MPI-parallelization upto IO file

CMakeLists.txt

@@ -74,7 +74,7 @@ add_subdirectory(src)
 
 #add_subdirectory(solvers)
 
-add_subdirectory(utilities)
+#add_subdirectory(utilities)
 
 #add_subdirectory(DEMSystems)
 add_subdirectory(testIO)

cmake/bashrc

@@ -29,7 +29,7 @@ export PATH="$pFlow_BIN_DIR:$PATH"
 
 export LD_LIBRARY_PATH="$pFlow_LIB_DIR:$LD_LIBRARY_PATH"
 
-export LD_LIBRARY_PATH="$Zoltan_DIR/build/lib:$LD_LIBRARY_PATH"
+export LD_LIBRARY_PATH="$Zoltan_DIR/lib:$LD_LIBRARY_PATH"
 
 
 #------------------------------------------------------------------------------

src/phasicFlow/CMakeLists.txt

@@ -6,6 +6,10 @@ types/types.cpp
 
 globals/error.cpp
 
+processors/processors.cpp
+processors/localProcessors.cpp
+processors/pFlowProcessors.cpp
+
 streams/token/tokenIO.cpp
 streams/token/token.cpp
 streams/iStream/IOstream.cpp
@@ -20,14 +24,10 @@ streams/TStream/oTstream.cpp
 streams/Fstream/iFstream.cpp
 streams/Fstream/oFstream.cpp
 streams/Fstream/fileStream.cpp
-streams/dataIO/dataIO.cpp
-streams/dataIO/dataIONoMPI.cpp 
 streams/streams.cpp 
 
 fileSystem/fileSystem.cpp
 
-processors/processors.cpp
-
 dictionary/dictionary.cpp
 dictionary/fileDictionary.cpp
 dictionary/entry/iEntry.cpp
@@ -39,6 +39,9 @@ containers/Field/Fields.cpp
 containers/List/anyList/anyList.cpp
 containers/pointField/pointFields.cpp
 
+#setFieldList/setFieldList.cpp
+#setFieldList/setFieldEntry.cpp
+
 Timer/Timer.cpp
 Timer/Timers.cpp
 
@@ -64,21 +67,58 @@ structuredData/plane/plane.cpp
 structuredData/domain/domain.cpp
 structuredData/domain/simulationDomain.cpp
 structuredData/domain/regularSimulationDomain.cpp
-structuredData/pointStructure/boundaryList.cpp
 structuredData/pointStructure/internalPoints.cpp
 structuredData/pointStructure/pointStructure.cpp
 structuredData/boundaries/boundaryBase/boundaryBase.cpp
 structuredData/boundaries/boundaryExit/boundaryExit.cpp
+structuredData/pointStructure/boundaryList.cpp
+
+commandLine/commandLine.cpp
 
 
 )
 
 set(link_libs)
-if(MPI_FOUND)
-	set(link_libs Kokkos::kokkos tbb PRIVATE MPI::MPI_CXX)
-else()
 set(link_libs Kokkos::kokkos tbb)
-endif()
 	
+
+
+if(pFlow_Build_MPI)
+
+	set(Zoltan_Install_DIR)
+	if(DEFINED ENV{Zoltan_DIR})
+	   set(Zoltan_Install_DIR $ENV{Zoltan_DIR})
+	else()
+	  set(Zoltan_Install_DIR $ENV{HOME}/PhasicFlow/Zoltan)
+	endif()
+	message(STATUS "Zoltan install directory is ${Zoltan_Install_DIR}")
+
+	set(ZOLTAN_PREFIX "${Zoltan_Install_DIR}" CACHE STRING "Zoltan install directory")
+
+	find_path(ZOLTAN_INCLUDE_DIR zoltan.h PATHS "${ZOLTAN_PREFIX}/include")
+
+	message(STATUS "Zoltan include path: ${ZOLTAN_INCLUDE_DIR}")
+
+	find_library(ZOLTAN_LIBRARY zoltan PATHS "${ZOLTAN_PREFIX}/lib")
+	message(STATUS "Zoltan lib path: ${ZOLTAN_LIBRARY}")
+	
+	list(APPEND SourceFiles
+	MPIParallelization/partitioning.cpp 
+	MPIParallelization/rcb1DPartitioning.cpp
+	MPIParallelization/domain/MPISimulationDomain.cpp
+    #MPIParallelization/dataIOMPI.cpp
+    MPIParallelization/procCommunication.cpp
+    MPIParallelization/boundaryProcessor.cpp
+    MPIParallelization/scatteredMasterDistributeChar.cpp
+	)
+	
+	list(APPEND link_libs MPI::MPI_CXX ${ZOLTAN_LIBRARY} -lm )
+	pFlow_add_library_install(phasicFlow SourceFiles link_libs)
+	target_include_directories(phasicFlow PUBLIC ./globals ${ZOLTAN_INCLUDE_DIR})
+
+else()
 	pFlow_add_library_install(phasicFlow SourceFiles link_libs)
 	target_include_directories(phasicFlow PUBLIC ./globals)
+endif()
+
+

src/phasicFlow/commandLine/commandLine.cpp

@@ -38,10 +38,10 @@ pFlow::commandLine::commandLine(word appName, word disptn)
 	CLI::App::add_flag_callback(
 		"--description",
 		[disptn, appName]() {
-			output<<"\n"<<yellowText(versoinCopyright)<<endl;
+			mOutput<<"\n"<<Yellow_Text(versoinCopyright)<<endl;
-			output<<yellowText(floatingPointDescription())<<endl<<endl;
+			mOutput<<Yellow_Text(floatingPointDescription())<<endl<<endl;
-			output<<"Description for "<< boldText(appName)<<":\n";
+			mOutput<<"Description for "<< Bold_Text(appName)<<":\n";
-			output<<"  "<<disptn<<endl;
+			mOutput<<"  "<<disptn<<endl;
 		},
 		"What does this app do?"
 		)->configurable(false);

src/phasicFlow/containers/Field/Field.cpp

@@ -185,11 +185,13 @@ template<template<class, class> class VectorField, class T, class PropType>
 bool pFlow::Field<VectorField, T, PropType>::read
 (
 	iIstream& is,
-	IOPattern::IOType iotype
+	const IOPattern& iop
 )
 {
 	
-	bool tokenFound;
+	bool tokenFound = true;
+	
+    if(iop.thisProcReadData())
         tokenFound = is.findToken(fieldKey_);
 
 	if( !tokenFound )
@@ -199,11 +201,12 @@ bool pFlow::Field<VectorField, T, PropType>::read
 		return false;
 	}
 	
-	if( !VectorType::read(is, iotype) )
+	if( !VectorType::read(is, iop) )
 	{
 		ioErrorInFile(is.name(), is.lineNumber())<<
 		"error in reading field data from field "<< this->name()<<endl;
 	}
+    if(iop.thisProcReadData())
 	    is.readEndStatement("Field::read");
 
 
@@ -213,14 +216,14 @@ bool pFlow::Field<VectorField, T, PropType>::read
 template<template<class, class> class VectorField, class T, class PropType>
 bool pFlow::Field<VectorField, T, PropType>::write(
 	iOstream& os, 
-	IOPattern::IOType iotype)const
+	const IOPattern& iop)const
 {
 
 	os.writeWordKeyword(fieldKey_)<<endl;
 
 	if(!os.check(FUNCTION_NAME))return false;
 
-	if(!VectorType::write(os, iotype)) return false;
+	if(!VectorType::write(os, iop)) return false;
 
 	os.endEntry();
 	if(!os.check(FUNCTION_NAME))return false;

src/phasicFlow/containers/Field/Field.hpp

@@ -27,7 +27,7 @@ Licence:
 
 #include "types.hpp"
 #include "Vector.hpp"
-
+#include "streams.hpp"
 
 namespace pFlow
 {
@@ -193,15 +193,15 @@ public:
 		bool writeField(iOstream& os)const;*/
 
 		
-		bool read(iIstream& is, IOPattern::IOType iotype);
+		bool read(iIstream& is, const IOPattern& iop);
 		
 
-		bool write(iOstream& os, IOPattern::IOType iotype )const;
+		bool write(iOstream& os, const IOPattern& iop )const;
 
 		template<typename HostMask>
 		bool write(
 			iOstream& os, 
-			IOPattern::IOType iotype, 
+			const IOPattern& iop, 
 			const HostMask& mask)const
 		{
 			
@@ -209,7 +209,7 @@ public:
 
 			if(!os.check(FUNCTION_NAME))return false;
 
-			if(!VectorType::write(os, iotype)) return false;
+			if(!VectorType::write(os, iop)) return false;
 
 			os.endEntry();
 			if(!os.check(FUNCTION_NAME))return false;

src/phasicFlow/containers/Vector/Vector.cpp

@@ -23,10 +23,10 @@ template<typename T, typename Allocator>
 bool pFlow::Vector<T, Allocator>::readVector
 (
 	iIstream& is,
-	IOPattern::IOType iotype
+	const IOPattern& iop
 )
 {
-	return readStdVector(is, vectorField(), iotype);
+	return readStdVector(is, vectorField(), iop);
 }
 
 
@@ -34,10 +34,10 @@ template<typename T, typename Allocator>
 bool pFlow::Vector<T, Allocator>::writeVector
 (
 	iOstream& os,
-	IOPattern::IOType iotype
+	const IOPattern& iop
 ) const
 {
-	return writeStdVector(os, vectorField(), iotype);	
+	return writeStdVector(os, vectorField(), iop);	
 }
 
 /*template<typename T, typename Allocator>

src/phasicFlow/containers/Vector/Vector.hpp

@@ -334,7 +334,7 @@ public:
 	inline 
 	auto getSpan()const
 	{
-		return span<const T>(this->data(), this->size());
+		return span<T>(const_cast<T*>(this->data()), this->size());
 	}
 
 	static constexpr bool isHostAccessible()
@@ -357,19 +357,19 @@ public:
 	inline VectorType operator -()const;
 
 	/// Read vector (assume ASCII in input)
-	bool readVector(iIstream& is, IOPattern::IOType iotype);
+	bool readVector(iIstream& is, const IOPattern& iop);
 
 	/// write vector 
-	bool writeVector(iOstream& os, IOPattern::IOType iotype) const;
+	bool writeVector(iOstream& os, const IOPattern& iop) const;
 
-	bool read(iIstream& is, IOPattern::IOType iotype)
+	bool read(iIstream& is, const IOPattern& iop)
 	{
-		return readVector(is, iotype);
+		return readVector(is, iop);
 	}
 
-	bool write(iOstream& os, IOPattern::IOType iotype)const
+	bool write(iOstream& os, const IOPattern& iop)const
 	{
-		return writeVector(os, iotype);
+		return writeVector(os, iop);
 	}
 
 };

src/phasicFlow/containers/Vector/stdVectorHelper.hpp

@@ -28,8 +28,8 @@ Licence:
 #include "span.hpp"
 #include "iOstream.hpp"
 #include "iIstream.hpp"
-#include "dataIO.hpp"
+#include "createDataIO.hpp"
-
+#include "pFlowProcessors.hpp"
 
 namespace pFlow
 {
@@ -54,10 +54,10 @@ inline
 bool writeSpan(
     iOstream& os, 
     const span<T>& sp, 
-    IOPattern::IOType iotype)
+    const IOPattern& iop)
 {
    
-   auto ioPtr = dataIO::create(iotype, IOPattern::exeMode());
+   auto ioPtr = createDataIO<T>(pFlowProcessors().localRunTypeName(), iop);
     
    if(!ioPtr)
 	{
@@ -73,32 +73,27 @@ bool writeSpan(
     return true; 
 }
 
-
 template<typename T, typename Allocator>
 bool writeStdVector
 (
 	iOstream& os, 
 	const std::vector<T,Allocator>& vec,
-	IOPattern::IOType iotype 
+	const IOPattern& iop 
 )
 {
-	span<T> sp( const_cast<T*>(vec.data()), vec.size());
+	auto sp = makeSpan(vec);
-
+	return writeSpan(os, sp, iop);
-	return writeSpan(os, sp, iotype);
 }
 
-	
-
-
 template<typename T, typename Allocator>
 bool readStdVector
 (
 	iIstream& is, 
 	std::vector<T,Allocator>& vec,
-	IOPattern::IOType iotype 
+	const IOPattern& iop 
 )
 {
-	auto ioPtr = dataIO::create(iotype, IOPattern::exeMode());
+	auto ioPtr = createDataIO<T>(pFlowProcessors().localRunTypeName(), iop);
 
 	if(!ioPtr)
 	{

src/phasicFlow/containers/VectorHD/VectorSingle.cpp

@@ -415,7 +415,7 @@ template<typename T, typename MemorySpace>
 INLINE_FUNCTION_H 
 auto pFlow::VectorSingle<T,MemorySpace>::getSpan()const
 {
-    return span<const T>(view_.data(), this->size());
+    return span<T>(const_cast<T*>(view_.data()), this->size());
 }
 
 template<typename T, typename MemorySpace>

src/phasicFlow/containers/VectorHD/VectorSingle.hpp

@@ -370,10 +370,10 @@ public:
 
 		/// Read vector from stream (ASCII)
 		FUNCTION_H
-		bool read(iIstream& is, IOPattern::IOType iotype)
+		bool read(iIstream& is, const IOPattern& iop)
 		{
 			std::vector<T> vecFromFile;
-			if(! readStdVector(is, vecFromFile, iotype)) return false;
+			if(! readStdVector(is, vecFromFile, iop)) return false;
 
 			this->assign(vecFromFile);
 
@@ -382,18 +382,18 @@ public:
 
 		/// Write the vector to os
 		FUNCTION_H
-		bool write(iOstream& os, IOPattern::IOType iotype)const
+		bool write(iOstream& os, const IOPattern& iop)const
 		{
 			auto hVec = hostVector();
 			auto sp = span<T>( const_cast<T*>(hVec.data()), hVec.size());
 			
-			return writeSpan(os, sp, iotype);
+			return writeSpan(os, sp, iop);
 			
 		}
 
 		template<typename HostMask>
 		FUNCTION_H
-		bool write(iOstream& os, IOPattern::IOType iotype, const HostMask& mask)const
+		bool write(iOstream& os, const IOPattern& iop, const HostMask& mask)const
 		{
 			auto hVec = hostVector();
 			
@@ -413,7 +413,7 @@ public:
 
 			auto sp = span<T>( finalField.data(), finalField.size());
 
-			return writeSpan(os, sp, iotype);
+			return writeSpan(os, sp, iop);
 
 		}
 

src/phasicFlow/containers/span/span.hpp

@@ -192,6 +192,42 @@ iOstream& operator<<(iOstream& os, const span<T>& s)
     return os;
 }
 
+template<typename T, template<class> class Container>
+span<T> makeSpan(Container<T>& container)
+{
+    return span<T>(container.data(), container.size());
+}
+
+template<typename T, template<class> class Container>
+span<T> makeSpan(const Container<T>& container)
+{
+    return span<T>(
+        const_cast<T*>(container.data()), 
+        container.size());
+}
+
+
+template<typename T>
+inline
+span<char> charSpan(span<T> s)
+{
+    auto el = sizeof(T);
+    return span<char>(
+        reinterpret_cast<char*>(s.data()),
+        s.size()*el);
+}
+
+template<typename T>
+inline
+span<const char> charSpan(span<const T> s)
+{
+    auto el = sizeof(T);
+    return span<const char>(
+        reinterpret_cast<const char*>(s.data()),
+        s.size()*el);
+}
+
+
 
 
 } // pFlow

src/phasicFlow/demComponent/demComponent.cpp

@@ -19,8 +19,8 @@ Licence:
 -----------------------------------------------------------------------------*/
 
 #include "demComponent.hpp"
-
+#include "systemControl.hpp"
-
+#include "Time.hpp"
 
 pFlow::demComponent::demComponent(const word& name, systemControl& control)
 :
@@ -29,3 +29,13 @@ pFlow::demComponent::demComponent(const word& name, systemControl& control)
 	time_(control.time()),
 	timers_(name, &control.timers())
 {}
+
+pFlow::real pFlow::demComponent::dt()const
+{
+	return time_.dt();
+}
+
+pFlow::real pFlow::demComponent::currentTime()const
+{
+    return time_.currentTime();
+}

src/phasicFlow/demComponent/demComponent.hpp

@@ -21,13 +21,15 @@ Licence:
 #ifndef __demComponent_hpp__ 
 #define __demComponent_hpp__
 
