Merge pull request #157 from PhasicFlow/develop

the need to provide neighborLength in domain dictionary is lifted. No…

DEMSystems/grainDEMSystem/grainDEMSystem.cpp

@@ -78,9 +78,14 @@ pFlow::grainDEMSystem::grainDEMSystem(
 	REPORT(0)<< "\nCreating surface geometry for grainDEMSystem . . . "<<END_REPORT;
 	geometry_ = geometry::create(Control(), Property());
 
+	REPORT(0)<<"Reading shape dictionary ..."<<END_REPORT;
+	grains_ = makeUnique<grainShape>(
+		pFlow::shapeFile__,
+		&Control().caseSetup(),
+		Property() );	
 
 	REPORT(0)<<"\nReading grain particles . . ."<<END_REPORT;
-	particles_ = makeUnique<grainFluidParticles>(Control(), Property());
+	particles_ = makeUnique<grainFluidParticles>(Control(), grains_());
 
 
 	insertion_ = makeUnique<grainInsertion>( 

DEMSystems/grainDEMSystem/grainDEMSystem.hpp

@@ -46,6 +46,8 @@ protected:
 
 	uniquePtr<geometry> 			geometry_ = nullptr;
 
+	uniquePtr<grainShape> 			grains_   = nullptr;
+
 	uniquePtr<grainFluidParticles>  particles_ = nullptr;
 
 	uniquePtr<grainInsertion> 		insertion_ = nullptr;

DEMSystems/grainDEMSystem/grainFluidParticles.cpp

@@ -35,8 +35,8 @@ void pFlow::grainFluidParticles::checkHostMemory()
 
 pFlow::grainFluidParticles::grainFluidParticles(
     systemControl &control,
-    const property &prop)
+    const grainShape& grains)
-    : grainParticles(control, prop),
+    : grainParticles(control, grains),
       fluidForce_(
           objectFile(
               "fluidForce",

DEMSystems/grainDEMSystem/grainFluidParticles.hpp

@@ -59,7 +59,7 @@ protected:
 public:
 
 	/// construct from systemControl and property 
-	grainFluidParticles(systemControl &control, const property& prop);
+	grainFluidParticles(systemControl &control, const grainShape& grains);
 
 	~grainFluidParticles() override = default;
 	

DEMSystems/sphereDEMSystem/sphereDEMSystem.cpp

@@ -74,13 +74,19 @@ pFlow::sphereDEMSystem::sphereDEMSystem(
 	property_ = makeUnique<property>(
 		propertyFile__,
     	Control().caseSetup().path());
+		
 
 	REPORT(0)<< "\nCreating surface geometry for sphereDEMSystem . . . "<<END_REPORT;
 	geometry_ = geometry::create(Control(), Property());
 
+	REPORT(0)<<"Reading shapes dictionary..."<<END_REPORT;
+	spheres_ = makeUnique<sphereShape>(
+		pFlow::shapeFile__, 
+		&Control().caseSetup(), 
+		Property());
 
 	REPORT(0)<<"\nReading sphere particles . . ."<<END_REPORT;
-	particles_ = makeUnique<sphereFluidParticles>(Control(), Property());
+	particles_ = makeUnique<sphereFluidParticles>(Control(), spheres_());
 
 
 	insertion_ = makeUnique<sphereInsertion>( 

DEMSystems/sphereDEMSystem/sphereDEMSystem.hpp

@@ -46,6 +46,8 @@ protected:
 
 	uniquePtr<geometry> 			geometry_ = nullptr;
 
+	uniquePtr<sphereShape> 			spheres_  = nullptr;
+
 	uniquePtr<sphereFluidParticles> particles_ = nullptr;
 
 	uniquePtr<sphereInsertion> 		insertion_ = nullptr;

DEMSystems/sphereDEMSystem/sphereFluidParticles.cpp

@@ -32,8 +32,8 @@ void pFlow::sphereFluidParticles::checkHostMemory()
 
 pFlow::sphereFluidParticles::sphereFluidParticles(
     systemControl &control,
-    const property &prop)
+    const sphereShape& shpShape)
-    : sphereParticles(control, prop),
+    : sphereParticles(control, shpShape),
       fluidForce_(
           objectFile(
               "fluidForce",

