Merge pull request #106 from PhasicFlow/develop

modification to the base code for MPI-developement up to processor bo…

src/Interaction/CMakeLists.txt

@@ -7,6 +7,8 @@ contactSearch/methods/cellBased/NBS/NBS.cpp
 contactSearch/methods/cellBased/NBS/cellsWallLevel0.cpp
 
 contactSearch/boundaries/boundaryContactSearch/boundaryContactSearch.cpp
+contactSearch/boundaries/twoPartContactSearch/twoPartContactSearchKernels.cpp
+contactSearch/boundaries/twoPartContactSearch/twoPartContactSearch.cpp
 contactSearch/boundaries/periodicBoundaryContactSearch/ppwBndryContactSearchKernels.cpp
 contactSearch/boundaries/periodicBoundaryContactSearch/ppwBndryContactSearch.cpp
 contactSearch/boundaries/periodicBoundaryContactSearch/wallBoundaryContactSearch.cpp
@@ -22,6 +24,13 @@ sphereInteraction/sphereInteractionsNonLinearModels.cpp
 sphereInteraction/sphereInteractionsNonLinearModModels.cpp
 )
 
+if(pFlow_Build_MPI)
+    list(APPEND SourceFiles 
+    contactSearch/boundaries/processorBoundaryContactSearch/processorBoundaryContactSearch.cpp
+    sphereInteraction/boundaries/processorBoundarySphereInteraction/processorBoundarySphereInteractions.cpp
+    )
+endif()
+
 set(link_libs Kokkos::kokkos phasicFlow Property Particles Geometry)
 
 pFlow_add_library_install(Interaction SourceFiles link_libs)

src/Interaction/contactSearch/ContactSearch/ContactSearch.hpp

@@ -130,9 +130,10 @@ public:
 		csPairContainerType& pwPairs,
 		bool force = false) override
 	{
-
 		ppTimer().start();
 
+		Particles().boundingSphere().updateBoundaries(DataDirection::SlaveToMaster);
+		
 		const auto& position = Particles().pointPosition().deviceViewAll();
 		const auto& flags = Particles().dynPointStruct().activePointsMaskDevice();
 		const auto& diam = Particles().boundingSphere().deviceViewAll();

src/Interaction/contactSearch/boundaries/periodicBoundaryContactSearch/ppwBndryContactSearch.hpp

@@ -36,15 +36,16 @@ public:
 	using NextType = deviceViewType1D<uint32>;
 
 private:
-	cells searchCells_;
 
-	HeadType head_{"periodic::head", 1, 1, 1};
+	cells    searchCells_;
 
-	NextType next_{"periodic::next", 1};
+	HeadType head_{ "periodic::head", 1, 1, 1 };
 
-	real sizeRatio_ = 1.0;
+	NextType next_{ "periodic::next", 1 };
 
-	uint32 nextCapacity_ = 0;
+	real     sizeRatio_ = 1.0;
+
+	uint32   nextCapacity_ = 0;
 
 	void checkAllocateNext(uint32 n);
 

src/Interaction/sphereInteraction/boundaries/boundarySphereInteraction/boundarySphereInteraction.hpp

@@ -143,7 +143,9 @@ public:
 	) override
     {
 		
-		notImplementedFunction;
+		pOutput<<"Function (hearChanges in boundarySphereInteractions)is not implmented Message "<<
+		 msg <<endl<<" name "<< this->name() <<" type "<< this->type()<<endl;;
+		//notImplementedFunction;
 		return true;
 	}
 

src/Interaction/sphereInteraction/boundaries/periodicBoundarySphereInteraction/periodicBoundarySIKernels.hpp

@@ -3,6 +3,7 @@ namespace pFlow::periodicBoundarySIKernels
 {
 
 template<typename ContactListType, typename ContactForceModel>
+inline
 void sphereSphereInteraction
 (
     real dt,
@@ -46,14 +47,6 @@ void sphereSphereInteraction
             
             if( ovrlp >0.0 )
             {
-                
-                /*auto Vi = thisVel[i];
-                auto Vj = mirrorVel[j];
-                auto wi = thisRVel[i];
-                auto wj = mirrorRVel[j];
-                auto Nij = (xj-xi)/dist;
-                auto Vr = Vi - Vj + cross((Ri*wi+Rj*wj), Nij);*/
-
                 auto Nij = (xj-xi)/dist;
                 auto wi = rVel[ind_i];
                 auto wj = rVel[ind_j];

src/Interaction/sphereInteraction/sphereInteraction/sphereInteraction.cpp

@@ -163,9 +163,16 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::iterate()
 	auto t = this->currentTime();
 	auto dt = this->dt();
 
-	//output<<"iter, t, dt "<< iter<<" "<< t << " "<<dt<<endl;
+	
 	bool broadSearch = contactSearch_().enterBroadSearch(iter, t, dt);
 
+	/*sphParticles_.diameter().updateBoundaries(DataDirection::SlaveToMaster);
+	sphParticles_.velocity().updateBoundaries(DataDirection::SlaveToMaster);
+	sphParticles_.rVelocity().updateBoundaries(DataDirection::SlaveToMaster);
+	sphParticles_.mass().updateBoundaries(DataDirection::SlaveToMaster);
+	sphParticles_.I().updateBoundaries(DataDirection::SlaveToMaster);
+	sphParticles_.propertyId().updateBoundaries(DataDirection::SlaveToMaster);*/
+	
 	
 	if(broadSearch)
 	{

src/Particles/CMakeLists.txt

@@ -16,6 +16,11 @@ Insertion/shapeMixture/shapeMixture.cpp
 Insertion/Insertion/Insertions.cpp
 )
 
+if(pFlow_Build_MPI)
+    list(APPEND SourceFiles 
+    particles/MPIParticleIdHandler/MPIParticleIdHandler.cpp)
+endif()
+
 set(link_libs Kokkos::kokkos phasicFlow Integration Property)
 
 pFlow_add_library_install(Particles SourceFiles link_libs)

src/Particles/SphereParticles/sphereParticles/sphereParticles.cpp

@@ -513,6 +513,14 @@ bool pFlow::sphereParticles::beforeIteration()
 		dynPointStruct().predict(dt, accelertion());
 		rVelIntegration_().predict(dt,rVelocity_, rAcceleration_);
 	intPredictTimer_.end();
+
+	propertyId_.updateBoundariesSlaveToMasterIfRequested();
+	diameter_.updateBoundariesSlaveToMasterIfRequested();
+	mass_.updateBoundariesSlaveToMasterIfRequested();
+	I_.updateBoundariesSlaveToMasterIfRequested();
+	rVelocity_.updateBoundariesSlaveToMasterIfRequested();
+	rAcceleration_.updateBoundariesSlaveToMasterIfRequested();
+	
 	
 	return true;
 }

src/Particles/particles/particleIdHandler/particleIdHandler.hpp

@@ -31,7 +31,12 @@ class particleIdHandler
 :
 	public uint32PointField_D
 {
-  
+
+private:
+
+	virtual 
+	bool initialIdCheck()=0;
+
 public:
 	
 	/// class info
@@ -53,7 +58,9 @@ public:
 	Pair<uint32, uint32> getIdRange(uint32 nNewParticles)=0;
 
 	virtual 
-	bool initialIdCheck()=0;
+	uint32 maxId()const = 0;
+
+	
 
 	// heat change for possible insertion of particles
 	// overrdie from internalField

src/Particles/particles/particles.cpp

@@ -78,7 +78,7 @@ pFlow::particles::particles(systemControl& control)
 {
 	this->addToSubscriber(dynPointStruct_);
 
