doc for integration

doc/header.html

@@ -4,7 +4,7 @@
 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
 <meta name="generator" content="Doxygen $doxygenversion"/>
-<meta name="description" content="PhasicFlow is an open-source parallel DEM package for simulating granular flow developed in C++ and can be exectued on both GPU (like cuda) and CPU.">
+<meta name="description" content="PhasicFlow is an open-source parallel DEM (discrete element method) package for simulating granular flow. It is developed in C++ and can be exectued on both GPU (like CUDA) and CPU.">
 <!--BEGIN PROJECT_NAME-->
 <title>$projectname: $title</title><!--END PROJECT_NAME-->
 <!--BEGIN !PROJECT_NAME-->

src/Integration/AdamsBashforth2/AdamsBashforth2.hpp

@@ -28,45 +28,68 @@ Licence:
 namespace pFlow
 {
 
-
+/**
+ * Second order Adams-Bashforth integration method for solving ODE
+ * 
+ * This is a one-step integration method and does not have prediction step.
+ * 
+ */
 class AdamsBashforth2
 :
 	public integration
 {
 protected:
 
+	/// dy at t-dt
 	realx3PointField_D& dy1_;
 
+	/// Range policy for integration kernel (alias)
 	using rpIntegration = Kokkos::RangePolicy<
 			DefaultExecutionSpace,
 			Kokkos::Schedule<Kokkos::Static>,
 			Kokkos::IndexType<int32>
 			>;
+
 public:
 
-	// type info
+	/// Type info
 	TypeInfo("AdamsBashforth2");
 
-	//// - Constructors
+	// - Constructors
+
+		/// Construct from components
 		AdamsBashforth2(
 			const word& baseName,
 			repository& owner,
 			const pointStructure& pStruct,
 			const word& method);
 
+		uniquePtr<integration> clone()const override
+		{
+			return makeUnique<AdamsBashforth2>(*this);
+		}
+
+		/// Destructor 
 		virtual ~AdamsBashforth2()=default;
 
-		// - add a virtual constructor 
+		/// Add this to the virtual constructor table 
 		add_vCtor(
 			integration,
 			AdamsBashforth2,
 			word);
 
 
-	//// - Methods
+	// - Methods
-		bool predict(real UNUSED(dt), realx3Vector_D& UNUSED(y), realx3Vector_D& UNUSED(dy)) override;
 
-		bool correct(real dt, realx3Vector_D& y, realx3Vector_D& dy) override;
+		bool predict(
+			real UNUSED(dt), 
+			realx3Vector_D& UNUSED(y), 
+			realx3Vector_D& UNUSED(dy)) override;
+
+		bool correct(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy) override;
 
 		bool setInitialVals(
 			const int32IndexContainer& newIndices,
@@ -77,15 +100,20 @@ public:
 			return false;
 		}
 		
-		uniquePtr<integration> clone()const override
+		/// Integrate on all points in the active range 
-		{
+		bool intAll(
-			return makeUnique<AdamsBashforth2>(*this);
+			real dt, 
-		}
+			realx3Vector_D& y, 
-
+			realx3Vector_D& dy, 
-		bool intAll(real dt, realx3Vector_D& y, realx3Vector_D& dy, range activeRng);
+			range activeRng);
 
+		/// Integrate on active points in the active range 
 		template<typename activeFunctor>
-		bool intRange(real dt, realx3Vector_D& y, realx3Vector_D& dy, activeFunctor activeP );
+		bool intRange(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			activeFunctor activeP );
 
 };
 

src/Integration/AdamsBashforth3/AdamsBashforth3.cpp

@@ -31,26 +31,8 @@ pFlow::AdamsBashforth3::AdamsBashforth3
 )
 :
 	integration(baseName, owner, pStruct, method),
-	/*dy1_(
-		owner.emplaceObject<realx3PointField_D>(
-			objectFile(
-				groupNames(baseName,"dy1"),
-				"",
-				objectFile::READ_IF_PRESENT,
-				objectFile::WRITE_ALWAYS),
-			pStruct,
-			zero3)),
-	dy2_(
-		owner.emplaceObject<realx3PointField_D>(
-			objectFile(
-				groupNames(baseName,"dy2"),
-				"",
-				objectFile::READ_IF_PRESENT,
-				objectFile::WRITE_ALWAYS),
-			pStruct,
-			zero3))*/
 	history_(
-		owner.emplaceObject<HistoryFieldType>(
+		owner.emplaceObject<pointField<VectorSingle,AB3History>>(
 			objectFile(
 				groupNames(baseName,"AB3History"),
 				"",