-#include "systemControl.hpp"
+#include "types.hpp"
-#include "Time.hpp"
+#include "typeInfo.hpp"
-
+#include "Timers.hpp"
 
 namespace pFlow
 {
 
+class systemControl;
+class Time;
 /**
  * A base class for every main component of DEM system.
  * 
@@ -96,18 +98,10 @@ public:
 		}
 
 		/// Time step of integration
-		inline
+		real dt()const;
-		real dt()const
-		{
-			return time_.dt();
-		}
 		
 		/// Current simulation time 
-		inline
+		real currentTime()const;
-		real currentTime()const
-		{
-			return time_.currentTime();
-		}
 		
 		inline
 		const auto& time()const

src/phasicFlow/dictionary/dictionary.hpp

@@ -218,6 +218,9 @@ public:
 		template<typename T>
 		bool addOrKeep(const word& keyword, const T& v);
 
+        template<typename T>
+        bool addOrReplace(const word& keyword, const T& v);
+
 		void clear();
 
 		/// pointer to a subdictionary 
@@ -384,8 +387,20 @@ T dictionary::getValOrSet
 	}
 }
 
+template <typename T>
+inline bool dictionary::addOrReplace
+(
+    const word &keyword, 
+    const T &v
+)
+{
+    uniquePtr<iEntry> ptr = makeUnique<dataEntry>(keyword, *this ,v);
+    return addPtr(keyword, ptr, false);
+}
+
+
+
 
 } // pFlow
 
-
 #endif // __dictionary_hpp__

src/phasicFlow/dictionary/fileDictionary.cpp

@@ -1,22 +1,50 @@
 #include "fileDictionary.hpp"
-#include "IOPattern.hpp"
 
 
-pFlow::fileDictionary::fileDictionary(const word &keyword)
+pFlow::fileDictionary::fileDictionary
+(
+    const objectFile & of, 
+    repository* owner
+)
 :
-    dictionary(keyword, true)
+    IOobject
+    (
+        of, 
+        IOPattern::IOPattern::AllProcessorsSimilar, 
+        owner
+    ),
+    dictionary
+    (
+        of.name(), 
+        true
+    )
 {
+    dictionary::name_ = IOobject::path().wordPath();
+    if(!IOobject::read())
+    {
+        fatalErrorInFunction<<
+        "Error in reading from dictionary "<< globalName()<<endl;
+        fatalExit;
+    }
 }
 
 pFlow::fileDictionary::fileDictionary(const word &keyword, const fileSystem &file)
 :
-    dictionary(keyword, file)
+    fileDictionary
-{
+    (
-}
+        objectFile
+        (
+            keyword,
+            file,
+            objectFile::READ_ALWAYS,
+            objectFile::WRITE_NEVER
+        ),
+        nullptr
+    )
+{}
 
 bool pFlow::fileDictionary::read(iIstream &is, const IOPattern &iop)
 {
-    
     return dictionary::read(is);
 }
 

src/phasicFlow/dictionary/fileDictionary.hpp

@@ -17,17 +17,18 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
+#ifndef __fileDictionary_hpp__
+#define __fileDictionary_hpp__
 
 #include "dictionary.hpp"
-
+#include "IOobject.hpp"
 
 namespace pFlow
 {
 
-class IOPattern;
-
 class fileDictionary
 :
+    public IOobject,
     public dictionary
 {
 public:
@@ -35,7 +36,7 @@ public:
     TypeInfo("fileDictionary");
 
     /// construct an empty dictionary with keyword and make it global/fileDictionary
-	fileDictionary(const word& keyword);
+	fileDictionary(const objectFile & of, repository* owner = nullptr);
 
 	/// construct a dictionary with name and read it from file 
 	fileDictionary(const word& keyword, const fileSystem& file);
@@ -43,11 +44,14 @@ public:
 
 
     /// read from stream 
-	virtual bool read(iIstream& is, const IOPattern& iop);
+    bool read(iIstream& is, const IOPattern& iop) override;
 
 	/// write to stream
-	virtual bool write(iOstream& os, const IOPattern& iop) const;
+	
+    bool write(iOstream& os, const IOPattern& iop) const override;
 
 };
 
 }
+
+#endif //__fileDictionary_hpp__

src/phasicFlow/fileSystem/fileSystem.cpp

@@ -21,7 +21,7 @@ Licence:
 
 #include "fileSystem.hpp"
 #include "error.hpp"
-#include "iOstream.hpp"
+#include "streams.hpp"
 
 
 bool pFlow::fileSystem::checkFileName(const word& name)
@@ -47,7 +47,6 @@ pFlow::fileSystem::fileSystem(const word & wPath)
 	path_(wPath),
 	isDir_(std::filesystem::is_directory(path_))
 {
-	std::cout<<"file name is " << fileName()<<std::endl;
 	if( !isDir_ && !checkFileName(fileName()))
 	{
 		fatalExit;
@@ -276,7 +275,7 @@ pFlow::fileSystem pFlow::operator /
 	const fileSystem& fs2 
 )
 {
-	fileSystem::pathType cmbPath(fs1.dirPath().path_ / fs2.dirPath().path_);
+	fileSystem::pathType cmbPath(fs1.dirPath().path_ / fs2.path_);
 
 	return fileSystem( cmbPath.c_str() );
 

src/phasicFlow/globals/error.cpp

@@ -30,7 +30,9 @@ Licence:
 
 
 
-static pFlow::Ostream& errorStream   = pFlow::errReport;
+//static pFlow::Ostream& errorStream   = pFlow::errReport;
+
+static pFlow::Ostream& errorStream   = pFlow::pOutput;
 
 
 pFlow::iOstream& fatalErrorMessage(const char* fileName, int linNumber )
@@ -57,9 +59,9 @@ pFlow::iOstream& notImplementedErrorMessage(const char*fnName, const char* fileN
 {
 
 	errorStream<<"\n>>> Fatal error in phasicFlow\n";
-	errorStream<<" Function "<< Red_Text(fnName) << " has not implmented yet!\n" <<
+	errorStream<<" Function "<< Red_Text(fnName) << " has not been implemented yet!\n" <<
-				 " Function definition is in source file "<< Red_Text(fileName) << 
+				 " File "<< Yellow_Text(fileName) << 
-	             " at line "<< Red_Text(lineNumber) <<'\n';
+	             " at line "<< Yellow_Text(lineNumber) <<'\n';
 	return errorStream;
 }
 

src/phasicFlow/processors/localProcessors.cpp

@@ -0,0 +1,117 @@
+#include "localProcessors.hpp"
+
+pFlow::localProcessors::localProcessors(const word &name)
+:
+    processors(),
+    localSize_(processors::globalSize()),
+    localRank_(processors::globalRank()),
+    name_(name)
+{
+#ifdef pFlow_Build_MPI
+    parrentCommunicator_ = pFlow::MPI::CommWorld;
+    localCommunicator_ = pFlow::MPI::CommWorld;
+#endif
+
+}
+
+pFlow::localProcessors::localProcessors
+(
+    const word &name, 
+    const std::vector<int> &ranks
+)
+:
+    processors(),
+    name_(name)
+{
+#ifdef pFlow_Build_MPI
+    parrentCommunicator_ = pFlow::MPI::CommWorld;
+    
+    if(ranks.size()> this->globalSize() )
+    {
+        fatalErrorInFunction<<
+        "the size of ranks is larger than parrent communicator size "<<endl;
+        fatalExit;
+    }
+
+    pFlow::MPI::Group globalGroup;
+    MPI_Comm_group(parrentCommunicator_, &globalGroup);
+
+    pFlow::MPI::Group localGroup;
+    MPI_Group_incl(globalGroup, ranks.size(), ranks.data(), &localGroup);
+ 
+    // Create the new communicator from that group of processes.
+    
+    CheckMPI( MPI_Comm_create(parrentCommunicator_, localGroup, &localCommunicator_), true);
+    
+    isPartOfLocal_ = localCommunicator_ != MPI::CommNull;
+    
+    if(isPartOfLocal_)
+    {
+        MPI_Comm_set_name(localCommunicator_, name.c_str());
+
+        MPI_Comm_size(localCommunicator_, &localSize_);
+        MPI_Comm_rank(localCommunicator_, &localRank_);
+    }
+
+#else
+
+    if(ranks.size()> 1 )
+    {
+        fatalErrorInFunction<< 
+        "rank size for processors should not be greater than 1.";
+        fatalExit;
+    }
+    localSize_ = processors::globalSize();
+    localRank_ = processors::globalRank();
+
+#endif
+}
+
+#ifdef pFlow_Build_MPI
+
+pFlow::localProcessors::localProcessors
+(
+    pFlow::MPI::Comm parrentComm, 
+    const word &name, 
+    const std::vector<int> &ranks
+)
+:
+    processors(),
+    name_(name)
+{
+    parrentCommunicator_ = parrentComm;
+    
+    int parSize;
+
+    MPI_Comm_size(parrentCommunicator_, &parSize);
+
+    if(ranks.size()> parSize )
+    {
+        fatalErrorInFunction<<
+        "the size of ranks is larger than parrent communicator size "<<endl;
+        fatalExit;
+    }
+
+    pFlow::MPI::Group parGroup;
+    MPI_Comm_group(parrentCommunicator_, &parGroup);
+
+    pFlow::MPI::Group localGroup;
+    MPI_Group_incl(parGroup, ranks.size(), ranks.data(), &localGroup);
+ 
+    // Create the new communicator from that group of processes.
+    
+    CheckMPI( MPI_Comm_create(parrentCommunicator_, localGroup, &localCommunicator_), true);
+    
+    isPartOfLocal_ = localCommunicator_ != MPI::CommNull;
+    
+    if(isPartOfLocal_)
+    {
+        MPI_Comm_set_name(localCommunicator_, name.c_str());
+
+        MPI_Comm_size(localCommunicator_, &localSize_);
+        MPI_Comm_rank(localCommunicator_, &localRank_);
+    }
+
+}
+
+#endif

src/phasicFlow/processors/localProcessors.hpp

@@ -0,0 +1,152 @@
+/*------------------------------- 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 __pFlowProcessors_hpp__
+#define __pFlowProcessors_hpp__
+
+
+#include "processors.hpp"
+#include "types.hpp"
+
+#ifdef pFlow_Build_MPI
+    #include "mpiTypes.hpp"
+#endif
+
+
+namespace pFlow
+{
+
+class localProcessors
+:
+    public processors
+{
+protected:
+
+#ifdef pFlow_Build_MPI
+    pFlow::MPI::Comm    parrentCommunicator_;
+
+    pFlow::MPI::Comm    localCommunicator_;
+#endif
+
+    int localSize_ = 0 ;
+
+    int localRank_ = -1;
+
+    bool isPartOfLocal_ = true;
+
+    word name_;
+
+public:
+
+        /// @brief Construct a local processor communication similar 
+        /// to global with specified name
+        /// @param name a given name to the local communicator 
+        localProcessors(const word& name);
+
+        
+        /// @brief Construct a local processor communication from global
+        /// communicator using a name and ranks 
+        /// @param name a given name to the local communicator 
+        /// @param ranks ranks to be included in the new communicator 
+        localProcessors(
+            const word& name, 
+            const std::vector<int>& ranks);
+
+    #ifdef pFlow_Build_MPI
+        localProcessors(
+            pFlow::MPI::Comm parrentComm, 
+            const word& name, 
+            const std::vector<int>& ranks);
+    #endif
+
+    // - Access 
+
+        /// @brief return name of the local communicator 
+        inline 
+        const auto& name()const
+        {
+            return name_;
+        }
+
+        inline
+        auto localRank()const
+        {
+            return localRank_;
+        }
+
+        inline 
+        auto localSize()const
+        {
+            return localSize_;
+        }
+
+    // - Methods 
+
+        inline
+        bool localMaster()const
+        {
+            return localRank_ == localMasterNo();
+        }
+
+        inline 
+        int localMasterNo()const
+        {
+            return 0;
+        }
+
+        inline 
+        bool localParallel()const
+        {
+            return localSize_>1;
+        }
+
+        inline
+        const char* localRunTypeName()
+        {
+            if(localParallel())
+                return "MPI";
+            else
+                return "regular";
+        }
+
+        inline
+        bool isThisActive()const
+        {
+            return isPartOfLocal_;
+        }
+
+    #ifdef pFlow_Build_MPI
+        inline 
+        auto parrentCommunicator()const
+        {
+            return parrentCommunicator_;
+        }
+
+        inline 
+        auto localCommunicator()const
+        {
+            return localCommunicator_;
+        }
+    #endif
+
+};
+
+}
+
+#endif

src/phasicFlow/processors/pFlowProcessors.cpp

@@ -0,0 +1,18 @@
+#include "pFlowProcessors.hpp"
+
+static pFlow::localProcessors pFlowProcessors__{"pFlowProcessors"};
+
+pFlow::localProcessors& pFlow::pFlowProcessors()
+{
+    return pFlowProcessors__;
+}
+
+void pFlow::initialize_pFlowProcessors()
+{
+    pFlowProcessors__ = localProcessors("pFlowProcessors");
+}
+
+void pFlow::initialize_pFlowProcessors(const std::vector<int>& ranks)
+{
+    pFlowProcessors__ = localProcessors("pFlowProcessors", ranks);
+}

src/phasicFlow/processors/pFlowProcessors.hpp

@@ -0,0 +1,14 @@
+
+#include "localProcessors.hpp"
+
+
+namespace pFlow
+{
+
+localProcessors& pFlowProcessors();
+
+void initialize_pFlowProcessors();
+
+void initialize_pFlowProcessors(const std::vector<int>& ranks);
+
+}

src/phasicFlow/processors/processors.cpp

@@ -21,7 +21,7 @@ Licence:
 #include "phasicFlowConfig.H"
 
 #ifdef pFlow_Build_MPI
-	#include <mpi.h>
+	#include "mpiCommunication.hpp"
 #endif
 
 // from PhasicFlow
@@ -29,7 +29,15 @@ Licence:
 #include "processors.hpp"
 #include "streams.hpp"
 
+static int numVarsInitialized__ = 0;
 
+#ifdef pFlow_Build_MPI
+
+    pFlow::MPI::DataType pFlow::MPI::realx3Type__;
+    pFlow::MPI::DataType pFlow::MPI::realx4Type__;
+    pFlow::MPI::DataType pFlow::MPI::int32x3Type__;
+    
+#endif
 
 void pFlow::processors::initProcessors(int argc, char *argv[])
 {
@@ -40,17 +48,31 @@ void pFlow::processors::initProcessors(int argc, char *argv[])
 		CheckMPI(MPI_Init(&argc, &argv), true);
 		isSelfInitialized_ = true;
 
-		processors::globalSize_ = MPI::COMM_WORLD.Get_size();
+        argc_ = argc;
-		processors::globalRank_ = MPI::COMM_WORLD.Get_rank();
+        argv_ = argv;
 
-		if(processors::isParallel())
+		MPI_Comm_rank(MPI_COMM_WORLD, &processors::globalRank_);
+        MPI_Comm_size(MPI_COMM_WORLD, &processors::globalSize_);
+        
+		
+		if(processors::globalParallel())
 		{
 			pFlow::pOutput.activatePrefix();
 			pFlow::pOutput.setPrefixNum(processors::globalRank_);	
 		}
 		
-		pFlow::mOutput.setMasterSlave(processors::isMaster());
+		pFlow::mOutput.setMasterSlave(processors::globalMaster());
-		pFlow::errReport.setMasterSlave(processors::isMaster());
+		pFlow::errReport.setMasterSlave(processors::globalMaster());
+
+        MPI_Type_contiguous(3, pFlow::MPI::Type<real>(), &pFlow::MPI::realx3Type__);
+		MPI_Type_commit(&pFlow::MPI::realx3Type__);
+
+        MPI_Type_contiguous(4, pFlow::MPI::Type<real>(), &pFlow::MPI::realx4Type__);
+		MPI_Type_commit(&pFlow::MPI::realx3Type__);
+
+		MPI_Type_contiguous(3, pFlow::MPI::Type<int32>(), &pFlow::MPI::int32x3Type__);
+		MPI_Type_commit(&pFlow::MPI::int32x3Type__);
+
 	}
 #else
 
