tutorial files modified for minor errors

All the problems were fixed

README.md

@@ -3,7 +3,7 @@
 </div>
 
 
-**PhasicFlow** is a parallel C++ code for performing DEM simulations. It can run on shared-memory multi-core computational units such as multi-core CPUs or GPUs (for now it works on CUDA-enabled GPUs). The parallelization method mainly relies on loop-level parallelization on a shared-memory computational unit. You can build and run PhasicFlow in serial mode on regular PCs, in parallel mode for multi-core CPUs, or build it for a GPU device to off-load computations to a GPU. In its current statues you can simulate millions of particles (up to 32M particles tested) on a single desktop computer. You can see the [performance tests of PhasicFlow](https://github.com/PhasicFlow/phasicFlow/wiki/Performance-of-phasicFlow) in the wiki page. 
+**PhasicFlow** is a parallel C++ code for performing DEM simulations. It can run on shared-memory multi-core computational units such as multi-core CPUs or GPUs (for now it works on CUDA-enabled GPUs). The parallelization method mainly relies on loop-level parallelization on a shared-memory computational unit. You can build and run PhasicFlow in serial mode on regular PCs, in parallel mode for multi-core CPUs, or build it for a GPU device to off-load computations to a GPU. In its current statues you can simulate millions of particles (up to 80M particles tested) on a single desktop computer. You can see the [performance tests of PhasicFlow](https://github.com/PhasicFlow/phasicFlow/wiki/Performance-of-phasicFlow) in the wiki page. 
 
 ## How to build?
 You can build PhasicFlow for CPU and GPU executions. [Here is a complete step-by-step procedure](https://github.com/PhasicFlow/phasicFlow/wiki/How-to-Build-PhasicFlow).
@@ -22,3 +22,19 @@ PhasicFlowPlus is and extension to PhasicFlow for simulating particle-fluid syst
 * [Kokkos](https://github.com/kokkos/kokkos) from National Technology & Engineering Solutions of Sandia, LLC (NTESS)
 * [CLI11 1.8](https://github.com/CLIUtils/CLI11) from University of Cincinnati.
 
+## How to cite PhasicFlow
+If you are using PhasicFlow in your research or industrial work, cite the following [article](https://www.sciencedirect.com/science/article/pii/S0010465523001662):
+```
+@article{NOROUZI2023108821,
+title = {PhasicFlow: A parallel, multi-architecture open-source code for DEM simulations},
+journal = {Computer Physics Communications},
+volume = {291},
+pages = {108821},
+year = {2023},
+issn = {0010-4655},
+doi = {https://doi.org/10.1016/j.cpc.2023.108821},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465523001662},
+author = {H.R. Norouzi},
+keywords = {Discrete element method, Parallel computing, CUDA, GPU, OpenMP, Granular flow}
+}
+```

src/Particles/Insertion/Insertion/Insertion.hpp

@@ -31,6 +31,28 @@ Licence:
 namespace pFlow
 {
 
+/**
+ * This class manages all the insertion regions for particles insertion
+ * in the simulation.
+ * 
+ * Any number of insertion regions can be defined in a simulation. The
+ * data for particle insertion is provided in particleInsertion file, which 
+ * looks like this. A list of insertion regions (class insertionRegion) can be defined in this file. 
+ * For more information see file insertionRegion.hpp. 
+ * \verbatim
+active  yes;
+
+region1
+{
+	// the data for insertionRegion
+}
+
+region2
+{
+	// Data for insertionRegion
+}
+ \endverbatim
+ */
 template<typename ShapeType>
 class Insertion
 :

src/Particles/Insertion/InsertionRegion/InsertionRegion.hpp

@@ -28,13 +28,18 @@ Licence:
 namespace pFlow
 {
 
+/**
+ * This manages insertion of particles from a region based on the ShapeType
+ *  
+ */
 template<typename ShapeType>
 class InsertionRegion
 :
 	public insertionRegion
 {
 protected:
-	// - type of particle shapes 
+
+	/// Ref to Shapes
 	const ShapeType& 	shapes_;
 
 	static bool checkForContact(
@@ -45,39 +50,52 @@ protected:
 
 public:
 
-	// - type info
+	/// Type info
 	TypeInfoTemplateNV("insertionRegion", ShapeType);
 
-	InsertionRegion(const dictionary& dict, const ShapeType& shapes);
+	// - Constructors
 
-	InsertionRegion(const InsertionRegion<ShapeType>& ) = default;
+		/// Construct from dictionary	
+		InsertionRegion(const dictionary& dict, const ShapeType& shapes);
 
-	InsertionRegion(InsertionRegion<ShapeType>&&) = default;
+		/// Copy
+		InsertionRegion(const InsertionRegion<ShapeType>& ) = default;
 
-	InsertionRegion<ShapeType>& operator=(const InsertionRegion<ShapeType>& ) = default;
+		/// Move
+		InsertionRegion(InsertionRegion<ShapeType>&&) = default;
 
-	InsertionRegion<ShapeType>& operator=(InsertionRegion<ShapeType>&&) = default;
+		/// Copy assignment
+		InsertionRegion<ShapeType>& operator=(const InsertionRegion<ShapeType>& ) = default;
 
+		/// Copy assignment
+		InsertionRegion<ShapeType>& operator=(InsertionRegion<ShapeType>&&) = default;
 
-	auto clone()const
-	{
-		return makeUnique<InsertionRegion<ShapeType>>(*this);
-	}
+		/// Clone
+		auto clone()const
+		{
+			return makeUnique<InsertionRegion<ShapeType>>(*this);
+		}
 
-	auto clonePtr()const
-	{
-		return new InsertionRegion<ShapeType>(*this);
-	}
+		/// Clone ptr
+		auto clonePtr()const
+		{
+			return new InsertionRegion<ShapeType>(*this);
+		}
 
+	// - Methods
 		
-	bool insertParticles
-	(
-		real currentTime,
-		real dt,
-		wordVector& names,
-		realx3Vector& pos,
-		bool& insertionOccured
-	);
+		/// Insert particles at currentTime
+		/// Check if currentTime is the right moment for 
+		/// particle insertion. Fill the vectors name, pos and signal
+		/// if particle insertion occured or not. 
+		bool insertParticles
+		(
+			real currentTime,
+			real dt,
+			wordVector& names,
+			realx3Vector& pos,
+			bool& insertionOccured
+		);
 
 	//bool read(const dictionary& dict);
 

src/Particles/Insertion/insertion/insertion.hpp

@@ -21,49 +21,58 @@ Licence:
 #ifndef __insertion_hpp__
 #define __insertion_hpp__
 
-
-#include "streams.hpp"
+#include "types.hpp"
+#include "virtualConstructor.hpp"
 
 namespace pFlow
 {
 
+// forward
 class particles;
 class dictionary;
 