src/Integration/AdamsBashforth3/AdamsBashforth3.hpp

@@ -30,10 +30,10 @@ namespace pFlow
 
 struct AB3History
 {
+	TypeInfoNV("AB3History");
+
 	realx3 dy1_={0,0,0};
 	realx3 dy2_={0,0,0};
-
-	TypeInfoNV("AB3History");
 };
 
 
@@ -65,21 +65,21 @@ iOstream& operator<<(iOstream& str, const AB3History& ab3)
 	return str;
 }
 
-
+/**
+ * Third order Adams-Bashforth integration method for solving ODE
+ * 
+ * This is a one-step integration method and does not have prediction step.
+ */
 class AdamsBashforth3
 :
 	public integration
 {
 protected:
 	
-	using HistoryFieldType = pointField<VectorSingle,AB3History>;
+	/// Integration history
-	//realx3PointField_D& dy1_;
+	pointField<VectorSingle,AB3History>& history_;
-
-	//realx3PointField_D& dy2_;
-
-	//  this is a device 
-	HistoryFieldType& history_;
 
+	/// Range policy for integration kernel
 	using rpIntegration = Kokkos::RangePolicy<
 			DefaultExecutionSpace,
 			Kokkos::Schedule<Kokkos::Static>,
@@ -91,23 +91,32 @@ public:
 	// type info
 	TypeInfo("AdamsBashforth3");
 
-	//// - Constructors
+	// - Constructors
+		
+		/// Construct from components
 		AdamsBashforth3(
 			const word& baseName,
 			repository& owner,
 			const pointStructure& pStruct,
 			const word& method);
 		
+		uniquePtr<integration> clone()const override
+		{
+			return makeUnique<AdamsBashforth3>(*this);
+		}
+
+		/// Destructor 
 		virtual ~AdamsBashforth3()=default;
 
-		// - add a virtual constructor 
+		/// Add this to the virtual constructor table 
 		add_vCtor(
 			integration,
 			AdamsBashforth3,
 			word);
 
 
-	//// - Methods
+	// - Methods
+
 		bool predict(
 			real UNUSED(dt),
 			realx3Vector_D & UNUSED(y),
@@ -126,18 +135,17 @@ public:
 			return false;
 		}
 
-		uniquePtr<integration> clone()const override
+		/// Integrate on all points in the active range 
-		{
+		bool intAll(
-			return makeUnique<AdamsBashforth3>(*this);
+			real dt, 
-		}
-
-		bool intAll(real dt, 
 			realx3Vector_D& y, 
 			realx3Vector_D& dy, 
 			range activeRng);
 
+		/// Integrate on active points in the active range 
 		template<typename activeFunctor>
-		bool intRange(real dt,
+		bool intRange(
+			real dt,
 			realx3Vector_D& y,
 			realx3Vector_D& dy,
 			activeFunctor activeP );

src/Integration/AdamsBashforth4/AdamsBashforth4.cpp

@@ -32,7 +32,7 @@ pFlow::AdamsBashforth4::AdamsBashforth4
 :
 	integration(baseName, owner, pStruct, method),
 	history_(
-		owner.emplaceObject<HistoryFieldType>(
+		owner.emplaceObject<pointField<VectorSingle,AB4History>>(
 			objectFile(
 				groupNames(baseName,"AB4History"),
 				"",

src/Integration/AdamsBashforth4/AdamsBashforth4.hpp

@@ -30,11 +30,12 @@ namespace pFlow
 
 struct AB4History
 {
+	TypeInfoNV("AB4History");
+
 	realx3 dy1_={0,0,0};
 	realx3 dy2_={0,0,0};
 	realx3 dy3_={0,0,0};
 	
-	TypeInfoNV("AB4History");
 };
 
 
@@ -68,23 +69,21 @@ iOstream& operator<<(iOstream& str, const AB4History& ab4)
 	return str;
 }
 
