initializeSystemCellLinkedLists();
+	system_.initializeSystemConfigurations();
+
+	/** INITIAL CONDITION */
+	ExecuteCorrectConfiguration();
+}
+
+double StructuralSimulation::RunSimulationFixedDurationJS(int number_of_steps)
+{
+	WriteBodyStatesToVtu write_states(in_output_, system_.real_bodies_);
+	GlobalStaticVariables::physical_time_ = 0.0;
+
+	/** Statistics for computing time. */
+	write_states.WriteToFile(GlobalStaticVariables::physical_time_);
+	int output_period = 100;
+	int ite = 0;	
+	Real dt = 0.0;
+	tick_count t1 = tick_count::now();
+	tick_count::interval_t interval;
+	/** Main loop */
+	while (ite < number_of_steps)
+	{
+		Real integration_time = 0.0;
+		int output_step = 0;
+		while (output_step < output_period)
+		{
+			RunSimulationStep(ite, dt, integration_time);
+			output_step++;
+		}
+		tick_count t2 = tick_count::now();
+		write_states.WriteToFile(GlobalStaticVariables::physical_time_);
+		tick_count t3 = tick_count::now();
+		interval += t3 - t2;
+	}
+	tick_count t4 = tick_count::now();
+	tick_count::interval_t tt;
+	tt = t4 - t1 - interval;
+	return tt.seconds();
+}

cases_high_level_simulation/high_level_simulation_class/solid_structural_simulation_class.h → SPHINXsys/src/for_3D_build/high_level_simulation_class/solid_structural_simulation_class.h

@@ -13,7 +13,6 @@
 
 using namespace SPH;
 using namespace std;
-using IndexPair = pair<int, int>;
 using GravityPair = pair<int, Vec3d>;
 using AccelTuple = tuple<int, BoundingBox, Vec3d>;
 using SpringDamperTuple = tuple<int, Vec3d, Real>;
@@ -28,7 +27,7 @@ class BodyPartByParticleTriMesh : public BodyPartByParticle
 class ImportedModel : public SolidBody
 {
 public:
-	ImportedModel(SPHSystem &system, string body_name, TriangleMeshShape* triangle_mesh_shape, Real resolution);
+	ImportedModel(SPHSystem &system, string body_name, TriangleMeshShape* triangle_mesh_shape, ParticleAdaptation* particle_adaptation);
 	~ImportedModel();
 };
 
@@ -46,7 +45,7 @@ class SolidBodyForSimulation
 	DampingWithRandomChoice<DampingPairwiseInner<indexVector, Vec3d>> damping_random_;
 
 public:
-	SolidBodyForSimulation(SPHSystem &system, string body_name, TriangleMeshShape& triangle_mesh_shape, Real resolution, Real physical_viscosity, LinearElasticSolid& material_model);
+	SolidBodyForSimulation(SPHSystem &system, string body_name, TriangleMeshShape& triangle_mesh_shape, ParticleAdaptation& particle_adaptation, Real physical_viscosity, LinearElasticSolid& material_model);
 	~SolidBodyForSimulation(){};
 
 	ImportedModel* GetImportedModel() { return &imported_model_; };
@@ -79,7 +78,7 @@ class StructuralSimulationInput
 	vector<Real> resolution_list_;
 	vector<LinearElasticSolid> material_model_list_;
 	Real physical_viscosity_;
-	vector<IndexPair> contacting_bodies_list_;
+	vector<array<int, 2>> contacting_bodies_list_;
 	// particle relaxation
 	bool particle_relaxation_;
 	// boundary conditions
@@ -96,7 +95,7 @@ class StructuralSimulationInput
 		vector<Real> resolution_list,
 		vector<LinearElasticSolid> material_model_list,
 		Real physical_viscosity,
-		vector<IndexPair> contacting_bodies_list
+		vector<array<int, 2>> contacting_bodies_list
 		);
 };
 
@@ -120,11 +119,11 @@ class StructuralSimulation
 		In_Output in_output_;
 
 		vector<TriangleMeshShape> body_mesh_list_;
-		vector<TriangleMeshShape> primitive_shape_list_;
+		vector<ParticleAdaptation> particle_adaptation_list_;
 
 		vector<SolidBodyForSimulation*> solid_body_list_;
 
-		vector<IndexPair> contacting_bodies_list_;
+		vector<array<int, 2>> contacting_bodies_list_;
 		vector<SolidContactBodyRelation*> contact_list_;
 		vector<solid_dynamics::ContactDensitySummation*> contact_density_list_;
 		vector<solid_dynamics::ContactForce*> contact_force_list_;
@@ -144,7 +143,9 @@ class StructuralSimulation
 
 		// for constructor, the order is important
 		void ScaleTranslationAndResolution();
+		void SetDefaultSystemResolutionMax();
 		void CreateBodyMeshList();
+		void CreateParticleAdaptationList();
 		void CalculateSystemBoundaries();
 		void InitializeElasticSolidBodies(bool particle_relaxation);
 		void InitializeContactBetweenTwoBodies(int first, int second);
@@ -171,11 +172,18 @@ class StructuralSimulation
 		void ExecuteContactUpdateConfiguration();
 		void RunSimulationStep(int &ite, Real &dt, Real &integration_time);
 
+		// Initialize simulation
+		void InitSimulation();
+
 	public:
 		StructuralSimulation(StructuralSimulationInput* input);
  		~StructuralSimulation();
 
+		//For c++
 		void RunSimulation(Real end_time);
+
+		//For JS
+		double RunSimulationFixedDurationJS(int number_of_steps);
 	};
 
 #endif //SOLID_STRUCTURAL_SIMULATION_CLASS_H

SPHINXsys/src/shared/materials/elastic_solid.h

@@ -110,9 +110,10 @@ namespace SPH {
 		LinearElasticSolid(Real rho_0, Real Youngs_modulus, Real poisson) : ElasticSolid()
 		{
 			material_name_ = "LinearElasticSolid";
-			rho0_ 	= rho_0;
-			E0_ = Youngs_modulus;
-			nu_ = poisson;
+			rho0_ = rho_0;
+			youngs_modulus_ = Youngs_modulus;
+			poisson_ratio_ = poisson;
+
 			assignDerivedMaterialParameters();
 		};
 		virtual ~LinearElasticSolid() {};