+/**
+ * Base class for particle insertion
+ */
 class insertion
 {
 protected:
-	// - insertion active 
+	
+	/// Is insertion active 
 	Logical 	active_ = "No";
 
-	// - check for collision / desabled for now 
+	/// Check for collision? It is not active now
 	Logical  	checkForCollision_ = "No";
 
-	// - particles 
+	/// Ref to particles 
 	particles& 				  particles_;
 
-	
+	/// Read from dictionary
 	bool readInsertionDict(const dictionary& dict);
 
+	/// Write to dictionary
 	bool writeInsertionDict(dictionary& dict)const;
 
 public:
 
-	// type info
+	/// Type info
 	TypeInfo("insertion");
 
+	/// Construct from component
 	insertion(particles& prtcl);
 
-
+	/// Destructor 
 	virtual ~insertion() = default;
 
+	/// is Insertion active 
 	bool isActive()const {
 		return active_();
 	}
 
-
+	/// read from iIstream
 	virtual bool read(iIstream& is) = 0;
 
+	/// write to iOstream
 	virtual bool write(iOstream& os)const = 0;
 
 

src/Particles/Insertion/insertionRegion/insertionRegion.hpp

@@ -31,67 +31,126 @@ namespace pFlow
 
 class dictionary;
 
+/**
+ * This class defines all the necessary enteties for defining an insertion
+ * region. 
+ * 
+ * Insertion region information are supplied through a dictionary in a file. 
+ * For example:
+\verbatim
+{
+	type 		cylinderRegion; // type of insertion region
+	rate 		15000;  // insertion rate (particles/s)
+	startTime	0;      // (s)
+	endTime		0.5;    // (s)
+	interval	0.025;  // (s)  
+
+	cylinderRegionInfo 
+	{
+		radius 	0.09;       	// radius of cylinder (m)
+   		p1 		(0.0 0.0 0.10); // (m,m,m)
+   		p2 		(0.0 0.0 0.11); // (m,m,m)
+	}
+   
+	setFields
+	{
+		velocity    realx3 (0.0 0.0 -0.6); // initial velocity of inserted particles 
+	}
+   
+	mixture
+	{
+		lightSphere 1; // mixture composition of inserted particles 
+	}
+} \endverbatim
+ *  
+ * More information on the above dictionary entries can be found in
+ * the table below.
+ * 
+ *  
+ * | Parameter | Type | Description | Optional [default value] |
+ * |----| :---: | ---- | ---- |
+ * | type | word | type of the insertion region with name ### | No |
+ * | rate | real | rate of insertion (particle/s) | No |
+ * | startTime | real | start of insertion (s) | No |
+ * | endTime | real | end of insertion (s) | No  |
+ * | interval | real | time interval between successive insertions (s) | No |
+ * | ###Info | dictionary | data for insertion region | No |
+ * | setFields | dictionary | set field for inserted particles (s) | Yes [empty dictionray] |
+ * | mixture | dictionary | mixture of particles to be inserted (s) | No |
+ * 
+ */
 class insertionRegion
 :
 	public timeFlowControl
 {
 protected:
 
-	// - name of the region 
+	/// name of the region 
 	word  		name_;
 
-	// - type of insertion region
+	/// type of insertion region
 	word		type_;
 
-	// peakable region of points
+	/// peakable region of points
 	uniquePtr<peakableRegion>  	pRegion_ = nullptr;
 
-	// mixture of shapes 
+	/// mixture of shapes 
 	uniquePtr<shapeMixture>  	mixture_ = nullptr;
 
-	// setFields for insertion region 
+	/// setFields for insertion region 
 	uniquePtr<setFieldList>     setFields_ = nullptr;
 
 
+	/// read from dictionary
 	bool readInsertionRegion(const dictionary& dict);
 
+	/// write to dictionary
 	bool writeInsertionRegion(dictionary& dict) const;
 
 
 public:
 
+	/// Type info
 	TypeInfoNV("insertionRegion");
 
-	//// - Constructors
+	// - Constructors
 
+		/// Construct from a dictionary
 		insertionRegion(const dictionary& dict);
 
+		/// Copy
 		insertionRegion(const insertionRegion& src);
 
+		/// Move 
 		insertionRegion(insertionRegion&&) = default;
 
+		/// Copy assignment
 		insertionRegion& operator=(const insertionRegion&);
 
+		/// Move assignment
 		insertionRegion& operator=(insertionRegion&&) = default;
 
-
+		/// Destructor 
 		~insertionRegion() = default;
 
 
-	//// - Methods 
+	// - Methods 
+
+		/// Const ref to setFields
 		const auto& setFields()const
 		{
 			return setFields_();
 		}
 
+		/// Const ref to name of the region
 		const auto& name()const
 		{
 			return name_;
 		}
 
+	// - IO operation
 
-	//// - IO operation
-
+		/// read from dictionary
 		bool read(const dictionary& dict)
 		{
 			if(!timeFlowControl::read(dict))return false;
@@ -99,14 +158,13 @@ public:
 			return readInsertionRegion(dict);
 		}
 
+		/// write to dictionary
 		bool write(dictionary& dict)const
 		{
 			if(!timeFlowControl::write(dict)) return false;
 
 			return writeInsertionRegion(dict);
 		}
-
-
 };
 
 } //pFlow

src/Particles/Insertion/insertionRegion/timeFlowControl.cpp

@@ -21,6 +21,17 @@ Licence:
 #include "timeFlowControl.hpp"
 #include "dictionary.hpp"
 
+size_t pFlow::timeFlowControl::numberToBeInserted(real currentTime)
+{
+	if(currentTime<startTime_)return 0;
+	if(currentTime>endTime_) return 0;
+
+	return static_cast<size_t>
+	( 
+		(currentTime - startTime_ + interval_)*rate_ - numInserted_ 
+	);
+}
+
 bool pFlow::timeFlowControl::readTimeFlowControl
 (
 	const dictionary& dict
@@ -60,3 +71,13 @@ pFlow::timeFlowControl::timeFlowControl
 	}
 
 }
+
+bool pFlow::timeFlowControl::insertionTime( real currentTime, real dt)
+{
+	if(currentTime < startTime_) return false;
+
+	if(currentTime > endTime_) return false;
+	if( mod(abs(currentTime-startTime_),interval_)/dt < 1 ) return true;
+
+	return false;
+}

src/Particles/Insertion/insertionRegion/timeFlowControl.hpp

@@ -29,32 +29,40 @@ namespace pFlow
 
 class dictionary;
 
+/**
+ *  Time control for particle insertion
+ */
 class timeFlowControl
 {
 protected:
 
+	/// start time of insertion
 	real startTime_;
 
+	/// end time of insertion 
 	real endTime_;
 
+	/// time interval between each insertion
 	real interval_;
 
+	/// rate of insertion 
 	real rate_;
 