-	idHandler_().initialIdCheck();
+	//idHandler_().initialIdCheck();
 }
 
 bool
@@ -87,7 +87,16 @@ pFlow::particles::beforeIteration()
 	zeroForce();
 	zeroTorque();
 
-	return dynPointStruct_.beforeIteration();
+	if( !dynPointStruct_.beforeIteration())
+  {
+    return false;
+  }
+
+  shapeIndex_.updateBoundariesSlaveToMasterIfRequested();
+  accelertion_.updateBoundariesSlaveToMasterIfRequested();
+  idHandler_().updateBoundariesSlaveToMasterIfRequested();
+
+  return true;
 }
 
 bool

src/Particles/particles/particles.hpp

@@ -181,6 +181,12 @@ public:
 		return contactTorque_;
 	}
 
+	inline 
+	uint maxId()const
+	{
+		return idHandler_().maxId();
+	}
+
 	bool         beforeIteration() override;
 
 	bool         iterate() override;

src/Particles/particles/regularParticleIdHandler/regularParticleIdHandler.cpp

@@ -9,6 +9,7 @@ pFlow::regularParticleIdHandler::regularParticleIdHandler
 :
     particleIdHandler(pStruct)
 {
+    initialIdCheck();
 }
 
 pFlow::Pair<pFlow::uint32, pFlow::uint32> 

src/Particles/particles/regularParticleIdHandler/regularParticleIdHandler.hpp

@@ -33,6 +33,7 @@ private:
     
     uint32 maxId_ = -1;
 
+  bool initialIdCheck()override; 
 public:
 
     ClassInfo("particleIdHandler<regular>");
@@ -50,7 +51,10 @@ public:
 
     Pair<uint32, uint32> getIdRange(uint32 nNewParticles)override;
 
-	bool initialIdCheck()override;
+	uint32 maxId()const override
+	{
+		return maxId_;
+	}
 
 };
 

src/phasicFlow/CMakeLists.txt

@@ -25,6 +25,7 @@ streams/TStream/oTstream.cpp
 streams/Fstream/iFstream.cpp
 streams/Fstream/oFstream.cpp
 streams/Fstream/fileStream.cpp
+streams/dataIO/dataIORegulars.cpp
 streams/streams.cpp 
 
 fileSystem/fileSystem.cpp
@@ -132,14 +133,14 @@ if(pFlow_Build_MPI)
 	message(STATUS "Zoltan lib path: ${ZOLTAN_LIBRARY}")
 	
 	list(APPEND SourceFiles
-	MPIParallelization/partitioning.cpp 
-	MPIParallelization/rcb1DPartitioning.cpp
+	MPIParallelization/domain/partitioning/partitioning.cpp 
+	MPIParallelization/domain/partitioning/rcb1DPartitioning.cpp
 	MPIParallelization/domain/MPISimulationDomain.cpp
-    #MPIParallelization/dataIOMPI.cpp
-    MPIParallelization/procCommunication.cpp
-    MPIParallelization/boundaryProcessor.cpp
-    MPIParallelization/scatteredMasterDistributeChar.cpp
-	MPIParallelization/processorBoundaryFields.cpp
+    MPIParallelization/dataIOMPI/dataIOMPIs.cpp
+    MPIParallelization/MPI/procCommunication.cpp
+    MPIParallelization/MPI/scatteredMasterDistributeChar.cpp
+	MPIParallelization/pointStructure/boundaries/boundaryProcessor.cpp
+	MPIParallelization/pointField/processorBoundaryFields.cpp
 	)
 	
 	list(APPEND link_libs MPI::MPI_CXX ${ZOLTAN_LIBRARY} -lm )

src/phasicFlow/containers/pointField/boundaryField/boundaryField/boundaryField.cpp

@@ -36,6 +36,25 @@ pFlow::boundaryField<T, MemorySpace>::boundaryField
 	internal_(internal)
 {}
 
+template<class T, class MemorySpace>
+typename pFlow::boundaryField<T, MemorySpace>::ProcVectorType& 
+pFlow::boundaryField<T, MemorySpace>::neighborProcField()
+{
+	static ProcVectorType dummyVector{"dummyVector"};
+	notImplementedFunction;
+	fatalExit;
+	return dummyVector;
+}
+
+template<class T, class MemorySpace>
+const typename pFlow::boundaryField<T, MemorySpace>::ProcVectorType& 
+pFlow::boundaryField<T, MemorySpace>::neighborProcField() const
+{
+	static ProcVectorType dummyVector{"dummyVector"};
+	notImplementedFunction;
+	fatalExit;
+	return dummyVector;
+}
 
 template<class T, class MemorySpace>
 pFlow::uniquePtr<pFlow::boundaryField<T, MemorySpace>>

src/phasicFlow/containers/pointField/boundaryField/boundaryField/boundaryField.hpp

@@ -26,6 +26,18 @@ Licence:
 namespace pFlow
 {
 
+
+// forward 
+template< class T, class MemorySpace>
+	class boundaryFieldList;
+
+enum class DataDirection
+{
+	MasterToSlave,
+	SlaveToMaster,
+	TwoWay
+};
+
 template< class T, class MemorySpace = void>
 class boundaryField
 :
@@ -43,12 +55,22 @@ public:
 
 	using FieldAccessType 	= scatteredFieldAccess<T, memory_space>;
 
-protected:
+	using ProcVectorType 	= VectorSingle<T,MemorySpace>;
 
+private:
+
+	/// friend et al. 
+	friend class boundaryFieldList<T,MemorySpace>;
+	
     /// @brief a ref to the internal field 
     InternalFieldType& 			internal_;
 
-	
+	virtual 
+	bool updateBoundary(int step, DataDirection direction)
+	{
+		return true;
+	}
+
 public:
 
 	TypeInfoTemplate211("boundaryField","none" ,T, memory_space::name());
@@ -78,7 +100,6 @@ public:
 		boundaryBase
 	);
 
-
 	bool hearChanges
 	(
 		real t,
@@ -116,6 +137,12 @@ public:
 			this->mirrorBoundary().indexList().deviceViewAll(),
 			internal_.deviceViewAll());
 	}
+	
+	virtual 
+	ProcVectorType& neighborProcField();
+
+	virtual
+	const ProcVectorType& neighborProcField()const;
 
 	void fill(const std::any& val)override
 	{

src/phasicFlow/containers/pointField/boundaryField/boundaryFieldList.hpp

@@ -43,6 +43,8 @@ protected:
 
     const boundaryList&         boundaries_;
 
+    uint32                      slaveToMasterUpdateIter_ = -1;
+
 public:
 
     boundaryFieldList(const boundaryList& boundaries, InternalFieldType& internal)
@@ -60,6 +62,29 @@ public:
         }
     }
 
+    void updateBoundaries(uint32 iter, DataDirection direction)
+    {
+        if( direction == DataDirection::SlaveToMaster 
+            && slaveToMasterUpdateIter_ == iter) return;
+        
+        // first step
+        for(auto b:*this)
+        {
+            b->updateBoundary(1, direction);
+        }
+
+        // second step
+        for(auto b:*this)
+        {
+            b->updateBoundary(2, direction);
+        }
+
+        if(direction == DataDirection::SlaveToMaster)
+        {
+            slaveToMasterUpdateIter_ = iter;
+        }
+    }
+
     void fill(const T& val)
     {
         for(auto& bf: *this)
@@ -68,6 +93,12 @@ public:
         }
     }
 
+    bool slaveToMasterUpdateRequested()const
+    {
+        return slaveToMasterUpdateIter_ != -1;
+    }
+
+    
 };
 
 }

src/phasicFlow/containers/pointField/boundaryField/generalBoundary/generalBoundary.cpp

