Merge pull request #94 from PhasicFlow/develop

pFlowToVTK and enhanced wall-particle search

src/Interaction/contactSearch/ContactSearch/ContactSearch.hpp

@@ -56,12 +56,12 @@ public:
 
 	ContactSearch(
 		const dictionary& csDict,
-		const box& domain,
+		const box& extDomain,
 	 	const particles& prtcl,
 	 	const geometry& geom,
 	 	Timers& timers)
 	:
-		contactSearch(csDict, domain, prtcl, geom, timers)
+		contactSearch(csDict, extDomain, prtcl, geom, timers)
 	{
 
 		auto method = dict().getVal<word>("method");
@@ -79,12 +79,13 @@ public:
 		uint32 wnTri    = this->Geometry().size();
 		const auto& wPoints = this->Geometry().points().deviceViewAll();
 		const auto& wVertices = this->Geometry().vertices().deviceViewAll();
+		const auto& wNormals = this->Geometry().normals().deviceViewAll();
 
 		ppwContactSearch_ = 
 			makeUnique<SearchMethodType>
 			(
 				nbDict,
-				this->domainBox(),
+				this->extendedDomainBox(),
 				minD,
 				maxD,
 				position,
@@ -93,7 +94,8 @@ public:
 				wnPoints,
 				wnTri,
 				wPoints,
-				wVertices
+				wVertices,
+				wNormals
 			);
 		REPORT(2)<<"Contact search algorithm for particle-particle is "<<
 				 Green_Text(ppwContactSearch_().typeName())<<END_REPORT;

src/Interaction/contactSearch/contactSearch/contactSearch.cpp

@@ -25,12 +25,12 @@ Licence:
 
 pFlow::contactSearch::contactSearch(
 	const dictionary& dict,
-	const box& domain,
+	const box& extDomain,
  	const particles& prtcl,
  	const geometry& geom,
  	Timers& timers)
 :
-	domainBox_(domain),
+	extendedDomainBox_(extDomain),
 	particles_(prtcl),
 	geometry_(geom),
 	ppTimer_("particle-particle contact search", &timers),
@@ -47,7 +47,7 @@ const pFlow::pointStructure &pFlow::contactSearch::pStruct() const
 
 pFlow::uniquePtr<pFlow::contactSearch> pFlow::contactSearch::create(
     const dictionary &dict,
-    const box &domain,
+    const box &extDomain,
     const particles &prtcl,
     const geometry &geom,
     Timers &timers)
@@ -60,7 +60,7 @@ pFlow::uniquePtr<pFlow::contactSearch> pFlow::contactSearch::create(
 	
 	if( dictionaryvCtorSelector_.search(model))
 	{
-		auto objPtr = dictionaryvCtorSelector_[model] (dict, domain, prtcl, geom, timers);
+		auto objPtr = dictionaryvCtorSelector_[model] (dict, extDomain, prtcl, geom, timers);
 		REPORT(2)<<"Model "<< Green_Text(model)<<" is created."<< END_REPORT;
 		return objPtr;
 	}

src/Interaction/contactSearch/contactSearch/contactSearch.hpp

@@ -42,7 +42,7 @@ class contactSearch
 {
 private:
 
-	const box& 	domainBox_;
+	const box& 	extendedDomainBox_;
 
 	const particles& 		particles_;
 
@@ -60,7 +60,7 @@ public:
 
 	contactSearch(
 		const dictionary& dict,
-		const box& domain,
+		const box& extDomain,
 	 	const particles& prtcl,
 	 	const geometry& geom,
 	 	Timers& timers);
@@ -88,9 +88,9 @@ public:
 		return dict_;
 	}
 
-	const auto& domainBox()const
+	const auto& extendedDomainBox()const
 	{
-		return domainBox_;
+		return extendedDomainBox_;
 	}
 
 	const auto& Particles()const
@@ -133,7 +133,7 @@ public:
 	static 
 	uniquePtr<contactSearch> create(
 		const dictionary& dict,
-		const box& domain,
+		const box& extDomain,
 	 	const particles& prtcl,
 	 	const geometry& geom,
 	 	Timers& timers);