+	/// number of inserted particles
 	size_t numInserted_ = 0;	
 
+
+	/// Read dictionary
 	bool readTimeFlowControl(const dictionary& dict);
 
+	/// Write to dictionary 
 	bool writeTimeFlowControl(dictionary& dict) const;
 
-	size_t numberToBeInserted(real currentTime)
-	{
-		if(currentTime<startTime_)return 0;
-		if(currentTime>endTime_) return 0;
-
-		return static_cast<size_t>( (currentTime - startTime_ + interval_)*rate_ - numInserted_ );
-	}
+	/// Return number of particles to be inserted at time currentTime
+	size_t numberToBeInserted(real currentTime);
 	
+	/// Add to numInserted
+	inline
 	size_t addToNumInserted(size_t newInserted)
 	{
 		return numInserted_ += newInserted;
@@ -62,30 +70,25 @@ protected:
 
 public:
 
-
+	/// Construct from dictionary 
 	timeFlowControl(const dictionary& dict);
 
+	/// Is currentTime the insertion moment?
+	bool insertionTime( real currentTime, real dt);
 	
-	bool insertionTime( real currentTime, real dt)
-	{
-		if(currentTime < startTime_) return false;
-
-		if(currentTime > endTime_) return false;
-		if( mod(abs(currentTime-startTime_),interval_)/dt < 1 ) return true;
-
-		return false;
-	}
-
+	/// Total number inserted so far
 	size_t totalInserted()const
 	{
 		return numInserted_;
 	}
 
+	/// Read from dictionary
 	bool read(const dictionary& dict)
 	{
 		return readTimeFlowControl(dict);
 	}
 
+	/// Write to dictionary 
 	bool write(dictionary& dict)const
 	{
 		return writeTimeFlowControl(dict);

src/Particles/Insertion/shapeMixture/shapeMixture.hpp

@@ -29,70 +29,95 @@ namespace pFlow
 
 class dictionary;
 
+/**
+ * Defines a mixture of particles for particle insertion.
+ *
+ * The mixture composition is defined based on the integer numbers.
+ * For example, if there are 3 shape names in the simulaiotn
+ * (shape1, shape2, and shape3), the mixture composition can be defined as:
+ * \verbatim
+ {
+	shape1 4;
+	shape2 2;
+	shape3 6;
+ }
+ \endverbatim
+ * 
+ */
 class shapeMixture
 {
-
 protected:
-	// - list of shape names 
+
+	/// List of shape names 
 	wordVector 		names_;
 
-	// - number composition 
+	/// Number composition 
 	uint32Vector   	number_;
 
-	// - number inserted of each shape 
+	/// Number of inserted particles of each shape 
 	uint32Vector   	numberInserted_;
 
+	/// Current number of inserted
 	uint32Vector      current_;
 
 public:
 
-	//- type Info
+	/// Type info
 	TypeInfoNV("shapeMixture");
 
-	//// - constrcutores 
+	// - Constrcutors 
 		
-		//
+		/// Construct from dictionary
 		shapeMixture(const dictionary & dict);
 
+		/// Copy
 		shapeMixture(const shapeMixture&) = default;
 
+		/// Move
 		shapeMixture(shapeMixture&&) = default;
 
+		/// Copy assignment 
 		shapeMixture& operator=(const shapeMixture&) = default;
 
+		/// Move assignment
 		shapeMixture& operator=(shapeMixture&&) = default;
 
-
+		/// Polymorphic copy
 		uniquePtr<shapeMixture> clone()const
 		{
 			return makeUnique<shapeMixture>(*this);
 		}
 
+		/// Polymorphic copy
 		shapeMixture* clonePtr()const
 		{
 			return new shapeMixture(*this);
 		}
 
 
-		//
+		/// Destructor 
 		~shapeMixture() = default;
 
-	//// - Methods 
+	// - Methods 
+
+		/// The name of the next shape that should be inserted
 		word getNextShapeName();
 
-
+		/// The name of the n next shapes that should be inserted
 		void getNextShapeNameN(size_t n, wordVector& names);
 
-
+		/// Size of mixture (names)
 		auto size()const {
 			return names_.size();
 		}
 
+		/// Total number inserted particles
 		auto totalInserted()const {
 			return sum(numberInserted_);
 		}
 
-	//// - IO operatoins 
+	// - IO operatoins 
+	
 		bool read(const dictionary& dict);
 
 		bool write(dictionary& dict) const;

src/Particles/SphereParticles/sphereParticles/sphereParticles.cpp

@@ -380,10 +380,13 @@ bool pFlow::sphereParticles::insertParticles
 		return false;
 	}
 
+
+
 	auto exclusionListAllPtr = getFieldObjectList(); 
 	
 	auto newInsertedPtr = pStruct().insertPoints( position, setField, time(), exclusionListAllPtr());
 	
+
 	if(!newInsertedPtr)
 	{
 		fatalErrorInFunction<<

src/Particles/SphereParticles/sphereParticles/sphereParticles.hpp

@@ -17,14 +17,13 @@ Licence:
   implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
 
 -----------------------------------------------------------------------------*/
-
-/*! 
-   @class pFlow::sphereParticles
-    
-   @brief Class for managing spherical particles 
-   
-   This is a top-level class that contains the essential components for
-   defining spherical prticles in a DEM simulation.
+/** 
+ * @class pFlow::sphereParticles
+ *   
+ * @brief Class for managing spherical particles 
+ *  
+ * This is a top-level class that contains the essential components for
+ * defining spherical prticles in a DEM simulation.
  */
 
 #ifndef __sphereParticles_hpp__

src/phasicFlow/containers/VectorHD/VectorSingle.hpp

@@ -544,18 +544,21 @@ public:
 				resize(maxInd+1);
 			}
 
-			if constexpr (isHostAccessible_)
-			{
-				fillSelected(deviceVectorAll(), indices.hostView(), indices.size(), val);
-				return true;
 			
-			}else
-			{
-				fillSelected(deviceVectorAll(), indices.deviceView(), indices.size(), val);
-				return true;
-			}
+			using policy = Kokkos::RangePolicy<
+			execution_space,
+			Kokkos::IndexType<int32> >;
+			auto dVec = deviceVectorAll();
+			auto dIndex = indices.deviceView();
 			
-			return false;
+			Kokkos::parallel_for(
+				"insertSetElement",
+				policy(0,indices.size()), LAMBDA_HD(int32 i){	
+				dVec(dIndex(i))= val;
+				});
+			Kokkos::fence();
+
+			return true;
 		}
 
 		INLINE_FUNCTION_H
@@ -597,13 +600,11 @@ public:
 		bool insertSetElement(const int32IndexContainer& indices, const Vector<T>& vals)
 		{
 