@@ -31,7 +31,8 @@ pFlow::generalBoundary::generalBoundary
 :
 	observer(&boundary, defaultMessage_),
 	boundary_(boundary),
-	pStruct_(pStruct)
+	pStruct_(pStruct),
+  isBoundaryMaster_(boundary.isBoundaryMaster())
 {}
 
 

src/phasicFlow/containers/pointField/boundaryField/generalBoundary/generalBoundary.hpp

@@ -45,16 +45,10 @@ private:
 
     const pointStructure&   pStruct_;
 
+    const bool              isBoundaryMaster_;
 
 	static inline
 	const message defaultMessage_{message::BNDR_RESET};
-				
-    template<typename BoundaryFieldType>
-    inline
-    bool checkForType()const
-    {
-        return typeName() == BoundaryFieldType::TYPENAME();
-    }
 
 public:
 
@@ -68,7 +62,6 @@ public:
     
     ~generalBoundary()override = default;
 	
-	
     inline
     uint32 thisBoundaryIndex()const
     {
@@ -93,6 +86,24 @@ public:
 		return boundary_.capacity();
 	}
 
+    inline 
+    auto neighborProcSize()const
+    {
+        return boundary_.neighborProcSize();
+    }
+
+    inline 
+    int neighborProcessorNo()const
+    {
+        return boundary_.neighborProcessorNo();
+    }
+
+    inline
+    int thisProcessorNo()const
+    {
+        return boundary_.thisProcessorNo();
+    }
+
     inline 
     const auto& boundary()const
     {
@@ -129,22 +140,17 @@ public:
         return pStruct_;
     }
 
+    inline
+    bool isBoundaryMaster()const
+    {
+        return isBoundaryMaster_;
+    }
+
     const Time& time()const;
 
 	virtual
 	void fill(const std::any& val)=0;
 
-    /*template<typename BoundaryFieldType>
-    BoundaryFieldType& thisField()
-    {
-        return static_cast<BoundaryFieldType&>(*this);
-    }
-
-    template<typename BoundaryFieldType>
-    const BoundaryFieldType& thisField()const
-    {
-        return static_cast<const BoundaryFieldType&>(*this);
-    }*/
 	
 };
 

src/phasicFlow/containers/pointField/internalField/internalField.hpp

@@ -181,6 +181,11 @@ public:
 		return field_.insertSetElement(indices, val);
 	}
 
+	inline const Time& time()const
+	{
+		return internalPoints_.time();
+	}
+
 	bool hearChanges
 	(
 		real t,

src/phasicFlow/containers/pointField/pointField/pointField.hpp

@@ -24,7 +24,7 @@ Licence:
 #include "pointStructure.hpp"
 #include "internalField.hpp"
 #include "boundaryFieldList.hpp"
-
+#include "Time.hpp"
 
 namespace pFlow
 {
@@ -103,6 +103,23 @@ public:
 			return static_cast<const InternalFieldType&>(*this);
 		}
 
+		void updateBoundaries(DataDirection direction)const
+		{
+			uint32 iter =  this->time().currentIter();
+			auto& bList = const_cast<boundaryFieldListType&>(boundaryFieldList_);
+			bList.updateBoundaries(iter, direction);
+		}
+
+		/// @brief update boundaries if it is requested previousely (slave to master). 
+		/// It only checks for SlaveToMaster direction.
+		void updateBoundariesSlaveToMasterIfRequested()
+		{
+			if(boundaryFieldList_.slaveToMasterUpdateRequested())
+			{
+				updateBoundaries(DataDirection::SlaveToMaster);
+			}
+		}
+
 		const auto& boundaryFields()const
 		{
 			return boundaryFieldList_;

src/phasicFlow/processors/localProcessors.cpp

@@ -1,3 +1,22 @@
+/*------------------------------- 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.
+
+-----------------------------------------------------------------------------*/
 #include "localProcessors.hpp"
 
 pFlow::localProcessors::localProcessors(const word &name)
@@ -8,8 +27,8 @@ pFlow::localProcessors::localProcessors(const word &name)
     name_(name)
 {
 #ifdef pFlow_Build_MPI
-    parrentCommunicator_ = pFlow::MPI::CommWorld;
-    localCommunicator_ = pFlow::MPI::CommWorld;
+    parrentCommunicator_ = MPI_COMM_WORLD;
+    localCommunicator_ = MPI_COMM_WORLD;
 #endif
 
 }
@@ -24,7 +43,7 @@ pFlow::localProcessors::localProcessors
     name_(name)
 {
 #ifdef pFlow_Build_MPI
-    parrentCommunicator_ = pFlow::MPI::CommWorld;
+    parrentCommunicator_ = MPI_COMM_WORLD;
     
     if(ranks.size()> this->globalSize() )
     {
@@ -33,17 +52,17 @@ pFlow::localProcessors::localProcessors
         fatalExit;
     }
 
-    pFlow::MPI::Group globalGroup;
+    MPI_Group globalGroup;
     MPI_Comm_group(parrentCommunicator_, &globalGroup);
 
-    pFlow::MPI::Group localGroup;
+    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;
+    isPartOfLocal_ = localCommunicator_ != MPI_COMM_NULL;
     
     if(isPartOfLocal_)
     {
@@ -71,7 +90,7 @@ pFlow::localProcessors::localProcessors
 
 pFlow::localProcessors::localProcessors
 (
-    pFlow::MPI::Comm parrentComm, 
+    MPI_Comm parrentComm, 
     const word &name, 
     const std::vector<int> &ranks
 )
@@ -92,17 +111,17 @@ pFlow::localProcessors::localProcessors
         fatalExit;
     }
 
-    pFlow::MPI::Group parGroup;
+    MPI_Group parGroup;
     MPI_Comm_group(parrentCommunicator_, &parGroup);
 
-    pFlow::MPI::Group localGroup;
+    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;
+    isPartOfLocal_ = localCommunicator_ != MPI_COMM_NULL;
     
     if(isPartOfLocal_)
     {

src/phasicFlow/processors/localProcessors.hpp

@@ -25,7 +25,7 @@ Licence:
 #include "types.hpp"
 
 #ifdef pFlow_Build_MPI
-    #include "mpiTypes.hpp"
+    #include "mpi.h"
 #endif
 
 
@@ -39,9 +39,9 @@ class localProcessors
 private:
 
 #ifdef pFlow_Build_MPI
-    pFlow::MPI::Comm    parrentCommunicator_;
+    MPI_Comm    parrentCommunicator_;
 
-    pFlow::MPI::Comm    localCommunicator_;
+    MPI_Comm    localCommunicator_;
 #endif
 
     int localSize_ = 1 ;
@@ -70,7 +70,7 @@ public:
 
     #ifdef pFlow_Build_MPI
         localProcessors(
-            pFlow::MPI::Comm parrentComm, 
+            MPI_Comm parrentComm, 
             const word& name, 
             const std::vector<int>& ranks);
     #endif

src/phasicFlow/processors/processors.cpp

@@ -58,11 +58,13 @@ void pFlow::processors::initProcessors(int argc, char *argv[])
 		if(processors::globalParallel())
 		{
 			pFlow::pOutput.activatePrefix();
-			pFlow::pOutput.setPrefixNum(processors::globalRank_);	
+			pFlow::pOutput.setPrefixNum(processors::globalRank_);
+			pFlow::errReport.activatePrefix();
+			pFlow::errReport.setPrefixNum(processors::globalRank_);
 		}
 		
 		pFlow::mOutput.setMasterSlave(processors::globalMaster());
-		pFlow::errReport.setMasterSlave(processors::globalMaster());
+		
 