@@ -64,6 +86,9 @@ void pFlow::processors::finalizeProcessors()
 #ifdef pFlow_Build_MPI
 	if(isSelfInitialized_ && !isFinalized())
 	{
+        MPI::TypeFree(&pFlow::MPI::realx3Type__);
+        MPI::TypeFree(&pFlow::MPI::realx4Type__);
+		MPI::TypeFree(&pFlow::MPI::int32x3Type__);
 		CheckMPI(MPI_Finalize(), true);
 	}
 #else
@@ -75,7 +100,7 @@ pFlow::processors::processors()
 {
 
 #ifdef pFlow_Build_MPI	
-	if(isParallel() && !isInitialized())
+	if(globalParallel() && !isInitialized())
 	{
 		fatalErrorInFunction<<
 		"MPI communication is not initialized yet!"<<endl;

src/phasicFlow/processors/processors.hpp

@@ -17,11 +17,11 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-
 #ifndef __processors_H__
 #define __processors_H__ 
 
 
+
 namespace pFlow
 {
 	// - Forward
@@ -64,6 +64,12 @@ protected:
 	static inline
 	int globalSize_ = 1;
 
+    static inline
+    int argc_ = 0;
+
+    static inline 
+    char** argv_ = nullptr;
+
 public:
 
 	/// Initialize MPI processors
@@ -77,28 +83,27 @@ public:
 	/// Constructor 
 	processors();
 	
-
 	/// Destructor 
 	~processors();
 	
 	/// Master processors number (globaly in MPI).
 	static inline
-	int masterNo()
+	int globalMasterNo()
 	{
 		return 0;
 	}
 
 	/// Is this a parallel MPI run.
 	static inline
-	bool isParallel()
+	bool globalParallel()
 	{
 		return processors::globalSize()>1;
 	}
 	
 	static inline
-	const char* runTypeName()
+	const char* globalRunTypeName()
 	{
-		if(isParallel())
+		if(globalParallel())
 		{
 			return "MPI";
 		}
@@ -117,9 +122,9 @@ public:
 	
 	/// Is this processor the master processor?
 	static inline
-	bool isMaster()
+	bool globalMaster()
 	{
-		return processors::globalRank() == processors::masterNo();
+		return processors::globalRank() == processors::globalMasterNo();
 	}
 	
 	/// Global size of processors
@@ -136,10 +141,30 @@ public:
 		return globalRank_;
 	}
 
+    static inline
+    int argc()
+    {
+        return argc_;
+    }
+
+    static inline 
+    char** argv()
+    {
+        return argv_;
+    }
+
 	/// Abort MPI run or regular run
 	static
 	void abort(int error);
 
+/*#ifdef pFlow_Build_MPI
+    static inline 
+    auto worldCommunicator()
+    {
+      return pFlow::MPI::CommWorld;  
+    }
+#endif*/
+
 }; //processors
 
 

src/phasicFlow/repository/IOobject/IOPattern.cpp

@@ -25,14 +25,11 @@ pFlow::IOPattern::IOPattern( IOType iotype)
 	ioType_(iotype),
 	globalSize_(processors::globalSize()),
 	globalRank_(processors::globalRank()),
-	isMaster_(processors::isMaster()),
+	isMaster_(processors::globalMaster()),
-	isParallel_(processors::isParallel())
+	isParallel_(processors::globalParallel())
 {}
 
 pFlow::word pFlow::IOPattern::exeMode()
 {
-    if(processors::isParallel())
+    return processors::globalRunTypeName();
-    	return word("MPI");
-    else
-    	return word("NoMPI");
 }

src/phasicFlow/repository/IOobject/IOPattern.hpp

@@ -116,6 +116,13 @@ public:
 		return isParallel_;
 	}
 
+    inline
+    bool thisCallRead()const
+    {
+        if(isMasterProcessorOnly() && !isMaster())return false;
+        return true;
+    }
+
 	inline
 	bool thisProcReadData()const
 	{
@@ -128,6 +135,7 @@ public:
 	bool thisProcWriteData()const
 	{
 		if(isAllProcessorsDifferent()) return true;
+        if(isMasterProcessorDistribute())return true;
 		return isMaster();
 	}
 

src/phasicFlow/repository/IOobject/IOfileHeader.cpp

@@ -17,7 +17,7 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-#include "processors.hpp"
+
 #include "IOfileHeader.hpp"
 #include "repository.hpp"
 
@@ -31,13 +31,11 @@ pFlow::uniquePtr<pFlow::iFstream> pFlow::IOfileHeader::inStream()const
 
 pFlow::uniquePtr<pFlow::oFstream> pFlow::IOfileHeader::outStream()const
 {
-
-	
 	auto osPtr = makeUnique<oFstream>(path(), outFileBinary());
 	
-	if(osPtr && owner_)
+	if(osPtr && owner())
 	{
-	 	auto outPrecision = owner_->outFilePrecision();
+	 	auto outPrecision = owner()->outFilePrecision();
 	 	osPtr->precision(outPrecision);
 	}
 
@@ -46,21 +44,19 @@ pFlow::uniquePtr<pFlow::oFstream> pFlow::IOfileHeader::outStream()const
 
 pFlow::IOfileHeader::IOfileHeader
 (
-	const objectFile& objf,
+	const objectFile& objf
-	const repository* owner
 )
 :
-	objectFile(objf),
+	objectFile(objf)
-	owner_(owner)
 {}
 
 pFlow::fileSystem pFlow::IOfileHeader::path() const
 {
 	fileSystem f;
 
-	if( owner_ )
+	if( owner() )
 	{
-		f = owner_->path()/localPath();	
+		f = owner()->path()/localPath();	
 
 	}else
 	{
@@ -72,8 +68,8 @@ pFlow::fileSystem pFlow::IOfileHeader::path() const
 
 bool pFlow::IOfileHeader::outFileBinary()const
 {
-	if(owner_)
+	if(owner())
-		return owner_->outFileBinary();
+		return owner()->outFileBinary();
 	else
 		return false;
 }
@@ -137,7 +133,6 @@ bool pFlow::IOfileHeader::writeHeader()const
 {
 
 	if( !this->readWriteHeader() ) return false;
-	if( !processors::isMaster() ) return false;
 	if( !implyWrite() ) return false;
 
 	return true;
@@ -186,7 +181,7 @@ bool pFlow::IOfileHeader::readHeader()const
 {
 	if( !implyRead())return false;
 	if( !this->readWriteHeader() ) return false;
-	return ioPattern().thisProcReadHeader();
+    return true;
 }
 
 bool pFlow::IOfileHeader::readHeader(iIstream& is, bool silent)
@@ -231,18 +226,6 @@ bool pFlow::IOfileHeader::readHeader(iIstream& is, bool silent)
 	return true;
 } 
 
-bool pFlow::IOfileHeader::writeData()const
-{
-	if(!implyWrite())return false;
-	return ioPattern().thisProcWriteData();
-}
-
-bool pFlow::IOfileHeader::readData()const
-{
-	if(!implyRead())return false;
-	return ioPattern().thisProcReadData();
-}
-
 bool pFlow::IOfileHeader::writeBanner(iOstream& os)const
 {
 	os<< 

src/phasicFlow/repository/IOobject/IOfileHeader.hpp

@@ -40,8 +40,6 @@ protected:
 	
 
 	//// - data members 
-		// owner repository
-		const repository* 	owner_ = nullptr;
 
 		// object name read from file 
 		word objectName_;
@@ -63,7 +61,7 @@ protected:
 public:
 
 	// with owner 
-	IOfileHeader(const objectFile& objf, const repository* owner = nullptr);
+	IOfileHeader(const objectFile& objf);
 
 	// - object name
 	const word& objectName()const
@@ -78,9 +76,10 @@ public:
 	}
 
 	// - pointer to owner repository 
+	virtual 
     const repository* owner()const
     {
-		return owner_;
+        return nullptr;
     }
 	
 	// - path to file name 
@@ -118,18 +117,13 @@ public:
 	/// Write the header to the file, typeName comes from the one read from file 
 	bool writeHeader(iOstream& os, bool forceWrite = false) const;
 
-	/// Check if the data should be written to file 
-	bool writeData()const;
-
 	/// Check if header should be read from file
 	bool readHeader()const;
 
 	/// Read the header in the file
 	bool readHeader(iIstream& is, bool silent=false);
 
-	/// Check if data should be read from file 
+	
-	/// Always return true
-	bool readData()const;
 	
 	/// write the banner 
 	bool writeBanner(iOstream& os)const;

src/phasicFlow/repository/IOobject/IOobject.cpp

@@ -25,39 +25,41 @@ Licence:
 pFlow::IOobject::IOobject
 (
     const objectFile&   objf, 
-	const repository* owner,
+    const IOPattern&    iop, 
-	uniquePtr<iObject>&& obj
+    repository*   owner
 )
 :
-	IOfileHeader(objf, owner),
+	IOfileHeader(objf),
-	object_(obj.release())
+	ioPattern_(iop),
+    owner_(owner)
 {
     
-	if(!read(this->readWriteHeader()))
+    if(owner_&& !owner->addToRepository(this))
     {
-		fatalErrorInFunction<<
-		"error in reading " << name() << " from path " << path()<<endl;
         fatalExit;
     }
 }
 
-
+pFlow::IOobject::~IOobject()
-pFlow::IOobject::IOobject
-(
-	const objectFile& objf,
-	const repository* owner,
-	uniquePtr<IOobject>&& obj
-)
-:
-	IOfileHeader(objf, owner),
-	object_( obj->object_.release())
 {
+    if(owner_)
+    {
+        owner_->removeFromRepository(this);
+    }
 }
 
-
+pFlow::repository* pFlow::IOobject::releaseOwner
-bool pFlow::IOobject::isObjectValid()const
+(
+    bool fromOwner
+)
 {   
-	return object_.get() != nullptr;
+    auto* old = owner_;
+    if(old && !fromOwner)
+    {
+        old->removeFromRepository(this);
+    }
+    owner_ = nullptr;
+    return old;
 }
 
 bool pFlow::IOobject::read(bool rdHdr)
@@ -65,12 +67,11 @@ bool pFlow::IOobject::read(bool rdHdr)
     
 	if( implyRead() )
 	{
-		if( rdHdr )
+		if( rdHdr & ioPattern().thisCallRead())
 		{	
 			if( auto ptrIS = inStream(); ptrIS )
 			{
 				if(!readHeader(ptrIS()))return false;
-				ptrIS.reset(nullptr);
 			}
 			else
 			{
@@ -80,10 +81,11 @@ bool pFlow::IOobject::read(bool rdHdr)
 			}
 		}
 
+        if(ioPattern().thisCallRead())
+        {
             if( auto ptrIS = inStream(); ptrIS )
             {
                 if(!read(ptrIS(), rdHdr))return false;              
-			
             }
             else
             {
@@ -93,6 +95,8 @@ bool pFlow::IOobject::read(bool rdHdr)
             }    
         }
 		
+	}	
+	
 	return true;
 }
 
@@ -100,6 +104,8 @@ bool pFlow::IOobject::read(bool rdHdr)
 bool pFlow::IOobject::write() const
 {
 	if(implyWrite())
+	{
+		if(ioPattern().thisProcWriteData())
         {
             if(auto ptrOS = outStream(); ptrOS )
             {
@@ -112,6 +118,7 @@ bool pFlow::IOobject::write() const
                 return false;
             }
         }
+	}
 
 	return true;
 }
@@ -119,18 +126,34 @@ bool pFlow::IOobject::write() const
 
 bool pFlow::IOobject::read(iIstream& is, bool rdHdr)
 {
-	if(rdHdr)
+	if(rdHdr && ioPattern().thisCallRead() )
 	{
 		if(!readHeader(is))return false;
 	}
-	return object_->read_object_t(is, ioPattern_);
+
+    if(ioPattern().thisCallRead())
+    {
+        return read(is, ioPattern());
+    }
+    else
+    {
+        return true;
+    }
+	
 }
 
 
 bool pFlow::IOobject::write(iOstream& os) const
 {
-	if(this->readWriteHeader())
+	if(this->writeHeader() && ioPattern().thisProcWriteHeader())
 		writeHeader(os, typeName());
     
-	return (object_->write_object_t(os, ioPattern_) && writeSeparator(os));
+    if(ioPattern().thisProcWriteData())
+	 {   //return (object_->write_object_t(os, ioPattern_) && writeSeparator(os));
+        notImplementedFunction;
+        //return object_->read_object_t(is, ioPattern_);
+        return false;
+     }
+    else
+        return true;
 }

src/phasicFlow/repository/IOobject/IOobject.hpp

@@ -25,7 +25,7 @@ Licence:
 
 
 #include "IOfileHeader.hpp"
-
+#include "IOPattern.hpp"
 
 namespace pFlow
 {
@@ -36,177 +36,49 @@ class IOobject
 :
 	public	IOfileHeader
 {
-
-private:
-
-	class iObject
-	{
-	public:
-
-		virtual ~iObject()=default;
-
-		// - clone 
-		virtual uniquePtr<iObject> clone() const = 0;
-
-		virtual word typeName()const = 0;
-
-		virtual bool read_object_t(iIstream& is, IOPattern iop) = 0;
-
-		virtual bool write_object_t(iOstream& os, IOPattern iop)const = 0;
-
-	};
-
-	template<typename dataType>
-	class object_t
-	:
-		public iObject
-	{
-	protected:
-		dataType 	data_;
-
-	public:
-
-		template<typename... Args,
-          		typename = std::enable_if_t<std::is_constructible<dataType, Args&&...>::value>>
-		object_t(Args&&... args)
-		:
-			data_(std::forward<Args>(args)...)
-		{
-			/*constexpr word msg(dataType::TYPENAME()+"input is not a member function.")
-			static_assert(std::is_member_function_pointer<decltype(&dataType::write)>::value,
-                  msg.c_str());*/
-		}
-
-		// cunstruct by copying data
-		object_t(const dataType& data): data_(data)
-		{}
-
-		
-		virtual uniquePtr<iObject> clone() const
-		{
-			return makeUnique<object_t>(*this);
-		}
-
-		virtual word typeName()const
-		{
-			return data_.typeName();
-		}
-
-		bool read_object_t(iIstream& is, IOPattern iop) override
-		{
-			return data_.read(is, iop);
-		}
-
-		bool write_object_t(iOstream& os, IOPattern iop)const override
-		{
-			return data_.write(os, iop);
-		}
-
-		auto& data()
-		{
-			return data_;
-		}
-
-		const auto& data()const
-		{
-			return data_;
-		}
-
-	};
-
 protected:
 
-	//// - data members
+    IOPattern       ioPattern_;
-
-		// underlaying data object 
-		uniquePtr<iObject> object_ = nullptr;
-
 
+    mutable repository* owner_;	
 
 public:
 
 	// - typeinfo
-	word typeName()const
+	virtual 
-	{
+    word typeName() const = 0;
-		return object_->typeName();
-	}
 
 	//// - Constructors
 
 		// - construct from components, transfer the ownership of iObject (object_t) to the 
 		//   onwner and read the object from file 
-		IOobject(const objectFile& objf, const repository* owner, uniquePtr<iObject>&& obj );
+		IOobject(
+            const objectFile&   objf, 
+            const IOPattern&    iop, 
+            repository*   owner);
         
-		// - construct from components, transfer the ownership of IOobject to the owner (no read happens)
+        ~IOobject();
-		IOobject(const objectFile& objf, const repository* owner, uniquePtr<IOobject>&& obj);
-		
-		
-		template<typename T, 
-			typename = std::enable_if_t<
-				!std::is_same<T, uniquePtr<IOobject::iObject>>::value && 
-				!std::is_same<T, uniquePtr<IOobject>>::value>>
-		IOobject(const objectFile& objf, const repository* owner, const T& data)
-		:
-			IOfileHeader(objf, owner),
-			object_(makeUnique<object_t<T>>(data))
-		{
-			if(!read(this->readWriteHeader()))
-			{
-				fatalErrorInFunction<<
-				"error in reading " << name() << " from path " << path()<<endl;
-				fatalExit;
-			}
-		}
-
-		
-		template<typename T, 
-			typename = std::enable_if_t<
-				!std::is_same<T, uniquePtr<IOobject::iObject>>::value && 
-				!std::is_same<T, uniquePtr<IOobject>>::value>>
-		IOobject(const objectFile& objf, const repository* owner,  T&& data)
-		:
-			IOfileHeader(objf, owner),
-			object_(makeUnique<object_t<T>>(data))
-		{
-			if(!read(this->readWriteHeader()))
-			{
-				fatalErrorInFunction<<
-				"error in reading " << name() << " from path " << path()<<endl;
-				fatalExit;
-			}
-		}		
 
