Doc for Geometry added

src/Geometry/geometry/demGeometry.hpp

@@ -27,13 +27,16 @@ Licence:
 namespace pFlow
 {
 
-
+/** base for geometry that manages control 
+ * 
+ */
 class demGeometry
 :
 	public demComponent
 {
 
 public:
+
 	demGeometry(systemControl& control)
 	:
 		demComponent("geometry", control)

src/Geometry/geometry/geometry.cpp

@@ -190,7 +190,7 @@ pFlow::geometry::geometry
 			objectFile(
 				"contactForceWall",
 				"",
-				objectFile::READ_IF_PRESENT,
+				objectFile::READ_NEVER,
 				objectFile::WRITE_ALWAYS),
 			surface(),
 			zero3) ),
@@ -199,7 +199,7 @@ pFlow::geometry::geometry
 			objectFile(
 				"stressWall",
 				"",
-				objectFile::READ_IF_PRESENT,
+				objectFile::READ_NEVER,
 				objectFile::WRITE_ALWAYS),
 			surface(),
 			zero3) )
@@ -271,6 +271,33 @@ pFlow::uniquePtr<pFlow::geometry>
 	return nullptr;
 }
 
+bool pFlow::geometry::beforeIteration()
+{ 
+	this->zeroForce();
+	return true;	
+}
+
+
+bool pFlow::geometry::afterIteration()
+{ 
+	
+	auto Force = contactForceWall_.deviceVectorAll();
+	auto area = triSurface_.area().deviceVectorAll();
+	auto stress = stressWall_.deviceVectorAll();
+	auto numTri =triSurface_.size();
+	
+
+	Kokkos::parallel_for(
+		"geometry::calculateStress",
+		numTri,
+		LAMBDA_HD(int32 i){
+			stress[i] = Force[i]/area[i];
+		});
+	Kokkos::fence();
+	return true;
+	
+}
+
 pFlow::uniquePtr<pFlow::geometry> 
 	pFlow::geometry::create(
 			systemControl& control,

src/Geometry/geometry/geometry.hpp

@@ -34,34 +34,51 @@ Licence:
 namespace pFlow
 {
 
+
+/**
+ * Base class for geometry for managing tri-surfaces, geometry motion, 
+ * and surface physical properties. 
+ * 
+ */
 class geometry
 :
 	public demGeometry
 {
 protected:
 
+	// - Protected members 
+
+		/// Const reference to physical property of materials 
 		const property& 	wallProperty_;
 
-	// - this object is owned by geometryRepository_ 
+		/// Repository to store geometry data at each simulation moment
 		repository&  		geometryRepository_;
 
-	// all triangles of walls 
+		/// All triangles in the set of wall surfaces 
 		multiTriSurface&  	triSurface_;
 
-	// 
+		/// The name of motion component of each wall surface 
 		wordField& 			motionComponentName_;
 
-	// 
+		/// Material name of each wall surface  
 		wordField&   		materialName_;
 		
+		/// Property id of each triangle in the set of wall surfaces
 		int8TriSurfaceField_D& 		propertyId_;
 
+		/// Contact force on each triangle in the set of wall surfaces
 		realx3TriSurfaceField_D& 	contactForceWall_;
 
+		/// Stress on ech triangle in the set of wall surfaces 
 		realx3TriSurfaceField_D&    stressWall_;
 
+	// - Protected member functions
+	
+		/// Find property id of each triangle based on the supplied material name
+		/// and the surface wall that the triangle belongs to. 
 		bool findPropertyId();
 
+		/// Initialize contact force to zero 
 		void zeroForce()
 		{
 			contactForceWall_.fill(zero3);
@@ -70,15 +87,15 @@ protected:
 
 public:
 
-	// - type info
+	/// Type info
 	TypeInfo("geometry");
 
-	//// - Constructors 
+	// - Constructors 
 		
-		// - empty
+		/// Construct from controlSystem and property, for reading from file
 		geometry(systemControl& control, const property& prop);
 
-		// - from components
+		/// Construct from components
 		geometry(systemControl& control,
 				 const property& prop,
 				 const multiTriSurface& triSurface,
@@ -86,6 +103,8 @@ public:
 				 const wordVector& propName
 				);
 
+		/// Construct from components and dictionary that contains 
+		/// motionModel
 		geometry(systemControl& control,
 				 const property& prop,
 				 const dictionary& dict,
@@ -93,9 +112,10 @@ public:
 				 const wordVector& motionCompName,
 				 const wordVector& propName);
 
-
+		/// Destructor
 		virtual ~geometry() = default;
 
+		/// Virtual constructor 
 		create_vCtor
 		(
 			geometry,
@@ -107,6 +127,7 @@ public:
 			(control, prop)
 		);
 
+		/// Virtual constructor 
 		create_vCtor
 		(
 			geometry,
@@ -120,135 +141,135 @@ public:
 			(control, prop, dict, triSurface, motionCompName, propName)
 		);
 
-	////- Methods 
+	//- Methods 
 
+		/// Size of tri-surface 
 		inline
 		auto size()const
 		{
 			return triSurface_.size();
 		}
 