         MPI_Type_contiguous(3, pFlow::MPI::Type<real>(), &pFlow::MPI::realx3Type__);
 		MPI_Type_commit(&pFlow::MPI::realx3Type__);

src/phasicFlow/repository/IOobject/IOPattern.hpp

@@ -41,7 +41,7 @@ public:
 	 * 
 	 * MasterProcessorDistribute: Read is done on master processor, but 
 	 * the data should be distributed between processors based on an externally 
-	 * specified pattern. Write is done on master processors and the data is 
+	 * specified pattern. Write is done on master processor and the data is 
 	 * collected from all processors (collection is done based on the externally 
 	 * specified pattern). 
 	 * 
@@ -146,7 +146,6 @@ public:
 	bool thisProcWriteData()const
 	{
 		if(isAllProcessorsDifferent()) return true;
-        if(isMasterProcessorDistribute())return true;
 		return isMaster();
 	}
 

src/phasicFlow/repository/IOobject/IOobject.cpp

@@ -118,8 +118,9 @@ bool pFlow::IOobject::readObject(bool rdHdr)
 
 bool pFlow::IOobject::writeObject() const
 {
-    
-	if(implyWrite()&& ioPattern().thisCallWrite())
+    if(!implyWrite()) return true;
+
+	if(ioPattern().thisCallWrite())
 	{
 		
         if(auto ptrOS = outStream(); ptrOS )
@@ -160,7 +161,9 @@ bool pFlow::IOobject::readObject(iIstream& is, bool rdHdr)
 bool pFlow::IOobject::writeObject(iOstream& os) const
 {
 	if(this->writeHeader() && ioPattern().thisProcWriteHeader())
-		writeHeader(os, typeName());
+	{
+        writeHeader(os, typeName());
+    }
     
     if(ioPattern().thisCallWrite())
 	 {   

src/phasicFlow/repository/systemControl/systemControl.cpp

@@ -199,7 +199,7 @@ bool pFlow::systemControl::operator++(int)
 
 		if (time().timersReportTime() && timersReport())
 		{
-			timers_.write(output, true);
+			timers_.write(mOutput, true);
 		}
 	}
 	else if (time().finalTime())
@@ -212,7 +212,7 @@ bool pFlow::systemControl::operator++(int)
 		}
 		writeToFileTimer_.end();
 
-		timers_.write(output, true);
+		timers_.write(mOutput, true);
 	}
 
 	return toContinue;

src/phasicFlow/streams/dataIO/dataIO.cpp

@@ -202,7 +202,7 @@ bool pFlow::dataIO<T>::writeData(iOstream& os, span<T> data)
 
 	if( ioPattern_.thisProcWriteData())
 	{
-		return writeDataAsciiBinary(os, data);
+		return writeDataAsciiBinary(os, bufferSpan_);
 	}
 	else
 	{
@@ -215,7 +215,7 @@ inline
 bool pFlow::dataIO<pFlow::word>::writeData(iOstream& os, span<word> data)
 {
     
-	if( ioPattern_.isParallel()	)
+	if( ioPattern_.isParallel()	&& ioPattern_.isMasterProcessorDistribute())
 	{
 		notImplementedFunction<<
 		"data transfer for type word is not supported in parallel mode!"<<endl;
@@ -232,7 +232,7 @@ bool pFlow::dataIO<pFlow::word>::writeData(iOstream& os, span<word> data)
 	
 	if( ioPattern_.thisProcWriteData())
 	{
-		return writeDataASCII(os, data);
+		return writeDataASCII(os, bufferSpan_);
 	}
 	else
 	{

src/phasicFlow/streams/dataIO/dataIO.hpp

@@ -31,8 +31,6 @@ Licence:
 #include "virtualConstructor.hpp"
 #include "pFlowProcessors.hpp"
 
-
-
 namespace pFlow
 {
 

src/phasicFlow/streams/dataIO/dataIOMPI.hpp

@@ -1,97 +0,0 @@
-#ifndef __datIOMPI_hpp__
-#define __datIOMPI_hpp__
-
-#include "dataIO.hpp"
-#include "pFlowProcessors.hpp"
-
-#ifdef pFlow_Build_MPI
-    #include "gatherMaster.hpp"
-#endif
-
-namespace pFlow
-{
-
-template<typename T>
-class dataIOMPI
-:
-	public dataIO<T>
-{
-protected:
-    
-    bool gatherData(span<T> data ) override
-    {
-        
-        if(this->ioPattern_.isAllProcessorsDifferent())
-        {
-            this->bufferSpan_ = data;
-            return true;
-        }
-        
-        if( this->ioPattern_.isMasterProcessorDistribute())
-        {
-
-#ifdef pFlow_Build_MPI
-            
-            auto gatherT = pFlow::MPI::gatherMaster<T>(pFlowProcessors());
-            
-            if(!gatherT.gatherData(data))
-            {
-                fatalErrorInFunction<<"Error in gathering data to master"<<endl;
-                return false;
-            }
-
-            this->buffer_ = gatherT.moveData();
-
-            this->bufferSpan_ = makeSpan(this->buffer_);
-
-            return true;
-#else
-            notImplementedFunction;
-            fatalExit;
-            return false;
-#endif //pFlow_Build_MPI
-        
-        }
-
-        if( this->ioPattern_.isMasterProcessorOnly() || this->ioPattern_.isAllProcessorSimilar() )
-        {
-            if( this->ioPattern_.isMaster() )
-            {
-                this->bufferSpan_ = data;
-            }
-            else
-            {
-                this->bufferSpan_ = span<T>(nullptr, 0);
-                return true;
-            }
-        }
-
-        return false;
-    }
-public:
-
-	TypeInfo("dataIO<MPI>");
-
-	dataIOMPI(const IOPattern& iop)
-    :
-        dataIO<T>(iop)
-    {}
-
-	dataIOMPI(const dataIOMPI&) = default;
-
-	dataIOMPI(dataIOMPI&&) = default;
-
-
-	dataIOMPI& operator=(const dataIOMPI&) = default;
-
-	dataIOMPI& operator=(dataIOMPI&&) = default;
-
-	~dataIOMPI() = default;
-
-};
-
-
-}
-
-
-#endif

src/phasicFlow/streams/dataIO/dataIORegulars.cpp

@@ -19,9 +19,15 @@ template class pFlow::dataIORegular<pFlow::int64>;
 template class pFlow::dataIO<pFlow::uint32>;
 template class pFlow::dataIORegular<pFlow::uint32>;
 
+template class pFlow::dataIO<pFlow::uint32x3>;
+template class pFlow::dataIORegular<pFlow::uint32x3>;
+
 template class pFlow::dataIO<pFlow::uint64>;
 template class pFlow::dataIORegular<pFlow::uint64>;
 
+template class pFlow::dataIO<size_t>;
+template class pFlow::dataIORegular<size_t>;
+
 template class pFlow::dataIO<pFlow::real>;
 template class pFlow::dataIORegular<pFlow::real>;
 

src/phasicFlow/streams/iStream/iIstream.hpp

@@ -260,6 +260,8 @@ inline iIstream& operator>>( iIstream& is, float& val);
 
 inline iIstream& operator>>( iIstream& is, double& val);
 
+inline iIstream& operator>>( iIstream& is, size_t& val);
+
 
 
 } // pFlow

src/phasicFlow/streams/iStream/iIstreamI.hpp

@@ -295,3 +295,35 @@ inline pFlow::iIstream& pFlow::operator>>( iIstream& is, double& val)
     return is;
 }
 
