to continue

tests/2d_examples/test_2d_diffusion_NeumannBC/diffusion_NeumannBC.cpp

@@ -53,7 +53,7 @@ int main(int ac, char *av[])
     //	Define the main numerical methods used in the simulation.
     //	Note that there may be data dependence on the constructors of these methods.
     //----------------------------------------------------------------------
-
+    SimpleDynamics<NormalDirectionFromBodyShape> diffusion_body_normal_direction(diffusion_body, diffusion_body_shape);
     SimpleDynamics<NormalDirectionFromBodyShape> wall_boundary_normal_direction(wall_Neumann, wall_shape_Neumann);
 
     DiffusionBodyRelaxation temperature_relaxation(

tests/2d_examples/test_2d_stfb/stfb.cpp

@@ -29,9 +29,9 @@ int main(int ac, char *av[])
     wall_boundary.generateParticles<BaseParticles, Lattice>(wall_boundary_shape);
 
     TransformShape<GeometricShapeBox> structure_shape(Transform(structure_translation), structure_halfsize, "Structure");
-    SolidBody structure(sph_system, structure_shape);
+    SolidBody structure(sph_system, structure_shape.getName());
     structure.defineMaterial<Solid>(rho_s);
-    structure.generateParticles<BaseParticles, Lattice>(floating_structure_shape);
+    structure.generateParticles<BaseParticles, Lattice>(structure_shape);
 
     ObserverBody observer(sph_system, "Observer");
     observer.defineAdaptationRatios(1.15, 2.0);
@@ -66,7 +66,7 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     SimpleDynamics<OffsetInitialPosition> structure_offset_position(structure, offset);
     SimpleDynamics<NormalDirectionFromBodyShape> wall_boundary_normal_direction(wall_boundary, wall_boundary_shape);
-    SimpleDynamics<NormalDirectionFromBodyShape> str_normal(structure);
+    SimpleDynamics<NormalDirectionFromBodyShape> str_normal(structure, structure_shape);
 
     Gravity gravity(Vecd(0.0, -gravity_g));
     SimpleDynamics<GravityForce<Gravity>> constant_gravity(water_block, gravity);

tests/2d_examples/test_2d_stretching/stretching.cpp

@@ -184,14 +184,15 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     //	Creating body, materials and particles.
     //----------------------------------------------------------------------
-    SolidBody beam_body(system, makeShared<Beam>("StretchingBody"));
-    beam_body.defineBodyLevelSetShape();
+    Beam beam_body_shape("StretchingBody");
+    SolidBody beam_body(system, beam_body_shape.getName());
+    LevelSetShape level_set_shape(beam_body, beam_body_shape);
     beam_body.defineMaterial<NonLinearHardeningPlasticSolid>(
         rho0_s, Youngs_modulus, poisson, yield_stress, hardening_modulus, saturation_flow_stress, saturation_exponent);
 
     (!system.RunParticleRelaxation() && system.ReloadParticles())
         ? beam_body.generateParticles<BaseParticles, Reload>(beam_body.getName())
-        : beam_body.generateParticles<BaseParticles, Lattice>(beam_body_shape);
+        : beam_body.generateParticles<BaseParticles, Lattice>(level_set_shape);
 
     ObserverBody beam_observer(system, "BeamObserver");
     beam_observer.generateParticles<ObserverParticles>(observation_location);
@@ -214,7 +215,7 @@ int main(int ac, char *av[])
         //----------------------------------------------------------------------
         using namespace relax_dynamics;
         SimpleDynamics<RandomizeParticlePosition> beam_body_random_particles(beam_body);
-        RelaxationStepInner beam_body_relaxation_step_inner(beam_body_inner);
+        RelaxationStepInner beam_body_relaxation_step_inner(beam_body_inner, level_set_shape);
         //----------------------------------------------------------------------
         //	Output for particle relaxation.
         //----------------------------------------------------------------------

tests/2d_examples/test_2d_water_entry_exit/test_2d_water_entry_exit.cpp

@@ -189,15 +189,18 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     //	Creating bodies with corresponding materials and particles.
     //----------------------------------------------------------------------
-    FluidBody water_block(sph_system, makeShared<WettingFluidBody>("WaterBody"));
+    WettingFluidBody water_block_shape("WaterBody");
+    FluidBody water_block(sph_system, water_block_shape.getName());
     water_block.defineMaterial<WeaklyCompressibleFluid>(rho0_f, c_f, mu_f);
     water_block.generateParticles<BaseParticles, Lattice>(water_block_shape);
 
