Merge pull request #156 from PhasicFlow/develop

Develop

cmake/autoComplete

@@ -1,8 +1,46 @@
 PF_cFlags="--description --help --version"
+AllTimeFolders=
+__getAllTime(){
+	files=( $(ls) )
+	deleteFiles=(settings caseSetup cleanThisCase VTK runThisCase stl postprocess postProcess) 
+	declare -A delk
+	for del in "${deleteFiles[@]}" ; do delk[$del]=1 ; done
+		# Tag items to remove, based on
+	for k in "${!files[@]}" ; do
+		[ "${delk[${files[$k]}]-}" ] && unset 'files[k]'
+	done
+		# Compaction
+	COMPREPLY=("${files[@]}")
+	AllTimeFolders="${files[@]}"
+}
+
+__getFields(){
+	__getAllTime
+	local -A unique_files=()
+
+	for dir in $AllTimeFolders; do
+	  # Check if the directory exists
+	  if [ ! -d "$dir" ]; then
+		continue  # Skip to the next directory
+	  fi
+		  
+	  files_in_dir=$(find "$dir" -maxdepth 1 -type f -printf '%f\n' | sort -u)
+	  
+	# Add filenames to the associative array (duplicates will be overwritten)
+	  while IFS= read -r filename; do
+		unique_files["$filename"]=1 # Just the key is important, value can be anything
+	  done <<< "$files_in_dir"
+	  
+	done
+	COMPREPLY=("${!unique_files[@]}")
+	AllTimeFolders=
+}
 
 _pFlowToVTK(){
     if [ "$3" == "--time" ]  ; then
-      COMPREPLY=( $(ls) )
+        __getAllTime
+    elif [ "$3" == "--fields" ]; then 
+    	__getFields
     else
         COMPREPLY=( $(compgen -W "$PF_cFlags --binary --no-geometry --no-particles --out-folder --time --separate-surfaces --fields" -- "$2") )
     fi
@@ -11,7 +49,7 @@ complete -F _pFlowToVTK pFlowToVTK
 
 _postprocessPhasicFlow(){
     if [ "$3" == "--time" ]; then
-      COMPREPLY=( $(ls) )
+      __getAllTime
     else
       COMPREPLY=( $(compgen -W "$PF_cFlags --out-folder --time --zeroFolder" -- "$2") )
     fi

src/Interaction/Models/grainContactForceModels.hpp

@@ -24,7 +24,6 @@ Licence:
 #include "cGAbsoluteLinearCF.hpp"
 #include "cGRelativeLinearCF.hpp"
 #include "cGNonLinearCF.hpp"
-#include "cGNonLinearCF2.hpp"
 
 #include "grainRolling.hpp"
 
@@ -43,8 +42,6 @@ using nonLimitedCGRelativeLinearGrainRolling = grainRolling<cGRelativeLinear<fal
 using limitedCGNonLinearGrainRolling   = grainRolling<cGNonLinear<true>>;
 using nonLimitedCGNonLinearGrainRolling = grainRolling<cGNonLinear<false>>;
 
-using limitedCGNonLinear2GrainRolling   = grainRolling<cGNonLinear2<true>>;
-using nonLimitedCGNonLinear2GrainRolling = grainRolling<cGNonLinear2<false>>;
 
 }
 

src/Interaction/contactSearch/contactSearch/contactSearch.cpp

@@ -93,7 +93,7 @@ bool pFlow::contactSearch::boundaryBroadSearch
 		bTimer_.start();
 		for(uint32 i=0u; i<6u; i++)
 		{
-			output<<" boundarySearch "<< i <<" for iter "<< ti.iter()<<endl;
+			//output<<" boundarySearch "<< i <<" for iter "<< ti.iter()<<endl;
 			if(!BoundaryBroadSearch(
 				i,
 				ti,

src/Interaction/sphereInteraction/boundaries/boundarySphereInteractionList.cpp

@@ -10,8 +10,8 @@ pFlow::boundarySphereInteractionList<CFModel, gMModel>::boundarySphereInteractio
 	boundaryListPtr<boundarySphereInteraction<CFModel,gMModel>>(),
 	boundaries_(sphPrtcls.pStruct().boundaries())
 {
-	
-	ForAllActiveBoundariesPtr(i, this)
+	output<<boundaries_.size()<<endl;
+	ForAllBoundariesPtr(i, this)
 	{
 		this->set(
 			i,