+inline pFlow::iIstream& pFlow::operator>>( iIstream& is, size_t& val)
+{
+    token t(is);
+    if (!t.good())
+    {
+        ioErrorInFile(is.name(), is.lineNumber())
+            << "Bad token - could not get double value";
+            fatalExit;
+        is.setBad();
+        return is;
+    }
+
+    if (t.isNumber())
+    {
+        val = static_cast<size_t>(t.number());
+    }
+    else
+    {
+        ioErrorInFile(is.name(), is.lineNumber())
+            << "Wrong token type - expected double value, found "
+            << t;
+            fatalExit;
+        is.setBad();
+        return is;
+    }
+
+    is.check(FUNCTION_NAME);
+    return is;
+}
+
+
+

src/phasicFlow/streams/streams.cpp

@@ -9,5 +9,5 @@ pFlow::processorOstream pFlow::pOutput(cout, "pFlow processorOstream");
 
 pFlow::Istream pFlow::input( std::cin, "sFlow Istream"); 
 
-pFlow::masterOstream pFlow::errReport( std::cerr, "pFlow error report stream");
+pFlow::processorOstream pFlow::errReport( std::cerr, "pFlow error report stream");
 

src/phasicFlow/streams/streams.hpp

@@ -28,12 +28,12 @@ namespace pFlow
 
 	extern Istream input; 
 
-	extern masterOstream errReport;
+	extern processorOstream errReport;
 
 }
 
 
-#define INFORMATION pFlow::mOutput<<boldChar<<magentaColor<<"> INFO: "<<defaultColor<<magentaColor
+#define INFORMATION pFlow::pOutput<<boldChar<<magentaColor<<"> INFO: "<<defaultColor<<magentaColor
 #define END_INFO defaultColor<<pFlow::endl
 
 #define REPORT(n) pFlow::mOutput.space(2*n)

src/phasicFlow/structuredData/boundaries/boundaryBase/boundaryBase.cpp

@@ -191,7 +191,8 @@ pFlow::boundaryBase::boundaryBase
 	internal_(internal),
 	boundaries_(bndrs),
 	thisBoundaryIndex_(thisIndex),
-	mirrorProcessoNo_(dict.getVal<uint32>("mirrorProcessorNo")),
+	neighborProcessorNo_(dict.getVal<int32>("neighborProcessorNo")),
+	isBoundaryMaster_(thisProcessorNo()>=neighborProcessorNo()),
 	name_(dict.name()),
 	type_(dict.getVal<word>("type"))
 {
@@ -231,13 +232,22 @@ pFlow::boundaryBase::thisPoints()const
    
 }
 
-typename pFlow::boundaryBase::pointFieldAccessType
-    pFlow::boundaryBase::neighborPoints()const
+pFlow::realx3Vector_D& pFlow::boundaryBase::neighborProcPoints()
 {
-    notImplementedFunction;
-    return pointFieldAccessType();
+	static realx3Vector_D dummyVector{"dummyVector"};
+	notImplementedFunction;
+	fatalExit;
+	return dummyVector;
 }
 
+const pFlow::realx3Vector_D& 
+pFlow::boundaryBase::neighborProcPoints()const
+{
+	static realx3Vector_D dummyVector{"dummyVector"};
+	notImplementedFunction;
+	fatalExit;
+	return dummyVector;
+}
 
 pFlow::realx3 pFlow::boundaryBase::displacementVectroToMirror() const
 {

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

@@ -51,42 +51,48 @@ public:
 
 private:
 
-	// friend et al. 
+	// friend et al.
 	friend boundaryList;
 
-	const plane& 	boundaryPlane_;
+	const plane&           boundaryPlane_;
 
-	/// list of particles indices on device 
-	uint32Vector_D 	indexList_;
+	/// list of particles indices on device
+	uint32Vector_D         indexList_;
 
 	/// list of particles indieces on host
-	mutable uint32Vector_H 	indexListHost_;
+	mutable uint32Vector_H indexListHost_;
 
 	/// device and host list are sync
-	mutable bool 			listsSync_ = false;
+	mutable bool           listsSync_ = false;
 
-	/// The length defined for creating neighbor list 
-	real  			neighborLength_;	
+	/// The length defined for creating neighbor list
+	real                   neighborLength_;
 
-	/// a reference to internal points 
-	internalPoints& internal_;
+	/// a reference to internal points
+	internalPoints&        internal_;
 
-	/// a reference to the list of boundaries 
+	/// a reference to the list of boundaries
 	/// (never use this in the constructor).
-	boundaryList& 	boundaries_;
+	boundaryList&          boundaries_;
 
-	uint32 			thisBoundaryIndex_;
+	uint32                 thisBoundaryIndex_;
 
-	uint32 			mirrorProcessoNo_;
+	int                    neighborProcessorNo_;
 
-	word 		name_;
+	bool                   isBoundaryMaster_;
 
-	word 		type_;
+	word                   name_;
+
+	word                   type_;
 
 protected:
 	
-	/// @brief set the size of indexList 
-	void setSize(uint32 newSize);
+	/// @brief Set the size of indexList. 
+	/// It is virtual to let derived classed to be aware of 
+	/// the fact that the size of boundary points has been changed.
+	/// So, any drived class that override this method should call 
+	/// boundaryBase::setSize(newSize) too. 
+	virtual void setSize(uint32 newSize);
 
 	void setNewIndices(const uint32Vector_D& newIndices);
 
@@ -116,6 +122,17 @@ protected:
 		}
 	}
 
+	/// Update this boundary data in two steps (1 and 2).
+	/// This is called after calling beforeIteration for 
+	/// all boundaries, so any particle addition, deletion,
+	/// and transfer has been finished up to this point.
+	/// This two-step update help to have a flexible mechanism
+	/// for data transfer, mostly for MPI related jobs. 
+	virtual 
+	bool updataBoundary(int step)
+	{
+		return true;
+	}
 	
 public:
 
@@ -213,6 +230,24 @@ public:
 		return indexList_.capacity();
 	}
 
+	inline 
+	int neighborProcessorNo()const
+	{
+		return neighborProcessorNo_;
+	}
+
+	inline 
+	int thisProcessorNo()const
+	{
+		return pFlowProcessors().localRank();
+	}
+
+	inline
+    bool isBoundaryMaster()const
+    {
+        return isBoundaryMaster_;
+    }
+
 	inline
 	uint32 thisBoundaryIndex()const
 	{
@@ -283,8 +318,22 @@ public:
 	
     pointFieldAccessType thisPoints()const;
 
+	/// @brief Return number of points in the neighbor processor boundary
+	virtual 
+	uint32 neighborProcSize()const
+	{
+		return 0;
+	}
+
+	/// @brief Return a reference to point positions in the neighbor
+	/// processor boundary.
     virtual
-    pointFieldAccessType neighborPoints()const;
+    realx3Vector_D& neighborProcPoints();
+
+	/// @brief Return a const reference to point positions in the 
+	/// neighbor processor boundary.
+	virtual
+	const realx3Vector_D& neighborProcPoints()const;
     
 	/// - static create 
 	static

src/phasicFlow/structuredData/boundaries/boundaryList.cpp

@@ -2,17 +2,17 @@
       O        C enter of
      O O       E ngineering and
     O   O      M ultiscale modeling of
-   OOOOOOO     F luid flow       
+   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 
+  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 
+  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.
 