-    SolidBody wall_boundary(sph_system, makeShared<WettingWallBody>("WallBoundary"));
+    WettingWallBody wall_boundary_shape("WallBoundary");
+    SolidBody wall_boundary(sph_system, wall_boundary_shape.getName());
     wall_boundary.defineMaterial<Solid>();
     wall_boundary.generateParticles<BaseParticles, Lattice>(wall_boundary_shape);
 
-    SolidBody cylinder(sph_system, makeShared<WettingCylinderBody>("Cylinder"));
+    WettingCylinderBody cylinder_shape("Cylinder");
+    SolidBody cylinder(sph_system, cylinder_shape.getName());
     cylinder.defineAdaptationRatios(1.15, 1.0);
     LevelSetShape cylinder_shape_level_set(cylinder, cylinder_shape);
     cylinder.defineMaterial<Solid>(rho0_s);

tests/2d_examples/test_2d_windows_frame_diffusion_D4/windows_frame_diffusion_D4.cpp

@@ -51,7 +51,7 @@ int main(int ac, char *av[])
     //	Define the main numerical methods used in the simulation.
     //	Note that there may be data dependence on the constructors of these methods.
     //----------------------------------------------------------------------
-
+    SimpleDynamics<NormalDirectionFromBodyShape> diffusion_body_normal_direction(diffusion_body, diffusion_body_shape);
     SimpleDynamics<NormalDirectionFromBodyShape> Robin_normal_direction_in(boundary_Robin_in, boundary_in_shape);
     SimpleDynamics<NormalDirectionFromBodyShape> Robin_normal_direction_ex(boundary_Robin_ex, boundary_ex_shape);
 

tests/2d_examples/test_2d_windows_frame_diffusion_D7/windows_frame_diffusion_D7.cpp

@@ -51,7 +51,7 @@ int main(int ac, char *av[])
     //	Define the main numerical methods used in the simulation.
     //	Note that there may be data dependence on the constructors of these methods.
     //----------------------------------------------------------------------
-
+    SimpleDynamics<NormalDirectionFromBodyShape> diffusion_body_normal_direction(diffusion_body, diffusion_body_shape);
     SimpleDynamics<NormalDirectionFromBodyShape> Robin_normal_direction_in(boundary_Robin_in, boundary_in_shape);
     SimpleDynamics<NormalDirectionFromBodyShape> Robin_normal_direction_ex(boundary_Robin_ex, boundary_ex_shape);
 

tests/3d_examples/test_3d_beam_pulling_pressure_load/beam_pulling_pressure_load.cpp

@@ -117,7 +117,8 @@ int main(int ac, char *av[])
     IOEnvironment io_environment(sph_system);
 
     /** Import a beam body, with corresponding material and particles. */
-    SolidBody beam_body(sph_system, makeShared<Beam>("beam"));
+    Beam beam_body_shape("Beam");
+    SolidBody beam_body(sph_system, beam_body_shape.getName());
     beam_body.defineMaterial<LinearElasticSolid>(rho, Youngs_modulus, poisson_ratio);
     beam_body.generateParticles<BaseParticles, Lattice>(beam_body_shape);
 

tests/3d_examples/test_3d_bending_circular_plate_parametric_cvt/test_3d_bending_circular_plate_parametric_cvt.cpp

@@ -230,13 +230,10 @@ return_data bending_circular_plate(Real dp_ratio)
     std::cout << "bb_system.first_: " << bb_system.first_ << std::endl;
     std::cout << "bb_system.second_: " << bb_system.second_ << std::endl;
 
-    // shell
-    auto shell_shape = makeShared<ComplexShape>("shell_shape" + std::to_string(int(dp_ratio * 1e3))); // keep all data for parameter study
-
     // starting the actual simulation
     SPHSystem system(bb_system, dp);
     system.setIOEnvironment(false);
-    SolidBody shell_body(system, shell_shape);
+    SolidBody shell_body(system, "shell_shape" + std::to_string(int(dp_ratio * 1e3)));
     shell_body.defineMaterial<LinearElasticSolid>(rho, E, mu);
     shell_body.generateParticles<SurfaceParticles, ShellCircle>(obj_vertices, sym_vec, particle_area, thickness);
     auto shell_particles = dynamic_cast<SurfaceParticles *>(&shell_body.getBaseParticles());