 		// - copy construct 
 		IOobject(const IOobject& src)=delete;	
 
 		// - move construct
-		IOobject(IOobject&& src) = default;
+		IOobject(IOobject&& src) = delete;
 		
 
-		// - make object from components, considering no owner for this object, and 
+        inline
-		//   read from file 
+        const IOPattern& ioPattern()const
-		//   Args are the arguments of object constructor 
+        {
-		template<typename T, typename... Args>
+            return ioPattern_;
-		static auto make(const objectFile& objf, Args&&... args);
+        }
 
-		// - construct object_t with the Args as the arguments of object constructor 
+        // - pointer to owner repository 
-		template<typename T, typename... Args>
+        const repository* owner()const override
-		static uniquePtr<iObject> make_object_t(Args&&... args);
+        {
-		
+            return owner_;
-
+        }
-	//// - Access to data object 
-
-		// - is object valid 
-		bool isObjectValid()const;
-
-		// - ref to data object
-		template<typename T>
-		auto& getObject();
-
-		// - const ref to data object 
-		template<typename T>
-		const auto& getObject()const;
 
+        repository* releaseOwner(bool fromOwner = false);
 
 	//// - IO operations 
 
@@ -222,6 +94,11 @@ public:
 		// - write to istream 
 		bool write(iOstream& os) const;
 
+        virtual 
+        bool write(iOstream& is, const IOPattern& iop)const = 0;
+
+        virtual 
+        bool read(iIstream& is, const IOPattern& iop) = 0;
 
 };
 

src/phasicFlow/repository/IOobject/IOobjectTemplates.cpp

@@ -19,7 +19,7 @@ Licence:
 -----------------------------------------------------------------------------*/
 
 
-template<typename T, typename... Args>
+/*template<typename T, typename... Args>
 auto pFlow::IOobject::make
 (
 	const objectFile& objf,
@@ -62,4 +62,4 @@ const auto& pFlow::IOobject::getObject()const
 		fatalExit;
 	}
 	return  static_cast<const object_t<T>&>(*object_).data();	
-}
+}*/

src/phasicFlow/repository/IOobject/objectFile.cpp

@@ -34,15 +34,13 @@ pFlow::objectFile::objectFile
 	const fileSystem& 	localPath,
 	const readFlag&   	rf, 
 	const writeFlag&  	wf,
-	IOPattern::IOType	ioType,
+	bool  rwHeader
-	bool  rwHdr
 )
 :
 	name_(name),
 	rFlag_(rf),
 	wFlag_(wf),
 	localPath_(localPath),
-	ioPattern_(ioType),
+	readWriteHeader_(rwHeader)	
-	readWriteHeader_(rwHdr)	
 {
 }

src/phasicFlow/repository/IOobject/objectFile.hpp

@@ -23,14 +23,10 @@ Licence:
 
 #include "types.hpp"
 #include "fileSystem.hpp"
-#include "IOPattern.hpp"
-
 
 namespace pFlow
 {
 
-
-
 class objectFile
 {
 public:
@@ -66,9 +62,7 @@ protected:
 	/// Number of bytes used for writing/reading real variable (used for binray)
 	int 		numBytesForReal_ = numBytesForReal__;
 	
-	IOPattern 	ioPattern_ = {IOPattern::MasterProcessorOnly};
+	/// Does the objectFile read & write the header?
-
-	/// Does the objectFile write the header or not
 	bool        readWriteHeader_ = true;
 
 public:
@@ -88,8 +82,7 @@ public:
 		const fileSystem& 	localPath,
 		const readFlag&   	rf = READ_NEVER,
 		const writeFlag&  	wf = WRITE_NEVER,
-		IOPattern::IOType	ioType = IOPattern::MasterProcessorOnly,
+		bool  rwHeader = true
-		bool  rwHdr = true
 	);
 
 	// copy construct 
@@ -156,11 +149,6 @@ public:
 		return wFlag_ == WRITE_NEVER;
 	}
 
-	const IOPattern& ioPattern()const
-	{
-		return ioPattern_;
-	}
-
 	inline 
 	bool readWriteHeader()const
 	{

src/phasicFlow/repository/Time/Time.cpp

@@ -104,6 +104,11 @@ pFlow::Time::Time(
 	}
 }
 
+pFlow::fileSystem pFlow::Time::localPath()const
+{
+    return fileSystem(timeName());
+}
+
 bool pFlow::Time::write
 (
 	bool verbose

src/phasicFlow/repository/Time/Time.hpp

@@ -70,10 +70,8 @@ public:
 
 
 	//// -  Methods
-		virtual fileSystem localPath()const
+		fileSystem localPath()const override;
-		{
+		
-			return fileSystem(timeName());
-		}
 	
 		// - geometry repository 
 		const repository& geometry()const

src/phasicFlow/repository/repository/repository.cpp

@@ -18,7 +18,6 @@ Licence:
 
 -----------------------------------------------------------------------------*/
 
-
 #include "repository.hpp"
 
 
@@ -42,10 +41,20 @@ pFlow::repository::repository
 
 pFlow::repository::~repository()
 {
+	for(auto& objcs: objects_)
+    {
+        objcs.second->releaseOwner(true);
+    }
+    for(auto& reps: repositories_)
+    {
+        reps.second->releaseOwner(true);
+    }
+
     if(owner_)
 	{
-		owner_->removeRepository(this);
+		owner_->removeFromRepository(this);
 	}
+    
 }
 
 pFlow::word pFlow::repository::name()const
@@ -106,26 +115,57 @@ bool pFlow::repository::addToRepository(repository* rep)
 	return true;
 }	
 
-bool pFlow::repository::removeRepository(repository* rep)
+bool pFlow::repository::removeFromRepository(repository* rep)
 {
 	auto name = rep->name();
 	return repositories_.erase(name) == 1; 
 }
 
+bool pFlow::repository::removeFromRepository(IOobject *io)
+{
+    auto name = io->name();
+	return objects_.erase(name) == 1; 
     
+}
+
+pFlow::repository *pFlow::repository::releaseOwner(bool fromOwner)
+{
+    auto* old = owner_;
+    if(old && !fromOwner)
+    {
+        old->removeFromRepository(this);
+    }
+    owner_ = nullptr;
+    return old;
+}
+
+bool pFlow::repository::addToRepository(IOobject* io)
+{
+    if( !objects_.insertIf(io->name(), io ) )
+	{
+		warningInFunction<<
+    	"Failed to add repository " << io->name() <<
+    	" to repository " << this->name() << 
+    	". It is already in this repository. \n";
+    	return false;
+	}
+
+	return true;
+}
 
 bool pFlow::repository::lookupObjectName(const word& nm)const
 {
 	return objects_.search(nm);
 }
 
-pFlow::word pFlow::repository::lookupObjectTypeName(
+pFlow::word pFlow::repository::lookupObjectTypeName
+(
 	const word& nm
 )const
 {
 	if(auto [iter, found] = objects_.findIf(nm); found)
 	{
-		return iter->second.typeName();
+		return iter->second->typeName();
 	}
 	else
 	{
@@ -143,13 +183,11 @@ bool pFlow::repository::globalLookupObjectName
 )const
 {	
 
-	
-	
 	if(!downward)
 	{	
 		// the object to start search and its owner 
-		auto object = this;
+		auto* object = this;
-		auto owner = object->owner();
+		auto* owner = object->owner();
 
 		// get to the top-most repository 
 		while(!owner)
@@ -245,10 +283,10 @@ bool pFlow::repository::write
 	{
 		if(verbose)
 		{
-			REPORT(1)<< "Writing to " << obj.second.path()<<END_REPORT;
+			REPORT(1)<< "Writing to " << obj.second->path()<<END_REPORT;
 		}
 		
-		if(!obj.second.write())
+		if(!obj.second->write())
 		{
 			return false;
 		}

src/phasicFlow/repository/repository/repository.hpp

@@ -45,7 +45,7 @@ protected:
 	repository* 	 owner_;
 
 	// - sorted names of objects with object index in vector of objects
-	wordMap<IOobject>  	objects_;
+	wordMap<IOobject*>  	objects_;
 
 	// - list of repositories that this repository owns
 	// - it is not a managed list of pointers!
@@ -100,61 +100,20 @@ public:
 		// - ref to this repository 
 		repository& thisRepository();
 		
-		// - add rep to this repository 
+		/// @brief add repository to this repository 
-		//   return false if the name already exists 
+		///   return false if the name already exists 
 		bool addToRepository(repository* rep);
 		
-		// - remove rep from the list of repositories 
+		/// @brief remove rep from the list of repositories 
-		bool removeRepository(repository* rep);
+		bool removeFromRepository(repository* rep);
 
+        /// @brief add IOobject to this repository
+        bool addToRepository(IOobject* io);
 
-	//// - Add/remove objects 
+    /// @brief remove rep from the list of repositories 
-
+		bool removeFromRepository(IOobject* io);
-		// - insert the object into repository if it does not exist
-		//   return a refernce to underlying data object, this reference never invalidated 
-		//   until it is deleted from repository.
-		//   issue a fatal error if it is already exists
-		//   ** one time construction and no move/copy of object ** 
-		template<typename T, typename... Args>
-		T& emplaceObject(const objectFile& objf, Args&&... args);
-		
-		// - insert the object into repository if it does not exist
-		//   return a refernce to underlying data object, this reference never invalidated 
-		//   until it is deleted from repository.
-		// - if the object already exist, after type check(if consistent), return the 
-		//   reference of the existing object and create no new object. 
-		//   ** one time construction and no move/copy of object ** 
-		template<typename T, typename... Args>
-		T& emplaceObjectOrGet(const objectFile& objf, Args&&... args);
-
-		// - insert the object into repository and replace if it already exists (old object is destroyed) 
-		//   return a refernce to underlying data object, this reference never invalidated 
-		//   until it is deleted from repository.
-		//   ** one time construction and no move/copy of object ** 
-		template<typename T, typename... Args>
-		T& emplaceReplaceObject(const objectFile& objf, Args&&... args);
-		
-
-		// - Insert_or_replace the IOobejct into repository and change its ownership  
-		//   to this repository, take effect only if the object does not belong to 
-		//   any other repository
-		template<typename T>
-		T& insertReplaceObject(uniquePtr<IOobject>&& ptr );
-		
-
-		// - Insert_or_replace the IOobejct into repository with new objectFile and   
-		//   change the ownership to this repository, take effect only if the object
-		//   does not belong to any other repository
-		template<typename T>
-		T& insertReplaceObject(const objectFile& objf, uniquePtr<IOobject>&& ptr );
-		
-		// - rease an object from this repository
-		bool eraseObject(const word& name)
-		{
-			return objects_.erase(name) == 1;
-		}
-
 
+        repository* releaseOwner(bool fromOwner = false);
 	//// - lookups and queries
 	
 		// - check if name of object exists

src/phasicFlow/repository/repository/repositoryTemplates.cpp

@@ -17,22 +17,7 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-
+/*
-template <typename Type1>
-pFlow::word pFlow::repository::reportTypeError (IOobject& object)
-{
-	word err;
-	err = "The requested object " + object.name() + " with type " + Type1::TYPENAME() + ", while the type " +
-	  	object.typeName() + "is found in repository " + this->name();
-
-	return err;
-}
-
-template <typename Type>
-bool pFlow::repository::checkForObjectType(IOobject& object)
-{
-	return Type::TYPENAME() == object.typeName();
-}
 
 template<typename T, typename... Args>
 T& pFlow::repository::emplaceObject(const objectFile& objf, Args&&... args)
@@ -142,6 +127,25 @@ T& pFlow::repository::insertReplaceObject(const objectFile& objf, uniquePtr<IOob
 }
 
 
+*/
+
+template <typename Type1>
+pFlow::word pFlow::repository::reportTypeError(IOobject& object)
+{
+	word err;
+	err = "Object " + object.name() + " with type " + Type1::TYPENAME() + 
+    "is requested, while the type " +
+	  	object.typeName() + "is found in repository " + this->name()+".";
+
+	return err;
+}
+
+template <typename Type>
+bool pFlow::repository::checkForObjectType(IOobject& object)
+{
+	return Type::TYPENAME() == object.typeName();
+}
+
 template<typename T>
 T& pFlow::repository::lookupObject(const word& name)
 {
@@ -150,14 +154,15 @@ T& pFlow::repository::lookupObject(const word& name)
 
     	if( checkType<T>(iter->second) )
     	{
-    		return iter->second.template getObject<T>();
+    		return static_cast<T&>(iter->second);
+            
 
     	}else
     	{
     		fatalErrorInFunction << 
     		reportTypeError<T>(iter->second)<<endl;
     		fatalExit;
-    		return iter->second.template getObject<T>();
+    		return static_cast<T&>(iter->second);
     	}
         
     }

src/phasicFlow/repository/systemControl/Control.hpp

@@ -1,47 +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 __Control_hpp__
-#define __Control_hpp__
-
-
-// top-level entity repository for the whole application 
-// Each application that is executed in pFlow, should have 
-// settings/systemControl file in it. 
-// This  repository holds two main repositories: Time and settings 
-
-#include "systemControl.hpp"
-#include "timeFolder.hpp"
-
-namespace pFlow
-{
-
-
-inline systemControl& Control()
-{
-	static systemControl control_;
-	return control_;
-}
-
-} // pFlow
-
-
-#endif // __Control_hpp__

src/phasicFlow/repository/systemControl/systemControl.cpp

@@ -25,6 +25,24 @@ Licence:
 #include "systemControl.hpp"
 #include "vocabs.hpp"
 
+bool pFlow::systemControl::readDomainDict()
+{
+    if(!domainDict_)
+    {
+        domainDict_ = makeUnique<fileDictionary>
+        (
+            objectFile
+            (
+                domainFile__,
+                "",
+                objectFile::READ_ALWAYS,
+                objectFile::WRITE_NEVER
+            ),
+            &settings()
+        );
+    }
+    return true;
+}
 
 pFlow::word pFlow::systemControl::getRunName
 (
@@ -108,55 +126,58 @@ pFlow::systemControl::systemControl
 	(	
 		getTopFolder(path)
 	),
-	settings_
-	(
-		settingsRepository__,
-		settingsFolder__,
-		this
-	),
-	caseSetup_
-	(
-		caseSetupRepository__,
-		caseSetupFolder__,
-		this
-	),
     settingsDict_
 	(
-		settings().emplaceObject<fileDictionary>
+        makeUnique<fileDictionary>
         (
             objectFile
             (
                 settingsFile__,
-				"",
+                settingsFolder__,
                 objectFile::READ_ALWAYS,
-				objectFile::WRITE_NEVER,
+                objectFile::WRITE_NEVER
-                IOPattern::AllProcessorsSimilar
             ),
-			settingsFile__
+            this   
         )
     ),
-	libs_(settingsDict_),
-	outFilePrecision_(
-		settingsDict_.getValOrSet("outFilePrecision", static_cast<uint64>(6))
-		),
     Time_
 	(
 		this,
-		settingsDict_
+		settingsDict_()
 	),
-	g_(
+	settings_
-		settingsDict_.getVal<realx3>("g")
+    (
+        makeUnique<repository>
+        (
+            settingsRepository__,
+            settingsFolder__,
+            this
+        )
     ),
-	domain_(
+	caseSetup_
-		settingsDict_.subDict("domain")
+	(
+        makeUnique<repository>
+        (
+            caseSetupRepository__,
+            caseSetupFolder__,
+            this
+        )
+	),
+	
+	libs_(settingsDict_()),
+	outFilePrecision_
+    (
+		settingsDict_().getValOrSet("outFilePrecision", static_cast<uint64>(6))
 	),
 	timers_(runName_),
 	timersReport_
 	(
-		settingsDict_.getValOrSet("timersReport", Logical("Yes"))
+		settingsDict_().getValOrSet("timersReport", Logical("Yes"))
 	),
 	writeToFileTimer_("Write to file", &timers_)	
-{}
+{
+    readDomainDict();
+}
 
 pFlow::systemControl::systemControl(
 		const real startTime, 
@@ -179,71 +200,62 @@ pFlow::systemControl::systemControl(
 	(	
 		getTopFolder(path)
 	),
-	settings_
-	(
-		settingsRepository__,
-		settingsFolder__,
-		this
-	),
-	caseSetup_
-	(
-		caseSetupRepository__,
-		caseSetupFolder__,
-		this
-	),
     settingsDict_
 	(
-		settings().emplaceObject<fileDictionary>
+        makeUnique<fileDictionary>
         (
             objectFile
             (
                 settingsFile__,
-				"",
+                settingsFolder__,
                 objectFile::READ_ALWAYS,
                 objectFile::WRITE_NEVER
             ),
-			settingsFile__
+            this   
         )
     ),
-	libs_(settingsDict_),
     Time_
 	(
 		this,
-		settingsDict_,
+		settingsDict_(),
 		startTime, 
 		endTime, 
 		saveInterval, 
 		startTimeName
 	),
+	settings_
+    (
+        makeUnique<repository>
+        (
+            settingsRepository__,
+            settingsFolder__,
+            this
+        )
+    ),
+	caseSetup_
+	(
+        makeUnique<repository>
+        (
+            caseSetupRepository__,
+            caseSetupFolder__,
+            this
+        )
+	),
+	libs_(settingsDict_()),
 	externalTimeControl_(true),
-	g_(
-		settingsDict_.getVal<realx3>("g")
-	),
-	domain_(
-		settingsDict_.subDict("domain")
-	),
 	timers_(runName_),
 	timersReport_
 	(
-		settingsDict_.getValOrSet("timersReport", Logical("Yes"))
+		settingsDict_->getValOrSet("timersReport", Logical("Yes"))
 	),
 	writeToFileTimer_("Write to file", &timers_)	
-{}
+{
+    readDomainDict();
+}
 
 pFlow::fileDictionary& pFlow::systemControl::domainDict()
 {
-	return 
+    return domainDict_();
-	settings().emplaceObjectOrGet<fileDictionary>
-	(
-		objectFile
-		(
-			domainFile__,
-			"",
-			objectFile::READ_ALWAYS,
-			objectFile::WRITE_NEVER
-		),
-		domainFile__
-	);
 }
 
 bool pFlow::systemControl::operator ++(int)

src/phasicFlow/repository/systemControl/systemControl.hpp

@@ -50,16 +50,19 @@ protected:
 	// - path to top-level folder 
 	const fileSystem 	topLevelFolder_;
 
