Pull webassembly and recent changes (#67)

* Verification cases thesis (#15) * ConstrainSolidBody renamed * constrain solid body reagion added * force boundary condition * force BC edited * Pressure bc (#16) * SurfacePressureFromSource added * SurfacePressureFromSource::Update * BC prob works but the particle normals are missing * time dependent surface pressure works * cube case moved to source tests * Add test folder (#18) * Translate body part (#45) * Feature/contact stent 2 (#10) * PositionSolidBody added * boundary condition works but breaks numerically * no message * first unit test added * indentation change * PositionSolidBody test * remove file * small fixes * position constraint changed works between start and end time * scaling boundary condition * PositionScaleSolidBody unit test * particel adaptation changed * system resolution ratio added to particle adaptation * add googletest to docker and workflow * unit test removed temporarily * unit rest removed * SolidParticleRelaxation added to update initial particle position * gtest added again * gtest install changed * gtest * gtest * gtest * gtest * cd path updated * change to shared pointers * unit test pointers changed * gtest added to docker * initialization changed * disable tests for simbody * errors fixed * TranslationSolidBody added; translation cylinder * whitespace * fixes * TranslateSolidBody corrected * writeToFile update * change SET to set * catch(out_of_range& e) added * change to size_t * cmake minimum removed * BoundingBox test changed * fix writeToFIle * test change * Feature/position bc stent (#34) * PositionSolidBody added * boundary condition works but breaks numerically * no message * first unit test added * indentation change * PositionSolidBody test * remove file * small fixes * position constraint changed works between start and end time * scaling boundary condition * PositionScaleSolidBody unit test * particel adaptation changed * system resolution ratio added to particle adaptation * add googletest to docker and workflow * unit test removed temporarily * unit rest removed * SolidParticleRelaxation added to update initial particle position * gtest added again * gtest install changed * gtest * gtest * gtest * gtest * cd path updated * change to shared pointers * unit test pointers changed * gtest added to docker * initialization changed * errors fixed * TranslationSolidBody added; translation cylinder * whitespace * fixes * TranslateSolidBody corrected * writeToFile update * change SET to set * catch(out_of_range& e) added * change to size_t * cmake minimum removed * BoundingBox test changed * fix writeToFIle * test change Co-authored-by: JohnVirtonomy <[email protected]> * -Werror only works for linux * TEST TranslateSolidBodyTuple * Update CMakeLists.txt remove werror flag for msvc * update from bitbucket 01.07.2021 * delete repeated files * brief information on google test in repo readme * delete clapack and simbody folder in root * google test works for windows but the unit test case did not copy stl file right in windows * now test_3d_unit works in windows. * information on installing google test in windows * add a comment on install ing for VS in windows * translation with same scale&unit test update * skip testing when [ci skip] in the commit message * update test_3d_unit - TranslateSolidBody not work * time-dependent-contact * number of time dep. contacts fixed * setup unit test for time dependent contact * Translate Solid Body fixed but tolerance is only 0.01 * output changed to 100 files always * 07.13.2021 update * typo * new files from bitbucket * update 07.13.2021 * time dependent contact fixed * time dep contact fixed * remove cout * time dep. contact tests finished * renaming * fix naming * move test class into seperate header * cmake changes * changing function names to lower case * change cmake list * small fix Co-authored-by: Ubuntu <virtonomy@SPHsimulation2.qg4qjrxycqxetcothedhm1ylih.ax.internal.cloudapp.net> Co-authored-by: JohnVirtonomy <[email protected]> Co-authored-by: Xiangyu Hu <[email protected]> Co-authored-by: Wen-Yang Chu <[email protected]> Co-authored-by: Xiangyu Hu <xiangyu.hu@tum> Co-authored-by: Xiangyu Hu <[email protected]> * TranslateSolidBodyPart added * particle relaxation fixed * change Get_ to get_ * checkIfPointInBoundingBox moved Co-authored-by: Ubuntu <virtonomy@SPHsimulation2.qg4qjrxycqxetcothedhm1ylih.ax.internal.cloudapp.net> Co-authored-by: JohnVirtonomy <[email protected]> Co-authored-by: Xiangyu Hu <[email protected]> Co-authored-by: Wen-Yang Chu <[email protected]> Co-authored-by: Xiangyu Hu <xiangyu.hu@tum> Co-authored-by: Xiangyu Hu <[email protected]> * update from bitbucket 07-30-2021 * replace the wrong gpuSPHinXsys * Simbody artifacts instead of installation * simbody variable added to cmake command * change path * conflict resolved * remove doubled test Co-authored-by: Ubuntu <virtonomy@SPHsimulation2.qg4qjrxycqxetcothedhm1ylih.ax.internal.cloudapp.net> Co-authored-by: JohnVirtonomy <[email protected]> Co-authored-by: Xiangyu Hu <[email protected]> Co-authored-by: Wen-Yang Chu <[email protected]> Co-authored-by: Xiangyu Hu <xiangyu.hu@tum> Co-authored-by: Xiangyu Hu <[email protected]> * Pressure bc (#20) * SurfacePressureFromSource added * SurfacePressureFromSource::Update * BC prob works but the particle normals are missing * stress relaxation changed to Kirchhof * time dependent surface pressure works * cube case moved to source tests * cube test removed * add overtime to position based tests * go back to last working state * back to working version Co-authored-by: Ubuntu <virtonomy@SPHbence.qg4qjrxycqxetcothedhm1ylih.ax.internal.cloudapp.net> * simulation class remvoed (#21) * fix numerical damping (#23) * Simbody lib seperate (#26) * remove submodules * simbody added on no lapack * simbody * cases user moved * scripts removed * simbody set to master * variables removed * 3d lib cmake * boost option * simbody linking to built libraries * renaming + 2D cmake * option subdir * werror * eigen in simbody * eigen added * eigen * eigen include * eigen * add wasmtbb * working wasm example * cmake changes * restore working wasm build * change memory pool for wasm * work on eigen Co-authored-by: wen-yang chu <[email protected]> * update simbody * Replace clapack (#27) * work on eigen * all tests pass with Eigen * macro renamed simbody * all SPH tests pass for static build * remove wasm files * first setup of spring on surface normal direction (#22) * first setup of spring on surface normal direction * adjusted combi of spring and pressure BC * correction of damping coefficient * simulation runs but too small time steps, only one vtu-file * consideration normal portion in opposite direction * creation of tests for vector calculations * simplification of vector norm calculation * small vector test working, but failing * small vector tests passing * angle tests added * correction of Vector Projection more test examples * correction of normal spring beam still spinning * adding of functions for vector calculations * change of spring force in right direction * debugging, still spinning after timestep 18 * change of vector calculation example * correction of normal spring force * for-loop removed, checking of spring & damping * area moved and considered in damping * adding gtest to CMakeLists * simplified dot_product_2 calculation * change from Vecd to Vec3d for calculations * changed Vector declaration and functions * correction of Spring and Damping Co-authored-by: JohnVirtonomy.io <[email protected]> * emscripten option to disable gtest (#28) * emscripten option to disable gtest * comment out compiling flags * bug fix Co-authored-by: wen-yang chu <[email protected]> * Fix zero pos particles (#31) * change pressure BC to be define by body part * SpringNormalOnSurfaceParticles