src/Interaction/sphereInteraction/sphereInteraction/sphereInteraction.cpp

@@ -145,6 +145,11 @@ pFlow::sphereInteraction<cFM,gMM, cLT>::sphereInteraction
 	{
 		fatalExit;
 	}
+
+	for(uint32 i=0; i<6; i++)
+	{
+		activeBoundaries_[i] = boundaryInteraction_[i].ppPairsAllocated();
+	}
 }
 
 template<typename cFM,typename gMM,template <class, class, class> class cLT>
@@ -190,11 +195,15 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::iterate()
 		ComputationTimer().start();
 
 		ForAllActiveBoundaries(i, boundaryInteraction_)
+		//for(size_t i=0; i<6; i++)
+		{
+			if(activeBoundaries_[i])
 			{
 				auto& BI = boundaryInteraction_[i];
 				BI.ppPairs().beforeBroadSearch();
 				BI.pwPairs().beforeBroadSearch();
 			}
+		}
 
 		ComputationTimer().end();
 		contactListMangementBoundaryTimer_.pause();	
@@ -214,6 +223,9 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::iterate()
 	}
 	
 	ForAllActiveBoundaries(i, boundaryInteraction_)
+	//for(size_t i=0; i<6; i++)
+	{
+		if(activeBoundaries_[i])
 		{
 			auto& BI = boundaryInteraction_[i];
 			if(!contactSearchRef.boundaryBroadSearch(
@@ -228,6 +240,7 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::iterate()
 				return false;
 			}
 		}
+	}
 	ComputationTimer().end();
 	
 	if(broadSearch && contactSearchRef.performedSearch())
@@ -246,11 +259,15 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::iterate()
 		ComputationTimer().start();
 		
 		ForAllActiveBoundaries(i, boundaryInteraction_)
+		//for(size_t i=0; i<6; i++)
+		{
+			if(activeBoundaries_[i])
 			{
 				auto& BI = boundaryInteraction_[i];
 				BI.ppPairs().afterBroadSearch();
 				BI.pwPairs().afterBroadSearch();
 			}
+		}
 
 		ComputationTimer().end();
 		contactListMangementBoundaryTimer_.end();
@@ -265,6 +282,7 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::iterate()
 	while(requireStep.anyElement(true) && step <= 10)
 	{
 		ForAllBoundaries(i, boundaryInteraction_)
+		//for(size_t i=0; i<6; i++)
 		{
 			if(requireStep[i] )
 			{
@@ -304,6 +322,7 @@ bool pFlow::sphereInteraction<cFM,gMM, cLT>::iterate()
 	while( requireStep.anyElement(true) && step < 20 )
 	{
 		ForAllBoundaries(i, boundaryInteraction_)
+		//for(size_t i=0; i<6; i++)
 		{
 			if(requireStep[i])
 			{

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

@@ -53,7 +53,7 @@ public:
         boundaryListPtr<BoundaryFieldType>(),
         boundaries_(boundaries)
     {
-        ForAllBoundaries(i, *this)
+        ForAllBoundariesPtr(i, this)
         {
             this->set
             (
@@ -69,13 +69,13 @@ public:
             && slaveToMasterUpdateIter_ == iter) return;
         
         // first step
-        ForAllBoundaries(i,*this)
+        ForAllBoundariesPtr(i,this)
         {
             this->boundaryPtr(i)->updateBoundary(1, direction);        
         }
 
         // second step
-        ForAllBoundaries(i,*this)
+        ForAllBoundariesPtr(i,this)
         {
             this->boundaryPtr(i)->updateBoundary(1, direction);
         }
@@ -88,7 +88,7 @@ public:
 
     void fill(const T& val)
     {
-        ForAllBoundaries(i, *this)
+        ForAllBoundariesPtr(i, this)
         {
             this->boundaryPtr(i)->fill(val);
         }

src/phasicFlow/eventManagement/subscriber.cpp

@@ -24,6 +24,11 @@ Licence:
 #include "observer.hpp"
 #include "message.hpp"
 