+    /// settingsDict fileDictionary
+	uniquePtr<fileDictionary> 	settingsDict_;
 
+    /// time repository
+    Time 			            Time_;
 
 	/// settings folder repository
-	repository 			settings_;
+	uniquePtr<repository> 		settings_;
 
 	/// caseSetup folder repository
-	repository 			caseSetup_;
+	uniquePtr<repository>       caseSetup_;
 
-	/// settingsDict fileDictionary
+    uniquePtr<fileDictionary>   domainDict_ = nullptr;
-	fileDictionary& 		settingsDict_;
 
 	/// extra libs to be loaded
 	dynamicLinkLibs 	        libs_;
@@ -67,19 +70,10 @@ protected:
 	/// precision for writing to file 
 	size_t 			outFilePrecision_ = 6;
 
-	/// time repository
-	Time 			Time_;
 
 	/// if time control is managed externaly
-
 	bool 			externalTimeControl_ = false;
 
-	// - acceleration 
-	realx3 			g_;
-
-	// - domain for dem world
-	box  			domain_;
-
 	// all timers
 	Timers 			timers_;
 
@@ -87,6 +81,8 @@ protected:
 
 	Timer 			writeToFileTimer_;
 
+    bool readDomainDict();
+
 	static word getRunName( const fileSystem& path);
 	
 	static word getTopFolder(const fileSystem& path);
@@ -104,25 +100,25 @@ public:
 		const fileSystem path = CWD() );
 
 	const repository& settings() const{
-		return settings_;
+		return settings_();
 	}
 
 	repository& settings(){
-		return settings_;
+		return settings_();
 	}
 
 	const repository& caseSetup()const{
-		return caseSetup_;
+		return caseSetup_();
 	}
 
 	repository& caseSetup(){
-		return caseSetup_;
+		return caseSetup_();
 	}
 
 	
 	const Time& time() const
 	{
-		return const_cast<Time&>(Time_);
+		return Time_;
 	}
 
 	Time& time()
@@ -156,11 +152,11 @@ public:
 	}
 
 	const fileDictionary& settingsDict()const{
-		return settingsDict_;
+		return settingsDict_();
 	}
 
 	fileDictionary& settingsDict(){
-		return settingsDict_;
+		return settingsDict_();
 	}
 
 	fileDictionary& domainDict();
@@ -171,14 +167,14 @@ public:
 		return runName_;
 	}
 
-	inline const realx3& g()const
+	inline const realx3 g()const
 	{
-		return g_;
+		return settingsDict_().getVal<realx3>("g");
 	}
 
-	inline const box& domain()const
+	inline box domain()
 	{
-		return domain_;
+		return box(domainDict().subDict("globalBox"));
 	}
 
 	bool operator ++(int);

src/phasicFlow/streams/dataIO/createDataIO.hpp

@@ -0,0 +1,35 @@
+#ifndef __createDataIO_hpp__
+#define __createDataIO_hpp__
+
+#include "uniquePtr.hpp"
+#include "dataIO.hpp"
+#include "dataIORegular.hpp"
+#include "dataIOMPI.hpp"
+
+namespace pFlow
+{
+
+template<typename T>
+uniquePtr<dataIO<T>> createDataIO(
+    const word& runType, const IOPattern& iop)
+{
+    if(runType == "regular")
+    {
+        return makeUnique<dataIORegular<T>>(iop);
+    }
+    else if(runType == "MPI")
+    {
+        return makeUnique<dataIOMPI<T>>(iop);
+    }
+    else
+    {
+        fatalErrorInFunction<< "not dataIO pattern is specified for this "<<
+        runType<<endl;
+        fatalExit;
+    }
+    return nullptr;
+}
+
+}
+
+#endif

src/phasicFlow/streams/dataIO/dataIO.cpp

@@ -1,34 +0,0 @@
-
-#include "dataIO.hpp"
-
-
-pFlow::uniquePtr<pFlow::dataIO> pFlow::dataIO::create
-(
-	IOPattern::IOType iotype, 
-	word exeMode
-)
-{
-	auto ioMode = angleBracketsNames("dataIO", exeMode);
-
-	if( wordvCtorSelector_.search(ioMode) )
-	{
-		auto objPtr = wordvCtorSelector_[ioMode] 
-			(
-				iotype,
-				exeMode
-			);
-		return objPtr;
-	}
-	else
-	{
-		printKeys
-		( 
-			fatalError << "Ctor Selector "<< Yellow_Text(ioMode) << " dose not exist. \n"
-			<<"Avaiable ones are: \n\n"
-			,
-			wordvCtorSelector_
-		);
-		fatalExit;
-	}
-	return nullptr;
-}

src/phasicFlow/streams/dataIO/dataIO.hpp

@@ -9,49 +9,37 @@
 #include "IOPattern.hpp"
 #include "iOstream.hpp"
 #include "iIstream.hpp"
-#include "virtualConstructor.hpp"
+
 
 
 namespace pFlow
 {
 
-class fileSystem;
+template<typename T>
-
-
 class dataIO
 {
-
-public:
-
-
-	static inline const uint64 ErrorReturn = static_cast<uint64>(-1);
-	
 protected:
 
 	IOPattern 	    ioPattern_;
 
-	word 		executionMode_;
+	std::vector<T> 	buffer_;
 
-	span<char> 			buffer_;
+    span<T>         bufferSpan_; 
 
-	template<typename T>
+
-	span<char> createSpan( span<T> sp )
+    /// gather data from all processors and put the results in buffer_
-	{
+	virtual bool gatherData(span<T> data) = 0;  
-		return span<char>( reinterpret_cast<char*>(sp.data()), sp.size()*sizeof(T) );
-	}
 
 public:
 
 	/// Type info
 	TypeInfo("dataIO");
 
-	dataIO(IOPattern::IOType iotype, word exeMode)
+	dataIO(const IOPattern& iop)
 	:
-	ioPattern_(iotype),
+	    ioPattern_(iop)
-	executionMode_(exeMode)
 	{}
 
-
 	dataIO(const dataIO&) = default;
 
 	dataIO(dataIO &&) = default;
@@ -62,199 +50,24 @@ public:
 
 	virtual ~dataIO() = default;
 
-	create_vCtor
-	(
-		dataIO,
-		word,
-		(
-			IOPattern::IOType iotype, 
-			word exeMode
-		),
-		(iotype, exeMode)
-	);
-
-	/// Gather data from all processors and put the results in 
-	/// buffer_
-	virtual bool gatherData(span<char> sp ) = 0;
-
 	/// Write data to the end of file from all processors.
 	/// This method should be called from all processors. 
-	template<typename T>
 	bool writeData(iOstream& os, span<T> data);
 
-	template<typename T>
+	bool readData(
-	bool readData(iIstream& is, std::vector<T>& data);
+        iIstream& is, 
+        std::vector<T>& data);
 
-	template<typename T>
 	bool readAscii(
 		iIstream& is,
 		std::vector<T>& vec	);
 
-	static
-	uniquePtr<dataIO> create(IOPattern::IOType iotype, word exeMode);
-
-
 };
 	
 
-template<>
-inline 
-bool dataIO::writeData<word>(iOstream& os, span<word> data)
-{
-	/*std::ostringstream ist();
-
-	for(auto i=0; i<data.size(); i++)
-	{
-		ist<< data[i]<<std::endl;
-	}
-
-	span<char> sp(ist.str().data(), ist.str().size());
-
-	if(!gatherData( sp) )
-	{
-		fatalErrorInFunction<<
-		"Error in gathering data for out stream "<< os.name()<<endl;
-		return false;
-	}
-
-	uint64 len = buffer_.size();
-	os<< len << endl;
-
-	if(!os.write(buffer_.data(), buffer_.size()))
-	{
-		fatalErrorInFunction<<
-    	"error in writing binary data to "<<os.name()<<endl;
-    	return false;
-	}*/
-
-	if( !data.writeASCII(os) )
-    {
-    	fatalErrorInFunction<<
-    	"error in writing ASCII data to "<<os.name()<<endl;
-    	return false;
-    }
-
-	return true;
-}
 
 }
 
 #include "dataIOTemplate.cpp"
 
 #endif
-
-
-
-/*bool writeDataToFileEndSTD(
-		const word& wordPath, 
-		const span<unsigned char>& data);
-
-	bool writeDataToFileEndMPI(
-		const word& wordPath, 
-		const span<unsigned char>& data);
-	
-	bool readDataSTD(
-		const word& wordPath,
-		const std::vector<uint64> chunkSizes,
-		span<unsigned char>& data,
-		uint64 binaryBlockStart);
-	
-	bool readDataMPI(
-		const word& wordPath, 
-		const std::vector<uint64> chunkSizes,
-		span<unsigned char>& data,
-		uint64 binaryBlockStart);
-
-	bool readMetaMPI(
-		const word& wordPath, 
-		std::vector<uint64>& chunkSizes,
-		uint64 startPosSearch,
-		uint64 &startPosBinaryBlock);
-
-	bool readMetaSTD(
-		const word& wordPath, 
-		std::vector<uint64>& chunkSizes,
-		uint64 startPosSearch,
-		uint64 &startPosBinaryBlock);
-
-	bool waitForAllMPI();
-
-	bool maxReduction( uint64& src, uint64& dst);
-
-	bool BcastPos(uint64 & pos);
-
-public:
-
-	dataIO(IOPattern::IOType iotype)
-	:
-		ioPattern_(iotype)
-	{}
-
-	~dataIO()=default;
-
-	template<typename T> 
-	bool writeDataEnd(
-		const word& wordPath,
-		const span<T>& data);
-
-	template<typename T>
-	bool writeAsciiEnd(
-		iOstream& os,
-		const span<T>& data);
-
-	template<typename T>
-	bool readDataBinary(
-		const word& wordPath, 
-		std::vector<T>& data,
-		uint64 startPos = 0);
-
-	template<typename T>
-	bool readAscii(
-		iIstream& is,
-		std::vector<T>& vec	);
-
-	template<typename T>
-	bool readData(
-		iIstream& is, 
-		std::vector<T>& vec,
-		bool resume = false); // resume only works for binary
-							  // for ascii, by default it starts from the current position
-
-
-	template<typename T>
-	bool writeData(iOstream& os,
-		const span<T>& data);
-
-	
-};
-
-template<>
-inline
-bool pFlow::dataIO::writeData<pFlow::word>
-(
-	iOstream& os,
-	const span<word>& data
-)
-{
-	if( !writeAsciiEnd(os, data) )
-    {
-        fatalErrorInFunction;
-        return false;
-    }
-	return true;	
-}
-
-template<>
-inline
-bool pFlow::dataIO::readData<pFlow::word>(
-	iIstream& is, 
-	std::vector<word>& vec,
-	bool resume)
-{
-	if(!readAscii(is, vec))
-	{
-		fatalErrorInFunction;
-		return false;
-	}
-	return true;
-}*/

src/phasicFlow/streams/dataIO/dataIONoMPI.cpp

@@ -1,20 +0,0 @@
-
-#include "dataIONoMPI.hpp"
-
-
-pFlow::dataIONoMPI::dataIONoMPI
-(
-	IOPattern::IOType iotype,
-	word exeMode
-)
-:
-	dataIO(iotype, exeMode)
-{}
-
-
-bool pFlow::dataIONoMPI::gatherData( span<char> sp )
-{
-	/// in serial mode, no gathering is required. 
-	buffer_ = sp;
-	return true;
-}

src/phasicFlow/streams/dataIO/dataIONoMPI.hpp

@@ -1,48 +0,0 @@
-#ifndef __datIONoMPI_hpp__
-#define __datIONoMPI_hpp__
-
-#include "dataIO.hpp"
-
-namespace pFlow
-{
-
-
-class dataIONoMPI
-:
-	public dataIO
-{
-protected:
-
-public:
-
-	TypeInfo("dataIO<NoMPI>");
-
-	dataIONoMPI(IOPattern::IOType iotype, word exeMode);
-
-	dataIONoMPI(const dataIONoMPI&) = default;
-
-	dataIONoMPI(dataIONoMPI&&) = default;
-
-
-	dataIONoMPI& operator=(const dataIONoMPI&) = default;
-
-	dataIONoMPI& operator=(dataIONoMPI&&) = default;
-
-	~dataIONoMPI() = default;
-
-	add_vCtor
-	(
-		dataIO,
-		dataIONoMPI,
-		word
-	);
-
-	bool gatherData(span<char> sp ) override;
-	
-};
-
-
-}
-
-
-#endif

src/phasicFlow/streams/dataIO/dataIORegular.hpp

@@ -0,0 +1,47 @@
+#ifndef __datIONoMPI_hpp__
+#define __datIONoMPI_hpp__
+
+#include "dataIO.hpp"
+
+namespace pFlow
+{
+template<typename T>
+class dataIORegular
+:
+	public dataIO<T>
+{
+protected:
+
+    bool gatherData(span<T> data ) override
+    {
+        /// in serial mode, no gathering is required. 
+        this->bufferSpan_ = data;
+        return true;
+    }
+
+public:
+
+	TypeInfo("dataIO<regular>");
+
+	dataIORegular(const IOPattern& iop)
+    :
+	    dataIO<T>(iop)
+    {}
+
+	dataIORegular(const dataIORegular&) = default;
+
+	dataIORegular(dataIORegular&&) = default;
+
+	dataIORegular& operator=(const dataIORegular&) = default;
+
+	dataIORegular& operator=(dataIORegular&&) = default;
+
+	~dataIORegular() = default;
+	
+};
+
+
+}
+
+
+#endif

src/phasicFlow/streams/dataIO/dataIOTemplate.cpp

@@ -1,9 +1,9 @@
 
 template<typename T>
-bool pFlow::dataIO::writeData(iOstream& os, span<T> data)
+bool pFlow::dataIO<T>::writeData(iOstream& os, span<T> data)
 {
 	/// first gather data from all processors (if any)
-	if(!gatherData( createSpan(data) ) )
+	if(!gatherData( data ) )
 	{
 		fatalErrorInFunction<<
 		"Error in gathering data for out stream "<< os.name()<<endl;
@@ -14,11 +14,14 @@ bool pFlow::dataIO::writeData(iOstream& os, span<T> data)
 	{
 		if( os.isBinary() )
 		{
-			// first write the size of data 		    
+			// first write the number of data
-			uint64 len = buffer_.size()/sizeof(T);
+			uint64 numData = bufferSpan_.size();
-			os<< len << endl;
+			os<< numData << endl;
 
