Particle insertion (domain check)

- Domain check is added to prevent points that are outside of internalDomainBox

src/Particles/Insertion/InsertionRegion/InsertionRegion.cpp

@@ -68,6 +68,16 @@ bool pFlow::InsertionRegion<ShapeType>::insertParticles
 	
 	if(newNum == 0) return true;
 
+	auto internalBox =  pStruct().internalDomainBox();
+
+	if( !(internalBox.minPoint() < internalBox.maxPoint()))
+	{
+		WARNING<<"Minimum point of internal point is not lower than "<<
+		"the maximum point \n"<<
+		"minimum point: "<< internalBox.minPoint()<<
+		"\nmaximum point:"<<internalBox.maxPoint()<<END_WARNING;
+	}
+
 	names.reserve(max(newNum,names.capacity()));
 	pos.reserve(max(newNum,pos.capacity()));
 	names.clear();
@@ -75,12 +85,6 @@ bool pFlow::InsertionRegion<ShapeType>::insertParticles
 
 	realVector diams("diams", newNum, 0, RESERVE());
 
-	for(uint32 i=0; i<newNum; i++)
-	{
-		uint32 idx;
-		shapes_.shapeNameToIndex(names[i], idx);
-		diams[i] = shapes_.boundingDiameter(idx);
-	}
 	
 	size_t n = 0;
 	uint32 idx;
@@ -94,6 +98,10 @@ bool pFlow::InsertionRegion<ShapeType>::insertParticles
 	{
 		
 		realx3 p = pReg.peek();
+
+		// check if point is inside internal box 
+		if(!internalBox.isInside(p))continue;
+
 		if( !checkForContact(pos, diams, p, d) )
 		{
 			names.push_back(name);

src/Particles/Insertion/InsertionRegion/InsertionRegion.hpp

@@ -22,6 +22,7 @@ Licence:
 #define __InsertionRegion_hpp__
 
 #include "dictionary.hpp"
+#include "pointStructure.hpp"
 #include "insertionRegion.hpp"
 
 namespace pFlow

src/Particles/Insertion/insertion/insertion.cpp

@@ -39,6 +39,12 @@ pFlow::insertion::insertion(particles& prtcl)
 	readInsertionDict(*this);
 }
 
+const pFlow::pointStructure&
+pFlow::insertion::pStruct() const
+{
+	return particles_.pStruct();
+}
+
 bool
 pFlow::insertion::read(iIstream& is, const IOPattern& iop)
 {

src/Particles/Insertion/insertion/insertion.hpp

@@ -27,6 +27,7 @@ namespace pFlow
 
 // forward
 class particles;
+class pointStructure;
 
 /**
  * Base class for particle insertion
@@ -88,6 +89,8 @@ public:
 		return particles_;
 	}
 
+	const pointStructure& pStruct()const;
+
 	inline bool readFromFile() const
 	{
 		return readFromFile_;

src/Particles/Insertion/insertionRegion/insertionRegion.cpp

@@ -158,6 +158,12 @@ pFlow::insertionRegion::insertionRegion(
 	}
 }
 
+const pFlow::pointStructure&
+pFlow::insertionRegion::pStruct() const
+{
+	return Insertion().pStruct();
+}
+
 pFlow::uint32
 pFlow::insertionRegion::numberToBeInserted(uint32 iter, real t, real dt)
 {

src/Particles/Insertion/insertionRegion/insertionRegion.hpp

@@ -31,6 +31,7 @@ namespace pFlow
 
 class dictionary;
 class insertion;
+class pointStructure;
 
 /**
  * This class defines all the necessary enteties for defining an insertion
@@ -92,7 +93,7 @@ private:
 	/// insertion region dictionary
 	const dictionary&         dict_;
 
-	/// ref to pointStructure
+	/// ref to insertion
 	const insertion&          insertion_;
 
 	/// @brief time control for insertion events
@@ -163,6 +164,8 @@ public:
 		return insertion_;
 	}
 
+	const pointStructure& pStruct()const;
+
 	inline bool insertionTime(uint32 iter, real t, real dt) const
 	{
 		return tControl_.timeEvent(iter, t, dt);

src/phasicFlow/setFieldList/setFieldEntryTemplates.cpp

@@ -23,7 +23,7 @@ template <typename Type>
 bool pFlow::setFieldEntry::checkForType()const
 {
 	word typeName( entry_.firstPart() );
-	return basicTypeName<Type>() == typeName;
+	return getTypeName<Type>() == typeName;
 };
 
 template <typename Type>

src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBase.hpp

@@ -153,12 +153,30 @@ public:
 		(dict, bplane, internal, bndrs, thisIndex)
 	);
 
+	/// The length from boundary plane into the domain 
+	/// where beyond that distance internal points exist.
+	/// By conventions is it always equal to neighborLength_  
+	real neighborLengthIntoInternal()const
+	{
+		return neighborLength_;
+	}
+
+	/// The distance length from boundary plane 
+	/// where neighbor particles exist in that distance. 
+	/// This length may be modified in each boundary type 
+	/// as required. In this case the boundaryExtensionLength
+	/// method should also be modified accordingly. 
 	virtual 
 	real neighborLength()const
 	{
 		return neighborLength_;
 	}
 
+	/// The extention length (in vector form) for the boundary
+	/// as required by  each boundary type. It is allowed for 
+	/// each boundary type to be extended outward to allow 
+	/// particles to stay more in its list before being removed 
+	/// from its list. 
 	virtual 
 	realx3 boundaryExtensionLength()const
 	{
@@ -240,6 +258,7 @@ public:
 
 	const boundaryBase& mirrorBoundary()const;
 	