+pFlow::subscriber::subscriber(const word& name)
+:
+	observerList_(message::numEvents())
+{}
+
 pFlow::subscriber::subscriber(const subscriber & src)
 {
 }

src/phasicFlow/eventManagement/subscriber.hpp

@@ -39,14 +39,14 @@ class subscriber
 private:
 
 	// - list of subsribed objectd that recieve updage messages 
-	mutable std::vector<List<observer*>> observerList_{message::numEvents()};
+	mutable std::vector<List<observer*>> observerList_;
 
 	//word subName_;
 
 public:
 
-	subscriber(const word& name)
-	{}
+	subscriber(const word& name);
+	
 
 	/// Copy constructor, only copies the name, not the list 
 	subscriber(const subscriber&);

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

@@ -27,6 +27,10 @@ Licence:
 #include "pointStructure.hpp"
 #include "boundaryBaseKernels.hpp"
 
+std::array<pFlow::word,6> pFlow::boundaryBase::types_={"none","none","none","none","none","none"};
+std::array<pFlow::real, 6> pFlow::boundaryBase::neighborLengths_={0.01,0.01,0.01,0.01,0.01,0.01};
+std::array<pFlow::real, 6> pFlow::boundaryBase::boundaryExtntionLengthRatios_ = {0.1,0.1,0.1,0.1,0.1,0.1};
+
 void pFlow::boundaryBase::setSize(uint32 newSize)
 {
 	indexList_.resize(newSize);
@@ -232,14 +236,16 @@ pFlow::boundaryBase::boundaryBase(
       boundaryPlane_(bplane),
       indexList_(groupNames("indexList", dict.name())),
       indexListHost_(groupNames("hostIndexList", dict.name())),
-      neighborLength_(dict.getVal<real>("neighborLength")),
-      boundaryExtntionLengthRatio_(dict.getVal<real>("boundaryExtntionLengthRatio")),
       internal_(internal),
       boundaries_(bndrs),
       thisBoundaryIndex_(thisIndex),
-      neighborProcessorNo_(dict.getVal<int32>("neighborProcessorNo")),
-      type_(makeUnique<word>(dict.getVal<word>("type")))
+      neighborProcessorNo_(dict.getVal<int32>("neighborProcessorNo"))
 {
+	types_[thisBoundaryIndex_] = dict.getVal<word>("type");
+	
+	neighborLengths_[thisBoundaryIndex_] = dict.getValMax<real>("neighborLength",0.0);
+	
+	boundaryExtntionLengthRatios_[thisBoundaryIndex_] = dict.getValMax<real>("boundaryExtntionLengthRatio",0.1);
 
     isBoundaryMaster_ = thisProcessorNo() >= neighborProcessorNo();
 

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

@@ -69,9 +69,6 @@ private:
 	/// list of particles indieces on host
 	mutable uint32Vector_H indexListHost_;
 
-	/// The length defined for creating neighbor list
-	real                   neighborLength_;
-
 	/// device and host list are sync
 	mutable bool           listsSync_ = false;
 
@@ -81,9 +78,6 @@ private:
 
 	bool                   isBoundaryMaster_;
 
-	/// the extra boundary extension beyound actual limits of boundary 
-	real 				   boundaryExtntionLengthRatio_;
-
 	/// a reference to internal points
 	internalPoints&        internal_;
 
@@ -95,10 +89,21 @@ private:
 
 	int                    neighborProcessorNo_;
 
-	uniquePtr<word>        type_;
+	/// The length defined for creating neighbor list
+	static std::array<real, 6> neighborLengths_;
+
+	static std::array<word, 6> types_;
 
 protected:
 	
+	/// the extra boundary extension beyound actual limits of the physical domain 
+	static std::array<real, 6> boundaryExtntionLengthRatios_;
+
+	real boundaryExtntionLengthRatio()const
+	{
+		return boundaryExtntionLengthRatios_[thisBoundaryIndex_];
+	}
+
 	/// @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.
@@ -212,11 +217,11 @@ public:
 