-			if(!os.write(buffer_.data(), buffer_.size()))
+            // write the bindary data
+            auto chBuffer = charSpan(bufferSpan_);
+
+			if(!os.write(chBuffer.data(), chBuffer.size()))
 			{
 				fatalErrorInFunction<<
 		    	"error in writing binary data to "<<os.name()<<endl;
@@ -28,13 +31,7 @@ bool pFlow::dataIO::writeData(iOstream& os, span<T> data)
 		}
 		else
 		{
-
+		    if( !bufferSpan_.writeASCII(os) )
-			/// cast the data into T
-			span<T> allData( 
-				reinterpret_cast<T*>(buffer_.data()), 
-				buffer_.size()/sizeof(T));
-		    
-		    if( !allData.writeASCII(os) )
 		    {
 		    	fatalErrorInFunction<<
 		    	"error in writing ASCII data to "<<os.name()<<endl;
@@ -50,20 +47,44 @@ bool pFlow::dataIO::writeData(iOstream& os, span<T> data)
 	}
 }
 
+template<>
+inline
+bool pFlow::dataIO<pFlow::word>::writeData(iOstream& os, span<word> data)
+{
+    notImplementedFunction;
+    fatalExit;
+    /// first gather data from all processors (if any)
+	if(!gatherData( data ) )
+	{
+		fatalErrorInFunction<<
+		"Error in gathering data for out stream "<< os.name()<<endl;
+		return false;
+	}
+
+	if( !bufferSpan_.writeASCII(os) )
+    {
+    	fatalErrorInFunction<<
+    	"error in writing ASCII data to "<<os.name()<<endl;
+    	return false;
+    }
+
+	return true;
+}
+
+
 template<typename T>
-bool pFlow::dataIO::readData
+bool pFlow::dataIO<T>::readData
 (
 	iIstream& is, 
 	std::vector<T>& data
 )
 {
-	
 	data.clear();
-
 	if(ioPattern_.thisProcReadData())
 	{
 		if(is.isBinary())
 		{
+            
 			// read length of data 			
 			token firstToken(is);
 			
@@ -98,7 +119,7 @@ bool pFlow::dataIO::readData
 }
 
 template<typename T>
-bool pFlow::dataIO::readAscii
+bool pFlow::dataIO<T>::readAscii
 (
 	iIstream& is,
 	std::vector<T>& vec
@@ -107,7 +128,6 @@ bool pFlow::dataIO::readAscii
 
 	if( !ioPattern_.thisProcReadData() ) return true;
 	
-
 	is.fatalCheck(FUNCTION_NAME);
 
 	vec.clear();
@@ -161,331 +181,10 @@ bool pFlow::dataIO::readAscii
 	
 	if(len>0&& len != vec.size())
 	{
-		warningInFunction<<"vector lendth specified "<< len << 
+		warningInFunction<<"vector length specified "<< len << 
 		" is different from number of elements "<< vec.size()<<endl;
 		return false;
 	}
 
 	return true;
 }
-
-/*template<typename T>
-bool pFlow::dataIO::writeDataEnd(
-	const word& wordPath,
-	const span<T>& data)
-{
-
-	if( ioPattern_.thisProcWriteData() )
-	{
-		span<unsigned char> charSpan(
-		reinterpret_cast<unsigned char*> (const_cast<T*>(data.data())),
-		data.size()*sizeof(T));
-
-		if( ioPattern_.isParallel() )
-		{
-			return writeDataToFileEndMPI(wordPath, charSpan);
-		}
-		else
-		{
-			return writeDataToFileEndSTD(wordPath, charSpan);
-		}
-	}
-	else
-	{
-		return true;
-	}
-
-	return false;
-}
-
-template<typename T>
-bool pFlow::dataIO::writeAsciiEnd
-(
-	iOstream& os,
-	const span<T>& data
-)
-{
-	if(ioPattern_.thisProcWriteData())
-	{
-		return data.writeASCII(os);
-	}
-	else
-		return true;
-}
-
-
-
-template<typename T>
-bool pFlow::dataIO::readDataBinary
-(
-	const word& wordPath, 
-	std::vector<T>& data,
-	uint64 startPos
-)
-{
-
-	std::vector<uint64> chunkSizes;
-	uint64 startPosBinaryBlock;
-
-	data.clear();
-	
-	if( ioPattern_.thisProcReadData())
-	{
-		
-		// read meta 
-		if(!readMetaSTD(
-				wordPath, 
-				chunkSizes, 
-				startPos,
-				startPosBinaryBlock))
-		{
-			fatalErrorInFunction;
-			return false;
-		}
-		
-		
-		if( ioPattern_.isMasterProcessor()  ||
-			ioPattern_.isAllProcessorSimilar()
-		)
-		{
-
-			auto sizeOfData = std::accumulate( 
-			chunkSizes.begin(), 
-			chunkSizes.end(),
-			static_cast<uint64>(0));
-			
-			
-			data.resize(sizeOfData/sizeof(T));
-
-			span<unsigned char> charSpan(
-				reinterpret_cast<unsigned char*>(data.data()),
-				data.size()*sizeof(T));
-
-			if(!readDataSTD(wordPath, chunkSizes, charSpan, startPosBinaryBlock))
-			{
-				fatalErrorInFunction;
-				return false;
-			}
-
-			return true;
-
-		}
-		else if( ioPattern_.isAllProcessorDifferent() )
-		{
-
-			if(chunkSizes.size() != ioPattern_.globalSize())
-			{
-				if( ioPattern_.isMaster())
-				{
-					auto sizeOfData = std::accumulate( 
-					chunkSizes.begin(), 
-					chunkSizes.end(),
-					static_cast<uint64>(0));
-					
-					
-					data.resize(sizeOfData/sizeof(T));
-
-					span<unsigned char> charSpan(
-						reinterpret_cast<unsigned char*>(data.data()),
-						data.size()*sizeof(T));
-
-					if(!readDataSTD(wordPath, chunkSizes, charSpan, startPosBinaryBlock))
-					{
-						fatalErrorInFunction;
-						return false;
-					}
-					return true;
-
-				}
-				else
-				{
-					return true;
-				}
-			}
-			else
-			{
-				auto thisProc = ioPattern_.globalRank();
-
-				data.resize(chunkSizes[thisProc]/sizeof(T));
-
-				span<unsigned char> charSpan(
-					reinterpret_cast<unsigned char*>(data.data()),
-					data.size()*sizeof(T));
-
-				
-				if( !readDataMPI(wordPath, chunkSizes, charSpan, startPosBinaryBlock) )
-				{
-					fatalErrorInFunction;
-					return false;
-				}
-				return true;	
-			}
-
-			
-		}
-		else
-		{
-			fatalErrorInFunction;
-			return false;	
-		}
-	}
-	else
-	{
-		return true;
-	}
-
-	return false;
-		
-	
-}
-
-template<typename T>
-bool pFlow::dataIO::readAscii
-(
-	iIstream& is,
-	std::vector<T>& vec
-)
-{
-
-	if( !ioPattern_.thisProcReadData() ) return true;
-	
-
-	is.fatalCheck(FUNCTION_NAME);
-
-	vec.clear();
-	
-	token firstToken(is);
-
-	size_t len = 0;
-	if( firstToken.isInt64())
-	{
-		len = firstToken.int64Token();
-		vec.reserve(len);
-		firstToken  = token(is);
-	}
-
-	T val{};
-	if( firstToken.isPunctuation() ) // start of vector 
-	{
-		if(firstToken != token::BEGIN_LIST)
-		{
-			warningInFunction
-			<< "expected token "<< token::BEGIN_LIST 
-			<< " but found "<< firstToken ;
-			return false;
-
-		}
-
-		token lastToken(is);
-		
-		is.fatalCheck(FUNCTION_NAME);
-		
-		while(!(lastToken.isPunctuation()
-             	&& lastToken == token::END_LIST ))
-		{
-
-			is.putBack(lastToken);
-			
-			is >> val;
-			vec.push_back(val);
-			
-			is >> lastToken;
-			is.fatalCheck(FUNCTION_NAME);
-		}
-
-	} else
-	{
-		warningInFunction
-		<< "expected token "<< token::BEGIN_LIST 
-		<< " but found "<< firstToken<<endl; ;
-		return false;
-	}
-	
-	if(len>0&& len != vec.size())
-	{
-		warningInFunction<<"vector lendth specified "<< len << 
-		" is different from number of elements "<< vec.size()<<endl;
-		return false;
-	}
-
-	return true;
-}
-
-template<typename T>
-bool pFlow::dataIO::readData
-(
-	iIstream& is, 
-	std::vector<T>& vec,
-	bool resume
-)
-{
-	if(is.isBinary())
-	{
-		uint64 currPos = 0;
-		if( resume )
-		{
-			currPos = is.tell();
-		}
-
-		if(! BcastPos(currPos) ) return false;
-		
-		if(!this->readDataBinary(is.name(), vec, currPos))
-		{
-			fatalErrorInFunction;
-			return false;
-		}
-
-		auto lastPos = lastPosRead_;
-		maxReduction( lastPos, lastPosRead_);
-		//std::cout<<"last post read "<< lastPosRead_<<std::endl;
-		
-		/// set the stream indicator to the last position 
-		is.seek(lastPosRead_);
-		
-		return true;
-	}
-	else
-	{
-		if(!readAscii(is, vec))
-		{
-			fatalErrorInFunction;
-			return false;
-		}
-		return true;
-	}
-}
-
-template<typename T>
-bool pFlow::dataIO::writeData
-(
-	iOstream& os,
-	const span<T>& sp
-)
-{
-	if( os.isBinary() )
-	{
-	    os.startOfBinaryStreaming();
-
-	    if(!writeDataEnd(os.name(), sp))
-	    {
-	        fatalErrorInFunction;
-	        return false;
-	    }
-
-	    os.endOfBinaryStreaming();
-
-	}
-	else
-	{
-	    if( !writeAsciiEnd(os, sp) )
-	    {
-	        fatalErrorInFunction;
-	        return false;
-	    }
-	}
-	return true; 
-
-}*/
-
-
-

src/phasicFlow/structuredData/box/box.hpp

@@ -97,6 +97,18 @@ public:
 			return max_;
 		}
 
+        INLINE_FUNCTION_HD
+        realx3& minPoint()
+        {
+            return min_;
+        }
+
+        INLINE_FUNCTION_HD
+        realx3& maxPoint()
+        {
+            return max_;
+        }
+
 	//// - IO operation 
 		FUNCTION_H
 		bool read(iIstream & is);

src/phasicFlow/structuredData/domain/domain.cpp

@@ -57,3 +57,24 @@ pFlow::domain::domain(const box& db)
 {
 
 }
+
+
+FUNCTION_H
+pFlow::iIstream& pFlow::operator >>(
+    pFlow::iIstream& is, 
+    pFlow::domain& d)
+{
+    box b;
+    is>>b; 
+    d = domain(b);
+    return is;
+}
+
+FUNCTION_H
+pFlow::iOstream& pFlow::operator << (
+    pFlow::iOstream& os, 
+    const pFlow::domain& d)
+{
+    os<< d.domainBox();
+    return os;
+}

src/phasicFlow/structuredData/domain/domain.hpp

@@ -156,17 +156,12 @@ bool operator ==(const domain& d1, const domain& d2)
 	return equal(d1, d2);
 }
 
-/*FUNCTION_H
+FUNCTION_H
-iIstream& operator >>(iIstream& is, box& b);
+iIstream& operator >>(iIstream& is, domain& d);
 
 FUNCTION_H
-iOstream& operator << (iOstream& os, const box& b);
+iOstream& operator << (iOstream& os, const domain& d);
 
-INLINE_FUNCTION_HD
-box extendBox(const box& b, const realx3& dl)
-{
-	return box(b.minPoint()-dl , b.maxPoint()+dl);
-}*/
 
 }
 

src/phasicFlow/structuredData/domain/regularSimulationDomain.cpp

@@ -50,37 +50,52 @@ bool pFlow::regularSimulationDomain::setThisDomain()
     return true;
 }
 
-pFlow::regularSimulationDomain::regularSimulationDomain(
+pFlow::regularSimulationDomain::regularSimulationDomain
-    const dictionary &dict)
-    : simulationDomain(dict)
-{
-}
-
-bool pFlow::regularSimulationDomain::updateDomains
 (
-	const realx3Vector& pointPos
+    const dictionary &dict
 )
-{
+:
-	thisNumPoints_ = pointPos.size();
+    simulationDomain(dict)
-	if(!createBoundaryDicts()) return false;
+{}
-	if(!setThisDomain()) return false;
 
+bool pFlow::regularSimulationDomain::initialUpdateDomains(span<realx3> pointPos)
+{
+    initialNumPoints_ = pointPos.size();
+    if(!setThisDomain()) return false;
+    if(!createBoundaryDicts()) return false;
     return true;
 }
 
-pFlow::uint32 pFlow::regularSimulationDomain::thisNumPoints() const
+pFlow::uint32 pFlow::regularSimulationDomain::initialNumberInThis() const
 {
-	return thisNumPoints_;	
+    return initialNumPoints_;
 }
 
-bool pFlow::regularSimulationDomain::transferBlockData
+/*bool pFlow::regularSimulationDomain::updateDomains(
+    span<realx3> pointPos,
+    pFlagTypeHost flags)
+{	
+    return true;
+}*/
+
+pFlow::uint32 pFlow::regularSimulationDomain::numberToBeImported() const
+{
+	return 0;	
+}
+
+pFlow::uint32 pFlow::regularSimulationDomain::numberToBeExported() const
+{
+    return 0;
+}
+
+bool pFlow::regularSimulationDomain::initialTransferBlockData
 (
 	span<char> src, 
 	span<char> dst,
-	uint32 sizeOfBlock
+	size_t sizeOfElement
 )
 {
-	size_t requiredSize = sizeOfBlock*thisNumPoints();
+	size_t requiredSize = sizeOfElement*initialNumberInThis();
 	if(dst.size() < requiredSize)
 	{
 		fatalErrorInFunction<< 
@@ -103,6 +118,54 @@ bool pFlow::regularSimulationDomain::transferBlockData
     return true;
 }
 
+bool pFlow::regularSimulationDomain::initialTransferBlockData
+(
+    span<realx3> src, 
+    span<realx3> dst
+)
+{
+    return initialTransferBlockData(
+        charSpan(src), 
+        charSpan(dst), 
+        sizeof(realx3)); 
+}
+
+bool pFlow::regularSimulationDomain::initialTransferBlockData
+(
+    span<real> src, 
+    span<real> dst
+)
+{
+    return initialTransferBlockData(
+        charSpan(src), 
+        charSpan(dst), 
+        sizeof(real)); 
+}
+
+bool pFlow::regularSimulationDomain::initialTransferBlockData
+(
+    span<uint32> src, 
+    span<uint32> dst
+)
+{
+    return initialTransferBlockData(
+        charSpan(src), 
+        charSpan(dst), 
+        sizeof(uint32)); 
+}
+
+bool pFlow::regularSimulationDomain::initialTransferBlockData
+(
+    span<int32> src, 
+    span<int32> dst
+)
+{
+    return initialTransferBlockData(
+        charSpan(src), 
+        charSpan(dst), 
+        sizeof(int32)); 
+}
+
 const pFlow::dictionary &pFlow::regularSimulationDomain::thisBoundaryDict() const
 {
     return globalDomainDict_.subDict("regularSimulationDomainBoundaries");

src/phasicFlow/structuredData/domain/regularSimulationDomain.hpp

@@ -13,7 +13,7 @@ class regularSimulationDomain
 {
 protected:
 
-	uint32 		thisNumPoints_=0;
+	uint32 		initialNumPoints_=0;
 
 	bool createBoundaryDicts() override;
 
@@ -35,16 +35,44 @@ public:
 		dictionary
 	);
 
-	bool updateDomains( 
+    bool initialUpdateDomains(span<realx3> pointPos) override;
-		const realx3Vector& pointPos)override;
 