-
+/**
+ * Fourth order Adams-Bashforth integration method for solving ODE
+ * 
+ * This is a one-step integration method and does not have prediction step.
+ */
 class AdamsBashforth4
 :
 	public integration
 {
 protected:
 
-	using HistoryFieldType = pointField<VectorSingle,AB4History>;
+	/// Integration history
-	//realx3PointField_D& dy1_;
+	pointField<VectorSingle,AB4History>& history_;
-
-	//realx3PointField_D& dy2_;
-
-
-
-	//  this is a device 
-	HistoryFieldType& history_;
 
+	/// Range policy for integration kernel
 	using rpIntegration = Kokkos::RangePolicy<
 			DefaultExecutionSpace,
 			Kokkos::Schedule<Kokkos::Static>,
@@ -93,32 +92,42 @@ protected:
 
 public:
 
-	// type info
+	/// Type info
 	TypeInfo("AdamsBashforth4");
 
-	//// - Constructors
+	// - Constructors
+		
+		/// Construct from components
 		AdamsBashforth4(
 			const word& baseName,
 			repository& owner,
 			const pointStructure& pStruct,
 			const word& method);
 		
+		uniquePtr<integration> clone()const override
+		{
+			return makeUnique<AdamsBashforth4>(*this);
+		}
+
+		/// Destructor
 		virtual ~AdamsBashforth4()=default;
 
-		// - add a virtual constructor 
+		/// Add a this to the virtual constructor table 
 		add_vCtor(
 			integration,
 			AdamsBashforth4,
 			word);
 
 
-	//// - Methods
+	// - Methods
+		
 		bool predict(
 			real UNUSED(dt),
 			realx3Vector_D & UNUSED(y),
 			realx3Vector_D& UNUSED(dy)) override;
 
-		bool correct(real dt, 
+		bool correct(
+			real dt, 
 			realx3Vector_D & y,
 			realx3Vector_D& dy) override;
 
@@ -131,18 +140,17 @@ public:
 			return false;
 		}
 
-		uniquePtr<integration> clone()const override
+		/// Integrate on all points in the active range 
-		{
+		bool intAll(
-			return makeUnique<AdamsBashforth4>(*this);
+			real dt, 
-		}
-
-		bool intAll(real dt, 
 			realx3Vector_D& y, 
 			realx3Vector_D& dy, 
 			range activeRng);
 
+		/// Integrate on active points in the active range 
 		template<typename activeFunctor>
-		bool intRange(real dt,
+		bool intRange(
+			real dt,
 			realx3Vector_D& y,
 			realx3Vector_D& dy,
 			activeFunctor activeP );

src/Integration/AdamsBashforth5/AdamsBashforth5.cpp

@@ -32,7 +32,7 @@ pFlow::AdamsBashforth5::AdamsBashforth5
 :
 	integration(baseName, owner, pStruct, method),
 	history_(
-		owner.emplaceObject<HistoryFieldType>(
+		owner.emplaceObject<pointField<VectorSingle,AB5History>>(
 			objectFile(
 				groupNames(baseName,"AB5History"),
 				"",

src/Integration/AdamsBashforth5/AdamsBashforth5.hpp

@@ -30,12 +30,12 @@ namespace pFlow
 
 struct AB5History
 {
+	TypeInfoNV("AB5History");
+
 	realx3 dy1_={0,0,0};
 	realx3 dy2_={0,0,0};
 	realx3 dy3_={0,0,0};
 	realx3 dy4_={0,0,0};
-
-	TypeInfoNV("AB5History");
 };
 
 
@@ -71,18 +71,21 @@ iOstream& operator<<(iOstream& str, const AB5History& ab5)
 	return str;
 }
 
-
+/**
+ * Fifth order Adams-Bashforth integration method for solving ODE
+ * 
+ * This is a one-step integration method and does not have prediction step.
+ */
 class AdamsBashforth5
 :
 	public integration
 {
 protected:
 
-	using HistoryFieldType = pointField<VectorSingle,AB5History>;
+	/// Integration history
-	
+	pointField<VectorSingle,AB5History>& history_;
-	//  this is a device 
-	HistoryFieldType& history_;
 