tests/3d_examples/test_3d_dambreak/dambreak.cpp

@@ -72,8 +72,8 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     //	Creating bodies with corresponding materials and particles.
     //----------------------------------------------------------------------
-    WaterBlock initial_water_block("WaterBody");
-    FluidBody water_block(sph_system, initial_water_block.getName());
+    WaterBlock water_block_shape("WaterBody");
+    FluidBody water_block(sph_system, water_block_shape.getName());
     water_block.defineMaterial<WeaklyCompressibleFluid>(rho0_f, c_f);
     water_block.generateParticles<BaseParticles, Lattice>(water_block_shape);
 

tests/3d_examples/test_3d_dambreak_elastic_plate_shell/test_3d_dambreak_elastic_plate_shell.cpp

@@ -172,9 +172,10 @@ int main(int ac, char *av[])
     wall_boundary.defineMaterial<Solid>();
     wall_boundary.generateParticles<BaseParticles, Lattice>(wall_boundary_shape);
 
-    SolidBody gate(sph_system, makeShared<MovingGate>("Gate"));
+    MovingGate gate_shape("Gate");
+    SolidBody gate(sph_system, gate_shape.getName());
     gate.defineMaterial<Solid>();
-    gate.generateParticles<BaseParticles, Lattice>();
+    gate.generateParticles<BaseParticles, Lattice>(gate_shape);
 
     SolidBody plate(sph_system, "Plate");
     plate.defineAdaptation<SPHAdaptation>(1.15, resolution_ref / resolution_shell);
@@ -216,7 +217,7 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     // solid
     SimpleDynamics<NormalDirectionFromBodyShape> wall_boundary_normal_direction(wall_boundary, wall_boundary_shape);
-    SimpleDynamics<NormalDirectionFromBodyShape> gate_normal_direction(gate);
+    SimpleDynamics<NormalDirectionFromBodyShape> gate_normal_direction(gate, gate_shape);
     SimpleDynamics<GateMotionConstraint> update_gate_position(gate);
     // Shell
     InteractionDynamics<thin_structure_dynamics::ShellCorrectConfiguration> plate_corrected_configuration(plate_inner);

tests/3d_examples/test_3d_elasticSolid_shell_collision/3d_elasticSolid_shell_collision.cpp

@@ -78,16 +78,18 @@ int main(int ac, char *av[])
     shell.defineMaterial<Solid>();
     shell.generateParticles<SurfaceParticles, Cylinder>();
 
-    SolidBody ball(sph_system, makeShared<GeometricShapeBall>(ball_center, ball_radius, "BallBody"));
+    GeometricShapeBall ball_shape(ball_center, ball_radius, "BallBody");
+    SolidBody ball(sph_system, ball_shape.getName());
+    LevelSetShape level_set_shape(ball, ball_shape);
+    level_set_shape.writeLevelSet(sph_system);
     ball.defineMaterial<NeoHookeanSolid>(rho0_s, Youngs_modulus, poisson);
     if (!sph_system.RunParticleRelaxation() && sph_system.ReloadParticles())
     {
         ball.generateParticles<BaseParticles, Reload>(ball.getName());
     }
     else
     {
-        ball.defineBodyLevelSetShape()->writeLevelSet(sph_system);
-        ball.generateParticles<BaseParticles, Lattice>();
+        ball.generateParticles<BaseParticles, Lattice>(level_set_shape);
     }
 
     ObserverBody ball_observer(sph_system, "BallObserver");
@@ -106,7 +108,7 @@ int main(int ac, char *av[])
         //----------------------------------------------------------------------
         using namespace relax_dynamics;
         SimpleDynamics<RandomizeParticlePosition> ball_random_particles(ball);
-        RelaxationStepInner ball_relaxation_step_inner(ball_inner);
+        RelaxationStepInner ball_relaxation_step_inner(ball_inner, level_set_shape);
         //----------------------------------------------------------------------
         //	Output for particle relaxation.
         //----------------------------------------------------------------------
@@ -143,7 +145,7 @@ int main(int ac, char *av[])
     //  Generally, we first define all the inner relations, then the contact relations.
     //----------------------------------------------------------------------
     InnerRelation ball_inner(ball);
-    ShellSurfaceContactRelation ball_contact(ball, {&shell});
+    ShellSurfaceContactRelation ball_contact(ball, level_set_shape, {&shell});
     ContactRelation ball_observer_contact(ball_observer, {&ball});
     //----------------------------------------------------------------------
     //	Define the main numerical methods used in the simulation.