DEMSystems/sphereDEMSystem/sphereFluidParticles.hpp

@@ -66,7 +66,7 @@ protected:
 public:
 
 	/// construct from systemControl and property 
-	sphereFluidParticles(systemControl &control, const property& prop);
+	sphereFluidParticles(systemControl &control, const sphereShape& shpShape);
 	
 	/// before iteration step 
 	bool beforeIteration() override;

solvers/grainGranFlow/createDEMComponents.hpp

@@ -17,10 +17,17 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
+REPORT(0)<<"Reading shape dictionary ..."<<END_REPORT;
+pFlow::grainShape grains
+(
+	pFlow::shapeFile__,
+	&Control.caseSetup(),
+	proprties
+);
 
 //
 REPORT(0)<<"\nReading sphere particles . . ."<<END_REPORT;
-pFlow::grainParticles grnParticles(Control, proprties);
+pFlow::grainParticles grnParticles(Control, grains);
 
 //
 REPORT(0)<<"\nCreating particle insertion object . . ."<<END_REPORT;

solvers/iterateSphereParticles/createDEMComponents.hpp

@@ -18,8 +18,16 @@ Licence:
 
 -----------------------------------------------------------------------------*/
 
+REPORT(0)<<"Reading shape dictionary ..."<<END_REPORT;
+pFlow::sphereShape spheres
+(
+	pFlow::shapeFile__,
+	&Control.caseSetup(),
+	proprties
+);
+
 //
 REPORT(0)<<"\nReading sphere particles . . ."<<END_REPORT;
-pFlow::sphereParticles sphParticles(Control, proprties);
+pFlow::sphereParticles sphParticles(Control, spheres);
 
 WARNING<<"Particle insertion has not been set yet!"<<END_WARNING;

solvers/sphereGranFlow/createDEMComponents.hpp

@@ -17,10 +17,18 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-
+REPORT(0)<<"Reading shapes dictionary..."<<END_REPORT;
+pFlow::sphereShape spheres
+(
+	pFlow::shapeFile__,
+	&Control.caseSetup(),
+	proprties
+);
 //
 REPORT(0)<<"\nReading sphere particles . . ."<<END_REPORT;
-pFlow::sphereParticles sphParticles(Control, proprties);
+
+
+pFlow::sphereParticles sphParticles(Control, spheres);
 
 //
 REPORT(0)<<"\nCreating particle insertion object . . ."<<END_REPORT;

src/Particles/GrainParticles/grainParticles/grainParticles.cpp

@@ -142,16 +142,11 @@ pFlow::grainParticles::getParticlesInfoFromShape(
 
 pFlow::grainParticles::grainParticles(
 	systemControl &control,
-	const property& prop
+	const grainShape& gShape
 )
 :
-	particles(control),
+	particles(control, gShape),
-	grains_
+	grains_(gShape),
-	(
-		shapeFile__,
-		&control.caseSetup(),
-		prop
-	),
 	propertyId_
 	(
 		objectFile

src/Particles/GrainParticles/grainParticles/grainParticles.hpp

@@ -48,7 +48,7 @@ public:
 private:
 
 	/// reference to shapes
-	ShapeType              grains_;
+	const ShapeType&       grains_;
 
 	/// property id on device
 	uint32PointField_D     propertyId_;
@@ -121,7 +121,7 @@ protected:
 public:
 
 	/// construct from systemControl and property
-	grainParticles(systemControl& control, const property& prop);
+	grainParticles(systemControl& control, const grainShape& gShape);
 