src/Interaction/contactSearch/methods/cellBased/NBS/NBS.cpp

@@ -32,7 +32,8 @@ pFlow::NBS::NBS
 	uint32 					nWallPoints,
 	uint32 					nWallElements,
 	const ViewType1D<realx3,memory_space>& 		wallPoints, 
-	const ViewType1D<uint32x3,memory_space>& 	wallVertices
+	const ViewType1D<uint32x3,memory_space>& 	wallVertices,
+  const ViewType1D<realx3,memory_space>& 		wallNormals 
 )
 : 
     particleWallContactSearchs<NBS>(
@@ -61,7 +62,8 @@ pFlow::NBS::NBS
 		nWallPoints,
 		nWallElements,
 		wallPoints,
-		wallVertices
+		wallVertices,
+    wallNormals
 	)
 {
 }

src/Interaction/contactSearch/methods/cellBased/NBS/NBS.hpp

@@ -80,7 +80,10 @@ protected:
 		if(!cellsWallLevel0_.broadSearch(
 			pwPairs,
 			NBSLevel0_.getSearchCells(),
-			NBSLevel0_.getCellIterator()))
+			NBSLevel0_.getCellIterator(),
+			pointPos,
+			diameter,
+			sizeRatio_))
 		{
 			fatalErrorInFunction<<
 			"Error in broadSearch for NBS (particle-wall)"<<endl;
@@ -105,7 +108,8 @@ public:
 			uint32 					nWallPoints,
 			uint32 					nWallElements,
 			const ViewType1D<realx3,memory_space>& 		wallPoints, 
-			const ViewType1D<uint32x3,memory_space>& 	wallVertices);
+			const ViewType1D<uint32x3,memory_space>& 	wallVertices,
+			const ViewType1D<realx3,memory_space>& 		wallNormals );
 		
 			
 		INLINE_FUNCTION_HD

src/Interaction/contactSearch/methods/cellBased/NBS/NBSLevel0.cpp

@@ -60,7 +60,6 @@ bool pFlow::NBSLevel0::findPairs
 			
 		}
 
-		Kokkos::fence();
 	}
 	
 	return true;

src/Interaction/contactSearch/methods/cellBased/NBS/cellsWallLevel0.cpp

@@ -26,18 +26,18 @@ pFlow::cellsWallLevel0::cellsWallLevel0
     real cellExtent, 
     uint32 numPoints, 
     uint32 numElements, 
-    const ViewType1D<realx3, 
+    const ViewType1D<realx3, memory_space> &points,
-    memory_space> &points,
+    const ViewType1D<uint32x3, memory_space> &vertices,
-    const ViewType1D<uint32x3, memory_space> &vertices
+	const ViewType1D<realx3, memory_space>& normals
 )
 :
     cellExtent_( max(cellExtent, 0.5 ) ),
     numElements_(numElements),
     numPoints_(numPoints),
     vertices_(vertices),
-    points_(points)
+    points_(points),
+	normals_(normals)
 {
-
     allocateArrays();
 }
 
@@ -45,8 +45,9 @@ bool pFlow::cellsWallLevel0::resetElements
 (
 	uint32 numElements, 
 	uint32 numPoints, 
-	ViewType1D<realx3, memory_space> &points, 
+	const ViewType1D<realx3, memory_space>& points, 
-	ViewType1D<uint32x3, memory_space> &vertices
+	const ViewType1D<uint32x3, memory_space>& vertices,
+	const ViewType1D<realx3, memory_space>& normals
 )
 {
 
@@ -54,6 +55,7 @@ bool pFlow::cellsWallLevel0::resetElements
 	numPoints_ = numPoints;
 	points_ 	= points;
 	vertices_ 	= vertices;
+	normals_ 	= normals;
 
 	allocateArrays();
 
@@ -64,7 +66,10 @@ bool pFlow::cellsWallLevel0::broadSearch
 (
 	csPairContainerType &pairs,
 	const cells& searchBox,  
-	const mapperNBS::CellIterator &particleMap
+	const mapperNBS::CellIterator &particleMap,
+	const deviceViewType1D<realx3>& pPoints,
+	const deviceViewType1D<real>&  pDiams,
+	real sizeRatio
 )
 {
 	
@@ -72,7 +77,7 @@ bool pFlow::cellsWallLevel0::broadSearch
 	
 	this->build(searchBox);
 	