+	/// Range policy for integration kernel
 	using rpIntegration = Kokkos::RangePolicy<
 			DefaultExecutionSpace,
 			Kokkos::Schedule<Kokkos::Static>,
@@ -91,32 +94,40 @@ protected:
 
 public:
 
-	// type info
+	/// Type info
 	TypeInfo("AdamsBashforth5");
 
-	//// - Constructors
+	// - Constructors
+		
 		AdamsBashforth5(
 			const word& baseName,
 			repository& owner,
 			const pointStructure& pStruct,
 			const word& method);
 
+		uniquePtr<integration> clone()const override
+		{
+			return makeUnique<AdamsBashforth5>(*this);
+		}
+
 		virtual ~AdamsBashforth5()=default;
 
-		// - add a virtual constructor 
+		/// Add this to the virtual constructor table 
 		add_vCtor(
 			integration,
 			AdamsBashforth5,
 			word);
 
 
-	//// - Methods
+	// - Methods
+		
 		bool predict(
 			real UNUSED(dt),
 			realx3Vector_D & UNUSED(y),
 			realx3Vector_D& UNUSED(dy)) override;
 
-		bool correct(real dt, 
+		bool correct(
+			real dt, 
 			realx3Vector_D & y,
 			realx3Vector_D& dy) override;
 
@@ -129,18 +140,17 @@ public:
 			return false;
 		}
 
-		uniquePtr<integration> clone()const override
+		/// Integrate on all points in the active range 
-		{
+		bool intAll(
-			return makeUnique<AdamsBashforth5>(*this);
+			real dt, 
-		}
-
-		bool intAll(real dt, 
 			realx3Vector_D& y, 
 			realx3Vector_D& dy, 
 			range activeRng);
 
+		/// Integrate on active points in the active range 
 		template<typename activeFunctor>
-		bool intRange(real dt,
+		bool intRange(
+			real dt,
 			realx3Vector_D& y,
 			realx3Vector_D& dy,
 			activeFunctor activeP );
@@ -184,4 +194,4 @@ bool pFlow::AdamsBashforth5::intRange(
 
 } // pFlow
 
-#endif //__integration_hpp__
+#endif //

src/Integration/AdamsMoulton3/AdamsMoulton3.hpp

@@ -28,19 +28,27 @@ Licence:
 namespace pFlow
 {
 
-
+/**
+ * Third order Adams-Moulton integration method for solving ODE
+ * 
+ * This is a predictor-corrector integration method.
+ */
 class AdamsMoulton3
 :
 	public integration
 {
 protected:
 
+	/// y at time t
 	realx3PointField_D& y0_;
 
+	/// dy at time t
 	realx3PointField_D& dy0_;
 
+	/// dy at time t-dt
 	realx3PointField_D& dy1_;
 
+	/// Range policy for integration kernel
 	using rpIntegration = Kokkos::RangePolicy<
 			DefaultExecutionSpace,
 			Kokkos::Schedule<Kokkos::Static>,
@@ -48,29 +56,44 @@ protected:
 			>;
 public:
 
-	// type info
+	/// Type info
 	TypeInfo("AdamsMoulton3");
 
-	//// - Constructors
+	// - Constructors
+
+		/// Construct from components
 		AdamsMoulton3(
 			const word& baseName,
 			repository& owner,
 			const pointStructure& pStruct,
 			const word& method);
 
+		uniquePtr<integration> clone()const override
+		{
+			return makeUnique<AdamsMoulton3>(*this);
+		}
+
+		/// Destructor 
 		virtual ~AdamsMoulton3()=default;
 
-		// - add a virtual constructor 
+		/// Add this to the virtual constructor table 
 		add_vCtor(
 			integration,
 			AdamsMoulton3,
 			word);
 
 
-	//// - Methods
+	// - Methods
-		bool predict(real dt, realx3Vector_D& y, realx3Vector_D& dy) override;
 
-		bool correct(real dt, realx3Vector_D& y, realx3Vector_D& dy) override;
+		bool predict(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy) override;
+
+		bool correct(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy) override;
 
 		bool setInitialVals(
 			const int32IndexContainer& newIndices,
@@ -81,20 +104,35 @@ public:
 			return true;
 		}
 