@@ -21,49 +21,44 @@ Licence:
 #include "boundaryList.hpp"
 #include "pointStructure.hpp"
 
-void pFlow::boundaryList::setExtendedDomain()
+void
+pFlow::boundaryList::setExtendedDomain()
 {
-	if(!listSet_)
+	if (!listSet_)
 	{
-		fatalErrorInFunction<<
-		"boundary list is not set yet and you used the objects."<<endl;
+		fatalErrorInFunction
+		  << "boundary list is not set yet and you used the objects." << endl;
 		fatalExit;
 	}
-	
-	realx3 lowerExt = 
-		boundary(0).boundaryExtensionLength() + 
-		boundary(2).boundaryExtensionLength() + 
-		boundary(4).boundaryExtensionLength();
-	
-	realx3 upperExt = 
-		boundary(1).boundaryExtensionLength()+
-		boundary(3).boundaryExtensionLength()+
-		boundary(5).boundaryExtensionLength();
-	
-	extendedDomain_ = pStruct_.simDomain().extendThisDomain
-	(
-		lowerExt,
-		upperExt
-	);
-	
-	
+
+	realx3 lowerExt = boundary(0).boundaryExtensionLength() +
+	                  boundary(2).boundaryExtensionLength() +
+	                  boundary(4).boundaryExtensionLength();
+
+	realx3 upperExt = boundary(1).boundaryExtensionLength() +
+	                  boundary(3).boundaryExtensionLength() +
+	                  boundary(5).boundaryExtensionLength();
+
+	extendedDomain_ = pStruct_.simDomain().extendThisDomain(lowerExt, upperExt);
 }
 
-bool pFlow::boundaryList::resetLists()
+bool
+pFlow::boundaryList::resetLists()
 {
 	clear();
 	listSet_ = false;
-    return true;
+	return true;
 }
 
-bool pFlow::boundaryList::updateLists()
+bool
+pFlow::boundaryList::updateNeighborLists()
 {
-    if(!listSet_)
+	if (!listSet_)
 	{
-		setLists();
+		createBoundaries();
 	}
 
-	std::array<real,6> dist;
+	std::array<real, 6> dist;
 	dist[0] = boundary(0).neighborLength();
 	dist[1] = boundary(1).neighborLength();
 	dist[2] = boundary(2).neighborLength();
@@ -71,71 +66,66 @@ bool pFlow::boundaryList::updateLists()
 	dist[4] = boundary(4).neighborLength();
 	dist[5] = boundary(5).neighborLength();
 
-	pStruct_.updateFlag(
-			extendedDomain_,
-			dist);
+	pStruct_.updateFlag(extendedDomain_, dist);
 
 	const auto& maskD = pStruct_.activePointsMaskDevice();
-	boundary(0).setSize( maskD.leftSize() );
-	boundary(1).setSize( maskD.rightSize() );
-	boundary(2).setSize( maskD.bottomSize() );
-	boundary(3).setSize( maskD.topSize() );
-	boundary(4).setSize( maskD.rearSize() );
-	boundary(5).setSize( maskD.frontSize() );
+	boundary(0).setSize(maskD.leftSize());
+	boundary(1).setSize(maskD.rightSize());
+	boundary(2).setSize(maskD.bottomSize());
+	boundary(3).setSize(maskD.topSize());
+	boundary(4).setSize(maskD.rearSize());
+	boundary(5).setSize(maskD.frontSize());
 
 	pStruct_.fillNeighborsLists(
-		boundary(0).indexList().deviceViewAll(),
-		boundary(1).indexList().deviceViewAll(),
-		boundary(2).indexList().deviceViewAll(),
-		boundary(3).indexList().deviceViewAll(),
-		boundary(4).indexList().deviceViewAll(),
-		boundary(5).indexList().deviceViewAll());
-	
-	
-	return true;	
+	  boundary(0).indexList().deviceViewAll(),
+	  boundary(1).indexList().deviceViewAll(),
+	  boundary(2).indexList().deviceViewAll(),
+	  boundary(3).indexList().deviceViewAll(),
+	  boundary(4).indexList().deviceViewAll(),
+	  boundary(5).indexList().deviceViewAll()
+	);
+
+	return true;
 }
 
-pFlow::boundaryList::boundaryList
-(
-    pointStructure& pStruct
-)
-: 
-	ListPtr<boundaryBase>(pStruct.simDomain().sizeOfBoundaries()),
-	pStruct_(pStruct),
-	timeControl_
-	(
-		pStruct.simDomain().subDict("boundaries"), 
-		"update",
-		pStruct.currentTime()
-	)
-{}
-
-bool pFlow::boundaryList::updateLists(uint32 iter, real t, real dt)
+pFlow::boundaryList::boundaryList(pointStructure& pStruct)
+  : ListPtr<boundaryBase>(pStruct.simDomain().sizeOfBoundaries()),
+    pStruct_(pStruct),
+    timeControl_(
+      pStruct.simDomain().subDict("boundaries"),
+      "update",
+      pStruct.currentTime()
+    )
 {
-	if( timeControl_.timeEvent(iter, t, dt))
+}
+
+bool
+pFlow::boundaryList::updateNeighborLists(uint32 iter, real t, real dt)
+{
+	if (timeControl_.timeEvent(iter, t, dt))
 	{
-		return updateLists();
+		return updateNeighborLists();
 	}
 	return true;
 }
 
-bool pFlow::boundaryList::setLists()
+bool
+pFlow::boundaryList::createBoundaries()
 {
-	if(listSet_)return true;
+	if (listSet_)
+		return true;
 
-	for(auto i=0; i<pStruct_.simDomain().sizeOfBoundaries();i++)
+	for (auto i = 0; i < pStruct_.simDomain().sizeOfBoundaries(); i++)
 	{
-		this->set
-		(
-			i,
-			boundaryBase::create
-			(
-				pStruct_.simDomain().boundaryDict(i),
-				pStruct_.simDomain().boundaryPlane(i),
-				pStruct_,
-				*this,
-				i
-			)
+		this->set(
+		  i,
+		  boundaryBase::create(
+		    pStruct_.simDomain().boundaryDict(i),
+		    pStruct_.simDomain().boundaryPlane(i),
+		    pStruct_,
+		    *this,
+		    i
+		  )
 		);
 	}
 	listSet_ = true;
@@ -146,81 +136,81 @@ bool pFlow::boundaryList::setLists()
 pFlow::box
 pFlow::boundaryList::internalDomainBox() const
 {
-	const auto& thisBox = pStruct_.thisDomain().domainBox();
-	
+	const auto&  thisBox = pStruct_.thisDomain().domainBox();
+
 	const realx3 lowerPointDisplacement = {
-		boundary(0).neighborLengthIntoInternal(), 
-		boundary(2).neighborLengthIntoInternal(), 
-		boundary(4).neighborLengthIntoInternal()};
+		boundary(0).neighborLengthIntoInternal(),
+		boundary(2).neighborLengthIntoInternal(),
+		boundary(4).neighborLengthIntoInternal()
+	};
 
 	const realx3 upperPointDisplacement = {
-		boundary(1).neighborLengthIntoInternal(), 
-		boundary(3).neighborLengthIntoInternal(), 
-		boundary(5).neighborLengthIntoInternal()};
-	
-	return {thisBox.minPoint() + lowerPointDisplacement, 
-			thisBox.maxPoint() - upperPointDisplacement};
+		boundary(1).neighborLengthIntoInternal(),
+		boundary(3).neighborLengthIntoInternal(),
+		boundary(5).neighborLengthIntoInternal()
+	};
+
+	return { thisBox.minPoint() + lowerPointDisplacement,
+		     thisBox.maxPoint() - upperPointDisplacement };
 }
 
 bool
 pFlow::boundaryList::beforeIteration(uint32 iter, real t, real dt)
 {
-	// it is time to update lists 
-	if(timeControl_.timeEvent(iter, t, dt))
+	// it is time to update lists
+	if (timeControl_.timeEvent(iter, t, dt) && !updateNeighborLists())
 	{
-		if(!updateLists())
+		fatalErrorInFunction;
+		return false;
+	}
+
+	for (auto bdry : *this)
+	{
+		if (!bdry->beforeIteration(iter, t, dt))
 		{
-			fatalErrorInFunction;
+			fatalErrorInFunction << "Error in beforeIteration in boundary "
+			                     << bdry->name() << endl;
 			return false;
 		}
 	}
 