 	~grainParticles() override = default;
 

src/Particles/Insertion/insertionRegion/insertionRegion.cpp

@@ -24,6 +24,7 @@ Licence:
 #include "particles.hpp"
 #include "twoPartEntry.hpp"
 #include "types.hpp"
+#include "shape.hpp"
 
 namespace pFlow
 {

src/Particles/SphereParticles/sphereParticles/sphereParticles.cpp

@@ -307,16 +307,11 @@ pFlow::sphereParticles::getParticlesInfoFromShape(
 
 pFlow::sphereParticles::sphereParticles(
 	systemControl &control,
-	const property& prop
+	const sphereShape& shpShape
 )
 :
-	particles(control),
+	particles(control, shpShape),
-	spheres_
+	spheres_(shpShape),
-	(
-		shapeFile__,
-		&control.caseSetup(),
-		prop
-	),
 	propertyId_
 	(
 		objectFile

src/Particles/SphereParticles/sphereParticles/sphereParticles.hpp

@@ -48,7 +48,7 @@ public:
 private:
 
 	/// reference to shapes
-	ShapeType              spheres_;
+	const ShapeType&              spheres_;
 
 	/// property id on device
 	uint32PointField_D     propertyId_;
@@ -124,7 +124,7 @@ protected:
 public:
 
 	/// construct from systemControl and property
-	sphereParticles(systemControl& control, const property& prop);
+	sphereParticles(systemControl& control, const sphereShape& shpShape);
 
 	~sphereParticles() override = default;
 

src/Particles/dynamicPointStructure/dynamicPointStructure.cpp

@@ -24,10 +24,11 @@ Licence:
 
 pFlow::dynamicPointStructure::dynamicPointStructure
 (
-	systemControl& control
+	systemControl& control,
+	real maxBSphere
 )
 :
-	pointStructure(control),
+	pointStructure(control, maxBSphere),
 	velocity_
 	(
 		objectFile(

src/Particles/dynamicPointStructure/dynamicPointStructure.hpp

@@ -57,7 +57,7 @@ public:
 
 	TypeInfo("dynamicPointStructure");
 
-	explicit dynamicPointStructure(systemControl& control);
+	explicit dynamicPointStructure(systemControl& control, real maxBSphere);
 
 	dynamicPointStructure(const dynamicPointStructure& ps) = delete;
 		

src/Particles/particles/particles.cpp

@@ -18,22 +18,12 @@ Licence:
 -----------------------------------------------------------------------------*/
 
 #include "particles.hpp"
+#include "shape.hpp"
 
-pFlow::particles::particles(systemControl& control)
+pFlow::particles::particles(systemControl& control, const shape& shapes)
   : observer(defaultMessage_),
     demComponent("particles", control),
-    dynPointStruct_(control),
+    dynPointStruct_(control, shapes.maxBoundingSphere()),
-    /*id_(
-      objectFile(
-        "id",
-        "",
-        objectFile::READ_IF_PRESENT,
-        objectFile::WRITE_ALWAYS
-      ),
-      dynPointStruct_,
-      static_cast<uint32>(-1),
-      static_cast<uint32>(-1)
-    ),*/
     shapeIndex_(
       objectFile(
         "shapeIndex",

src/Particles/particles/particles.hpp

@@ -25,11 +25,14 @@ PARTICULAR PURPOSE.
 #include "demComponent.hpp"
 #include "dynamicPointStructure.hpp"
 #include "particleIdHandler.hpp"
-#include "shape.hpp"
+//#include "shape.hpp"
 
 namespace pFlow
 {
 
+
+class shape;
+
 class particles
   : public observer
   , public demComponent
@@ -96,7 +99,7 @@ public:
 	// type info
 	TypeInfo("particles");
 
-	explicit particles(systemControl& control);
+	explicit particles(systemControl& control, const shape& shapes);
 
 	inline const auto& dynPointStruct() const
 	{

src/Particles/particles/shape/shape.hpp

@@ -37,7 +37,7 @@ private:
   	const property& 	property_; 
 
 	/// list of property ids of shapes (index)
-	uint32Vector			shapePropertyIds_;
+	uint32Vector		shapePropertyIds_;
 
 	/// list of material names 
 	wordVector 			materialNames_;

src/phasicFlow/structuredData/domain/regularSimulationDomain.cpp

@@ -72,10 +72,11 @@ bool pFlow::regularSimulationDomain::setThisDomain()
 
 pFlow::regularSimulationDomain::regularSimulationDomain
 (
-    systemControl& control
+    systemControl& control,
+    real maxBsphere
 )
 :
-    simulationDomain(control)
+    simulationDomain(control, maxBsphere)
 {}
 
 bool pFlow::regularSimulationDomain::initialUpdateDomains(span<realx3> pointPos)

src/phasicFlow/structuredData/domain/regularSimulationDomain.hpp

@@ -44,7 +44,7 @@ public:
 