with body part * option to use inner or outer surface for spring * zero position of particles fixed * fix BodyPartByParticle (#34) * Dynamic heart (#29) * change pressure BC to be define by body part * SpringNormalOnSurfaceParticles with body part * option to use inner or outer surface for spring * zero position of particles fixed * adding function to avoid LevelSetComplexShape * "virtual" added to comply with github CI test * both options for normalDirectionCalculation * "virtual" removed since no change in CI test * additional findNormalDirection dor 2D_build * comment to see if geometry_level_set is called * accelaration output added to vtu * adding displacement output & removing density * Vec3d to Vecd * adding normal vectors to vtu-File * von Mises Strain implemented * CMake name change to differentiate BUILD_TEST * test for strain calculation * correction of von Mises strain calculation * displ., normal, strain output calc. added in 2D Co-authored-by: JohnVirtonomy <[email protected]> * Fix wasm merge2 (#37) * add EMSCRIPTEN macro to disable macro * remove image stuff with emscripten * simbody static lib with emscripten Co-authored-by: Wen-Yang Chu <[email protected]> Co-authored-by: JohnVirtonomy <[email protected]> * Production 1 freatures (#32) * cherry pick fixing zero position * option to write levelset data * fix BodyPartByParticle * small_shift changed * small shift changed back * fix normal calculation bug Co-authored-by: JohnVirtonomy <[email protected]> * vtu ouput update (#39) * SurfaceOnlyBodyStatesRecordingToVtu class * class, functions for only surface particles output * comment out cout of number of surface particles * ShapeSurface in constructor only called at start * correction of surface ouput; still some issues * final correction of surface particle output Co-authored-by: JohnVirtonomy <[email protected]> * add writer for vtu file to string * revert commit * add writer for vtu file to string (#40) * add small shift option to level set (#38) * add small shift option to level set * throw exceptions if instability occurs * fix comment * Kirchhof relaxation stability improved, removed B_ * fix 2D error * 2d self contact changed Co-authored-by: JohnVirtonomy <[email protected]> * Triangle mesh from buffer constructor (#44) * triangle mesh buffer constructor * Triangle mesh from buffer only for emcc * structural simulation to gitHub (#41) * structural simulation to gitHub * change class * fix wasm compilation Co-authored-by: JohnVirtonomy <[email protected]> Co-authored-by: BenceVirtonomy <[email protected]> * Surface spring (#45) * surface spring constraint added with test * add surface fixation * surface spring * better exception * findTBB edit * change error message Co-authored-by: JohnVirtonomy <[email protected]> Co-authored-by: Ubuntu <virtonomy@SPHsimulation2.qg4qjrxycqxetcothedhm1ylih.ax.internal.cloudapp.net> Co-authored-by: JohnVirtonomy <[email protected]> Co-authored-by: Xiangyu Hu <[email protected]> Co-authored-by: Wen-Yang Chu <[email protected]> Co-authored-by: Xiangyu Hu <xiangyu.hu@tum> Co-authored-by: Xiangyu Hu <[email protected]> Co-authored-by: Ubuntu <virtonomy@SPHbence.qg4qjrxycqxetcothedhm1ylih.ax.internal.cloudapp.net> Co-authored-by: JohnVirtonomy <[email protected]> Co-authored-by: JohnVirtonomy.io <[email protected]> Co-authored-by: Antonov548 <[email protected]> Co-authored-by: mrezavandVirtonomy <[email protected]>
Virtonomy · Oct 22, 2021 · faa88ca · faa88ca
1 parent efcd778
commit faa88ca
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diff --git a/3rd_party/simbody b/3rd_party/simbody
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -12,13 +12,13 @@ option(STATIC_BUILD "STATIC_BUILD" 0)
 option(ONLY_3D "ONLY_3D" 0)
 option(BUILD_WITH_SIMBODY "BUILD_WITH_SIMBODY" 0)
 option(EMSCRIPTEN "EMSCRIPTEN" 0)
-option(BUILD_TESTS "BUILD_TESTS" 1)
+option(BUILD_SPHINXSYS_TESTS "BUILD_SPHINXSYS_TESTS" 1)
 