 	/// The length from boundary plane into the domain 
 	/// where beyond that distance internal points exist.
-	/// By conventions is it always equal to neighborLength_  
+	/// By conventions is it always equal to neighborLengths_[i]  
 	inline
 	real neighborLengthIntoInternal()const
 	{
-		return neighborLength_;
+		return neighborLengths_[thisBoundaryIndex_];
 	}
 
 	/// The distance length from boundary plane 
@@ -224,10 +229,9 @@ public:
 	/// This length may be modified in each boundary type 
 	/// as required. In this case the boundaryExtensionLength
 	/// method should also be modified accordingly.  
-	virtual 
 	real neighborLength()const
 	{
-		return (1+boundaryExtntionLengthRatio_)*neighborLength_;
+		return (1+boundaryExtntionLengthRatio())*neighborLengthIntoInternal();
 	}
 
 	/// The extention length (in vector form) for the boundary
@@ -235,10 +239,9 @@ public:
 	/// each boundary type to be extended outward to allow 
 	/// particles to stay more in its list before being removed 
 	/// from its list.  
-	virtual 
 	realx3 boundaryExtensionLength()const
 	{
-		return -boundaryExtntionLengthRatio_*neighborLength_ * boundaryPlane_.normal();
+		return -boundaryExtntionLengthRatio()*neighborLengthIntoInternal() * boundaryPlane_.normal();
 	}
 
 	/// Is this iter the right time for updating bounday list
@@ -257,7 +260,7 @@ public:
 	inline
 	const word& type()const
 	{
-		return type_();
+		return types_[thisBoundaryIndex_];
 	}
 
 	inline

src/phasicFlow/structuredData/boundaries/boundaryList.cpp

@@ -144,7 +144,7 @@ pFlow::boundaryList::createBoundaries()
 	if (listSet_)
 		return true;
 
-	ForAllBoundaries(i, *this)
+	ForAllBoundariesPtr(i, this)
 	{
 		this->set(
 		  i,
@@ -200,7 +200,7 @@ pFlow::boundaryList::beforeIteration(const timeInfo& ti, bool force)
 
 	while(callAgain.anyElement(true) && step <= 10u)
 	{
-		ForAllBoundaries(i,*this)
+		ForAllBoundariesPtr(i,this)
 		{
 			if(callAgain[i])
 			{
@@ -239,7 +239,7 @@ pFlow::boundaryList::beforeIteration(const timeInfo& ti, bool force)
 		step++;
 	}
 	
-	ForAllBoundaries(i,*this)
+	ForAllBoundariesPtr(i,this)
 	{
 		boundary(i).updataBoundaryData(1);
 	}
@@ -248,7 +248,7 @@ pFlow::boundaryList::beforeIteration(const timeInfo& ti, bool force)
 		bdry->updataBoundaryData(1);
 	}*/
 
-	ForAllBoundaries(i,*this)
+	ForAllBoundariesPtr(i,this)
 	{
 		boundary(i).updataBoundaryData(2);
 	}
@@ -263,7 +263,7 @@ pFlow::boundaryList::beforeIteration(const timeInfo& ti, bool force)
 bool
 pFlow::boundaryList::iterate(const timeInfo& ti, bool force)
 {
-	ForAllBoundaries(i, *this)
+	ForAllBoundariesPtr(i, this)
 	{
 		if (!boundary(i).iterate(ti))
 		{
@@ -293,7 +293,7 @@ pFlow::boundaryList::afterIteration(const timeInfo& ti, bool force)
 	int step = 1;
 	while(callAgain.anyElement(true)&& step <=10)
 	{
-		ForAllBoundaries(i,*this)
+		ForAllBoundariesPtr(i,this)
 		{
 			if(callAgain[i])
 			{

src/phasicFlow/structuredData/boundaries/boundaryListPtr.hpp

@@ -34,35 +34,19 @@ template<typename BoundaryType>
 class boundaryListPtr 
 {
 private:
-	std::array<BoundaryType*,6> 		boundaries_;
+	std::array<BoundaryType*,6> 		baseBoundaries_;
 
 	std::bitset<6>						activeBoundaries_=0B000000;
 
 public:
 
 	boundaryListPtr():
-		boundaries_({nullptr, nullptr, nullptr, nullptr, nullptr, nullptr})
+		baseBoundaries_({nullptr, nullptr, nullptr, nullptr, nullptr, nullptr})
 	{}
 