 	TypeInfo("simulationDomain<regular>");
 
-	explicit regularSimulationDomain(systemControl& control);
+	explicit regularSimulationDomain(systemControl& control, real maxBsphere);
 
 	~regularSimulationDomain() final = default;
 

src/phasicFlow/structuredData/domain/simulationDomain.cpp

@@ -28,12 +28,14 @@ bool pFlow::simulationDomain::prepareBoundaryDicts()
 	
     dictionary& boundaries = this->subDict("boundaries");
 
-    real neighborLength = boundaries.getVal<real>("neighborLength");
-
 	real boundaryExtntionLengthRatio = 
         boundaries.getValOrSetMax("boundaryExtntionLengthRatio", static_cast<real>(0.1));
 	
-    uint32 updateInterval = 
+    real neighborLength = boundaries.getValOrSetMax<real>(
+		"neighborLength", 
+		(1+boundaryExtntionLengthRatio)*maxBoundingSphere_);
+
+	uint32 updateInterval = 
         boundaries.getValOrSetMax<uint32>("updateInterval", 1u);
 
     uint32 neighborListUpdateInterval = 
@@ -82,7 +84,7 @@ bool pFlow::simulationDomain::prepareBoundaryDicts()
     return true;
 }
 
-pFlow::simulationDomain::simulationDomain(systemControl &control)
+pFlow::simulationDomain::simulationDomain(systemControl &control, real maxBSphere)
     : fileDictionary(
           objectFile(
               domainFile__,
@@ -90,9 +92,10 @@ pFlow::simulationDomain::simulationDomain(systemControl &control)
               objectFile::READ_ALWAYS,
               objectFile::WRITE_NEVER),
           &control.settings()),
-      globalBox_(subDict("globalBox"))
+      globalBox_(subDict("globalBox")),
+	  maxBoundingSphere_(maxBSphere)
 {
-    if( !prepareBoundaryDicts() )
+	if( !prepareBoundaryDicts() )
     {
         fatalErrorInFunction<<
             "Error in preparing dictionaries for boundaries"<<endl;
@@ -118,16 +121,15 @@ pFlow::simulationDomain::boundaryPlane(uint32 i) const
 }
 
 pFlow::uniquePtr<pFlow::simulationDomain>
-pFlow::simulationDomain::create(systemControl& control)
+pFlow::simulationDomain::create(systemControl& control, real maxBSphere)
 {
 	word sType = angleBracketsNames(
         "simulationDomain", 
         pFlowProcessors().localRunTypeName());
 
-
 	if( systemControlvCtorSelector_.search(sType) )
 	{
-		return systemControlvCtorSelector_[sType] (control);
+		return systemControlvCtorSelector_[sType] (control, maxBSphere);
 	}
 	else
 	{

src/phasicFlow/structuredData/domain/simulationDomain.hpp

@@ -44,6 +44,7 @@ private:
 	/// @brief acutal limits of the global box of  simulation
 	box 			globalBox_;
 
+	real 			maxBoundingSphere_;
 	static constexpr uint32 sizeOfBoundaries_ = 6;
 
 	static 
@@ -70,7 +71,7 @@ public:
 	TypeInfo("simulationDomain");
 
 	/// Constrcut from components 
-	explicit simulationDomain(systemControl& control);
+	explicit simulationDomain(systemControl& control, real maxBSphere);
 	
 	/// Destructor 
 	~simulationDomain() override = default;
@@ -80,8 +81,8 @@ public:
 	(
 		simulationDomain,
 		systemControl,
-		(systemControl& control),
+		(systemControl& control, real maxBSphere),
-		(control)	
+		(control, maxBSphere)	
 	);
 
 	const auto& globalBox()const
@@ -189,7 +190,7 @@ public:
 	const plane& boundaryPlane(uint32 i)const;
 	
 	static
-	uniquePtr<simulationDomain> create(systemControl& control);
+	uniquePtr<simulationDomain> create(systemControl& control, real maxBSphere);
 