-			//Info<<"start of insertSetElement vecotsingle"<<endInfo;
 			if(indices.size() == 0)return true;
 			if(indices.size() != vals.size())return false;
 
 			auto maxInd = indices.max(); 
-			/*output<<"maxInd "<< maxInd<<endl;
-			output<<"size() "<< size()<<endl;*/
+			
 			if(this->empty() || maxInd > size()-1 )
 			{
 				resize(maxInd+1);

src/phasicFlow/setFieldList/setFieldEntryTemplates.cpp

@@ -158,6 +158,7 @@ void* pFlow::setFieldEntry::setPointFieldSelected
 	if( pointField<VectorDual,Type>::TYPENAME() == fieldTypeName )
 	{
 		
+		
 		auto& field = owner.lookupObject<pointField<VectorDual,Type>>(fName);
 		if(field.insertSetElement(selected, value))
 			return &field;

src/phasicFlow/structuredData/pointStructure/pointStructure.cpp

@@ -379,11 +379,13 @@ pFlow::uniquePtr<pFlow::int32IndexContainer> pFlow::pointStructure::insertPoints
 		pos)
 		)return nullptr;
 
+	
 	if(!pointFlag_.insertSetElement(
 		newPointsPtr(),
 		static_cast<int8>(PointFlag::ACTIVE))
 		)return nullptr;
 
+	
 	setNumMaxPoints();
 	auto minInd = newPointsPtr().min();
 	auto maxInd = newPointsPtr().max();
@@ -393,6 +395,7 @@ pFlow::uniquePtr<pFlow::int32IndexContainer> pFlow::pointStructure::insertPoints
 
 	for(auto sfEntry:setField)
 	{
+
 		if(void* fieldPtr = 
 			sfEntry.setPointFieldSelectedAll( 
 				owner, 

tutorials/postprocessPhasicFlow/segregation/settings/particlesDict

@@ -41,7 +41,7 @@ setFields
 	{
 		velocity 		realx3 	(0 0 0); // linear velocity (m/s)
 		acceleration 	realx3 	(0 0 0); // linear acceleration (m/s2)
-		rotVelocity 	realx3 	(0 0 0); // rotational velocity (rad/s)
+		r	Velocity 	realx3 	(0 0 0); // rotational velocity (rad/s)
 		shapeName 		word	smallSphere; // name of the particle shape 
 	}
 
@@ -53,8 +53,7 @@ setFields
 			selectRandomInfo
 			{
 				begin 	0;			// begin index of points
-				end 	30000;		// end index of points 
-				number  29999;			// stride for selector 
+				end 	29999;		// end index of points 
 			}
 			fieldValue  // fields that the selector is applied to 
 			{