-	for(auto& bdry:*this)
+	for (auto bdry : *this)
 	{
-		if( !bdry->beforeIteration(iter, t, dt))
-		{
-			fatalErrorInFunction<<
-			"Error in beforeIteration in boundary "<<bdry->name()<<endl;
-			return false;
-		}
-		
+		bdry->updataBoundary(1);
 	}
 
-    return true;
+	for (auto bdry : *this)
+	{
+		bdry->updataBoundary(2);
+	}
+
+	return true;
 }
 
-bool pFlow::boundaryList::iterate
-(
-	uint32 iter, 
-	real t, 
-	real dt
-)
+bool
+pFlow::boundaryList::iterate(uint32 iter, real t, real dt)
 {
-	for(auto& bdry:*this)
+	for (auto& bdry : *this)
 	{
-		if( !bdry->iterate(iter, t, dt))
+		if (!bdry->iterate(iter, t, dt))
 		{
-			fatalErrorInFunction<<
-			"Error in iterate in boundary "<<bdry->name()<<endl;
-			return false;
-		}
-	}
-    return true;
-}
-
-bool pFlow::boundaryList::afterIteration
-(
-	uint32 iter, 
-	real t, 
-	real dt
-)
-{
-    for(auto& bdry:*this)
-	{
-		if( !bdry->afterIteration(iter, t, dt))
-		{
-			fatalErrorInFunction<<
-			"Error in afterIteration in boundary "<<bdry->name()<<endl;
+			fatalErrorInFunction << "Error in iterate in boundary "
+			                     << bdry->name() << endl;
+			return false;
+		}
+	}
+	return true;
+}
+
+bool
+pFlow::boundaryList::afterIteration(uint32 iter, real t, real dt)
+{
+	for (auto& bdry : *this)
+	{
+		if (!bdry->afterIteration(iter, t, dt))
+		{
+			fatalErrorInFunction << "Error in afterIteration in boundary "
+			                     << bdry->name() << endl;
 			return false;
 		}
 	}

src/phasicFlow/structuredData/boundaries/boundaryList.hpp

@@ -40,24 +40,23 @@ class boundaryList
 private:
 
 	//// - data members
-		pointStructure& 		pStruct_;
+	pointStructure& pStruct_;
 
-		baseTimeControl 		timeControl_;
+	baseTimeControl timeControl_;
 
-		domain 					extendedDomain_;
+	domain          extendedDomain_;
 
-		box 					internalDomainBox_;
+	box             internalDomainBox_;
 
-		bool                    listSet_ = false;
+	bool            listSet_ = false;
 
-		void setExtendedDomain();		
+	void setExtendedDomain();
 
-		bool resetLists();
-
-		/// @brief update neighbor list of boundaries regardless
-		/// of the time intervals 
-		bool updateLists();
+	bool resetLists();
 
+	/// @brief update neighbor list of boundaries regardless
+	/// of the time intervals
+	bool updateNeighborLists();
 
 public:
 	
@@ -66,16 +65,16 @@ public:
 	
 
 	//// - Constructors
-	boundaryList(pointStructure& pStruct);
+	explicit boundaryList(pointStructure& pStruct);
 
 
-  	~boundaryList() = default;
+  	virtual ~boundaryList() = default;
 
 	/// @brief update neighbor list of boundaries based on 
 	/// the time intervals
-	bool updateLists(uint32 iter, real t, real dt);
+	bool updateNeighborLists(uint32 iter, real t, real dt);
 
-	bool setLists();
+	bool createBoundaries();
 
 	inline
 	const pointStructure& pStruct()const
@@ -115,8 +114,6 @@ public:
 
 	box internalDomainBox()const;
 	
-	
-
 	bool beforeIteration(uint32 iter, real t, real dt);
 
 	bool iterate(uint32 iter, real t, real dt);

src/phasicFlow/structuredData/domain/regularSimulationDomain.cpp

@@ -51,9 +51,9 @@ bool pFlow::regularSimulationDomain::createBoundaryDicts()
 			return false;
 		}
 
-		if(!bDict.add("mirrorProcessorNo",(uint32) processors::globalRank()))
+		if(!bDict.add("neighborProcessorNo",(uint32) processors::globalRank()))
 		{
-			fatalErrorInFunction<<"error in adding mirrorProcessorNo to "<< bName <<
+			fatalErrorInFunction<<"error in adding neighborProcessorNo to "<< bName <<
 			" in dictionary "<< boundaries.globalName()<<endl;
 			return false;
 		}
@@ -84,7 +84,7 @@ bool pFlow::regularSimulationDomain::createBoundaryDicts()
 
 bool pFlow::regularSimulationDomain::setThisDomain()
 {
-	thisDomain_ = domain(globalBox_);
+	thisDomain_ = domain(globalBox());
     return true;
 }
 
@@ -126,11 +126,23 @@ pFlow::uint32 pFlow::regularSimulationDomain::numberToBeExported() const
     return 0;
 }
 
-bool pFlow::regularSimulationDomain::initialTransferBlockData
-(
-	span<char> src, 
-	span<char> dst,
-	size_t sizeOfElement
+bool
+pFlow::regularSimulationDomain::domainActive() const
+{
+	return true;
+}
+
+const pFlow::domain&
+pFlow::regularSimulationDomain::thisDomain() const
+{
+	return thisDomain_;
+}
+
+bool
+pFlow::regularSimulationDomain::initialTransferBlockData(
+  span<char> src,
+  span<char> dst,
+  size_t     sizeOfElement
 ) const
 {
 	size_t requiredSize = sizeOfElement*initialNumberInThis();
@@ -209,7 +221,3 @@ const pFlow::dictionary &pFlow::regularSimulationDomain::thisBoundaryDict() cons
     return this->subDict("regularBoundaries");
 }
 
-bool pFlow::regularSimulationDomain::requiresDataTransfer()const
-{
-    return false;
-}

src/phasicFlow/structuredData/domain/regularSimulationDomain.hpp

@@ -2,17 +2,17 @@
       O        C enter of
      O O       E ngineering and
     O   O      M ultiscale modeling of
-   OOOOOOO     F luid flow       
+   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 
+  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 
+  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.
 
@@ -26,81 +26,70 @@ Licence:
 namespace pFlow
 {
 
-class regularSimulationDomain
-:
+class regularSimulationDomain 
+: 
 	public simulationDomain
 {
-protected:
+private:
 
-	uint32 		initialNumPoints_=0;
+	domain thisDomain_;
 
-	bool createBoundaryDicts() override;
+	uint32 initialNumPoints_ = 0;
 
-	bool setThisDomain()override;
+	bool   createBoundaryDicts() final;
+
+	bool   setThisDomain() final;
 
 public:
 
 	TypeInfo("simulationDomain<regular>");
 
-	regularSimulationDomain(systemControl& control);
+	explicit regularSimulationDomain(systemControl& control);
 
-	virtual
-	~regularSimulationDomain()=default;
-	
-	add_vCtor
-	(
-		simulationDomain,
-		regularSimulationDomain,
-		systemControl
-	);
+	~regularSimulationDomain() final = default;
 
-    bool initialUpdateDomains(span<realx3> pointPos) override;
+	add_vCtor(simulationDomain, regularSimulationDomain, systemControl);
 
-    uint32 initialNumberInThis()const override;
+	bool   initialUpdateDomains(span<realx3> pointPos) final;
 