 	/// @brief  Boundary name based on boundary index 
 	/// @param i boundary index (range from 0 to 5) 

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

@@ -92,7 +92,8 @@ bool pFlow::pointStructure::initializePoints(const PointsTypeHost &points)
 
 pFlow::pointStructure::pointStructure
 (
-    systemControl& control
+    systemControl& control, 
+    real maxBSphere
 )
 :
     IOobject
@@ -111,7 +112,7 @@ pFlow::pointStructure::pointStructure
   	internalPoints(),
 	simulationDomain_
 	(
-		simulationDomain::create(control)
+		simulationDomain::create(control, maxBSphere)
 	),
     //pointSorting_(simulationDomain_->subDictOrCreate("pointSorting")),
 	boundaries_
@@ -137,6 +138,7 @@ pFlow::pointStructure::pointStructure
 
 pFlow::pointStructure::pointStructure(
     systemControl& control,
+    real maxBSphere, 
     const realx3Vector &posVec)
 :
 	IOobject
@@ -155,7 +157,7 @@ pFlow::pointStructure::pointStructure(
   	internalPoints(),
 	simulationDomain_
 	(
-		simulationDomain::create(control)
+		simulationDomain::create(control, maxBSphere)
 	),
     //pointSorting_(simulationDomain_->subDictOrCreate("pointSorting")),
 	boundaries_

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

@@ -80,11 +80,12 @@ public:
 	//// - Constructors 
 
 		/// an empty pointStructure, good for reading from file 
-		explicit pointStructure(systemControl& control);
+		explicit pointStructure(systemControl& control, real maxBSphere);
 
 		/// construct from point positions, assume all points are active
 		pointStructure(
             systemControl& control,
+			real maxBSphere,
 			const realx3Vector& posVec);
 
 		pointStructure(const pointStructure&) = delete;

utilities/pFlowToVTK/pointFieldToVTK.cpp

@@ -57,7 +57,7 @@ bool pFlow::PFtoVTK::convertTimeFolderPointFields(
     filename = vtk.fileName().wordPath();
 
     REPORT(1);
-    auto pStruct = pointStructure(control);
+    auto pStruct = pointStructure(control, 0.0005);
 
     // get a list of files in this timeFolder;
 
@@ -146,7 +146,7 @@ bool pFlow::PFtoVTK::convertTimeFolderPointFieldsSelected(
     filename = vtk.fileName().wordPath();
 
     REPORT(1);
-    auto pStruct = pointStructure(control);
+    auto pStruct = pointStructure(control, 0.0005);
 
     // get a list of files in this timeFolder;
 

utilities/particlesPhasicFlow/particlesPhasicFlow.cpp

@@ -88,7 +88,7 @@ int main( int argc, char* argv[] )
 
 		auto finalPos = pointPosition().getFinalPosition();
 
-		pStructPtr = pFlow::makeUnique<pFlow::pointStructure>(Control, finalPos);
+		pStructPtr = pFlow::makeUnique<pFlow::pointStructure>(Control, 0.0005, finalPos);
 
 
 		REPORT(1)<< "Created pStruct with "<< pStructPtr().size() << " points and capacity "<<
@@ -98,7 +98,7 @@ int main( int argc, char* argv[] )
     else
 	{
 		// read the content of pStruct from 0/pStructure
-		pStructPtr = pFlow::makeUnique<pFlow::pointStructure>(Control);
+		pStructPtr = pFlow::makeUnique<pFlow::pointStructure>(Control, 0.0005);
 
 	}
 

utilities/postprocessPhasicFlow/postprocess.cpp

@@ -65,7 +65,7 @@ bool pFlow::postprocess::processTimeFolder(real time, const word& tName, const f
 	control_.time().setTime(time);
 
 	REPORT(1)<<"Reading pointStructure"<<END_REPORT;
-	pointStructure pStruct(control_);
+	pointStructure pStruct(control_, 0.0005);
 
 	// first delete the object to remove fields from repository 
 	pointToCell_.reset(nullptr);