tutorials/sphereGranFlow/RotaryAirLockValve/ReadMe.md

@@ -0,0 +1,209 @@
+# Problem Definition
+The problem is to simulate a Rotary Air-Lock Valve. The external diameter of rotor is about 21 cm. There is one type of particle in this simulation. Particles are inserted into the inlet of the valve from t=**0** s.
+* **28000** particles with **5 mm** diameter are inserted into the valve with the rate of **4000 particles/s**. 
+* The rotor starts its ortation at t = 1.25 s at the rate of 2.1 rad/s. 
+
+
+<html>
+<body>
+<div align="center"><b>
+	a view of the Rotary Air-Lock Valve while rotating 
+</div></b>
+<div align="center">
+<img src="https://github.com/PhasicFlow/phasicFlow/blob/media/media/rotaryAirLock.gif", width=700px>
+</div>
+<div align="center"><i>
+	particles are colored according to time of insertion
+</div></i>
+</body>
+</html>
+
+# Setting up the Case
+As it has been explained in the previous simulations, the simulation case setup is based on text-based scripts. Here, the simulation case setup files are stored into three folders: `caseSetup`, `setting`, and `stl`  (see the above folders). See next the section for more information on how we can setup the geometry and its rotation.
+  
+## Geometry 
+
+### Defining rotation axis
+In file `settings/geometryDict` the information of rotating axis of rotor and its speed of rotation are defined. The rotation starts at t = **1.25 s** and ends at t = **7 s**.
+
+```C++
+// information for rotatingAxisMotion motion model 
+rotatingAxisMotionInfo
+{
+	rotAxis 
+	{
+
+		// first point for the axis of rotation
+		p1 (0.561547 0.372714 0.000);
+
+		// second point for the axis of rotation
+		p2 (0.561547 0.372714 0.010);
+
+		// rotation speed (rad/s)
+		omega 2.1;
+
+		// Start time of Geometry Rotating (s)
+		startTime 1.25;
+		
+		// End time of Geometry Rotating (s)
+		endTime 7;
+	}
+}
+```
+### Surfaces 
+In `settings/geometryDict` file, the surfaces component are defined to form a Rotating Air-Lock Valve. All surface components are supplied in stl file format. All stl files should be stored under 'stl' folder. 
+
+```C++
+surfaces
+{
+	gear
+	{
+		// type of the wall
+		type 	 stlWall;
+
+		// file name in stl folder
+		file 	 gear.stl;
+
+		// material name of this wall
+		material wallMat;
+
+		// motion component name 
+		motion 	 rotAxis;
+	}
+	surfaces
+	{
+		// type of the wall
+		type 	 stlWall;
+
+		// file name in stl folder
+		file 	 surfaces.stl;
+
+		// material name of this wall
+		material wallMat;
+
+		// motion component name 
+		motion 	 none;
+}
+```
+## Defining particles 
+### Diameter and material of spheres 
+In the `caseSetup/sphereShape` the diameter and the material name of the particles are defined.
+
+<div align="center"> 
+in <b>caseSetup/sphereShape</b> file
+</div>
+
+```C++
+// names of shapes
+names 		(sphere);
+
+// diameter of shapes 
+diameters 	(0.005);
+
+// material names for shapes 
+materials	(sphereMat);
+```
+### Insertion of Particles 
+Insertion of particles starts from t = 0 s and ends at t = 7 s. A box is defined for the port from which particles are being inderted. The rate of insertion is 4000 particles per second. 
+
+<div align="center"> 
+in <b>settings/particleInsertion</b> file
+</div>
+
+```C++
+topRegion
+{
+
+	// type of insertion region
+	type  boxRegion;
+
+	// insertion rate (particles/s)
+	rate 	  4000;
+
+	// Start time of Particles insertion (s)
+	startTime 	  0;
+
+	// End time of Particles insertion (s)	
+	endTime   	  7;
+
+	// Time interval between each insertion (s)
+	interval       0.025;
+
+	// Coordinates of BoxRegion (m,m,m)
+	boxRegionInfo 
+	{
+		min ( 0.48 0.58 0.01 ); // (m,m,m)
+		max ( 0.64 0.59 0.05 ); // (m,m,m)
+	}
+
+	setFields
+	{
+		// initial velocity of inserted particles
+		velocity    realx3 (0.0 -0.6 0.0);  
+	}
+
+	mixture
+	{
+		sphere 1;  
+	}
+}
+```
+
+## Interaction between particles
+ In `caseSetup/interaction` file, material names and properties and interaction parameters are defined. Since we are defining 1 material type in the simulation, the interaction matrix is 2x2 (interactions are symmetric).
+ ```C++
+ // a list of materials names
+materials   (sphereMat  wallMat);
+
+// density of materials [kg/m3]
+densities   (1000    2500);
+
+contactListType   sortedContactList;
+
+model
+{
+    contactForceModel nonLinearNonLimited;
+
+    rollingFrictionModel normal;
+   
+    /*
+    Property (sphereMat-sphereMat  sphereMat-wallMat
+                                  wallMat-wallMat);
+    */
+   
+    // Young modulus [Pa]
+    Yeff  (1.0e6 1.0e6
+                 1.0e6);
+
+    // Shear modulus [Pa]
+    Geff  (0.8e6 0.8e6
+                 0.8e6);
+
+    // Poisson's ratio [-]
+    nu    (0.25 0.25
+                0.25);
+
+    // coefficient of normal restitution
+    en    (0.7  0.8
+                1.0);
+
+    // coefficient of tangential restitution
+   et    (1.0   1.0
+                1.0);
+
+    // dynamic friction
+    mu    (0.3  0.35
+                0.35);
+
+    // rolling friction
+    mur   (0.1  0.1
+                0.1);     
+}
+```
+# Performing simulation and seeing the results 
+To perform simulations, enter the following commands one after another in the terminal. 
+
+Enter `$ particlesPhasicFlow` command to create the initial fields for particles (here the simulaiton has no particle at the beginning).  
+Enter `$ geometryPhasicFlow` command to create the geometry.  
+At last, enter `$ sphereGranFlow` command to start the simulation.  
+After finishing the simulation, you can use  `$ pFlowtoVTK` to convert the results into vtk format stored in ./VTK folder.

tutorials/sphereGranFlow/RotaryAirLockValve/caseSetup/interaction

@@ -0,0 +1,83 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// a list of materials names
+materials   (sphereMat  wallMat);
+
+// density of materials [kg/m3]
+densities   (1000    2500);
+
+contactListType   sortedContactList;
+
+model
+{
+    contactForceModel nonLinearNonLimited;
+
+    rollingFrictionModel normal;
+   
+    /*
+    Property (sphereMat-sphereMat  sphereMat-wallMat
+                                  wallMat-wallMat);
+    */
+   
+    // Young modulus [Pa]
+    Yeff  (1.0e6 1.0e6
+                 1.0e6);
+
+    // Shear modulus [Pa]
+    Geff  (0.8e6 0.8e6
+                 0.8e6);
+
+    // Poisson's ratio [-]
+    nu    (0.25 0.25
+                0.25);
+
+    // coefficient of normal restitution
+    en    (0.7  0.8
+                1.0);
+
+    // coefficient of tangential restitution
+   et    (1.0   1.0
+                1.0);
+
+    // dynamic friction
+    mu    (0.3  0.35
+                0.35);
+
+    // rolling friction
+    mur   (0.1  0.1
+                0.1);     
+}
+
+contactSearch
+{
+    // method for broad search particle-particle
+    method			NBS;
+
+    // method for broad search particle-wall
+    wallMapping		cellMapping;
+
+    NBSInfo
+    {
+    // each 10 timesteps, update neighbor list
+    updateFrequency	10;
+
+    // bounding box size to particle diameter (max)
+    sizeRatio	1.1;
+    }
+
+   cellMappingInfo
+    {
+    // each 20 timesteps, update neighbor list
+    updateFrequency 10;
+
+    // bounding box for particle-wall search (> 0.5)
+    cellExtent     0.6;        
+    }
+}