-		uniquePtr<integration> clone()const override
+		/// Prediction step on all points in the active range
-		{
+		bool predictAll(
-			return makeUnique<AdamsMoulton3>(*this);
+			real dt, 
-		}
+			realx3Vector_D& y, 
-
+			realx3Vector_D& dy, 
-		bool predictAll(real dt, realx3Vector_D& y, realx3Vector_D& dy, range activeRng);
+			range activeRng);
 
+		/// Prediction step on active points in the active range
 		template<typename activeFunctor>
-		bool predictRange(real dt, realx3Vector_D& y, realx3Vector_D& dy, activeFunctor activeP);
+		bool predictRange(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			activeFunctor activeP);
 
-		bool intAll(real dt, realx3Vector_D& y, realx3Vector_D& dy, range activeRng);
+		/// Integrate on all points in the active range
+		bool intAll(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			range activeRng);
 
+		/// Integrate on active points in the active range
 		template<typename activeFunctor>
-		bool intRange(real dt, realx3Vector_D& y, realx3Vector_D& dy, activeFunctor activeP );
+		bool intRange(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			activeFunctor activeP);
 
 };
 
@@ -176,4 +214,4 @@ bool pFlow::AdamsMoulton3::intRange(
 
 } // pFlow
 
-#endif //__integration_hpp__
+#endif //

src/Integration/AdamsMoulton4/AdamsMoulton4.hpp

@@ -28,21 +28,30 @@ Licence:
 namespace pFlow
 {
 
-
+/**
+ * Fourth order Adams-Moulton integration method for solving ODE
+ * 
+ * This is a predictor-corrector integration method.
+ */
 class AdamsMoulton4
 :
 	public integration
 {
 protected:
 
+	/// y at time t
 	realx3PointField_D& y0_;
 
+	/// dy at time t
 	realx3PointField_D& dy0_;
 
+	/// dy at time t-dt
 	realx3PointField_D& dy1_;
 
+	/// dy at time t-2*dt
 	realx3PointField_D& dy2_;
 
+	/// Range policy for integration kernel 
 	using rpIntegration = Kokkos::RangePolicy<
 			DefaultExecutionSpace,
 			Kokkos::Schedule<Kokkos::Static>,
@@ -50,29 +59,44 @@ protected:
 			>;
 public:
 
-	// type info
+	/// Type info
 	TypeInfo("AdamsMoulton4");
 
-	//// - Constructors
+	// - Constructors
+		
+		/// Construct from components
 		AdamsMoulton4(
 			const word& baseName,
 			repository& owner,
 			const pointStructure& pStruct,
 			const word& method);
 
+		uniquePtr<integration> clone()const override
+		{
+			return makeUnique<AdamsMoulton4>(*this);
+		}
+
+		/// Destructor 
 		virtual ~AdamsMoulton4()=default;
 
-		// - add a virtual constructor 
+		// Add this to the virtual constructor table 
 		add_vCtor(
 			integration,
 			AdamsMoulton4,
 			word);
 
 
-	//// - Methods
+	// - Methods
-		bool predict(real dt, realx3Vector_D& y, realx3Vector_D& dy) override;
 
-		bool correct(real dt, realx3Vector_D& y, realx3Vector_D& dy) override;
+		bool predict(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy) override;
+
+		bool correct(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy) override;
 
 		bool setInitialVals(
 			const int32IndexContainer& newIndices,
@@ -83,20 +107,35 @@ public:
 			return true;
 		}
 
-		uniquePtr<integration> clone()const override
+		/// Prediction step on all points in the active range
-		{
+		bool predictAll(
-			return makeUnique<AdamsMoulton4>(*this);
+			real dt, 
-		}
+			realx3Vector_D& y, 
-
+			realx3Vector_D& dy, 
-		bool predictAll(real dt, realx3Vector_D& y, realx3Vector_D& dy, range activeRng);
+			range activeRng);
 
+		/// Prediction step on active points in the active range
 		template<typename activeFunctor>
-		bool predictRange(real dt, realx3Vector_D& y, realx3Vector_D& dy, activeFunctor activeP);
+		bool predictRange(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			activeFunctor activeP);
 
-		bool intAll(real dt, realx3Vector_D& y, realx3Vector_D& dy, range activeRng);
+		/// Integrate on all points in the active range
+		bool intAll(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			range activeRng);
 
