using new TriangleMeshDistance for triangle mesh shape

modules/structural_simulation/structural_simulation_class.cpp

@@ -303,9 +303,9 @@ void StructuralSimulation::createBodyMeshList()
     {
         std::string relative_input_path_copy = relative_input_path_;
 #ifdef __EMSCRIPTEN__
-        body_mesh_list_.push_back(makeShared<TriangleMeshShapeSTL>(reinterpret_cast<const uint8_t *>(imported_stl_list_[i].ptr), translation_list_[i], scale_stl_, imported_stl_list_[i].name));
+        body_mesh_list_.push_back(makeShared<TriangleMeshShapeGeneric>(reinterpret_cast<const uint8_t *>(imported_stl_list_[i].ptr), translation_list_[i], scale_stl_, imported_stl_list_[i].name));
 #else
-        body_mesh_list_.push_back(makeShared<TriangleMeshShapeSTL>(relative_input_path_copy.append(imported_stl_list_[i]), translation_list_[i], scale_stl_, imported_stl_list_[i]));
+        body_mesh_list_.push_back(makeShared<TriangleMeshShapeGeneric>(relative_input_path_copy.append(imported_stl_list_[i]), translation_list_[i], scale_stl_, imported_stl_list_[i]));
 #endif
     }
 }

src/for_3D_build/geometries/TriangleMeshDistance.h

@@ -301,7 +301,7 @@ inline tmd::Result tmd::TriangleMeshDistance::signed_distance(const std::array<d
     Result result = this->unsigned_distance(p);
 
     const std::array<int, 3> &triangle = this->triangles[result.triangle_id];
-    Vec3d pseudonormal;
+    Vec3d pseudonormal(0.0, 0.0, 0.0);
     switch (result.nearest_entity)
     {
     case tmd::NearestEntity::V0:

tests/3d_examples/test_3d_beam_pulling_pressure_load/beam_pulling_pressure_load.cpp

@@ -36,7 +36,7 @@ class Beam : public ComplexShape
     {
         std::string fname_ = "./input/beam.stl";
         Vecd translation(0.0, 0.0, 0.0);
-        add<TriangleMeshShapeSTL>(fname_, translation, 0.001);
+        add<TriangleMeshShapeGeneric>(fname_, translation, 0.001);
     }
 };
 

tests/3d_examples/test_3d_heart_volume_change/excitation_contraction.h

@@ -63,7 +63,7 @@ class Heart : public ComplexShape
   public:
     explicit Heart(const std::string &shape_name) : ComplexShape(shape_name)
     {
-        add<TriangleMeshShapeSTL>(full_path_to_myocardium, translation, length_scale);
+        add<TriangleMeshShapeGeneric>(full_path_to_myocardium, translation, length_scale);
     }
 };
 /** Set diffusion relaxation method. */

tests/3d_examples/test_3d_nonlinear_wave_fsi/nonlinear_wave_fsi.cpp

@@ -187,7 +187,7 @@ int main(int ac, char *av[])
     /** mass properties of the fixed spot. */
     SimTK::Body::Rigid fixed_spot_info(SimTK::MassProperties(1, SimTK::Vec3(0), SimTK::UnitInertia(1)));
     /** mass properties of the structure. */
-    StructureSystemForSimbody structure_multibody(structure, makeShared<TriangleMeshShapeSTL>(stl_structure_path, translation_str, StructureScale));
+    StructureSystemForSimbody structure_multibody(structure, makeShared<TriangleMeshShapeGeneric>(stl_structure_path, translation_str, StructureScale));
     SimTK::Body::Rigid structure_info(*structure_multibody.body_part_mass_properties_);
     /** Free mobilizer */
     SimTK::MobilizedBody::Free tethered_struct(matter.Ground(), SimTK::Transform(SimTK::Vec3(translation_str[0], translation_str[1], translation_str[2])), structure_info, SimTK::Transform(SimTK::Vec3(0.0, 0.0, 0.0)));

tests/3d_examples/test_3d_nonlinear_wave_fsi/nonlinear_wave_fsi.h

@@ -268,7 +268,7 @@ class FloatingStructure : public ComplexShape
   public:
     explicit FloatingStructure(const std::string &shape_name) : ComplexShape(shape_name)
     {
-        add<TriangleMeshShapeSTL>(stl_structure_path, translation_str, StructureScale);
+        add<TriangleMeshShapeGeneric>(stl_structure_path, translation_str, StructureScale);
     }
 };
 
@@ -299,7 +299,7 @@ class WaterBlock : public ComplexShape
         Vecd water_pos(0.5 * DW, 0.5 * (DL - EXS), 0.5 * WH);
         Transform translation_water(water_pos);
         add<TransformShape<GeometricShapeBox>>(Transform(translation_water), halfsize_water);
-        subtract<TriangleMeshShapeSTL>(stl_structure_path, translation_str, StructureScale);
+        subtract<TriangleMeshShapeGeneric>(stl_structure_path, translation_str, StructureScale);
     }
 };
 

tests/3d_examples/test_3d_particle_relaxation/particle_relaxation.cpp

@@ -30,7 +30,7 @@ class SolidBodyFromMesh : public ComplexShape
     explicit SolidBodyFromMesh(const std::string &shape_name) : ComplexShape(shape_name)
     {
         Vecd translation(0.0, 0.0, 0.0);
-        add<TriangleMeshShapeSTL>(full_path_to_file, translation, 1.0);
+        add<TriangleMeshShapeGeneric>(full_path_to_file, translation, 1.0);
     }
 };
 //-----------------------------------------------------------------------------------------------------------

tests/3d_examples/test_3d_particle_relaxation_single_resolution/particle_relaxation_single_resolution_3D.cpp