-	uint32 thisNumPoints()const override;
+    uint32 initialNumberInThis()const override;
 
+	/*bool updateDomains(
+		span<realx3> pointPos,
+        pFlagTypeHost flags) override;*/
    
-	bool transferBlockData(
+	uint32 numberToBeImported()const override;
+
+	uint32 numberToBeExported()const override;
+
+	bool initialTransferBlockData(
 		span<char> src, 
 		span<char> dst,
-		uint32 sizeOfBlock) override;
+		size_t sizeOfElement) override;
+
+
+    /// @brief 
+    /// @param src 
+    /// @param dst 
+    /// @return 
+    bool initialTransferBlockData(
+        span<realx3> src,
+        span<realx3> dst) override;
+
+    bool initialTransferBlockData(
+        span<real> src,
+        span<real> dst) override;
+
+    bool initialTransferBlockData(
+        span<uint32> src,
+        span<uint32> dst) override;
+
+    bool initialTransferBlockData(
+        span<int32> src,
+        span<int32> dst) override;
+    
 	
 	const dictionary& thisBoundaryDict()const override;
 

src/phasicFlow/structuredData/domain/simulationDomain.cpp

@@ -19,7 +19,7 @@ Licence:
 -----------------------------------------------------------------------------*/
 
 #include "simulationDomain.hpp"
-#include "processors.hpp"
+#include "pFlowProcessors.hpp"
 
 pFlow::simulationDomain::simulationDomain(const dictionary& dict)
 :
@@ -32,10 +32,10 @@ pFlow::simulationDomain::simulationDomain(const dictionary& dict)
 pFlow::uniquePtr<pFlow::simulationDomain> 
     pFlow::simulationDomain::create(const dictionary &dict)
 {
-    
 	word sType = angleBracketsNames(
         "simulationDomain", 
-        processors::runTypeName());
+        pFlowProcessors().localRunTypeName());
+
 
 	if( dictionaryvCtorSelector_.search(sType) )
 	{

src/phasicFlow/structuredData/domain/simulationDomain.hpp

@@ -17,19 +17,22 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-
 #ifndef __simulationDomain_hpp__
 #define __simulationDomain_hpp__
 
-#include "domain.hpp"
+#include <array>
-#include "virtualConstructor.hpp"
-#include "Vectors.hpp"
 
+#include "domain.hpp"
+#include "span.hpp"
 #include "streams.hpp"
+#include "virtualConstructor.hpp"
+#include "pointFlag.hpp"
 
 namespace pFlow
 {
 
+//class pFlagTypeHost;
+
 class simulationDomain
 {
 private:
@@ -84,23 +87,64 @@ public:
 	virtual 
 	const dictionary& thisBoundaryDict()const = 0;
 	
+    virtual 
+    bool initialUpdateDomains(span<realx3> pointPos) = 0;
 
     virtual
-	bool updateDomains(
+    uint32 initialNumberInThis()const = 0;
-		const realx3Vector& pointPos) = 0;
-
-	//virtual getImportExportList() = 0;
-
-	//virtual getNumberInThisList() = 0;
 
     virtual 
-	uint32 thisNumPoints()const = 0;
+	bool initialTransferBlockData(
-
-	virtual 
-	bool transferBlockData(
 		span<char> src, 
 		span<char> dst,
-		uint32 sizeOfBlock) = 0;
+		size_t sizeOfElement) = 0;
+    
+    virtual 
+    bool initialTransferBlockData(
+        span<realx3> src,
+        span<realx3> dst) = 0;
+    
+    virtual
+    bool initialTransferBlockData(
+        span<real> src,
+        span<real> dst) = 0;
+
+    virtual
+    bool initialTransferBlockData(
+        span<uint32> src,
+        span<uint32> dst) = 0;
+    
+    virtual 
+    bool initialTransferBlockData(
+        span<int32> src,
+        span<int32> dst) = 0;
+    
+    
+    /*template<typename T>
+    bool initialTransferBlockData(
+        span<T> src,
+        span<T> dst )
+    {
+        size_t el=sizeof(T);
+        return initialTransferBlockData
+        (
+            charSpan(src), 
+            charSpan(dst), 
+            el
+        );
+    }*/  
+
+
+
+    /// @brief Number of points to be imported after updating domains 
+	/// @return number of points
+	virtual
+	uint32 numberToBeImported()const = 0;
+
+    virtual 
+    uint32 numberToBeExported()const = 0;
+
+	
 
 	virtual 
 	bool requiresDataTransfer() const = 0;

src/phasicFlow/structuredData/infinitePlane/infinitePlane.hpp

@@ -137,6 +137,33 @@ public:
 			return t*normal_ + p;
 		}
 
+        INLINE_FUNCTION_HD
+        bool parallel(const infinitePlane& pln)const
+        {
+            return  equal(normal_, pln.normal_) ||
+                    equal(normal_,-pln.normal_);
+        }
+
+        INLINE_FUNCTION_HD
+        bool parallelTouch(const infinitePlane& pln)const
+        {
+            if(equal(normal_, pln.normal_) && equal(d_, pln.d_))return true;
+            if(equal(normal_,-pln.normal_) && equal(d_,-pln.d_))return true;
+            return false;
+        }
+
+        INLINE_FUNCTION_HD
+        const auto& normal()const
+        {
+            return normal_;
+        }
+
+        INLINE_FUNCTION_HD
+        const auto& d()const
+        {
+            return d_;
+        }
+
 	//// - IO operation 
 
 		FUNCTION_H

src/phasicFlow/structuredData/plane/plane.cpp

@@ -54,13 +54,11 @@ pFlow::plane pFlow::plane::parallelPlane(real distance)const
 	return plane(pp1, pp2, pp3, pp4);
 }
 
-bool pFlow::plane::validPlane4
+bool pFlow::plane::validPlane4(
-(
     const realx3 &p1,
     const realx3 &p2,
     const realx3 &p3,
-	const realx3& p4
+    const realx3 &p4)
-)
 {
 	if( !validPlane3(p1,p2,p3)) return false;
 	if( !infinitePlane(p1,p2,p3).pointOnPlane(p4)) return false;

src/phasicFlow/structuredData/plane/plane.hpp

@@ -122,6 +122,7 @@ public:
 	// return the parallel plane to this plane 
 	plane parallelPlane(real distance)const;
 
+
 	static 
 	bool validPlane4(
 		const realx3& p1, 

src/phasicFlow/structuredData/pointStructure/internalPoints.cpp

@@ -173,20 +173,48 @@ pFlow::internalPoints::internalPoints
 }
 
 
-const pFlow::internalPoints::pFlagTypeDevice& 
+const pFlow::pFlagTypeDevice& 
 	pFlow::internalPoints::activePointsMaskD() const 
 {
 	return pFlagsD_;
 }
 
 
-const pFlow::internalPoints::pFlagTypeHost&
+const pFlow::pFlagTypeHost&
 	pFlow::internalPoints::activePointsMaskH() const
 {
 	syncPFlag();
 	return pFlagsH_;
 }
 
+FUNCTION_H
+const pFlow::realx3Field_D& 
+    pFlow::internalPoints::pointPosition()const
+{
+    return pointPosition_;
+}
+
+pFlow::hostViewType1D<pFlow::realx3> 
+    pFlow::internalPoints::activePointsHost() const
+{
+    auto maskH = activePointsMaskH();
+    auto pointsH = pointPositionHost();
+
+    hostViewType1D<realx3> aPoints("Active pointst", maskH.numActive());
+    auto aRange = maskH.activeRange();
+    uint32 n = 0;
+    for(auto i=aRange.start(); i<aRange.end(); i++)
+    {
+        if( maskH.isActive(i) )
+        {
+            aPoints[n] = pointsH[i];
+            n++;
+        }
+    }
+
+    return aPoints;
+}
+
 FUNCTION_H
 pFlow::realx3Field_D &pFlow::internalPoints::pointPosition()
 {
@@ -218,13 +246,13 @@ FUNCTION_H
 bool pFlow::internalPoints::read
 (
 	iIstream& is, 
-	IOPattern::IOType iotype
+	const IOPattern& iop
 )
 {
 	
 	Field<Vector, realx3 , vecAllocator<realx3>> fRead("internalPoints", "internalPoints");
 
-	if( !fRead.read(is, iotype))
+	if( !fRead.read(is, iop))
 	{
 		fatalErrorInFunction<<
 		"Error in reading pointPosition from stream "<< is.name()<<endl;
@@ -249,16 +277,16 @@ FUNCTION_H
 bool pFlow::internalPoints::write
 (
 	iOstream& os, 
-	IOPattern::IOType iotype
+	const IOPattern& iop
 )const
 {
 	if( pFlagsD_.isAllActive())
 	{
-		return pointPosition_.write(os, iotype);
+		return pointPosition_.write(os, iop);
 	}
 	else
 	{
-		return pointPosition_.write(os, iotype, activePointsMaskH());
+		return pointPosition_.write(os, iop, activePointsMaskH());
 	}
 }
 

src/phasicFlow/structuredData/pointStructure/internalPoints.hpp

@@ -47,11 +47,6 @@ public:
 
 	using execution_space 	= typename pointsType::execution_space;
 
-	using pFlagTypeDevice 	= pointFlag<execution_space>;
-
-	using pFlagTypeHost 	= pointFlag<DefaultHostExecutionSpace>;
-
-
 protected:
 
 	//// - data members
@@ -120,11 +115,19 @@ public:
 		FUNCTION_H
         realx3Field_D& pointPosition();
 
-		/*INLINE_FUNCTION_H
+        INLINE_FUNCTION_H
-		auto pointPositionHostAll()
+        auto pointPositionHost()const
         {
-			return pointPosition_.hostVectorAll();
+            return pointPosition_.hostVector();
-		}*/
+        }
+
+        INLINE_FUNCTION_H
+        auto pointPositionDevice()const
+        {
+            return pointPosition_.deviceVector();
+        }
+
+		hostViewType1D<realx3> activePointsHost()const;
 
 		// - size of data structure
 		INLINE_FUNCTION_H
@@ -216,12 +219,12 @@ public:
 		
 		/// Read 
 		FUNCTION_H
-		bool read(iIstream& is, IOPattern::IOType iotype);
+		bool read(iIstream& is, const IOPattern& iop);
 		
 
 		/// Write 
 		FUNCTION_H
-		bool write(iOstream& os, IOPattern::IOType iotype)const;	
+		bool write(iOstream& os, const IOPattern& iop)const;	
 
 };
 

src/phasicFlow/structuredData/pointStructure/pointFlag.hpp

@@ -244,6 +244,9 @@ public:
 
 };
 
+using pFlagTypeDevice 	= pointFlag<DefaultExecutionSpace>;
+
+using pFlagTypeHost 	= pointFlag<DefaultHostExecutionSpace>;
 
 }
 

src/phasicFlow/structuredData/pointStructure/pointFlagKernels.hpp

@@ -258,8 +258,6 @@ void pFlow::pointFlag<ExecutionSpace>::fillNeighborsLists
 			});
 		Kokkos::fence();	
 	}
-	
-
 }
 
 template<typename ExecutionSpace>

src/phasicFlow/structuredData/pointStructure/pointStructure.cpp

@@ -1,3 +1,4 @@
+
 /*------------------------------- phasicFlow ---------------------------------
       O        C enter of
      O O       E ngineering and
@@ -19,53 +20,61 @@ Licence:
 -----------------------------------------------------------------------------*/
 
 #include "pointStructure.hpp"
-#include "simulationDomain.hpp"
+#include "systemControl.hpp"
+#include "vocabs.hpp"
 
-#include "streams.hpp"
 
-bool pFlow::pointStructure::distributePoints
+bool pFlow::pointStructure::setupPointStructure(const realx3Vector &points)
-(
-	const realx3Vector &points
-)
 {
-	uint32 thisN = simulationDomain_->thisNumPoints();
+    if(!simulationDomain_->initialUpdateDomains(points.getSpan()))
+    {
+        fatalErrorInFunction<<
+        "error in updating domains"<<endl;
+        return false;
+    }
     
-    Field<Vector, realx3 , vecAllocator<realx3>> internal(
+    uint32 thisN = simulationDomain_->initialNumberInThis();
-        "internalPoints", 
-        "internalPoints", 
-        thisN, 
-        thisN, 
-        RESERVE());
 
-    
+    Field<Vector, realx3 , vecAllocator<realx3>> internal
-    auto l = sizeof(realx3);
-    auto pointsSpan = span<char>(
-        reinterpret_cast<char*>
     (
-			const_cast<realx3*>(points.data())
+        "internalPoints", 
-		), 
+        "internalPoints", 
-        points.size()*l );
+        thisN, 
+        thisN, 
+        RESERVE()
+    );
     
-    auto internalSpan = span<char>(reinterpret_cast<char*>(internal.data()), internal.size()*l);
+    auto pSpan  = makeSpan(points); 
+    auto iSpan  = internal.getSpan();
     
-    if(!simulationDomain_->transferBlockData(pointsSpan, internalSpan, l))
+    if(!simulationDomain_->initialTransferBlockData(pSpan, iSpan))
     {
         fatalErrorInFunction<<
         "Error in transfering the block data "<<endl;
         return false;
     }
     
-    pointPosition_.assign(internal.vectorField());
+    if( !initializePoints(internal) )
+    {
+        fatalErrorInFunction;
+        return false;
+    }
 
+    boundaries_.updateLists();
+
+    return false;
+}
+
+
+bool pFlow::pointStructure::initializePoints(const realx3Vector &points)
+{
+    pointPosition_.assign(points.vectorField());
 
     pFlagsD_ = pFlagTypeDevice(pointPosition_.capacity(), 0, pointPosition_.size());
     pFlagSync_ = false;
     syncPFlag();
 
-    
-
     return true;
-
 }
 
 pFlow::pointStructure::pointStructure
@@ -73,7 +82,19 @@ pFlow::pointStructure::pointStructure
     systemControl& control
 )
 :
-	demComponent("particlesCM", control),
+    IOobject
+    (
+        objectFile
+        (
+            pointStructureFile__,
+            "",
+            objectFile::READ_ALWAYS,
+            objectFile::WRITE_ALWAYS
+        ),
+        IOPattern::MasterProcessorDistribute,
+        &control.time()
+    ),
+	demComponent("particlesCenterMass", control),
   	internalPoints(),
 	simulationDomain_
 	(
@@ -84,37 +105,52 @@ pFlow::pointStructure::pointStructure
 		simulationDomain_(),
 		*this
 	)
-{}
+{
+    REPORT(0)<< "Reading point structure from file"<<
+    IOobject::localPath()<<END_REPORT;
+
+    if( !IOobject::read() )
+    {
+        fatalErrorInFunction<<
+        "Error in reading from file "<<IOobject::localPath()<<endl;
+    }
+}
 
 
 pFlow::pointStructure::pointStructure(
     systemControl& control,
     const realx3Vector &posVec)
 :
-	demComponent("particlesCM", control), 
+	IOobject
+    (
+        objectFile
+        (
+            pointStructureFile__,
+            "",
+            objectFile::READ_NEVER,
+            objectFile::WRITE_ALWAYS
+        ),
+        IOPattern::MasterProcessorDistribute,
+        &control.time()
+    ),
+	demComponent("particlesCenterMass", control),
   	internalPoints(),
-	simulationDomain_(
+	simulationDomain_
-		simulationDomain::create(control.domainDict())),
+	(
-	boundaries_(
+		simulationDomain::create(control.domainDict())
+	),
+	boundaries_
+	(
 		simulationDomain_(),
-		*this)
+		*this
+	)
 {
-    if(!simulationDomain_->updateDomains(posVec) )
+    if(!setupPointStructure(posVec))
     {
         fatalErrorInFunction<<
-        "Failed to update domains."<<endl;
+        "Error in seting up pointStructure"<<endl;
         fatalExit;
     }
-
-    boundaries_.updateLists();
-
-    if( !distributePoints(posVec) )
-    {
-        fatalErrorInFunction<<"Faild to distributes poinst"<<endl;
-        fatalExit;
-    }
-
-    
 }
 
 bool pFlow::pointStructure::beforeIteration()
@@ -134,28 +170,49 @@ bool pFlow::pointStructure::afterIteration()
 
 bool pFlow::pointStructure::read(
     iIstream &is,
-    IOPattern::IOType iotype)
+    const IOPattern& iop)
 {
-    Field<Vector, realx3 , vecAllocator<realx3>> fRead("file_internalPoints", "internalPoints");
     