tests/3d_examples/test_3d_muscle_activation/src/muscle_activation.cpp

@@ -66,9 +66,9 @@ int main(int ac, char *av[])
     //	Creating bodies with corresponding materials and particles.
     //----------------------------------------------------------------------
     TransformShape<GeometricShapeBox> muscle_body_shape(Transform(translation_myocardium), halfsize_myocardium, "MyocardiumMuscleBody");
-    SolidBody muscle_body(sph_system, muscle_body_shape);
+    SolidBody muscle_body(sph_system, muscle_body_shape.getName());
     muscle_body.defineMaterial<ActiveMuscle<Muscle>>(rho0_s, bulk_modulus, fiber_direction, sheet_direction, a0, b0);
-    muscle_body.generateParticles<BaseParticles, Lattice>();
+    muscle_body.generateParticles<BaseParticles, Lattice>(muscle_body_shape);
     //----------------------------------------------------------------------
     //	Define body relation map.
     //	The contact map gives the topological connections between the bodies.

tests/3d_examples/test_3d_muscle_soft_body_contact/muscle_soft_body_contact.cpp

@@ -62,14 +62,16 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     //	Creating bodies with corresponding materials and particles.
     //----------------------------------------------------------------------
-    SolidBody myocardium_body(sph_system, makeShared<Myocardium>("MyocardiumBody"));
+    Myocardium myocardium_body_shape("MyocardiumBody");
+    SolidBody myocardium_body(sph_system, myocardium_body_shape.getName());
     myocardium_body.defineMaterial<NeoHookeanSolid>(rho0_s, Youngs_modulus, poisson);
-    myocardium_body.generateParticles<BaseParticles, Lattice>();
+    myocardium_body.generateParticles<BaseParticles, Lattice>(myocardium_body_shape);
 
-    SolidBody moving_plate(sph_system, makeShared<MovingPlate>("MovingPlate"));
+    MovingPlate moving_plate_shape("MovingPlate");
+    SolidBody moving_plate(sph_system, moving_plate_shape.getName());
     moving_plate.defineAdaptationRatios(1.15, 1.5);
     moving_plate.defineMaterial<NeoHookeanSolid>(rho0_s, Youngs_modulus, poisson);
-    moving_plate.generateParticles<BaseParticles, Lattice>();
+    moving_plate.generateParticles<BaseParticles, Lattice>(moving_plate_shape);
     //----------------------------------------------------------------------
     //	Define body relation map.
     //	The contact map gives the topological connections between the bodies.
@@ -78,8 +80,8 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     InnerRelation myocardium_body_inner(myocardium_body);
     InnerRelation moving_plate_inner(moving_plate);
-    SurfaceContactRelation myocardium_plate_contact(myocardium_body, {&moving_plate});
-    SurfaceContactRelation plate_myocardium_contact(moving_plate, {&myocardium_body});
+    SurfaceContactRelation myocardium_plate_contact(myocardium_body, myocardium_body_shape, {&moving_plate});
+    SurfaceContactRelation plate_myocardium_contact(moving_plate, moving_plate_shape, {&myocardium_body});
     //----------------------------------------------------------------------
     //	Define the numerical methods used in the simulation.
     //	Note that there may be data dependence on the sequence of constructions.

tests/3d_examples/test_3d_muscle_solid_contact/muscle_solid_contact.cpp

@@ -62,22 +62,24 @@ int main(int ac, char *av[])
     //----------------------------------------------------------------------
     //	Creating bodies with corresponding materials and particles.
     //----------------------------------------------------------------------
-    SolidBody myocardium_body(sph_system, makeShared<Myocardium>("MyocardiumBody"));
+    Myocardium myocardium_body_shape("MyocardiumBody");
+    SolidBody myocardium_body(sph_system, myocardium_body_shape.getName());
     myocardium_body.defineMaterial<NeoHookeanSolid>(rho0_s, Youngs_modulus, poisson);
-    myocardium_body.generateParticles<BaseParticles, Lattice>();
+    myocardium_body.generateParticles<BaseParticles, Lattice>(myocardium_body_shape);
 