-	void set(size_t i, uniquePtr<BoundaryType>&& ptr )
-	{
-		if( i > boundaries_.size() )
-		{
-			fatalErrorInFunction<<
-			"Out of range access of boundaryListPtr members. List size is "<<
-			size() << "and you are accessing "<< i << "\n";
-			fatalExit;
-		}
+	boundaryListPtr(const boundaryListPtr&)=delete;
 
-		if(boundaries_[i]) delete boundaries_[i];
-		boundaries_[i] = ptr.release();
-
-		if(boundaries_[i])
-		{
-			// query if this boundary active or not
-			activeBoundaries_.set(i,boundaries_[i]->isActive());	
-		}
-	}
+	boundaryListPtr(boundaryListPtr&&)=default;
 
 	~boundaryListPtr()
 	{
@@ -71,7 +55,7 @@ public:
 
 	void clear()
 	{
-		for(auto& bndry:boundaries_)
+		for(auto& bndry:baseBoundaries_)
 		{
 			if(bndry != nullptr)
 			{
@@ -82,16 +66,36 @@ public:
 		activeBoundaries_.reset();
 	}
 
+	void set(size_t i, uniquePtr<BoundaryType>&& ptr )
+	{
+		if( i > baseBoundaries_.size() )
+		{
+			fatalErrorInFunction<<
+			"Out of range access of boundaryListPtr members. List size is "<<
+			size() << "and you are accessing "<< i << "\n";
+			fatalExit;
+		}
+
+		if(baseBoundaries_[i]) delete baseBoundaries_[i];
+		baseBoundaries_[i] = ptr.release();
+
+		if(baseBoundaries_[i])
+		{
+			// query if this boundary active or not
+			activeBoundaries_.set(i,baseBoundaries_[i]->isActive());	
+		}
+	}
+
 	// - access to ith element
 	inline    
 	BoundaryType& operator[](size_t i)
 	{
-		if(boundaries_[i]== nullptr)
+		if(baseBoundaries_[i]== nullptr)
 		{
 			fatalErrorInFunction<<"Accessing nullptr element"<<endl;
 			fatalExit;
 		}
-		return *boundaries_[i];
+		return *(baseBoundaries_[i]);
 	}
 	
 	// - const access to ith element
@@ -99,34 +103,34 @@ public:
 	inline  
 	const BoundaryType& operator[](size_t i) const
 	{
-		if(boundaries_[i]== nullptr)
+		if(baseBoundaries_[i]== nullptr)
 		{
 			fatalErrorInFunction<<"Accessing nullptr element"<<endl;
 			fatalExit;
 		}
-		return *boundaries_[i];
+		return *(baseBoundaries_[i]);
 	}
 
 	inline
 	BoundaryType* boundaryPtr(size_t i)
 	{
-		if(boundaries_[i]== nullptr)
+		if(baseBoundaries_[i]== nullptr)
 		{
 			fatalErrorInFunction<<"Accessing nullptr element"<<endl;
 			fatalExit;
 		}
-		return boundaries_[i];
+		return baseBoundaries_[i];
 	}
 
 	inline
 	const BoundaryType* boundaryPtr(size_t i)const 
 	{
-		if(boundaries_[i]== nullptr)
+		if(baseBoundaries_[i]== nullptr)
 		{
 			fatalErrorInFunction<<"Accessing nullptr element"<<endl;
 			fatalExit;
 		}
-		return boundaries_[i];
+		return baseBoundaries_[i];
 	}
 
 	inline constexpr
@@ -178,7 +182,7 @@ public:
 