-	this->particleWallFindPairs(pairs, particleMap);
+	this->particleWallFindPairs(pairs, particleMap, pPoints, pDiams, sizeRatio);
 	
 	return true;
 }
@@ -104,7 +109,10 @@ bool pFlow::cellsWallLevel0::build(const cells & searchBox)
 bool pFlow::cellsWallLevel0::particleWallFindPairs
 (
 	csPairContainerType &pairs, 
-	const mapperNBS::CellIterator &particleMap
+	const mapperNBS::CellIterator &particleMap,
+	const deviceViewType1D<realx3>& pPoints,
+	const deviceViewType1D<real>&  pDiams,
+	real sizeRatio
 )
 {
 
@@ -113,7 +121,7 @@ bool pFlow::cellsWallLevel0::particleWallFindPairs
 	while (getFull)
 	{
 		
-		getFull = findPairsElementRangeCount(pairs, particleMap);
+		getFull = findPairsElementRangeCount(pairs, particleMap, pPoints, pDiams, sizeRatio);
 		
 		if(getFull)
 		{
@@ -137,14 +145,14 @@ bool pFlow::cellsWallLevel0::particleWallFindPairs
 pFlow::int32 pFlow::cellsWallLevel0::findPairsElementRangeCount
 (
 	csPairContainerType &pairs, 
-	const mapperNBS::CellIterator &particleMap
+	const mapperNBS::CellIterator &particleMap,
+	const deviceViewType1D<realx3>& pPoints,
+	const deviceViewType1D<real>&  pDiams,
+	real sizeRatio
 )
 {
 	uint32 getFull =0;
 			
-	//const auto pwPairs = pairs;
-	const auto elementBox = elementBox_;
-	
 	
 	Kokkos::parallel_reduce(
 		"pFlow::cellsWallLevel0::findPairsElementRangeCount",
@@ -155,7 +163,10 @@ pFlow::int32 pFlow::cellsWallLevel0::findPairsElementRangeCount
 			
 			const uint32 iTri = teamMember.league_rank();
 
-			const auto triBox = elementBox[iTri];
+			const auto triBox = elementBox_[iTri];
+			const auto triPlane = infinitePlane(
+				normals_[iTri], 
+				points_[vertices_[iTri].x()]);
 
 			uint32 getFull2 = 0;
 
@@ -175,10 +186,13 @@ pFlow::int32 pFlow::cellsWallLevel0::findPairsElementRangeCount
 						while( n != particleMap.NoPos)
 						{
 							// id is wall id the pair is (particle id, wall id)
+							if( abs(triPlane.pointFromPlane(pPoints[n]))< pDiams[n]*sizeRatio*cellExtent_)
+							{
 								if( pairs.insert(
 									static_cast<csIdType>(n),
 									static_cast<csIdType>(iTri) ) == -1 )
 									innerUpdate++;
+							}
 							n = particleMap.next(n);
 						
 						}

src/Interaction/contactSearch/methods/cellBased/NBS/cellsWallLevel0.hpp

@@ -60,6 +60,9 @@ private:
 	// - ref to points in the trisurface (borrowed)
 	ViewType1D<realx3, memory_space> 	points_;
 
+	// - ref to normal vectors of triangles (borrowed)
+	ViewType1D<realx3, memory_space> 	normals_;
+
 	// cell range of element/triangle bounding box
 	ViewType1D<iBoxType, memory_space> 	elementBox_;
 	
@@ -88,7 +91,8 @@ public:
 		uint32 					numPoints,
 		uint32 					numElements,
 		const ViewType1D<realx3,memory_space>& 		points, 
-		const ViewType1D<uint32x3,memory_space>& 	vertices);
+		const ViewType1D<uint32x3,memory_space>& 	vertices,
+		const ViewType1D<realx3, memory_space>& normals);
 	
 
 	
@@ -97,8 +101,9 @@ public:
 	bool resetElements( 
 		uint32 		numElements,
 		uint32      numPoints,
-		ViewType1D<realx3, memory_space>& points, 
+		const ViewType1D<realx3, memory_space>& points, 
-		ViewType1D<uint32x3, memory_space>& vertices);
+		const ViewType1D<uint32x3, memory_space>& vertices,
+		const ViewType1D<realx3, memory_space>& normals);
 	