+		/// Number of points in the set of surface walls 
 		inline
 		auto numPoints()const
 		{
 			return triSurface_.numPoints();
 		}
 
+		/// Number of triangles in the set of surface walls 
 		inline
 		auto numTriangles()const
 		{
 			return size();
 		}
 
+		/// Access to the points
 		inline
 		const auto& points()const
 		{
 			return triSurface_.points();
 		}
 
+		/// Access to the vertices 
 		inline
 		const auto& vertices()const
 		{
 			return triSurface_.vertices();
 		}
 
+		/// Obtain an object for accessing triangles 
 		inline auto getTriangleAccessor()const
 		{
 			return triSurface_.getTriangleAccessor();
 		}
 
+		/// Surface 
 		inline auto& surface()
 		{
 			return triSurface_;
 		}
 
+		/// Surface 
 		inline const auto& surface()const
 		{
 			return triSurface_;
 		}
 
+		/// Access to contact force
 		inline
 		realx3TriSurfaceField_D& contactForceWall()
 		{
 			return contactForceWall_;
 		}
 
+		/// Access to contact force
 		inline
 		const realx3TriSurfaceField_D& contactForceWall() const
 		{
 			return contactForceWall_;
 		}
 
+		/// Access to property 
 		inline const auto& wallProperty()const
 		{
 			return wallProperty_;
 		}
 
-		// owner repository
+		/// Owner repository
 		inline
 		const repository& owner()const
 		{
 			return geometryRepository_;
 		}
 
+		/// Owner repository
 		inline
 		repository& owner()
 		{
 			return geometryRepository_;
 		}
 
+		/// Path to the repository folder 
 		inline auto path()
 		{
 			return owner().path();
 		}
 
+		/// The name of motion model 
 		virtual 
 		word motionModelTypeName()const = 0;
 
+		/// Motion model index of triangles 
 		virtual
 		const int8Vector_HD& 			triMotionIndex() const =0;
 
+		/// Motion model index of points 
 		virtual 
 		const int8Vector_HD& 			pointMotionIndex()const = 0;
 
+		/// Property ide of triangles 
 		const int8TriSurfaceField_D& 	propertyId() const
 		{
 			return propertyId_;
 		}
 
-		bool beforeIteration() override { 
+		/// Operations before each iteration 
+		bool beforeIteration() override;
 
-			this->zeroForce();
+		/// Operations after each iteration
-			return true;
+		bool afterIteration() override;
 
-		}
+	//- IO
-
-		bool afterIteration() override { 
-			
-			auto Force = contactForceWall_.deviceVectorAll();
-			auto area = triSurface_.area().deviceVectorAll();
-			auto stress = stressWall_.deviceVectorAll();
-			auto numTri =triSurface_.size();
-			
-
-			Kokkos::parallel_for(
-				"geometry::calculateStress",
-				numTri,
-				LAMBDA_HD(int32 i){
-					stress[i] = Force[i]/area[i];
-				});
-			Kokkos::fence();
-			return true;
-			
-		}
 
+		/// write 
 		bool write()const
 		{
 			return owner().write();
 		}
 
 
-		// static 
+	//- Static members 
 
 		static
 		uniquePtr<geometry> create(systemControl& control, const property& prop);

src/Geometry/geometryMotion/geometryMotion.cpp

@@ -18,38 +18,6 @@ Licence:
 
 -----------------------------------------------------------------------------*/
 
-template<typename MotionModel>
-bool pFlow::geometryMotion<MotionModel>::moveGeometry()
-{
-
-	real dt = this->dt();
-	real t = this->currentTime();
-
-	auto pointMIndex= pointMotionIndex_.deviceVector();
-	auto mModel = motionModel_.getModel(t);
-	realx3* points = triSurface_.pointsData_D();
-	auto numPoints = triSurface_.numPoints();
-
-
-	Kokkos::parallel_for(
-		"geometryMotion<MotionModel>::movePoints",
-		numPoints,
-		LAMBDA_HD(int32 i){
-			auto newPos = mModel.transferPoint(pointMIndex[i], points[i], dt);
-			points[i] = newPos;
-		});
-
-	Kokkos::fence();
-
-	// move the motion components 
-	motionModel_.move(t,dt);
-
-	// end of calculations 
-	moveGeomTimer_.end();
-
-	return true;
-}
-
 template<typename MotionModel>
 bool pFlow::geometryMotion<MotionModel>::findMotionIndex()
 {
@@ -88,6 +56,7 @@ bool pFlow::geometryMotion<MotionModel>::findMotionIndex()
 	return true;
 }
 
+
 template<typename MotionModel>
 pFlow::geometryMotion<MotionModel>::geometryMotion
 (
@@ -180,6 +149,13 @@ pFlow::geometryMotion<MotionModel>::geometryMotion
 	findMotionIndex();
 }
 