tutorials/sphereGranFlow/RotaryAirLockValve/caseSetup/particleInsertion

@@ -0,0 +1,54 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */
+objectName particleInsertion;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// is insertion active?
+active  yes;
+
+// not implemented for yes
+collisionCheck No;
+
+/*
+one region is considered for inserting particles. 
+*/
+topRegion
+{
+
+	// type of insertion region
+	type  boxRegion;
+
+	// insertion rate (particles/s)
+	rate 	  4000;
+
+	// Start time of Particles insertion (s)
+	startTime 	  0;
+
+	// End time of Particles insertion (s)	
+	endTime   	  7;
+
+	// Time Interval between each insertion (s)
+	interval       0.025;
+
+	// Coordinates of BoxRegion (m,m,m)
+	boxRegionInfo 
+	{
+		min ( 0.48 0.58 0.01 ); // (m,m,m)
+		max ( 0.64 0.59 0.05 ); // (m,m,m)
+	}
+
+	setFields
+	{
+		// initial velocity of inserted particles
+		velocity    realx3 (0.0 -0.6 0.0);  
+	}
+
+	mixture
+	{
+		sphere 1;  
+	}
+}

tutorials/sphereGranFlow/RotaryAirLockValve/caseSetup/sphereShape

@@ -0,0 +1,19 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName particleInsertion;
+objectType dicrionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+objectName 	sphereDict;
+objectType 	sphereShape;
+
+// names of shapes
+names 		(sphere);
+
+// diameter of shapes 
+diameters 	(0.005);
+
+// material names for shapes 
+materials	(sphereMat);

tutorials/sphereGranFlow/RotaryAirLockValve/settings/geometryDict

@@ -0,0 +1,66 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	geometryDict;
+objectType 	dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxisMotion; 
+
+// information for rotatingAxisMotion motion model 
+rotatingAxisMotionInfo
+{
+	rotAxis 
+	{
+
+		// first point for the axis of rotation
+		p1 (0.561547 0.372714 0.000);
+
+		// second point for the axis of rotation
+		p2 (0.561547 0.372714 0.010);
+
+		// rotation speed (rad/s)
+		omega 2.1;
+
+		// Start time of Geometry Rotating (s)
+		startTime 1.25;
+		
+		// End time of Geometry Rotating (s)
+		endTime 7;
+	}
+}
+
+surfaces
+{
+	gear
+	{
+		// type of the wall
+		type 	 stlWall;
+
+		// file name in stl folder
+		file 	 gear.stl;
+
+		// material name of this wall
+		material wallMat;
+
+		// motion component name 
+		motion 	 rotAxis;
+	}
+surfaces
+	{
+		// type of the wall
+		type 	 stlWall;
+
+		// file name in stl folder
+		file 	 surfaces.stl;
+
+		// material name of this wall
+		material wallMat;
+
+		// motion component name 
+		motion 	 none;
+}
+

tutorials/sphereGranFlow/RotaryAirLockValve/settings/particlesDict

@@ -0,0 +1,43 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	geometryDict;
+objectType 	dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+setFields
+{
+	defaultValue 
+	{
+		// linear velocity (m/s)
+		velocity 	realx3 	(0 0 0);
+
+		// linear acceleration (m/s2)
+		acceleration 	realx3 	(0 0 0);
+
+		// rotational velocity (rad/s)
+		rVelocity 	realx3 	(0 0 0);
+
+		// name of the particle shape
+		shapeName 	word	sphere;
+	}
+
+	selectors
+	{}
+}
+
+// positions particles 
+positionParticles
+{
+
+	// creates the required fields with zero particles (empty).
+	method empty;
+
+	// maximum number of particles in the simulation
+	maxNumberOfParticles 	50000;
+
+	// perform initial sorting based on morton code?
+	mortonSorting 		Yes;
+}

tutorials/sphereGranFlow/RotaryAirLockValve/settings/settingsDict

@@ -0,0 +1,48 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	geometryDict;
+objectType 	dictionary;
+fileFormat  ASCII;
+/*---------------------------------------------------------------------------*/
+
+run		rotatingValve;
+
+// time step for integration (s)
+dt			0.00001;
+
+// start time for simulation
+startTime		0;
+
+// end time for simulation
+endTime			7;
+
+// time interval for saving the simulation
+saveInterval	0.05;
+
+// maximum number of digits for time folder
+timePrecision	6;
+
+// gravity vector (m/s2) 
+g		(0 -9.8 0);
+
+/*
+	Simulation domain every particles that goes outside this domain is deleted.
+*/
+
+domain 
+{
+	min (0.397538  0.178212 0.00);
+	max (0.725537  0.600214 0.06);
+}
+
+// integration method 
+integrationMethod	AdamsBashforth3;
+
+// report timers?
+timersReport		Yes;
+
+// time interval for reporting timers
+timersReportInterval		  0.01;	                
+

tutorials/sphereGranFlow/RotatingDrumWithBaffles/settings/particlesDict

@@ -16,7 +16,7 @@ setFields
 		// linear acceleration (m/s2) 		
 		acceleration 	realx3 	(0 0 0);
 		// rotational velocity (rad/s) 		
-		rotVelocity 	realx3 	(0 0 0);
+		rVelocity 		realx3 	(0 0 0);
 		// name of the particle shape   		
 		shapeName 		word	smallSphere; 	
 	}

tutorials/sphereGranFlow/V-blender/settings/particlesDict

@@ -24,7 +24,7 @@ setFields
 		acceleration 	realx3 	(0 0 0);
 		
 		// rotational velocity (rad/s)
-		rotVelocity 	realx3 	(0 0 0);
+		rVelocity	 	realx3 	(0 0 0);
 		
 		// name of the particle shape
 		shapeName 	word	smallSphere;

tutorials/sphereGranFlow/binarySystemOfParticles/settings/particlesDict

@@ -41,7 +41,7 @@ setFields
 	{
 		velocity 		realx3 	(0 0 0); // linear velocity (m/s)
 		acceleration 	realx3 	(0 0 0); // linear acceleration (m/s2)
-		rotVelocity 	realx3 	(0 0 0); // rotational velocity (rad/s)
+		rVelocity 		realx3 	(0 0 0); // rotational velocity (rad/s)
 		shapeName 		word	smallSphere; // name of the particle shape 
 	}
 

tutorials/sphereGranFlow/layeredSiloFilling/settings/particlesDict

@@ -13,7 +13,7 @@ setFields
 	{
 		velocity 		realx3 	(0 0 0); 		// linear velocity (m/s)
 		acceleration 	realx3 	(0 0 0); 		// linear acceleration (m/s2)
-		rotVelocity 	realx3 	(0 0 0);  		// rotational velocity (rad/s)
+		rVelocity 		realx3 	(0 0 0);  		// rotational velocity (rad/s)
 		shapeName 		word	lightSphere; 	// name of the particle shape 
 	}
 

tutorials/sphereGranFlow/rotatingDrumMedium/settings/particlesDict

@@ -19,7 +19,7 @@ setFields
 	{
 		velocity 		realx3 	(0 0 0); // linear velocity (m/s)
 		acceleration 	realx3 	(0 0 0); // linear acceleration (m/s2)
-		rotVelocity 	realx3 	(0 0 0); // rotational velocity (rad/s)
+		rVelocity 		realx3 	(0 0 0); // rotational velocity (rad/s)
 		shapeName 		word	glassBead; // name of the particle shape 
 	}
 

tutorials/sphereGranFlow/rotatingDrumSmall/settings/particlesDict

@@ -19,7 +19,7 @@ setFields
 	{
 		velocity 		realx3 	(0 0 0); // linear velocity (m/s)
 		acceleration 	realx3 	(0 0 0); // linear acceleration (m/s2)
-		rotVelocity 	realx3 	(0 0 0); // rotational velocity (rad/s)
+		rVelocity 		realx3 	(0 0 0); // rotational velocity (rad/s)
 		shapeName 		word	sphere1; // name of the particle shape 
 	}
 

tutorials/sphereGranFlow/screwConveyor/README.md

@@ -0,0 +1,208 @@
+# Simulating a screw conveyor {#screwConveyor}
+## Problem definition
+The problem is to simulate a screw conveyorwith the diameter 0.2 m and the length 1 m and 20 cm pitch. It is filled with 30,000 4-mm spherical particles. The timestep for integration is 0.00001 s.
+<div align="center"><b>
+a view of rotating drum
+
+![]()
+</b></div>
+
+***
+
+## Setting up the case 
+PhasicFlow simulation case setup is based on the text-based scripts that we provide in two folders located in the simulation case folder: `settings` and `caseSetup` (You can find the case setup files in the above folders.