 if(EMSCRIPTEN)
     set(STATIC_BUILD 1)
     set(BUILD_WITH_SIMBODY 1)
     set(ONLY_3D 1)
-    set(BUILD_TESTS 1)
+    set(BUILD_SPHINXSYS_TESTS 1)
     add_definitions(-D__SIMBODY_WITHOUT_LAPACK__)
     add_definitions(-D__EIGEN__)
     add_definitions(-D__EMSCRIPTEN__)
@@ -128,10 +128,12 @@ endif()
 
 add_subdirectory(SPHINXsys)
 
-if(BUILD_TESTS)
+if(BUILD_SPHINXSYS_TESTS)
     add_subdirectory(tests)
 endif()
 
 if(ACTIVATE_CUDA)
     add_subdirectory(cases_test_gpu)
 endif()
+
+add_subdirectory(modules)
diff --git a/SPHINXsys/src/for_2D_build/geometries/level_set_supplementary.cpp b/SPHINXsys/src/for_2D_build/geometries/level_set_supplementary.cpp
@@ -88,9 +88,9 @@ namespace SPH {
 			}
 	}
 	//=================================================================================================//
-	void LevelSetDataPackage::markNearInterface()
+	void LevelSetDataPackage::markNearInterface(Real small_shift_factor)
 	{
-		Real small_shift = 0.75 * grid_spacing_;
+		Real small_shift = small_shift_factor * grid_spacing_;
 		//corner averages, note that the first row and first column are not used 
 		PackageTemporaryData<Real> corner_averages;
 		for (int i = 1; i != AddressSize(); ++i)

diff --git a/SPHINXsys/src/for_2D_build/particles/solid_particles_supplementary.cpp b/SPHINXsys/src/for_2D_build/particles/solid_particles_supplementary.cpp
@@ -32,4 +32,34 @@ namespace SPH {
 			+ 3.0 * sigmaxy * sigmaxy);
 	}
 	//=================================================================================================//
+	Vecd ElasticSolidParticles::displacement(size_t particle_i) //not tested in 2D
+	{
+		Vecd disp = pos_n_[particle_i] - pos_0_[particle_i];
+		return disp;
+	}
+	//=================================================================================================//
+	Vecd ElasticSolidParticles::normal(size_t particle_i) //not tested in 2D
+	{
+		Vecd normal_vec = n_[particle_i];
+		return normal_vec;
+	}
+	//=================================================================================================//
+	Real ElasticSolidParticles::von_Mises_strain(size_t particle_i) //not tested in 2D
+	{
+
+		Mat2d F = F_[particle_i];
+		Mat2d epsilon = 0.5 * (~F * F - Mat2d(1.0)); //calculation of the Green-Lagrange strain tensor
+
+
+		Real epsilonxx = epsilon(0, 0);
+		Real epsilonyy = epsilon(1, 1);
+		Real epsilonzz = 0; 			//z-components zero for 2D measures
+		Real epsilonxy = epsilon(0, 1);
+		Real epsilonxz = 0; 			//z-components zero for 2D measures
+		Real epsilonyz = 0; 			//z-components zero for 2D measures
+
+		return sqrt( (1.0 / 3.0) * (std::pow(epsilonxx - epsilonyy, 2.0) + std::pow(epsilonyy - epsilonzz, 2.0) + std::pow(epsilonzz - epsilonxx, 2.0))
+		 + 2.0 * (std::pow(epsilonxy, 2.0) + std::pow(epsilonyz, 2.0) + std::pow(epsilonxz, 2.0)));
+	}
+	//=================================================================================================//
 }
diff --git a/SPHINXsys/src/for_3D_build/geometries/complex_shape_image_mesh.cpp b/SPHINXsys/src/for_3D_build/geometries/complex_shape_image_mesh.cpp
@@ -1,3 +1,5 @@
+#ifndef __EMSCRIPTEN__
+
 #include "complex_shape_image_mesh.h"
 #include "image_mesh_shape.h"
 
@@ -161,4 +163,6 @@ namespace SPH
 		return BoundingBox(lower_bound, upper_bound);
 	}
 	//=================================================================================================//
-}
+}
+
+#endif // __EMSCRIPTEN__
diff --git a/SPHINXsys/src/for_3D_build/geometries/complex_shape_image_mesh.h b/SPHINXsys/src/for_3D_build/geometries/complex_shape_image_mesh.h
@@ -31,6 +31,8 @@
 #ifndef COMPLEX_SHAPE_IMAGE_MESH_H
 #define COMPLEX_SHAPE_IMAGE_MESH_H
 