 
 	INLINE_FUNCTION_HD
@@ -116,18 +121,27 @@ public:
 	bool broadSearch(
 		csPairContainerType& pairs,
 		const cells& searchBox, 
-		const mapperNBS::CellIterator& particleMap);
+		const mapperNBS::CellIterator& particleMap,
+		const deviceViewType1D<realx3>& pPoints,
+		const deviceViewType1D<real>&  pDiams,
+		real sizeRatio);
 	
 
 	bool build(const cells& searchBox);
 	
 	bool particleWallFindPairs(
 		csPairContainerType& pairs, 
-		const mapperNBS::CellIterator& particleMap);
+		const mapperNBS::CellIterator& particleMap,
+		const deviceViewType1D<realx3>& pPoints,
+		const deviceViewType1D<real>&  pDiams,
+		real sizeRatio);
 
 	int32 findPairsElementRangeCount(
 		csPairContainerType& pairs, 
-		const mapperNBS::CellIterator& particleMap); 
+		const mapperNBS::CellIterator& particleMap,
+		const deviceViewType1D<realx3>& pPoints,
+		const deviceViewType1D<real>&  pDiams,
+		real sizeRatio); 
 	
 
 

src/Interaction/sphereInteraction/sphereInteraction.cpp

@@ -134,7 +134,7 @@ pFlow::sphereInteraction<cFM,gMM, cLT>::sphereInteraction
 {
 	contactSearch_ = contactSearch::create(
 	subDict("contactSearch"),
-	prtcl.thisDomain().domainBox(),
+	prtcl.extendedDomain().domainBox(),
 	prtcl,
 	geom,
 	timers());

src/phasicFlow/fileSystem/fileSystem.cpp

@@ -281,6 +281,15 @@ pFlow::fileSystem pFlow::operator /
 
 }
 
+pFlow::fileSystem pFlow::operator /
+(
+	const fileSystem& fs1,
+	const word& dir2 
+)
+{
+	return fs1/fileSystem(dir2, "");
+}
+
 pFlow::fileSystem pFlow::operator +
 (
 	const fileSystem& fs1,

src/phasicFlow/fileSystem/fileSystem.hpp

@@ -50,7 +50,13 @@ fileSystem operator /
 (
 	const fileSystem& fs1,
     const fileSystem& fs2
- );
+);
+
+fileSystem operator /
+(
+	const fileSystem& fs1,
+    const word& dir2
+);
 
 fileSystem operator +
 (

src/phasicFlow/repository/Time/timeControl.cpp

@@ -117,6 +117,15 @@ pFlow::timeControl::timeControl(
 	checkForOutputToFile();
 }
 
+pFlow::real pFlow::timeControl::setTime(real t)
+{
+	real tmp = currentTime_;
+	currentTime_ = t;
+	lastSaved_ = t;
+	checkForOutputToFile();
+	return tmp;
+}
+
 pFlow::word pFlow::timeControl::timeName()const
 {
 	if(managedExternaly_)
@@ -167,8 +176,6 @@ void pFlow::timeControl::checkForOutputToFile()
 	}
 
 	outputToFile_ = save;
-
-
 }
 
 bool pFlow::timeControl::timersReportTime()const

src/phasicFlow/repository/Time/timeControl.hpp

@@ -108,14 +108,8 @@ public:
 		return dt_;
 	}
 
-	real setTime(real t)
+	real setTime(real t);
-	{
+	
-		real tmp = currentTime_;
-		currentTime_ = t;
-		lastSaved_ = t;
-		checkForOutputToFile();
-		return tmp;
-	}
 
 	void setStopAt(real sT)
 	{

src/phasicFlow/repository/systemControl/systemControl.hpp

@@ -31,7 +31,6 @@ Licence:
 #include "types.hpp"
 #include "Time.hpp"
 #include "fileDictionary.hpp"
-#include "box.hpp"
 #include "Timers.hpp"
 #include "dynamicLinkLibs.hpp"
 #include "Set.hpp"
@@ -176,11 +175,6 @@ public:
 		return settingsDict_().getVal<realx3>("g");
 	}
 
-	/*inline box domain()
-	{
-		return box(domainDict().subDict("globalBox"));
-	}*/
-
 	bool operator ++(int);
 
 	void setSaveTimeFolder(

src/phasicFlow/structuredData/pointStructure/pointStructure.hpp

@@ -148,6 +148,12 @@ public:
 			return simulationDomain_().thisDomain();
 		}
 
+		inline 
+		const auto& extendedDomain()const
+		{
+			return boundaries_.extendedDomain();
+		}
+		
 	// - IO methods 
 
 		/// @brief read the point structure from the input stream.

utilities/CMakeLists.txt

@@ -5,7 +5,7 @@ add_subdirectory(particlesPhasicFlow)
 
 add_subdirectory(geometryPhasicFlow)
 