+		/// Integrate on active points in the active range
 		template<typename activeFunctor>
-		bool intRange(real dt, realx3Vector_D& y, realx3Vector_D& dy, activeFunctor activeP );
+		bool intRange(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			activeFunctor activeP );
 
 };
 
@@ -182,4 +221,4 @@ bool pFlow::AdamsMoulton4::intRange(
 
 } // pFlow
 
-#endif //__integration_hpp__
+#endif //

src/Integration/AdamsMoulton5/AdamsMoulton5.hpp

@@ -28,23 +28,33 @@ Licence:
 namespace pFlow
 {
 
-
+/**
+ * Fifth order Adams-Moulton integration method for solving ODE
+ * 
+ * This is a predictor-corrector integration method.
+ */
 class AdamsMoulton5
 :
 	public integration
 {
 protected:
 
+	/// y at time t
 	realx3PointField_D& y0_;
 
+	/// dy at time t
 	realx3PointField_D& dy0_;
 
+	/// dy at time t-dt
 	realx3PointField_D& dy1_;
 
+	/// dy at time t-2*dt
 	realx3PointField_D& dy2_;
 
+	/// dy at time t-3*dt
 	realx3PointField_D& dy3_;
 
+	/// Range policy for integration kernel 
 	using rpIntegration = Kokkos::RangePolicy<
 			DefaultExecutionSpace,
 			Kokkos::Schedule<Kokkos::Static>,
@@ -52,16 +62,24 @@ protected:
 			>;
 public:
 
-	// type info
+	/// Type info
 	TypeInfo("AdamsMoulton5");
 
-	//// - Constructors
+	// - Constructors
+		
+		/// Construct from components
 		AdamsMoulton5(
 			const word& baseName,
 			repository& owner,
 			const pointStructure& pStruct,
 			const word& method);
 		
+		uniquePtr<integration> clone()const override
+		{
+			return makeUnique<AdamsMoulton5>(*this);
+		}
+
+		/// Destructor 
 		virtual ~AdamsMoulton5()=default;
 
 		// - add a virtual constructor 
@@ -71,10 +89,17 @@ public:
 			word);
 
 
-	//// - Methods
+	// - Methods
-		bool predict(real dt, realx3Vector_D& y, realx3Vector_D& dy) override;
 		
-		bool correct(real dt, realx3Vector_D& y, realx3Vector_D& dy) override;
+		bool predict(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy) override;
+
+		bool correct(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy) override;
 
 		bool setInitialVals(
 			const int32IndexContainer& newIndices,
@@ -85,20 +110,35 @@ public:
 			return true;
 		}
 
-		uniquePtr<integration> clone()const override
+		/// Prediction step on all points in the active range
-		{
+		bool predictAll(
-			return makeUnique<AdamsMoulton5>(*this);
+			real dt, 
-		}
+			realx3Vector_D& y, 
-
+			realx3Vector_D& dy, 
-		bool predictAll(real dt, realx3Vector_D& y, realx3Vector_D& dy, range activeRng);
+			range activeRng);
 
+		/// Prediction step on active points in the active range
 		template<typename activeFunctor>
-		bool predictRange(real dt, realx3Vector_D& y, realx3Vector_D& dy, activeFunctor activeP);
+		bool predictRange(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			activeFunctor activeP);
 
-		bool intAll(real dt, realx3Vector_D& y, realx3Vector_D& dy, range activeRng);
+		/// Integrate on all points in the active range
+		bool intAll(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			range activeRng);
 
+		/// Integrate on active points in the active range
 		template<typename activeFunctor>
-		bool intRange(real dt, realx3Vector_D& y, realx3Vector_D& dy, activeFunctor activeP );
+		bool intRange(
+			real dt, 
+			realx3Vector_D& y, 
+			realx3Vector_D& dy, 
+			activeFunctor activeP );
 
 };
 

src/Integration/integration/integration.hpp

@@ -31,32 +31,71 @@ Licence:
 namespace pFlow
 {
 
-
+/**
+ * Base class for integrating the first order ODE (IVP) 
+ * 
+ * The ODE should be in the following form:
+ *\f[ 
+	 \frac{dy}{dt} = f(y,t)
+  \f]
+ * for example the equation of motion is in the following form:
+ *\f[ 
+	m\frac{d\vec{v}}{dt} = m\vec{g} + \sum \vec{f_c}(\vec{v},t)
+  \f]
+ *
+ * The integration method can be either one-step or predictor-corrector type.
+ * 
+ */
 class integration
 {
 protected:
 