+#ifndef __EMSCRIPTEN__
+
 #define _SILENCE_EXPERIMENTAL_FILESYSTEM_DEPRECATION_WARNING
 
 #include "base_geometry.h"
@@ -88,3 +90,5 @@ namespace SPH
 }
 
 #endif //COMPLEX_SHAPE_IMAGE_MESH_H
+
+#endif // __EMSCRIPTEN__
diff --git a/SPHINXsys/src/for_3D_build/geometries/geometry.cpp b/SPHINXsys/src/for_3D_build/geometries/geometry.cpp
@@ -17,6 +17,17 @@ namespace SPH
 		polymesh.scaleMesh(scale_factor);
 		triangle_mesh_ = generateTriangleMesh(polymesh.transformMesh(translation));
 	}
+#ifdef __EMSCRIPTEN__
+	//=================================================================================================//
+	TriangleMeshShape::TriangleMeshShape(const uint8_t* buffer, Vec3d translation, Real scale_factor)
+		: Shape("TriangleMeshShape")
+	{
+		SimTK::PolygonalMesh polymesh;
+		polymesh.loadStlBuffer(buffer);
+		polymesh.scaleMesh(scale_factor);
+		triangle_mesh_ = generateTriangleMesh(polymesh.transformMesh(translation));
+	}
+#endif
 	//=================================================================================================//
 	TriangleMeshShape::TriangleMeshShape(Vec3d halfsize, int resolution, Vec3d translation)
 		: Shape("TriangleMeshShape")
@@ -146,6 +157,7 @@ namespace SPH
 	//=================================================================================================//
 	Vec3d ComplexShape::findClosestPoint(const Vec3d &input_pnt)
 	{
+		//std::cout << "ComplexShape::findSignedDistance(const Vec3d &input_pnt) called";
 		return complex_shape_mesh_->findClosestPoint(input_pnt);
 	}
 	//=================================================================================================//

diff --git a/SPHINXsys/src/for_3D_build/geometries/geometry.h b/SPHINXsys/src/for_3D_build/geometries/geometry.h
@@ -69,6 +69,10 @@ namespace SPH
 	public:
 		//constructor for load stl file from out side
 		TriangleMeshShape(std::string file_path_name, Vec3d translation, Real scale_factor);
+#ifdef __EMSCRIPTEN__
+		//constructor for load stl file from buffer
+		TriangleMeshShape(const uint8_t* buffer, Vec3d translation, Real scale_factor);
+#endif
 		// constructor for brick geometry
 		TriangleMeshShape(Vec3d halfsize, int resolution, Vec3d translation);
 		// constructor for sphere geometry
@@ -90,12 +94,10 @@ namespace SPH
 
 	class ComplexShape : public Shape
 	{
-		Vec3d findClosestPoint(const Vec3d &input_pnt);
-
 	public:
 		ComplexShape() : Shape("ComplexShape") { complex_shape_mesh_ = nullptr; };
 		ComplexShape(std::string complex_shape_name) : Shape(complex_shape_name) { complex_shape_mesh_ = nullptr; };
-		ComplexShape(ComplexShapeMesh*complex_shape_mesh) : Shape("ComplexShape") { complex_shape_mesh_ = complex_shape_mesh; };
+		ComplexShape(ComplexShapeMesh* complex_shape_mesh) : Shape("ComplexShape") { complex_shape_mesh_ = complex_shape_mesh; };
 		virtual ~ComplexShape() {};
 		virtual BoundingBox findBounds() override;
 
@@ -125,11 +127,13 @@ namespace SPH
 		virtual bool checkNearSurface(const Vec3d &input_pnt, Real threshold);
 		/** Signed distance is negative for point within the complex shape. */
 		virtual Real findSignedDistance(const Vec3d &input_pnt);
+		/** find closest point on the surface */
+		virtual Vec3d findClosestPoint(const Vec3d &input_pnt);
 		/** Normal direction point toward outside of the complex shape. */
 		virtual Vec3d findNormalDirection(const Vec3d &input_pnt);
 
 	protected:
-		/** shape container<pointer to geomtry, operation> */
+		/** shape container<pointer to geometry, operation> */
 
 		ComplexShapeMesh* complex_shape_mesh_;
 	};

diff --git a/SPHINXsys/src/for_3D_build/geometries/image_mesh_shape.cpp b/SPHINXsys/src/for_3D_build/geometries/image_mesh_shape.cpp
@@ -1,3 +1,5 @@
+#ifndef __EMSCRIPTEN__
+
 #include "image_mesh_shape.h"
 
 namespace SPH
@@ -69,3 +71,5 @@ namespace SPH
 	//=================================================================================================//
 
 }
+
+#endif // __EMSCRIPTEN__
diff --git a/SPHINXsys/src/for_3D_build/geometries/image_mesh_shape.h b/SPHINXsys/src/for_3D_build/geometries/image_mesh_shape.h
@@ -31,6 +31,8 @@
 #ifndef IMAGE_MESH_SHAPE_H
 #define IMAGE_MESH_SHAPE_H
 