+template<typename MotionModel>
+bool pFlow::geometryMotion<MotionModel>::beforeIteration() 
+{ 
+	geometry::beforeIteration();
+	return true;
+}
+
 template<typename MotionModel>
 bool pFlow::geometryMotion<MotionModel>::iterate()
 {
@@ -191,3 +167,42 @@ bool pFlow::geometryMotion<MotionModel>::iterate()
 	}
 	return true;
 }
+
+template<typename MotionModel>
+bool pFlow::geometryMotion<MotionModel>::afterIteration() 
+{
+	geometry::afterIteration();
+	return true;
+}
+
+template<typename MotionModel>
+bool pFlow::geometryMotion<MotionModel>::moveGeometry()
+{
+
+	real dt = this->dt();
+	real t = this->currentTime();
+
+	auto pointMIndex= pointMotionIndex_.deviceVector();
+	auto mModel = motionModel_.getModel(t);
+	realx3* points = triSurface_.pointsData_D();
+	auto numPoints = triSurface_.numPoints();
+
+
+	Kokkos::parallel_for(
+		"geometryMotion<MotionModel>::movePoints",
+		numPoints,
+		LAMBDA_HD(int32 i){
+			auto newPos = mModel.transferPoint(pointMIndex[i], points[i], dt);
+			points[i] = newPos;
+		});
+
+	Kokkos::fence();
+
+	// move the motion components 
+	motionModel_.move(t,dt);
+
+	// end of calculations 
+	moveGeomTimer_.end();
+
+	return true;
+}

src/Geometry/geometryMotion/geometryMotion.hpp

@@ -17,8 +17,6 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-
-
 #ifndef __geometryMotion_hpp__
 #define __geometryMotion_hpp__
 
@@ -29,7 +27,11 @@ Licence:
 namespace pFlow
 {
 
-
+/**
+ * 	A class that represent surfaces in the simulation and moves surfaces 
+ * based on the MotionModelType. MotionModelType can be any motion model. 
+ * 
+ */
 template<typename MotionModelType>
 class	geometryMotion 
 :
@@ -41,34 +43,34 @@ public:
 
 protected: 
 	
-
+	/// Ref to motion model 
 	MotionModel& 		motionModel_;
 	
-	// motion indext mapped on each surface 
+	/// motion indext mapped on each surface 
 	int32Vector_HD  	motionIndex_;
 
-	// motion index mapped on each triangle 
+	/// motion index mapped on each triangle 
 	int8Vector_HD 		triMotionIndex_; 
 
 	/// motion index mapped on each point 
 	int8Vector_HD		pointMotionIndex_;
 
-	// timer for moveGeometry
+	/// timer for moveGeometry
 	Timer 				moveGeomTimer_;			
 
-	
+	/// determine the motion index of each triangle 
 	bool findMotionIndex();
 	
 public:
 
-	// type info
+	/// Type info
 	TypeInfoTemplate("geometry", MotionModel);
 
-	//// - Constructors
+	// - Constructors
 		
 		geometryMotion(systemControl& control, const property& prop);
 
-		// construct from components 
+		
 		geometryMotion(
 			systemControl& control,
 			const property& prop,
@@ -77,8 +79,8 @@ public:
 			const wordVector& propName,
 			const MotionModel& motionModel);
 
-		// - construct from components and dictionary that contains 
+		/// Construct from components and dictionary that contains 
-		//   motionModel
+		/// motionModel
 		geometryMotion(systemControl& control,
 				 const property& prop,
 				 const dictionary& dict,
@@ -86,8 +88,7 @@ public:
 				 const wordVector& motionCompName,
 				 const wordVector& propName);
 
-
+		/// Add virtual constructor 
-
 		add_vCtor
 		(
 			geometry,
@@ -95,6 +96,7 @@ public:
 			systemControl
 		);
 
+		/// Add virtual constructor 
 		add_vCtor
 		(
 			geometry,
@@ -102,48 +104,47 @@ public:
 			dictionary
 		);
 
-	//// - Methods
+	// - Methods
 
+		/// Obtain motion model at time t 
 		auto getModel(real t)const
 		{
 			return motionModel_.getModel(t);
 		}
 
+		/// TypeName / TypeInfo of motion model 
 		word motionModelTypeName()const override
 		{
 			return motionModel_.typeName();
 		}
 
+		/// Access to motion model index of triangles 
 		const int8Vector_HD& triMotionIndex()const override
 		{
 			return triMotionIndex_;
 		}
 
+		/// Access to motion model index of points 
 		const int8Vector_HD& pointMotionIndex()const override
 		{
 			return pointMotionIndex_;
 		}
 
-	// - iterate
+		/// Operations before each iteration 
-	bool beforeIteration() override { 
+		bool beforeIteration() override;
-		geometry::beforeIteration();
-		return true;
-	}
 
+		/// Iterate geometry one time step  
 		bool iterate() override ;
 
-	bool afterIteration() override {
+		/// Operations after each iteration 
-		geometry::afterIteration();
+		bool afterIteration() override;
-		return true;
-	}
-
 
+		/// Move geometry 
 		bool moveGeometry();
 
 };
 
-
+} // pFlow
-}
 
 #include "geometryMotion.cpp"