+	// - Protected data members 
+
+		/// The owner repository that all fields are storred in
 		repository& owner_;
 
+		/// The base name for integration 
 		const word baseName_;
 
+		/// A reference to pointStructure
 		const pointStructure& pStruct_;
 
 public:
 
-	// type info
+	/// Type info
 	TypeInfo("integration");
 
-	//// - Constructors
+
+	// - Constructors
+
+		/// Construct from components
 		integration(
 			const word& baseName,
 			repository& owner,
 			const pointStructure& pStruct,
 			const word& method);
 
+		/// Copy constructor 
+		integration(const integration&) = default;
+
+		/// Move constructor
+		integration(integration&&) = default;
+
+		/// Copy assignment 
+		integration& operator = (const integration&) = default;
+
+		/// Move assignment
+		integration& operator = (integration&&) = default;
+
+		/// Polymorphic copy/cloning
+		virtual 
+		uniquePtr<integration> clone()const=0;
+
+		/// Destructor 
 		virtual ~integration()=default;
 
-		// - add a virtual constructor 
+		/// Add a virtual constructor 
 		create_vCtor(
 			integration,
 			word,
@@ -67,35 +106,49 @@ public:
 			(baseName, owner, pStruct, method) );
 
 
-	//// - Methods
+	// - Methods
 
+		/// Const ref to pointStructure
+		inline
 		const auto& pStruct()const
 		{
 			return pStruct_;
 		}
 
-		virtual bool predict(real dt, realx3Vector_D& y, realx3Vector_D& dy) = 0;
+		/// Base name
-
+		inline
-		virtual bool correct(real dt, realx3Vector_D& y, realx3Vector_D& dy) = 0;
-
-		virtual bool setInitialVals(
-				const int32IndexContainer& newIndices,
-				const realx3Vector& y) = 0;
-
-		virtual bool needSetInitialVals()const = 0;
-
-		virtual uniquePtr<integration> clone()const=0;
-
 		const word& baseName()const
 		{
 			return baseName_;
 		}
 
+		/// Ref to the owner repository
+		inline
 		repository& owner()
 		{
 			return owner_;
 		}
 
+		/// Prediction step in integration
+		virtual 
+		bool predict(real dt, realx3Vector_D& y, realx3Vector_D& dy) = 0;
+
+		/// Correction/main integration step
+		virtual 
+		bool correct(real dt, realx3Vector_D& y, realx3Vector_D& dy) = 0;
+
+		/// Set the initial values for new indices 
+		virtual 
+		bool setInitialVals(
+				const int32IndexContainer& newIndices,
+				const realx3Vector& y) = 0;
+
+		/// Check if the method requires any set initial vals
+		virtual 
+		bool needSetInitialVals()const = 0;
+
+
+	/// Create the polymorphic object based on inputs
 	static
 		uniquePtr<integration> create(
 			const word& baseName,
@@ -103,7 +156,7 @@ public:
 			const pointStructure& pStruct,
 			const word& method);
 
-};
+}; // integration
 
 } // pFlow
 

src/Integration/integration/integrations.hpp

@@ -1,28 +0,0 @@
-/*------------------------------- phasicFlow ---------------------------------
-      O        C enter of
-     O O       E ngineering and
-    O   O      M ultiscale modeling of
-   OOOOOOO     F luid flow       
-------------------------------------------------------------------------------
-  Copyright (C): www.cemf.ir
-  email: hamid.r.norouzi AT gmail.com
-------------------------------------------------------------------------------  
-Licence:
-  This file is part of phasicFlow code. It is a free software for simulating 
-  granular and multiphase flows. You can redistribute it and/or modify it under
-  the terms of GNU General Public License v3 or any other later versions. 
- 
-  phasicFlow is distributed to help others in their research in the field of 
-  granular and multiphase flows, but WITHOUT ANY WARRANTY; without even the
-  implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
-
------------------------------------------------------------------------------*/
-
-#ifndef __integrations_hpp__
-#define __integrations_hpp__
-
-#include "integration.hpp"
-#include "AdamsBashforth2.hpp"
-#include "AdamsBashforth3.hpp"
-
-#endif

src/Particles/dynamicPointStructure/dynamicPointStructure.hpp

@@ -24,7 +24,7 @@ Licence:
 