+    Field<Vector, realx3 , vecAllocator<realx3>> 
+        fRead("file_internalPoints", "internalPoints");   
 
-
+	if( !fRead.read(is, iop))
-	if( !fRead.read(is, iotype))
 	{
 		fatalErrorInFunction<<
 		"Error in reading pointPosition from stream "<< is.name()<<endl;
 		return false;
 	}
 
-    if(!simulationDomain_->updateDomains(fRead))
+    return setupPointStructure(fRead);
+}
+
+bool pFlow::pointStructure::write
+(
+    iOstream& os, 
+    const IOPattern& iop
+)const
+{
+    
+    hostViewType1D<realx3> pointsH;
+
+    if(isAllActive())
+    {
+        pointsH = pointPositionHost();
+    }
+    else
+    {
+        pointsH = activePointsHost();
+    }
+
+    auto data = span<realx3>(pointsH.data(), pointsH.size());
+    
+    if( !writeSpan(os, data, iop) )
     {
         fatalErrorInFunction<<
-        "error in updating domains"<<endl;
+        "Error in writing pointStructure in stream "<<
+        os.name()<<endl;
         return false;
     }
 
-    boundaries_.updateLists();
+    return true;
-
-	return distributePoints(fRead);
-    
 }

src/phasicFlow/structuredData/pointStructure/pointStructure.hpp

@@ -20,10 +20,12 @@ Licence:
 #ifndef __pointStructure_hpp__
 #define __pointStructure_hpp__
 
+#include "IOobject.hpp"
 #include "demComponent.hpp"
 #include "internalPoints.hpp"
 #include "simulationDomain.hpp"
 #include "boundaryList.hpp"
+#include "streams.hpp"
 
 
 
@@ -33,6 +35,7 @@ namespace pFlow
 
 class pointStructure
 :
+    public IOobject,
     public demComponent,
 	public internalPoints
 {
@@ -44,7 +47,9 @@ protected:
 	boundaryList 				boundaries_;
     
 
-	bool distributePoints(const realx3Vector& points);
+    bool setupPointStructure(const realx3Vector& points);
+
+    bool initializePoints(const realx3Vector& points);
 
 public:
 
@@ -63,19 +68,12 @@ public:
             systemControl& control,
 			const realx3Vector& posVec);
 
-		// - copy construct
-		//
-		//   should be changed, may causs undefined behavior 
-		//////////////////////////////////////////////////////////////
 		pointStructure(const pointStructure&) = delete;
 
 		// - no move construct 
 		pointStructure(pointStructure&&) = delete;
 
-		// - copy assignment 
+		
-		//
-		//   should be changed, may causs undefined behavior 
-		//////////////////////////////////////////////////////////////
 		pointStructure& operator=(const pointStructure&) = delete;
 
 		// - no move assignment 
@@ -122,15 +120,14 @@ public:
 
 		/// @brief read the point structure from the input stream.
 		/// @param is: input stream
-		/// @param iotype: type of input pattern
+		/// @param iop: type of input pattern
 		/// @return true on success
-		FUNCTION_H
+		bool read(iIstream& is, const IOPattern& iop) override;
-		bool read(iIstream& is, IOPattern::IOType iotype);
 		
 
 		/// Write 
-		/*FUNCTION_H
+		bool write(iOstream& os, const IOPattern& iop)const override;
-		bool write(iOstream& os, IOPattern::IOType iotype)const;	*/
+        
 		
 		
 		
@@ -141,6 +138,16 @@ public:
 };
 
 
+/*inline iOstream& operator << (iOstream& os, const pointStructure& ps )
+{	
+	if( !ps.write(os, IOPattern::AllProcessorsDifferent) )
+	{
+		ioErrorInFile(os.name(), os.lineNumber());
+		fatalExit;
+	}
+	return os; 
+}*/
+
 } // pFlow
 
 

src/phasicFlow/structuredData/trisurfaceStructure/stlFile.hpp

@@ -106,10 +106,10 @@ public:
 		size_t size()const;
 		
 		// - vertecies of ith solid
-		const realx3x3Vector& solid(label i)const;
+		const realx3x3Vector& solid(uint64 i)const;
 
 		// - name of ith solid 
-		const word& name(label i)const;
+		const word& name(uint64 i)const;
 
 };
 

src/phasicFlow/types/triple/triple.hpp

@@ -146,6 +146,8 @@ struct triple
 		/// access component
 		INLINE_FUNCTION_HD const T & z()const { return z_; }
 
+        INLINE_FUNCTION_HD const T& comp(uint32 i) const {return *(this+i);}
+
 	//// methods
 
 		/// Dot product of two vectors

src/setHelpers/finalize.hpp

@@ -23,7 +23,7 @@ Licence:
 
 // initilized and finalize should be placed in onc scope 
 }
-pFlow::output<< "\nFinalizing host/device execution space ...."<<pFlow::endl;
+REPORT(0)<< "\nFinalizing host/device execution space ...."<<END_REPORT;
 Kokkos::finalize();
 
 

src/setHelpers/setProperty.hpp

@@ -22,7 +22,7 @@ Licence:
 #ifndef __setProperty_hpp__
 #define __setProperty_hpp__
 
-REPORT(0)<<"\nReading proprties . . . "<<endREPORT;
+REPORT(0)<<"\nReading proprties . . . "<<END_REPORT;
 
 auto proprties = pFlow::property(Control.caseSetup().path()+pFlow::propertyFile__);
 

src/setHelpers/setSurfaceGeometry.hpp

@@ -21,7 +21,7 @@ Licence:
 #ifndef __setSurfaceGeometry_hpp__
 #define __setSurfaceGeometry_hpp__
 
-REPORT(0)<< "\nCreating surface geometry . . . "<<endREPORT;
+REPORT(0)<< "\nCreating surface geometry . . . "<<END_REPORT;
 auto surfGeometryPtr = pFlow::geometry::create(Control, proprties);
 auto& surfGeometry = surfGeometryPtr();
 

utilities/CMakeLists.txt

@@ -1,13 +1,13 @@
 
 #add_subdirectory(checkPhasicFlow)
 
-#add_subdirectory(particlesPhasicFlow)
+add_subdirectory(particlesPhasicFlow)
 
 #add_subdirectory(geometryPhasicFlow)
 
 #add_subdirectory(pFlowToVTK)
 
-#add_subdirectory(Utilities)
+add_subdirectory(Utilities)
 
 #add_subdirectory(postprocessPhasicFlow)
 

utilities/Utilities/CMakeLists.txt

@@ -2,15 +2,17 @@
 set(SourceFiles 
 readFromTimeFolder.cpp
 readControlDict.cpp
-vtkFile/vtkFile.cpp
+#vtkFile/vtkFile.cpp
-geometryPhasicFlow/Wall/Wall.cpp 
+#geometryPhasicFlow/Wall/Wall.cpp 
-geometryPhasicFlow/planeWall/planeWall.cpp 
+#geometryPhasicFlow/planeWall/planeWall.cpp 
-geometryPhasicFlow/stlWall/stlWall.cpp
+#geometryPhasicFlow/stlWall/stlWall.cpp
-geometryPhasicFlow/cylinderWall/cylinderWall.cpp
+#geometryPhasicFlow/cylinderWall/cylinderWall.cpp
-geometryPhasicFlow/cuboidWall/cuboidWall.cpp
+#geometryPhasicFlow/cuboidWall/cuboidWall.cpp
 )
 
-set(link_libs Kokkos::kokkos phasicFlow Particles Geometry)
+#set(link_libs Kokkos::kokkos phasicFlow Particles Geometry)
+
+set(link_libs Kokkos::kokkos phasicFlow)
 
 pFlow_add_library_install(Utilities SourceFiles link_libs)
 

utilities/Utilities/geometryPhasicFlow/cylinderWall/cylinderWall.cpp

@@ -49,7 +49,7 @@ bool pFlow::cylinderWall::createCylinder(
 	real L = zAx.length();
 
 	
-	realx3Vector r1P(numDiv + 1), r2P(numDiv + 1);
+	realx3Vector r1P("r1P",numDiv + 1), r2P("r1P",numDiv + 1);
 	real dTheta = 2 * Pi / numDiv;
 	real theta = 0;
 

utilities/Utilities/geometryPhasicFlow/stlWall/stlWall.cpp

@@ -42,7 +42,7 @@ bool pFlow::stlWall::readSTLWall
 		return false;
 	}
 
-	for(label i=0; i<stl.size(); i++)
+	for(uint64 i=0; i<stl.size(); i++)
 	{
 		auto it = triangles_.end();
 		triangles_.insert(it, stl.solid(i).begin(), stl.solid(i).end());

utilities/Utilities/readFromTimeFolder.hpp

@@ -20,7 +20,7 @@ Licence:
 #ifndef __readFromTimeFolder_hpp__
 #define __readFromTimeFolder_hpp__
 
-
+#include "vocabs.hpp"
 #include "repository.hpp"
 #include "pointFields.hpp"
 #include "utilityFunctions.hpp"

utilities/particlesPhasicFlow/CMakeLists.txt

@@ -6,6 +6,8 @@ positionOrdered/positionOrdered.cpp
 #positionRandom/positionRandom.cpp
 empty/empty.cpp
 )
-set(link_lib phasicFlow Kokkos::kokkos Interaction Utilities)
+#set(link_lib phasicFlow Kokkos::kokkos Interaction Utilities)
+
+set(link_lib phasicFlow Kokkos::kokkos Utilities)
 
 pFlow_make_executable_install(particlesPhasicFlow source_files link_lib)

utilities/particlesPhasicFlow/particlesPhasicFlow.cpp

@@ -21,25 +21,14 @@ Licence:
 
 #include "positionParticles.hpp"
 #include "pointStructure.hpp"
-#include "setFields.hpp"
+//#include "setFields.hpp"
 #include "systemControl.hpp"
 #include "commandLine.hpp"
 #include "vocabs.hpp"
 
 //#include "readControlDict.hpp"
 
-using pFlow::output;
+using namespace pFlow;
-using pFlow::endl;
-using pFlow::dictionary;
-using pFlow::uniquePtr;
-using pFlow::IOobject;
-using pFlow::objectFile;
-using pFlow::fileSystem;
-using pFlow::pointStructure;
-using pFlow::pointStructureFile__;
-using pFlow::positionParticles;
-using pFlow::commandLine;
-using pFlow::setFieldList;
 
 int main( int argc, char* argv[] )
 {
@@ -83,7 +72,7 @@ int main( int argc, char* argv[] )
 // this should be palced in each main 
 #include "initialize_Control.hpp"
 
-	auto objCPDict = IOobject::make<dictionary>
+	auto objCPDict = IOobject::make<fileDictionary>
 	(
 		objectFile
 		(
@@ -92,11 +81,10 @@ int main( int argc, char* argv[] )
 			objectFile::READ_ALWAYS,
 			objectFile::WRITE_ALWAYS
 		),
-		"particlesDict",
+		"particlesDict"
-		true
 	);
 
-	auto& cpDict = objCPDict().getObject<dictionary>();
+	auto& cpDict = objCPDict().getObject<fileDictionary>();
 
 	pointStructure* pStructPtr = nullptr;
 
@@ -128,19 +116,19 @@ int main( int argc, char* argv[] )
 
 		pStructPtr = &pStruct;
 
-
 		REPORT(1)<< "Created pStruct with "<< pStruct.size() << " points and capacity "<<
 		pStruct.capacity()<<" . . ."<< END_REPORT;
 
-		REPORT(1)<< "Writing pStruct to " << Control.time().path()+ pointStructureFile__<< END_REPORT<<endl<<endl;
+		//REPORT(1)<< "Writing pStruct to " << Control.time().path()+ pointStructureFile__<< END_REPORT<<endl<<endl;
         
-		if( !Control.time().write())
+		/*if( !Control.time().write())
 		{
 			fatalErrorInFunction<<
 			"ERRor in writing to file. \n ";
 			return 1; 
+		}*/
 	}
-	}else
+    else
 	{
 
 		auto& pStruct = Control.time().emplaceObject<pointStructure>
@@ -163,8 +151,8 @@ int main( int argc, char* argv[] )
 
 	if(!positionOnly)
 	{
-
+        WARNING<< "setFields is not active "<<END_WARNING;
-		auto& pStruct = *pStructPtr;
+	/*	auto& pStruct = *pStructPtr;
 
 		auto& sfDict = cpDict.subDict("setFields");
 
@@ -197,10 +185,16 @@ int main( int argc, char* argv[] )
 				return 1;
 			}
 			output<<endl;
-		}
+		}*/
 	}
 
-	Control.time().write(true);
+	
+    if( !Control.time().write(true))
+    {
+        fatalErrorInFunction<<
+        "ERRor in writing to file. \n ";
+        return 1; 
+    }
 	REPORT(0)<< Green_Text("\nFinished successfully.\n")<<END_REPORT;
 
 

utilities/particlesPhasicFlow/positionParticles/positionParticles.cpp

@@ -23,7 +23,7 @@ Licence:
 #include "cylinder.hpp"
 #include "sphere.hpp"
 #include "cells.hpp"
-#include "contactSearchFunctions.hpp"
+//#include "contactSearchFunctions.hpp"
 
 #include "streams.hpp"
 
@@ -32,20 +32,20 @@ pFlow::realx3Vector pFlow::positionParticles::sortByMortonCode(realx3Vector& pos
 {
 	struct indexMorton
 	{
-		size_t morton;
+		uint64 morton;
-		size_t index;
+		uint64 index;
 	};
 
-	realx3 minP = min(position);
+	/*realx3 minP = min(position);
 	realx3 maxP = max(position);
 	real cellsize = maxDiameter();
-	cells<size_t> allCells( box(minP, maxP), cellsize);
+	cells<uint64> allCells( box(minP, maxP), cellsize);
 
 	Vector<indexMorton> indMor(position.size(),RESERVE());
 
 	indMor.clear();
 
-	size_t ind=0;
+	uint64 ind=0;
 	for(const auto& p:position)
 	{
 		auto cellInd = allCells.pointIndex(p);
@@ -68,9 +68,10 @@ pFlow::realx3Vector pFlow::positionParticles::sortByMortonCode(realx3Vector& pos
 	for(auto& ind:indMor)
 	{
 		sortedPos.push_back( position[ind.index] );
-	}
+	}*/
 
-	return sortedPos;
+    WARNING<<"Morton sorting is inactive!"<<END_WARNING;
+	return position;
 }
 
 
@@ -80,7 +81,7 @@ pFlow::positionParticles::positionParticles
 	const dictionary& dict
 )
 {
-	maxNumberOfParticles_ = dict.getValOrSet("maxNumberOfParticles", static_cast<size_t>(10000));
+	maxNumberOfParticles_ = dict.getValOrSet("maxNumberOfParticles", static_cast<uint64>(10000));
 	
 	mortonSorting_ = dict.getValOrSet("mortonSorting", Logical("Yes"));
 
@@ -90,11 +91,13 @@ pFlow::positionParticles::positionParticles
 	}
 	else if(dict.containsDictionay("cylinder"))
 	{
-		region_ = makeUnique<region<cylinder>>(dict.subDict("cylinder"));
+        WARNING<<"cylinder region is not set!"<<END_WARNING;
+		//region_ = makeUnique<region<cylinder>>(dict.subDict("cylinder"));
 	}
 	else if(dict.containsDictionay("sphere"))
 	{
-		region_ = makeUnique<region<sphere>>(dict.subDict("sphere"));
+        WARNING<<"sphere region is not set!"<<END_WARNING;
+		//region_ = makeUnique<region<sphere>>(dict.subDict("sphere"));
 	}
 	else
 	{
@@ -112,7 +115,7 @@ pFlow::realx3Vector pFlow::positionParticles::getFinalPosition()
 	}
 	else
 	{
-		realx3Vector vec(position().capacity(), RESERVE());
+		realx3Vector vec("final position",position().capacity(), 0 , RESERVE());
 		vec.assign( position().begin(), position().end());
 		
 		return std::move(vec);
@@ -132,7 +135,7 @@ pFlow::uniquePtr<pFlow::positionParticles>
 
 	if( dictionaryvCtorSelector_.search(method) )
 	{
-		return dictionaryvCtorSelector_[method] (dict);
+		return dictionaryvCtorSelector_[method] (control, dict);
 	}
 	else
 	{