@@ -20,6 +20,7 @@ using namespace SPH;
 Vec3d domain_upper_bound(2.3, 4.5, 0.3);
 Vecd translation(0.0, 0.0, 0.0);
 Real scaling = 1.0; */
+
 //----------------------------------------------------------------------
 //	Setting for the second geometry.
 //	To use this, please commenting the setting for the first geometry.
@@ -40,18 +41,45 @@ Real scaling = 2.5;
 //----------------------------------------------------------------------
 BoundingBox system_domain_bounds(domain_lower_bound, domain_upper_bound);
 Real dp_0 = (domain_upper_bound[0] - domain_lower_bound[0]) / 100.0;
-//----------------------------------------------------------------------
-//	define the imported model.
-//----------------------------------------------------------------------
+//--------------------------------------------------------------------
 class SolidBodyFromMesh : public ComplexShape
 {
   public:
     explicit SolidBodyFromMesh(const std::string &shape_name) : ComplexShape(shape_name)
     {
-        add<ExtrudeShape<TriangleMeshShapeSTL>>(4.0 * dp_0, full_path_to_file, translation, scaling);
-        subtract<TriangleMeshShapeSTL>(full_path_to_file, translation, scaling);
+        add<ExtrudeShape<TriangleMeshShapeGeneric>>(4.0 * dp_0, full_path_to_file, translation, scaling);
+        subtract<TriangleMeshShapeGeneric>(full_path_to_file, translation, scaling);
     }
 };
+//----------------------------------------------------------------------
+//	Setting for the second geometry.
+//	To use this, please commenting the setting for the first geometry.
+//----------------------------------------------------------------------
+//std::string full_path_to_file = "./input/fluid.stl";
+//----------------------------------------------------------------------
+//	Basic geometry parameters and numerical setup.
+//----------------------------------------------------------------------
+//Vec3d domain_lower_bound(-0.036, -0.046, -0.011);
+//Vec3d domain_upper_bound(0.036, 0.093, 0.072);
+//Vecd translation(0.0, 0.0, 0.0);
+//Real scaling = 1.0;
+
+//----------------------------------------------------------------------
+//	Below are common parts for the two test geometries.
+//----------------------------------------------------------------------
+//BoundingBox system_domain_bounds(domain_lower_bound, domain_upper_bound);
+//Real dp_0 = (domain_upper_bound[0] - domain_lower_bound[0]) / 100.0;
+//----------------------------------------------------------------------
+//	define the imported model.
+//----------------------------------------------------------------------
+//class SolidBodyFromMesh : public ComplexShape
+//{
+//  public:
+//    explicit SolidBodyFromMesh(const std::string &shape_name) : ComplexShape(shape_name)
+//    {
+//        add<TriangleMeshShapeGeneric>(full_path_to_file, translation, scaling);
+//    }
+//};
 //-----------------------------------------------------------------------------------------------------------
 //	Main program starts here.
 //-----------------------------------------------------------------------------------------------------------

tests/3d_examples/test_3d_pkj_lv_electrocontraction/pkj_lv_electrocontraction.h

@@ -93,7 +93,7 @@ class Heart : public ComplexShape
     explicit Heart(const std::string &shape_name) : ComplexShape(shape_name)
     {
         Vecd translation(0.0, 0.0, 0.0);
-        add<TriangleMeshShapeSTL>(full_path_to_lv, translation, length_scale);
+        add<TriangleMeshShapeGeneric>(full_path_to_lv, translation, length_scale);
     }
 };
 /** Set diffusion relaxation. */

tests/3d_examples/test_3d_self_contact/3d_self_contact.cpp

@@ -35,7 +35,7 @@ class Coil : public ComplexShape
   public:
     explicit Coil(const std::string &shape_name) : ComplexShape(shape_name)
     {
-        add<TriangleMeshShapeSTL>(full_path_to_file, Vecd::Zero(), 1.0);
+        add<TriangleMeshShapeGeneric>(full_path_to_file, Vecd::Zero(), 1.0);
     }
 };
 class StationaryPlate : public ComplexShape

tests/3d_examples/test_3d_shell_particle_relaxation/test_3d_shell_particle_relaxation.cpp

@@ -32,7 +32,7 @@ class ImportedShellModel : public ComplexShape
   public:
     explicit ImportedShellModel(const std::string &shape_name) : ComplexShape(shape_name)
     {
-        add<TriangleMeshShapeSTL>(full_path_to_geometry, Vecd::Zero(), 1.0);
+        add<TriangleMeshShapeGeneric>(full_path_to_geometry, Vecd::Zero(), 1.0);
     }
 };
 //--------------------------------------------------------------------------

tests/modules/bernoulli_beam_struct_sim/bernoulli_beam_struct_sim.cpp

@@ -20,7 +20,7 @@ TEST(BernoulliBeam20x, Pressure)
     SharedPtr<SaintVenantKirchhoffSolid> material = makeShared<SaintVenantKirchhoffSolid>(rho_0, Youngs_modulus, poisson);
     std::vector<SharedPtr<SaintVenantKirchhoffSolid>> material_model_list = {material};
 
-    SharedPtr<TriangleMeshShapeSTL> specimen = makeShared<TriangleMeshShapeSTL>("./input/bernoulli_beam_20x.stl", Vec3d::Zero(), scale_stl, "bernoulli_beam_20x");
+    SharedPtr<TriangleMeshShapeGeneric> specimen = makeShared<TriangleMeshShapeGeneric>("./input/bernoulli_beam_20x.stl", Vec3d::Zero(), scale_stl, "bernoulli_beam_20x");
     BoundingBox fixation = specimen->getBounds();
     fixation.second_[0] = fixation.first_[0] + 0.01;