+All the commands should be entered in the terminal while the current working directory is the simulation case folder (at the top of the `caseSetup` and `settings`).
+ 
+
+### Creating particles
+
+Open the file  `settings/particlesDict`. Two dictionaries, `positionParticles` and `setFields` position particles and set the field values for the particles. 
+In dictionary `positionParticles`, the positioning `method` is `positionOrdered`, which position particles in order in the space defined by `box`. `box` space is defined by two corner points `min` and `max`. In dictionary `positionOrderedInfo`, `numPoints` defines number of particles; `diameter`, the distance between two adjacent particles, and `axisOrder` defines the axis order for filling the space by particles. 
+
+<div align="center"> 
+in <b>settings/particlesDict</b> file
+</div>
+
+```C++
+positionParticles
+{
+	method empty;     		// creates the required fields with zero particles (empty). 
+
+	maxNumberOfParticles 	50000; // maximum number of particles in the simulation
+	mortonSorting 			Yes;    // perform initial sorting based on morton code?   
+
+}
+```
+
+Enter the following command in the terminal to create the particles and store them in `0` folder.
+
+`> particlesPhasicFlow`
+ 
+### Creating geometry
+In file `settings/geometryDict` , you can provide information for creating geometry. Each simulation should have a `motionModel` that defines a model for moving the surfaces in the simulation. `rotatingAxisMotion` model defines a fixed axis which rotates around itself. The dictionary `rotAxis` defines an motion component with `p1` and `p2` as the end points of the axis and `omega` as the rotation speed in rad/s. You can define more than one motion component in a simulation. 
+
+<div align="center"> 
+in <b>settings/geometryDict</b> file
+</div>
+
+```C++
+motionModel rotatingAxisMotion; 
+.
+.
+.
+rotatingAxisMotionInfo
+{
+	rotAxis 
+	{
+		p1 (1.09635 0.2010556 0.22313511);	// first point for the axis of rotation 
+		p2 (0.0957492 0.201556 0.22313511);	// second point for the axis of rotation
+		omega 3; 		// rotation speed (rad/s)
+		startTime 5;
+		endTime 30;
+	}
+}
+
+```
+In the dictionary `surfaces` you can define all the surfaces (shell) in the simulation. Two main options are available: built-in geometries in PhasicFlow, and providing surfaces with stl file. Here we use built-in geometries. In `cylinder` dictionary, a cylindrical shell with end helix, `material` name `prop1`, `motion` component `none` is defined. `helix` define  plane helix at center of  cylindrical shell, `material` name `prop1` and `motion` component `rotAxis`.'rotAxis' is use for helix because it is rotating and 'none' is use for shell because It is motionless.
+
+<div align="center"> 
+in <b>settings/geometryDict</b> file
+</div>
+
+```C++
+surfaces
+{
+	helix
+	{
+		type 	 stlWall;  	// type of the wall
+		file 	 helix.stl;	// file name in stl folder		
+		material prop1;   // material name of this wall
+		motion 	 rotAxis;	// motion component name 
+	}
+
+	shell
+	{
+		type 	 stlWall;  	// type of the wall
+		file 	 shell.stl;	// file name in stl folder		
+		material prop1;   // material name of this wall
+		motion 	 none;		// motion component name 
+	}
+
+}
+
+```
+
+Enter the following command in the terminal to create the geometry and store it in `0/geometry` folder.
+
+`> geometryPhasicFlow`
+
+### Defining properties and interactions 
+In the file `caseSetup/interaction` , you find properties of materials. `materials` defines a list of material names in the simulation and `densities` sets the corresponding density of each material name. model dictionary defines the interaction model for particle-particle and particle-wall interactions. `contactForceModel` selects the model for mechanical contacts (here nonlinear model with limited tangential displacement) and `rollingFrictionModel` selects the model for calculating rolling friction. Other required prosperities should be defined in this dictionary. 
+
+<div align="center"> 
+in <b>caseSetup/interaction</b> file
+</div>
+
+```C++
+materials      (prop1);    // a list of materials names
+densities      (1000.0);   // density of materials [kg/m3]
+
+contactListType   sortedContactList; 
+
+model
+{
+   contactForceModel nonLinearNonLimited;
+   rollingFrictionModel normal;
+
+   Yeff  (1.0e6);       // Young modulus [Pa]
+
+   Geff  (0.8e6);       // Shear modulus [Pa]
+
+   nu    (0.25);        // Poisson's ratio [-]
+
+   en    (0.7);         // coefficient of normal restitution
+
+   et    (1.0);         // coefficient of tangential restitution 
+
+   mu    (0.3);         // dynamic friction 
+
+   mur   (0.1);         // rolling friction 
+        
+}
+```
+
+Dictionary `contactSearch` sets the methods for particle-particle and particle-wall contact search. `method` specifies the algorithm for finding neighbor list for particle-particle contacts and `wallMapping` shows how particles are mapped onto walls for finding neighbor list for particle-wall contacts. `updateFrequency` sets the frequency for updating neighbor list and `sizeRatio` sets the size of enlarged cells (with respect to particle diameter) for finding neighbor list. Larger `sizeRatio` include more particles in the neighbor list and you require to update it less frequent. 
+
+<div align="center"> 
+in <b>caseSetup/interaction</b> file
+</div>
+
+```C++
+contactSearch
+{
+   method         NBS;           // method for broad search particle-particle
+   wallMapping    cellMapping;   // method for broad search particle-wall 
+
+   NBSInfo
+   {
+      updateFrequency 10;        // each 20 timesteps, update neighbor list 
+      sizeRatio      1.1;        // bounding box size to particle diameter (max)
+   }
+
+   cellMappingInfo
+   {
+      updateFrequency 10;        // each 20 timesteps, update neighbor list  
+      cellExtent     0.6;        // bounding box for particle-wall search (> 0.5)
+   }
+
+}
+```
+
+In the file `caseSetup/sphereShape`, you can define a list of `names` for shapes (`shapeName` in particle field), a list of diameters for shapes and their `properties` names. 
+
+<div align="center"> 
+in <b>caseSetup/sphereShape</b> file
+</div>
+
+```C++
+names 		(sphere1); 	// names of shapes 
+diameters 	(0.01);	        // diameter of shapes 
+materials	(prop1);	// material names for shapes 
+```
+
+Other settings for the simulation can be set in file `settings/settingsDict`. The dictionary `domain` defines the a rectangular bounding box with two corner points for the simulation. Each particle that gets out of this box, will be deleted automatically. 
+
+<div align="center"> 
+in <b>settings/settingsDict</b> file
+</div>
+
+```C++
+dt 		0.0001; 	// time step for integration (s)
+startTime 	0; 		// start time for simulation 
+endTime 	20;	 	// end time for simulation 
+saveInterval 	0.05; 		// time interval for saving the simulation
+timePrecision   6;		// maximum number of digits for time folder 
+g 		(0 -9.8 0);     // gravity vector (m/s2) 
+
+domain 
+{
+	min (0.0 -0.06 0.001);
+	max (1.2 1 0.5);
+}
+
+integrationMethod 		AdamsBashforth3; 	// integration method 
+
+timersReport 			Yes;  	                // report timers?
+
+timersReportInterval    	0.01;	                // time interval for reporting timers
+```
+
+## Running the case 