+#ifndef __EMSCRIPTEN__
+
 #define _SILENCE_EXPERIMENTAL_FILESYSTEM_DEPRECATION_WARNING
 
 #include "base_geometry.h"
@@ -85,4 +87,6 @@ namespace SPH
 	};
 }
 
+#endif // __EMSCRIPTEN__
+
 #endif //IMAGE_MESH_SHAPE_H
diff --git a/SPHINXsys/src/for_3D_build/geometries/level_set_supplementary.cpp b/SPHINXsys/src/for_3D_build/geometries/level_set_supplementary.cpp
@@ -106,9 +106,10 @@ namespace SPH {
 				}
 	}
 	//=================================================================================================//
-	void LevelSetDataPackage::markNearInterface() 
-	{
-		Real small_shift = 0.75 * grid_spacing_;
+	void LevelSetDataPackage::markNearInterface(Real small_shift_factor) 
+	{	
+		 // small_shift_factor = 0.75 by default, can be increased for difficult geometries for smoothing
+		Real small_shift = small_shift_factor * grid_spacing_;
 		//corner averages, note that the first row and first column are not used 
 		PackageTemporaryData<Real> corner_averages;
 		for (int i = 1; i != AddressSize(); ++i)

diff --git a/SPHINXsys/src/for_3D_build/particles/solid_particles_supplementary.cpp b/SPHINXsys/src/for_3D_build/particles/solid_particles_supplementary.cpp
@@ -31,4 +31,34 @@ namespace SPH {
 			+ 3.0 * (sigmaxy * sigmaxy + sigmaxz * sigmaxz + sigmayz * sigmayz));
 	}
 	//=================================================================================================//
+	Vecd ElasticSolidParticles::displacement(size_t particle_i)
+	{
+		Vecd disp = pos_n_[particle_i] - pos_0_[particle_i];
+		return disp;
+	}
+	//=================================================================================================//
+	Vecd ElasticSolidParticles::normal(size_t particle_i)
+	{
+		Vecd normal_vec = n_[particle_i];
+		return normal_vec;
+	}
+	//=================================================================================================//
+	Real ElasticSolidParticles::von_Mises_strain(size_t particle_i)
+	{
+
+		Mat3d F = F_[particle_i];
+		Mat3d epsilon = 0.5 * (~F * F - Matd(1.0)); //calculation of the Green-Lagrange strain tensor
+
+
+		Real epsilonxx = epsilon(0, 0);
+		Real epsilonyy = epsilon(1, 1);
+		Real epsilonzz = epsilon(2, 2);
+		Real epsilonxy = epsilon(0, 1);
+		Real epsilonxz = epsilon(0, 2);
+		Real epsilonyz = epsilon(1, 2);
+
+		return sqrt( (1.0 / 3.0) * (std::pow(epsilonxx - epsilonyy, 2.0) + std::pow(epsilonyy - epsilonzz, 2.0) + std::pow(epsilonzz - epsilonxx, 2.0))
+		 + 2.0 * (std::pow(epsilonxy, 2.0) + std::pow(epsilonyz, 2.0) + std::pow(epsilonxz, 2.0)));
+	}
+	//=================================================================================================//
 }
diff --git a/SPHINXsys/src/shared/bodies/base_body.cpp b/SPHINXsys/src/shared/bodies/base_body.cpp
@@ -74,12 +74,18 @@ namespace SPH
 		return body_domain_bounds_;
 	}
 	//=================================================================================================//
-	void SPHBody::writeParticlesToVtuFile(std::ofstream &output_file)
+	void SPHBody::writeParticlesToVtuFile(std::ostream &output_file)
 	{
 		base_particles_->writeParticlesToVtuFile(output_file);
 		newly_updated_ = false;
 	}
 	//=================================================================================================//
+	void SPHBody::writeSurfaceParticlesToVtuFile(std::ofstream &output_file, ShapeSurface& surface_particles)
+	{
+		base_particles_->writeSurfaceParticlesToVtuFile(output_file, surface_particles);
+		newly_updated_ = false;
+	}
+	//=================================================================================================//
 	void SPHBody::writeParticlesToPltFile(std::ofstream &output_file)
 	{
 		if (newly_updated_)
@@ -184,7 +190,7 @@ namespace SPH
 			if (fabs(phi) < particle_spacing_min_)
 				tagAParticle(i);
 		}
-		std::cout << "Number of surface particles : " << body_part_particles_.size() << std::endl;
+		//std::cout << "Number of surface particles : " << body_part_particles_.size() << std::endl;
 	}
 	//=================================================================================================//
 	ShapeSurfaceLayer::ShapeSurfaceLayer(SPHBody *body, Real layer_thickness)