-#add_subdirectory(pFlowToVTK)
+add_subdirectory(pFlowToVTK)
 
 add_subdirectory(Utilities)
 

utilities/Utilities/CMakeLists.txt

@@ -1,8 +1,8 @@
 
 set(SourceFiles 
 readFromTimeFolder.cpp
-readControlDict.cpp
+#readControlDict.cpp
-#vtkFile/vtkFile.cpp
+vtkFile/vtkFile.cpp
 geometryPhasicFlow/Wall/Wall.cpp 
 geometryPhasicFlow/planeWall/planeWall.cpp 
 #geometryPhasicFlow/stlWall/stlWall.cpp

utilities/pFlowToVTK/CMakeLists.txt

@@ -1,7 +1,7 @@
 
 set(source_files 
 pFlowToVTK.cpp 
-geometric.cpp 
+#geometric.cpp 
 )
 set(link_lib phasicFlow Kokkos::kokkos Utilities)
 

utilities/pFlowToVTK/pFlowToVTK.cpp

@@ -18,29 +18,19 @@ Licence:
 
 -----------------------------------------------------------------------------*/
 
-
+#include "vocabs.hpp"
 #include "systemControl.hpp"
-#include "pointFieldToVTK.hpp"
-#include "triSurfaceFieldToVTK.hpp"
 #include "timeFolder.hpp"
 #include "commandLine.hpp"
 #include "ranges.hpp"
-#include "readControlDict.hpp"
+#include "Vectors.hpp"
+#include "phasicFlowKokkos.hpp"
+#include "pointFieldToVTK.hpp"
+//#include "triSurfaceFieldToVTK.hpp"
+//#include "readControlDict.hpp"
 
 
-using pFlow::word;
+using namespace pFlow;
-using pFlow::wordVector;
-using pFlow::geometryFolder__;
-using pFlow::timeFolder;
-using pFlow::fileSystem;
-using pFlow::wordList;
-using pFlow::IOfileHeader;
-using pFlow::objectFile;
-using pFlow::output;
-using pFlow::endl;
-using pFlow::multiTriSurface;
-using pFlow::commandLine;
-using pFlow::realCombinedRange;
 
 int main(int argc, char** argv )
 {
@@ -69,6 +59,12 @@ int main(int argc, char** argv )
 		"path to output folder of VTK",
 		"path");
 	
+	bool separateSurfaces = false;
+	cmds.addOption(
+		"-s,--separate-surfaces",
+		separateSurfaces,
+		"surfaces in the geometry are converted separatedly");
+
 	wordVector fields;
 	bool 			 allFields = true;
 	cmds.addOption("-f,--fields",
@@ -92,7 +88,7 @@ int main(int argc, char** argv )
 
 
 	timeFolder folders(Control);
-	fileSystem destFolder = fileSystem(outFolder)/geometryFolder__;
+	fileSystem destFolder = fileSystem(outFolder)/word(geometryFolder__);
 	fileSystem destFolderField = fileSystem(outFolder);
 	wordList geomfiles{"triSurface"};
 
@@ -117,11 +113,11 @@ int main(int argc, char** argv )
 
 	do
 	{
-
+		Control.time().setTime(folders.time());
 		if( !validRange.isMember( folders.time() ) )continue;
 		
-		output<< "time: " << cyanText( folders.time() )<<" s" <<endl;
+		output<< "time: " << Cyan_Text( folders.time() )<<" s" <<endl;
-		if(!noGoem)
+		/*if(!noGoem)
 		{	
 			fileSystem geomFolder = folders.folder()/geometryFolder__;
 			if(!pFlow::TSFtoVTK::convertTimeFolderTriSurfaceFields(geomFolder, folders.time(), destFolder, "surface"))
@@ -129,7 +125,7 @@ int main(int argc, char** argv )
 				fatalExit;
 				return 1;
 			}	
-		}
+		}*/
 
 		if(!noParticle)
 		{
@@ -137,17 +133,15 @@ int main(int argc, char** argv )
 			if(allFields)
 			{
 				if( !pFlow::PFtoVTK::convertTimeFolderPointFields(
-					folders.folder(),
+					Control,
-					folders.time(),
 					destFolderField,
-					"sphereFields" )
+					"sphereFields" ))
-				)
 				{
 					fatalExit;
 				}
 			}else
 			{
-				if(!pFlow::PFtoVTK::convertTimeFolderPointFieldsSelected(
+				/*if(!pFlow::PFtoVTK::convertTimeFolderPointFieldsSelected(
 					folders.folder(),
 					folders.time(),
 					destFolderField,
@@ -157,7 +151,7 @@ int main(int argc, char** argv )
 				)
 				{
 					fatalExit;
-				}
+				}*/
 			}	
 		}
 		