+	/// the actual boundary plane of this boundary 
 	const plane& boundaryPlane()const
 	{
 		return boundaryPlane_;

src/phasicFlow/structuredData/boundaries/boundaryList.cpp

@@ -143,12 +143,27 @@ bool pFlow::boundaryList::setLists()
 	return true;
 }
 
-bool pFlow::boundaryList::beforeIteration
-(
-	uint32 iter, 
-	real t, 
-	real dt
-)
+pFlow::box
+pFlow::boundaryList::internalDomainBox() const
+{
+	const auto& thisBox = pStruct_.thisDomain().domainBox();
+	
+	const realx3 lowerPointDisplacement = {
+		boundary(0).neighborLengthIntoInternal(), 
+		boundary(2).neighborLengthIntoInternal(), 
+		boundary(4).neighborLengthIntoInternal()};
+
+	const realx3 upperPointDisplacement = {
+		boundary(1).neighborLengthIntoInternal(), 
+		boundary(3).neighborLengthIntoInternal(), 
+		boundary(5).neighborLengthIntoInternal()};
+	
+	return {thisBox.minPoint() + lowerPointDisplacement, 
+			thisBox.maxPoint() - upperPointDisplacement};
+}
+
+bool
+pFlow::boundaryList::beforeIteration(uint32 iter, real t, real dt)
 {
 	// it is time to update lists 
 	if(timeControl_.timeEvent(iter, t, dt))

src/phasicFlow/structuredData/boundaries/boundaryList.hpp

@@ -46,6 +46,8 @@ private:
 
 		domain 					extendedDomain_;
 
+		box 					internalDomainBox_;
+
 		bool                    listSet_ = false;
 
 		void setExtendedDomain();		
@@ -105,6 +107,16 @@ public:
 		return extendedDomain_;
 	}
 
+	inline
+	const auto& extendedDomainBox()const
+	{
+		return extendedDomain_.domainBox();
+	}
+
+	box internalDomainBox()const;
+	
+	
+
 	bool beforeIteration(uint32 iter, real t, real dt);
 
 	bool iterate(uint32 iter, real t, real dt);

src/phasicFlow/structuredData/box/box.hpp

@@ -79,10 +79,12 @@ public:
 
 	//// - Methods 
 
+		
 		INLINE_FUNCTION_HD
 		bool isInside(const realx3& point)const
 		{
-			return point > min_ && point <max_;
+			// box planes are also included as the inside of the box 
+			return point >= min_ && point <=max_;
 		}
 
 		INLINE_FUNCTION_HD

src/phasicFlow/structuredData/cylinder/cylinder.hpp

@@ -90,7 +90,9 @@ public:
 			auto p1Point = point-p1_;
 			auto H = cross(p1Point , axisVector_);
 			auto H2 = dot(H,H);
-			if( H2 < radius2_*axisVector2_)
+
+			// the shell itslef is considered as inside point 
+			if( H2 <= radius2_*axisVector2_)
 			{
 				real t = dot(p1Point, axisVector_)/axisVector2_;
 				if(t >= 0.0 && t <= 1.0)

src/phasicFlow/structuredData/infinitePlane/infinitePlane.hpp

@@ -103,6 +103,12 @@ public:
 			return pointFromPlane(p)>=0;
 		}
 
+		INLINE_FUNCTION_HD
+		bool pointInNegativeSide(const realx3& p)const
+		{
+			return pointFromPlane(p)<0;
+		}
+
 		INLINE_FUNCTION_HD
 		bool inPositiveDistance(const realx3& p, real dist)const
 		{	
@@ -114,14 +120,7 @@ public:
 		bool inNegativeDistance(const realx3& p, real dist)const
 		{	
 			real d = pointFromPlane(p);
-			return d < 0.0 && d <= -dist;
-		}
-
-
-		INLINE_FUNCTION_HD
-		bool pointInNegativeSide(const realx3& p)const
-		{
-			return pointFromPlane(p)<0;
+			return d < 0.0 && d >= -dist;
 		}
 
 		INLINE_FUNCTION_HD

src/phasicFlow/structuredData/pointStructure/internalPoints/pointFlagKernels.hpp

@@ -543,7 +543,7 @@ pFlow::uint32 pFlow::pointFlag<ExecutionSpace>::changeCapacity
 	while( emptySpots < reqEmptySpots )
 	{
 		newCap = newCap*pFlow::gSettings::vectorGrowthFactor__+1;
-		uint32 emptySpots = newCap - numActive_;
+		emptySpots = newCap - numActive_;
 	}
 	
 	viewType newFlags(flags_.label(), newCap);

src/phasicFlow/structuredData/pointStructure/pointStructure/pointStructure.hpp

@@ -154,6 +154,12 @@ public:
 			return boundaries_.extendedDomain();
 		}
 
+		inline 
+		auto internalDomainBox()const
+		{
+			return boundaries_.internalDomainBox();
+		}
+		
 	// - IO methods 
 
 		/// @brief read the point structure from the input stream.

src/phasicFlow/structuredData/sphere/sphere.hpp

@@ -76,7 +76,7 @@ public:
 		{
 			auto cPoint = point-center_;
 			auto dist2 = dot(cPoint,cPoint);
-			return dist2 < radius2_;
+			return dist2 <= radius2_;
 
 		}