diff --git a/SPHINXsys/src/shared/bodies/base_body.h b/SPHINXsys/src/shared/bodies/base_body.h
@@ -52,6 +52,7 @@ namespace SPH
 	class BaseParticles;
 	class BaseCellLinkedList;
 	class SPHBodyRelation;
+	class ShapeSurface;
 
 	/**
 	 * @class SPHBody
@@ -110,7 +111,8 @@ namespace SPH
 		virtual void assignBaseParticles(BaseParticles *base_particles);
 		void allocateConfigurationMemoriesForBufferParticles();
 
-		virtual void writeParticlesToVtuFile(std::ofstream &output_file);
+		virtual void writeParticlesToVtuFile(std::ostream &output_file);
+		virtual void writeSurfaceParticlesToVtuFile(std::ofstream &output_file, ShapeSurface& surface_particles);
 		virtual void writeParticlesToPltFile(std::ofstream &output_file);
 		virtual void writeParticlesToXmlForRestart(std::string &filefullpath);
 		virtual void readParticlesFromXmlForRestart(std::string &filefullpath);
@@ -207,13 +209,28 @@ namespace SPH
 		IndexVector body_part_particles_; /**< Collection particle in this body part. */
 
 		BodyPartByParticle(SPHBody *body, std::string body_part_name)
-			: BodyPartByShape(body, body_part_name){};
+			: BodyPartByShape(body, body_part_name),
+			body_part_bounds_(Vecd(0), Vecd(0)), body_part_bounds_set_(false)
+		{};
 
 		virtual ~BodyPartByParticle(){};
 
+		void setBodyPartBounds(BoundingBox bbox){
+			body_part_bounds_ = bbox;
+			body_part_bounds_set_ = true;
+		};
+
+		BoundingBox getBodyPartBounds(){
+			if (!body_part_bounds_set_) std::cout << "WARNING: the body part bounds are not set for BodyPartByParticle." << std::endl;
+			return body_part_bounds_;
+		}
+
 	protected:
 		void tagAParticle(size_t particle_index);
 		virtual void tagBodyPart() override;
+
+		BoundingBox body_part_bounds_;
+		bool body_part_bounds_set_;
 	};
 
 	/**

diff --git a/SPHINXsys/src/shared/common/image_mhd.h b/SPHINXsys/src/shared/common/image_mhd.h
@@ -30,6 +30,8 @@
 #ifndef IMAGE_MHD_H
 #define IMAGE_MHD_H
 
+#ifndef __EMSCRIPTEN__
+
 #include "small_vectors.h"
 #include "sph_data_containers.h"
 
@@ -161,4 +163,6 @@ namespace SPH {
 
 #include "image_mhd.hpp"
 
+#endif //__EMSCRIPTEN__
+
 #endif //IMAGE_MHD_H
diff --git a/SPHINXsys/src/shared/common/image_mhd.hpp b/SPHINXsys/src/shared/common/image_mhd.hpp
@@ -21,13 +21,16 @@
 *                                                                           *
 * --------------------------------------------------------------------------*/
 /**
-* @file image_mesh_shape.h
+* @file image_mhd.hpp
 * @brief x
 * @details x
 *			x
 * @author	Yijin Mao
 */
-#pragma once
+#ifndef IMAGE_MHD_HPP
+#define IMAGE_MHD_HPP
+
+#ifndef __EMSCRIPTEN__
 
 #include "image_mhd.h"
 #include "boost/algorithm/string.hpp"
@@ -521,3 +524,6 @@ namespace SPH {
 
 	}
 }
+#endif __EMSCRIPTEN__
+
+#endif IMAGE_MHD_HPP