 #include "Time.hpp"
 #include "pointFields.hpp"
-#include "integrations.hpp"
+#include "integration.hpp"
 #include "uniquePtr.hpp"
 
 namespace pFlow
@@ -57,17 +57,6 @@ public:
 
 	dynamicPointStructure(const dynamicPointStructure& ps) = default;
 
-	/*dynamicPointStructure(const dynamicPointStructure& ps):
-		pointStructure(ps),
-		time_(ps.time_),
-		integrationMethod_(ps.integrationMethod_),
-		velocity_(ps.velocity_),
-		integrationPos_(ps.integrationPos_->clone()),
-		integrationVel_(ps.integrationVel_->clone())
-	{
-
-	}*/
-
 		
 		// - no move construct 
 	dynamicPointStructure(dynamicPointStructure&&) = delete;

src/demComponent/demComponent.hpp

@@ -28,22 +28,37 @@ Licence:
 namespace pFlow
 {
 
+/**
+ * A base class for every main component of DEM system.
+ * 
+ * This class provides abstraction at a very high level for any solver/utility
+ * that forces the derived component (i.e. particles, geometry, and etc) to 
+ * advance over time when iterate is called in time a loop.
+ * 
+ */
 class demComponent
 {
 protected:
 
+	// - Protected data members 
+
+		/// Name of the DEM component 
 		word 	componentName_;
 
-
+		/// Reference to systemControl 
 		systemControl& control_;
 
-
+		/// All timers (if any) of this component
 		Timers 	timers_;
 
 public:
 
+	/// Type info
 	TypeInfo("demComponent");
 
+	// - Constructors
+	
+		/// construct from components
 		demComponent(const word& name, systemControl& control)
 		:
 			componentName_(name),
@@ -51,47 +66,94 @@ public:
 			timers_(name, &control.timers())
 		{}
 
+		/// No copy constructor
+		demComponent(const demComponent&) = delete;
+
+		/// No move constructor 
+		demComponent(demComponent&&) = delete;
+
+		/// No copy assignment
+		demComponent& operator = (const demComponent&) = delete;
+
+		/// No move assignment 
+		demComponent& operator =(demComponent&&) = delete;
+
+		/// destructor 
 		virtual ~demComponent() = default;
 
 	
+	// - Member functions 
+
+		/// Const ref to systemControl
+		inline
 		const auto& control()const
 		{
 			return control_;
 		}
 
+		/// Ref to systemControl
+		inline
 		auto& control()
 		{
 			return control_;
 		}
 
+		/// Time step of integration
 		inline
 		real dt()const
 		{
 			return control_.time().dt();
 		}
 
+		/// Current simulation time 
 		inline
 		real currentTime()const
 		{
 			return control_.time().currentTime();
 		}
 
-	auto& timers(){
+		/// Const ref to timers
+		inline
+		const auto& timers() const
+		{
 			return timers_;
 		}
 
-	const auto& timers() const{
+		/// Ref to timers
+		inline
+		auto& timers()
+		{
 			return timers_;
 		}
 
+		/// This is called before the start of time loop
+		virtual
+		bool beforeTimeLoop()
+		{
+			notImplementedFunction;
+			return false;
+		}
 
-	virtual bool beforeIteration() = 0;
+		/// This is called in time loop, before iterate
+		virtual 
+		bool beforeIteration() = 0;
 
+		/// This is called in time loop. Perform the main calculations 
+		/// when the component should evolve along time.
+		virtual 
+		bool iterate() = 0;
 
-	virtual bool iterate() = 0;
+		/// This is called in time loop, after iterate.
+		virtual 
+		bool afterIteration() = 0;
 
-
+		/// This is called after the time loop
-	virtual bool afterIteration() = 0;
+		virtual
+		bool afterTimeLoop()
+		{
+			notImplementedFunction;
+			return false;
+		}
 
 };