 }
 
-#define ForAllBoundaries(i,bndryList) for(size_t i = 0ul; i<(bndryList).size(); i++)
+#define ForAllBoundaries(i,bndryList) for(size_t i = 0ul; i<bndryList.size(); i++)
 #define ForAllBoundariesPtr(i,bndryList) for(size_t i = 0ul; i<bndryList->size(); i++)
 #define ForAllActiveBoundaries(i,bndryList) for(size_t i = bndryList.firstActive(); i<bndryList.size(); i=bndryList.nextActive(i))
 #define ForAllActiveBoundariesPtr(i,bndryList) for(size_t i = bndryList->firstActive(); i<bndryList->size(); i=bndryList->nextActive(i))

src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.cpp

@@ -33,23 +33,11 @@ pFlow::boundaryPeriodic::boundaryPeriodic
 )
 :
 	boundaryBase(dict, bplane, internal, bndrs, thisIndex),
-	mirrorBoundaryIndex_(dict.getVal<uint32>("mirrorBoundaryIndex")),
-	extensionLength_(dict.getVal<real>("boundaryExtntionLengthRatio"))
+	mirrorBoundaryIndex_(dict.getVal<uint32>("mirrorBoundaryIndex"))
 {
-	extensionLength_ = max(extensionLength_, static_cast<real>(0.1));
-}
 	
-pFlow::real pFlow::boundaryPeriodic::neighborLength() const
-{
-    return (1+extensionLength_)*neighborLengthIntoInternal();
 }
 
-pFlow::realx3 pFlow::boundaryPeriodic::boundaryExtensionLength() const
-{
-    return -extensionLength_*neighborLengthIntoInternal()*boundaryBase::boundaryPlane().normal();
-}
-
-
 bool pFlow::boundaryPeriodic::beforeIteration(
 	uint32 step, 
 	const timeInfo& ti, 
@@ -59,22 +47,25 @@ bool pFlow::boundaryPeriodic::beforeIteration(
 {
 	if(step==1)
 	{
+		boundaryBase::beforeIteration(step, ti, updateIter, iterBeforeUpdate, callAgain);
 		callAgain = true;
+		return true;
 	}
-	else
-	{
+
+	
 	callAgain = false;
 	// nothing have to be done
 	if(empty())
 	{
 		return true;
 	}
-
+	//output<<this->thisBoundaryIndex()<<"  ->"<<ti.iter()<<" update called\n";
 	if(!performBoundarytUpdate())
 	{
 		return true;
 	}
 
+	//output<<this->thisBoundaryIndex()<<"  ->"<< ti.iter()<<" update is being performed \n";
 	uint32 s = size();
 	uint32Vector_D transferFlags("transferFlags",s+1, s+1, RESERVE()); 
 	transferFlags.fill(0u);
@@ -116,10 +107,10 @@ bool pFlow::boundaryPeriodic::beforeIteration(
 		mirrorBoundaryIndex(), 
 		transferVec
 	);
-	}
 	
 	return true;
 	
+	
 }
 
 bool pFlow::boundaryPeriodic::iterate(const timeInfo& ti)

src/phasicFlow/structuredData/boundaries/boundaryPeriodic/boundaryPeriodic.hpp

@@ -35,8 +35,6 @@ private:
 
 	uint32 mirrorBoundaryIndex_;
 
-	real extensionLength_ = 0.1;
-
 public:
 
 	TypeInfo("boundary<periodic>");
@@ -58,9 +56,6 @@ public:
 		dictionary
 	);
 
-	real neighborLength()const override;
-
-	realx3 boundaryExtensionLength()const override;
 
 	bool beforeIteration(
 		uint32 step, 

src/phasicFlow/structuredData/boundaries/boundaryReflective/boundaryReflective.hpp

@@ -34,9 +34,9 @@ private:
 
 	real                      restitution_ = 0.95;
 
-    word        velocityName_{"velocity"};
+    inline static word        velocityName_{"velocity"};
 	
-    word        diameterName_{"diameter"};
+    inline static word        diameterName_{"diameter"};
 
 public:
 

src/phasicFlow/structuredData/domain/simulationDomain.cpp

@@ -75,7 +75,7 @@ bool pFlow::simulationDomain::prepareBoundaryDicts()
             return false;
 		}
 
-		bDict.addOrReplace("boundaryExtntionLengthRatio", boundaryExtntionLengthRatio);
+		bDict.addOrKeep("boundaryExtntionLengthRatio", boundaryExtntionLengthRatio);
 
 	}