-	bool initialThisDomainActive()const override
-	{
-		return true;
-	}
+	uint32 initialNumberInThis() const final;
 
-	/*bool updateDomains(
-		span<realx3> pointPos,
-        pFlagTypeHost flags) override;*/
-   
-	uint32 numberToBeImported()const override;
+	uint32 numberToBeImported() const final;
 
-	uint32 numberToBeExported()const override;
+	uint32 numberToBeExported() const final;
+
+	/// @brief Is this domain active?
+	/// Active mean, there is particle in it and
+	/// boundaries and other entities of simulation domains are valid
+	bool domainActive() const final;
+
+	/// @brief return the simulation domain of this processor
+	const domain& thisDomain() const final;
 
 	bool initialTransferBlockData(
-		span<char> src, 
-		span<char> dst,
-		size_t sizeOfElement) const override;
+	  span<char> src,
+	  span<char> dst,
+	  size_t     sizeOfElement
+	) const final;
 
+	/// @brief
+	/// @param src
+	/// @param dst
+	/// @return
+	bool initialTransferBlockData(span<realx3> src, span<realx3> dst)
+	  const final;
 
-    /// @brief 
-    /// @param src 
-    /// @param dst 
-    /// @return 
-    bool initialTransferBlockData(
-        span<realx3> src,
-        span<realx3> dst) const override;
+	bool initialTransferBlockData(span<real> src, span<real> dst)
+	  const final;
 
-    bool initialTransferBlockData(
-        span<real> src,
-        span<real> dst) const override;
+	bool initialTransferBlockData(span<uint32> src, span<uint32> dst)
+	  const final;
 
-    bool initialTransferBlockData(
-        span<uint32> src,
-        span<uint32> dst) const override;
+	bool initialTransferBlockData(span<int32> src, span<int32> dst)
+	  const final;
 
-    bool initialTransferBlockData(
-        span<int32> src,
-        span<int32> dst) const override;
-    
-	
-	const dictionary& thisBoundaryDict()const override;
+	const dictionary& thisBoundaryDict() const final;
 
-	bool requiresDataTransfer() const override;
 };
 
 }

src/phasicFlow/structuredData/domain/simulationDomain.cpp

@@ -52,8 +52,14 @@ pFlow::domain pFlow::simulationDomain::extendThisDomain
 	return domain({minP, maxP});
 }
 
+const pFlow::plane&
+pFlow::simulationDomain::boundaryPlane(uint32 i) const
+{
+	return thisDomain().boundaryPlane(i);
+}
+
 pFlow::uniquePtr<pFlow::simulationDomain>
-	pFlow::simulationDomain::create(systemControl &control)
+pFlow::simulationDomain::create(systemControl& control)
 {
 	word sType = angleBracketsNames(
         "simulationDomain", 

src/phasicFlow/structuredData/domain/simulationDomain.hpp

@@ -39,33 +39,27 @@ class simulationDomain
 :
 	public fileDictionary
 {
-private:
+private:	
 
-static inline constexpr uint32 sizeOfBoundaries_ = 6;
-
-static 
-inline const std::array<word,6>  boundaryNames_ = 
-{
-	"left", "right", 
-	"bottom", "top",
-	"rear", "front"
-};
-
-protected:	
-
-	//fileDictionary 	globalDomainDict_ ;
-
-	/// @brief acutal limits of the simulation domain
+	/// @brief acutal limits of the global box of  simulation
 	box 			globalBox_;
 
-	/// @brief the actual limits of this processor domain 
-	domain 			thisDomain_;
 
-	bool 			boundariesSet_ = false;
+	static constexpr uint32 sizeOfBoundaries_ = 6;
+
+	static 
+	inline const std::array<word,6>  boundaryNames_ = 
+	{
+		"left", "right", 
+		"bottom", "top",
+		"rear", "front"
+	};
 	
-	virtual bool    createBoundaryDicts() = 0;
+	virtual 
+	bool createBoundaryDicts() = 0;
 
-	virtual bool    setThisDomain() = 0;
+	virtual 
+	bool setThisDomain() = 0;
 
 public:
 
@@ -73,11 +67,10 @@ public:
 	TypeInfo("simulationDomain");
 
 	/// Constrcut from components 
-	simulationDomain(systemControl& control);
+	explicit simulationDomain(systemControl& control);
 	
 	/// Destructor 
-	virtual 
-	~simulationDomain() = default;
+	~simulationDomain() override = default;
 	
 
 	create_vCtor
@@ -88,6 +81,11 @@ public:
 		(control)	
 	);
 
+	const auto& globalBox()const
+	{
+		return globalBox_;
+	}
+
 	virtual 
 	const dictionary& thisBoundaryDict()const = 0;
 	
@@ -97,9 +95,6 @@ public:
     virtual
     uint32 initialNumberInThis()const = 0;
 
-	virtual 
-	bool initialThisDomainActive()const = 0;
-
     virtual 
 	bool initialTransferBlockData(
 		span<char> src, 
@@ -139,9 +134,7 @@ public:
             charSpan(dst), 
             el
         );
-    } 
-
-
+    }
 
     /// @brief Number of points to be imported after updating domains 
 	/// @return number of points
@@ -151,40 +144,46 @@ public:
     virtual 
     uint32 numberToBeExported()const = 0;
 
-	
-
+	/// @brief Is this domain active?
+	/// Active mean, there is particle in it and 
+	/// boundaries and other entities of simulation domains are valid  
 	virtual 
-	bool requiresDataTransfer() const = 0;
-
-	inline 
-	const auto& thisDomain()const
-	{
-		return thisDomain_;
-	}
+	bool domainActive()const = 0;
 
 	
+	/// @brief return the simulation domain of this processor 
+	virtual 
+	const domain& thisDomain()const = 0;
+	
+	
 	domain extendThisDomain(
 		const realx3& lowerPointExtension, 
 		const realx3& upperPointExtension)const;
 
+	/// @brief The original dictionary supplied by the user as input 
 	inline 
 	const auto& globalBoundaryDict()const
 	{
 		return static_cast<const fileDictionary&>(*this);
 	}
 
+	/// @brief return a const ref to dicrionary of boundary i of this processor 
 	inline
 	const dictionary& boundaryDict(uint32 i)const
 	{
 		return thisBoundaryDict().subDict(bundaryName(i));
 	}
 	
-	inline
-	const auto& boundaryPlane(uint32 i)const
-	{
-		return thisDomain_.boundaryPlane(i);
-	}
+	/// @brief return a const ref to the plane of boundary i of this processor 
+	const plane& boundaryPlane(uint32 i)const;
+	
 
+	static
+	uniquePtr<simulationDomain> create(systemControl& control);
+
+	/// @brief  Boundary name based on boundary index 
+	/// @param i boundary index (range from 0 to 5) 
+	/// @return const reference to name of the boundary 
 	static inline
 	const word& bundaryName(uint32 i)
 	{
@@ -197,9 +196,6 @@ public:
 		return boundaryNames_.size();
 	}
 	
-	static
-	uniquePtr<simulationDomain> create(systemControl& control);
-
 }; // simulationDomain
 
 

src/phasicFlow/structuredData/pointStructure/pointStructure/pointStructure.cpp

@@ -55,7 +55,7 @@ bool pFlow::pointStructure::setupPointStructure(const PointsTypeHost &points)
         thisN, 
         RESERVE()
     );
-    
+
     auto pSpan  = points.getSpan();
     
     if(auto iSpan  = internal.getSpan(); 
@@ -72,7 +72,7 @@ bool pFlow::pointStructure::setupPointStructure(const PointsTypeHost &points)
         return false;
     }
 
-    boundaries_.setLists();
+    boundaries_.createBoundaries();
 
     return true;
 }