-    SolidBody moving_plate(sph_system, makeShared<MovingPlate>("MovingPlate"));
+    MovingPlate moving_plate_shape("MovingPlate");
+    SolidBody moving_plate(sph_system, moving_plate_shape.getName());
     moving_plate.defineMaterial<SaintVenantKirchhoffSolid>(rho0_s, Youngs_modulus, poisson);
-    moving_plate.generateParticles<BaseParticles, Lattice>();
+    moving_plate.generateParticles<BaseParticles, Lattice>(moving_plate_shape);
     //----------------------------------------------------------------------
     //	Define body relation map.
     //	The contact map gives the topological connections between the bodies.
     //	Basically the the range of bodies to build neighbor particle lists.
     //  Generally, we first define all the inner relations, then the contact relations.
     //----------------------------------------------------------------------
     InnerRelation myocardium_body_inner(myocardium_body);
-    SurfaceContactRelation myocardium_plate_contact(myocardium_body, {&moving_plate});
-    SurfaceContactRelation plate_myocardium_contact(moving_plate, {&myocardium_body});
+    SurfaceContactRelation myocardium_plate_contact(myocardium_body, myocardium_body_shape, {&moving_plate});
+    SurfaceContactRelation plate_myocardium_contact(moving_plate, moving_plate_shape, {&myocardium_body});
     //----------------------------------------------------------------------
     //	Define the numerical methods used in the simulation.
     //	Note that there may be data dependence on the sequence of constructions.
@@ -117,8 +119,7 @@ int main(int ac, char *av[])
     SimTK::GeneralForceSubsystem forces(MBsystem);
     SimTK::CableTrackerSubsystem cables(MBsystem);
     /** mass properties of the fixed spot. */
-    TransformShape<GeometricShapeBox> moving_plate_shape(Transform(translation_moving_plate), halfsize_moving_plate, "Plate");
-    SimpleDynamics<NormalDirectionFromBodyShape> moving_plate_normal_direction(moving_plate);
+    SimpleDynamics<NormalDirectionFromBodyShape> moving_plate_normal_direction(moving_plate, moving_plate_shape);
     SolidBodyPartForSimbody plate_multibody(moving_plate, moving_plate_shape);
     /** Mass properties of the constrained spot.
      * SimTK::MassProperties(mass, center of mass, inertia)

tests/3d_examples/test_3d_network/network.cpp

@@ -51,9 +51,11 @@ int main(int ac, char *av[])
     SPHSystem sph_system(system_domain_bounds, dp_0);
     sph_system.handleCommandlineOptions(ac, av)->setIOEnvironment();
     /** Creat a body, corresponding material and particles. */
-    TreeBody tree_on_sphere(sph_system, makeShared<GeometricShapeBall>(Vec3d::Zero(), 1.0, "Sphere"));
-    tree_on_sphere.defineBodyLevelSetShape()->writeLevelSet(sph_system);
-    tree_on_sphere.generateParticles<BaseParticles, Network>(starting_point, second_point, iteration_levels, grad_factor);
+    GeometricShapeBall ball_shape(Vec3d::Zero(), 1.0, "Sphere");
+    TreeBody tree_on_sphere(sph_system, ball_shape.getName());
+    LevelSetShape level_set_shape(tree_on_sphere, ball_shape);
+    level_set_shape.writeLevelSet(sph_system);
+    tree_on_sphere.generateParticles<BaseParticles, Network>(ball_shape, starting_point, second_point, iteration_levels, grad_factor);
     /** Write particle data. */
     BodyStatesRecordingToVtp write_states(sph_system);
     write_states.writeToFile(0);

tests/3d_examples/test_3d_passive_cantilever/passive_cantilever.cpp

@@ -73,9 +73,10 @@ int main(int ac, char *av[])
     SPHSystem sph_system(system_domain_bounds, resolution_ref);
     sph_system.handleCommandlineOptions(ac, av);
     /** create a Cantilever body, corresponding material, particles and reaction model. */
-    SolidBody cantilever_body(sph_system, makeShared<Cantilever>("CantileverBody"));
+    Cantilever cantilever_body_shape("CantileverBody");
+    SolidBody cantilever_body(sph_system, cantilever_body_shape.getName());
     cantilever_body.defineMaterial<Muscle>(rho0_s, bulk_modulus, fiber_direction, sheet_direction, a0, b0);
-    cantilever_body.generateParticles<BaseParticles, Lattice>();
+    cantilever_body.generateParticles<BaseParticles, Lattice>(cantilever_body_shape);
     /** Define Observer. */
     ObserverBody cantilever_observer(sph_system, "CantileverObserver");
     cantilever_observer.generateParticles<ObserverParticles>(observation_location);