utilities/pFlowToVTK/pointFieldToVTK.hpp

@@ -25,13 +25,15 @@ Licence:
 #include <regex>
 
 #include "vtkFile.hpp"
+#include "systemControl.hpp"
+#include "pointStructure.hpp"
 #include "pointFields.hpp"
-#include "IOobject.hpp"
+
 
 namespace pFlow::PFtoVTK
 {
 
-template<typename IntType, typename IncludeMaskType>
+/*template<typename IntType, typename IncludeMaskType>
 bool addIntPointField(
 	iOstream& 	os,
 	word 		fieldName,
@@ -53,7 +55,7 @@ bool addRealx3PointField(
 	word 		fieldName,
 	int32 		numActivePoints,
 	realx3* 	field,
-	IncludeMaskType includeMask );
+	IncludeMaskType includeMask );*/
 
 bool regexCheck(word TYPENAME, word fieldType)
 {
@@ -69,14 +71,10 @@ bool regexCheck(word TYPENAME, word fieldType)
 template<typename Type>
 bool checkFieldType(word objectType)
 {
-	//if( pointField<VectorSingle,Type>::TYPENAME() == objectType )return true;
+	return regexCheck(pointField<Type>::TYPENAME(), objectType);
-	//if( pointField<VectorSingle,Type, HostSpace>::TYPENAME() == objectType ) return true;
-	//if( pointField<VectorDual, Type>::TYPENAME() == objectType )return true;
-	return regexCheck(pointField<VectorSingle,Type>::TYPENAME(), objectType);
-	
 }
 
-template<typename T>
+/*template<typename T>
 bool convertIntPointField
 (
 	iOstream& os,
@@ -113,10 +111,10 @@ bool convertIntPointField
 		pStruct.numActive(),
 		data,
 		pStruct.activePointsMaskH() );
-}
+}*/
 
 
-bool convertRealTypePointField(
+/*bool convertRealTypePointField(
 	iOstream& os,
 	const IOfileHeader& header,
 	const pointStructure& pStruct)
@@ -144,9 +142,9 @@ bool convertRealTypePointField(
 		pStruct.numActive(),
 		data,
 		pStruct.activePointsMaskH() );
-}
+}*/
 
-bool convertRealx3TypePointField(
+/*bool convertRealx3TypePointField(
 	iOstream& os,
 	const IOfileHeader& header,
 	const pointStructure& pStruct)
@@ -174,50 +172,45 @@ bool convertRealx3TypePointField(
 		pStruct.numActive(),
 		data,
 		pStruct.activePointsMaskH() );
-}
+}*/
 
 
-template<typename IncludeMaskType>
 bool addUndstrcuturedGridField(
 	iOstream& 	os,
-	int32 		numActivePoints,
 	realx3* 	position,
-	IncludeMaskType includeMask)
+	uint32 		numPoints)
 {
 
-	auto [iFirst, iLast] = includeMask.activeRange();
-
 	os<< "DATASET UNSTRUCTURED_GRID\n";
-	os<< "POINTS "<< numActivePoints << " float\n"; 
+	os<< "POINTS "<< numPoints << " float\n"; 
 	
-	if(numActivePoints==0) return true;
+	if(numPoints==0) return true;
 	
-	for(int32 i=iFirst; i<iLast; ++i)
+	for(uint32 i=0; i<numPoints; i++)
 	{
-		if(includeMask(i))
 		os<< position[i].x()<<' '<< position[i].y()<<' '<<position[i].z()<<'\n';
 	}
 
-	os<<"CELLS "<< numActivePoints<<' '<< 2*numActivePoints<<'\n';
+	os<<"CELLS "<< numPoints<<' '<< 2*numPoints<<'\n';
-	for(int32 i=0; i<numActivePoints; i++)
+	for(uint32 i=0; i<numPoints; i++)
 	{
 		os<< 1 <<' '<< i<<'\n';
 	}
 
-	os<<"CELL_TYPES "<< numActivePoints<<'\n';
+	os<<"CELL_TYPES "<< numPoints<<'\n';
 
-	for(int32 i=0; i<numActivePoints; i++)
+	for(int32 i=0; i<numPoints; i++)
 	{
 		os<< 1 <<'\n';
 	}
 	
-	os << "POINT_DATA " << numActivePoints << endl;
+	os << "POINT_DATA " << numPoints << endl;
 
 	return true;
 }
 
 
-template<typename IntType, typename IncludeMaskType>
+/*template<typename IntType, typename IncludeMaskType>
 bool addIntPointField(
 	iOstream& 	os,
 	word 		fieldName,
@@ -238,9 +231,9 @@ bool addIntPointField(
 	}
 
 	return true;
-}
+}*/
 
-template<typename IncludeMaskType>
+/*template<typename IncludeMaskType>
 bool addRealPointField(
 	iOstream& 	os,
 	word 		fieldName,
@@ -260,9 +253,9 @@ bool addRealPointField(
 			os<< field[i] <<'\n';
 	}
 	return true;
-}
+}*/
 
-template<typename IncludeMaskType>
+/*template<typename IncludeMaskType>
 bool addRealx3PointField(
 	iOstream& 	os,
 	word 		fieldName,
@@ -283,16 +276,16 @@ bool addRealx3PointField(
 	}
 
 	return true;
-}
+}*/
 
 
 bool convertTimeFolderPointFields( 
-	fileSystem timeFolder,
+	systemControl& control,
-	real time,
 	fileSystem destPath,
 	word bName)
 {
 
+	fileSystem timeFolder = control.time().path();
 	// check if pointStructure exist in this folder 
 	IOfileHeader pStructHeader(
 		objectFile(
@@ -304,36 +297,35 @@ bool convertTimeFolderPointFields(
 
 	if( !pStructHeader.headerOk(true) )
 	{
-		output<<yellowColor<<"Time folder "<< timeFolder <<
+		output<<yellowColor<<"Time folder "<< control.time().path() <<
 		" does not contain any pStructure data file. Skipping this folder . . ."
 		<<defaultColor<<nl;
 		return true;
 	}
 
-	vtkFile vtk(destPath, bName, time);
+	vtkFile vtk(destPath, bName, control.time().currentTime());
 
 	if(!vtk) return false;
 
-	auto pStructObjPtr = IOobject::make<pointStructure>(pStructHeader);
+	
-	auto& pStruct = pStructObjPtr().getObject<pointStructure>();
+	auto pStruct = pointStructure(control);
 
 	// get a list of files in this timeFolder;
 
-	auto posVec = std::as_const(pStruct).pointPosition().hostVectorAll();
+	auto posVec = pStruct.pointPositionHost();
 	auto* pos = posVec.data();
 
-	REPORT(1)<<"Writing pointStructure to vtk file with "<< yellowText(pStruct.numActive())
+	REPORT(1)<<"Writing pointStructure to vtk file with "<< Yellow_Text(pStruct.numActive())
-					 <<" active particles"<<endREPORT;
+					 <<" active particles"<<END_REPORT;
 	addUndstrcuturedGridField(
 		vtk(),
-		pStruct.numActive(),
 		pos,
-		pStruct.activePointsMaskH());
+		pStruct.numActive());
 
-	auto fileList = containingFiles(timeFolder);
+	//auto fileList = containingFiles(timeFolder);
 
 
-	for(auto& file:fileList)
+	/*for(auto& file:fileList)
 	{
 		IOfileHeader fieldHeader(
 			objectFile(
@@ -350,7 +342,7 @@ bool convertTimeFolderPointFields(
 			convertRealTypePointField(vtk(), fieldHeader, pStruct);
 			convertRealx3TypePointField(vtk(), fieldHeader, pStruct);
 		}
-	}
+	}*/
 
 	return true;
 }
@@ -367,7 +359,7 @@ bool convertTimeFolderPointFieldsSelected(
 {
 
 	// check if pointStructure exist in this folder 
-	IOfileHeader pStructHeader(
+	/*IOfileHeader pStructHeader(
 		objectFile(
 			pointStructureFile__,
 			timeFolder,
@@ -438,7 +430,7 @@ bool convertTimeFolderPointFieldsSelected(
 				REPORT(1)<<"Could not find "<<yellowText(fieldAddress) <<" skipping . . ."<<endREPORT;
 			}
 		}
-	}
+	}*/
 
 	return true;
 }