+The solver for this simulation is `sphereGranFlow`. Enter the following command in the terminal. Depending on the computational power, it may take a few minutes to a few hours to complete. 
+
+`> sphereGranFlow`
+
+## Post processing 
+After finishing the simulation, you can render the results in Paraview. To convert the results to VTK format, just enter the following command in the terminal. This will converts all the results (particles and geometry) to VTK format and store them in folder `VTK/`. 
+
+`> pFlowToVTK`

tutorials/sphereGranFlow/screwConveyor/caseSetup/interaction

@@ -0,0 +1,54 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName interaction;
+objectType dicrionary;
+fileFormat 	ASCII;
+/*---------------------------------------------------------------------------*/
+
+materials      (prop1);    // a list of materials names
+densities      (1000.0);   // density of materials [kg/m3]
+
+contactListType   sortedContactList; 
+
+model
+{
+   contactForceModel nonLinearNonLimited;
+   rollingFrictionModel normal;
+
+   Yeff  (1.0e6);       // Young modulus [Pa]
+
+   Geff  (0.8e6);       // Shear modulus [Pa]
+
+   nu    (0.25);        // Poisson's ratio [-]
+
+   en    (0.7);         // coefficient of normal restitution
+
+   et    (1.0);         // coefficient of tangential restitution 
+
+   mu    (0.3);         // dynamic friction 
+
+   mur   (0.1);         // rolling friction 
+        
+}
+
+
+contactSearch
+{
+   method         NBS;           // method for broad search particle-particle
+   wallMapping    cellMapping;   // method for broad search particle-wall 
+
+   NBSInfo
+   {
+      updateFrequency 10;        // each 20 timesteps, update neighbor list 
+      sizeRatio      1.1;        // bounding box size to particle diameter (max)
+   }
+
+   cellMappingInfo
+   {
+      updateFrequency 10;        // each 20 timesteps, update neighbor list  
+      cellExtent     0.6;        // bounding box for particle-wall search (> 0.5)
+   }
+
+}

tutorials/sphereGranFlow/screwConveyor/caseSetup/particleInsertion

@@ -0,0 +1,46 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName particleInsertion;
+objectType dicrionary;
+fileFormat 	ASCII;
+/*---------------------------------------------------------------------------*/
+
+
+active  yes;          // is insertion active?
+
+collisionCheck No;   // not implemented for yes
+
+/*
+five layers of particles are packed one-by-one using 5 insertion steps. 
+*/
+
+layer0
+{
+   type		      cylinderRegion; // type of insertion region
+   rate 	      5000;  // insertion rate (particles/s)
+   startTime 	  0;      // (s)
+   endTime   	  100;    // (s)
+   interval       0.03;  //s  
+
+   cylinderRegionInfo 
+   {
+   	radius 	0.09;       // radius of cylinder (m)
+   	p1 (0.22 0.73 0.25); // (m,m,m)
+   	p2 (0.22 0.742 0.25); // (m,m,m)
+   }
+   
+   setFields
+   {
+     velocity    realx3 (0.0 -0.6 -0); // initial velocity of inserted particles 
+   }
+   
+   mixture
+   {
+      sphere1 1; // mixture composition of inserted particles 
+      
+   }
+}
+
+

tutorials/sphereGranFlow/screwConveyor/caseSetup/sphereShape

@@ -0,0 +1,12 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */ 
+objectName 	sphereDict;
+objectType 	sphereShape;
+fileFormat 	ASCII;
+/*---------------------------------------------------------------------------*/
+
+names 		(sphere1); 	// names of shapes 
+diameters 	(0.01);	// diameter of shapes 
+materials	(prop1);	// material names for shapes 

tutorials/sphereGranFlow/screwConveyor/cleanThisCase

@@ -0,0 +1,7 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+
+ls | grep -P "^(([0-9]+\.?[0-9]*)|(\.[0-9]+))$" | xargs -d"\n" rm -rf
+rm -rf VTK 
+
+#------------------------------------------------------------------------------

tutorials/sphereGranFlow/screwConveyor/runThisCase

@@ -0,0 +1,21 @@
+#!/bin/sh
+cd ${0%/*} || exit 1    # Run from this directory
+echo "\n<--------------------------------------------------------------------->"
+echo "1) Creating particles"
+echo "<--------------------------------------------------------------------->\n"
+particlesPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "2) Creating geometry"
+echo "<--------------------------------------------------------------------->\n"
+geometryPhasicFlow
+
+echo "\n<--------------------------------------------------------------------->"
+echo "3) Running the case"
+echo "<--------------------------------------------------------------------->\n"
+sphereGranFlow
+
+
+
+
+#------------------------------------------------------------------------------

tutorials/sphereGranFlow/screwConveyor/settings/geometryDict

@@ -0,0 +1,45 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	geometryDict;
+objectType 	dictionary;
+fileFormat 	ASCII;
+/*---------------------------------------------------------------------------*/
+
+// motion model: rotating object around an axis
+motionModel rotatingAxisMotion; 
+
+surfaces
+{
+	helix
+	{
+		type 	 stlWall;  	// type of the wall
+		file 	 helix.stl;	// file name in stl folder		
+		material prop1;   // material name of this wall
+		motion 	 rotAxis;	// motion component name 
+	}
+
+	shell
+	{
+		type 	 stlWall;  	// type of the wall
+		file 	 shell.stl;	// file name in stl folder		
+		material prop1;   // material name of this wall
+		motion 	 none;		// motion component name 
+	}
+
+}
+
+
+rotatingAxisMotionInfo
+{
+	rotAxis 
+	{
+		p1 (1.09635 0.2010556 0.22313511);	// first point for the axis of rotation 
+		p2 (0.0957492 0.201556 0.22313511);	// second point for the axis of rotation
+		omega 3; 		// rotation speed (rad/s)
+		startTime 5;
+		endTime 30;
+	}
+}
+

tutorials/sphereGranFlow/screwConveyor/settings/particlesDict

@@ -0,0 +1,40 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	particlesDict;
+objectType 	dictionary;
+fileFormat 	ASCII;
+/*---------------------------------------------------------------------------*/
+
+
+// positions particles 
+positionParticles
+{
+	method empty;     		// creates the required fields with zero particles (empty). 
+
+	maxNumberOfParticles 	50000; // maximum number of particles in the simulation
+	mortonSorting 			Yes;    // perform initial sorting based on morton 
+
+}
+
+setFields
+{
+	defaultValue 
+	{
+		// linear velocity (m/s)
+		velocity 	realx3 	(0 0 0);
+
+		// linear acceleration (m/s2)
+		acceleration 	realx3 	(0 0 0);
+
+		// rotational velocity (rad/s)
+		rVelocity 	realx3 	(0 0 0);
+
+		// name of the particle shape
+		shapeName 	word	sphere1;
+	}
+
+	selectors
+	{}
+}

tutorials/sphereGranFlow/screwConveyor/settings/settingsDict

@@ -0,0 +1,38 @@
+/* -------------------------------*- C++ -*--------------------------------- *\ 
+|  phasicFlow File                                                            | 
+|  copyright: www.cemf.ir                                                     | 
+\* ------------------------------------------------------------------------- */  
+objectName 	settingsDict;
+objectType 	dictionary;
+fileFormat 	ASCII;
+/*---------------------------------------------------------------------------*/
+
+run 			layerdSiloFilling;
+
+dt 				0.0001; 	// time step for integration (s)
+
+startTime 		0; 			// start time for simulation 
+
+endTime 		20;	 		// end time for simulation 
+
+saveInterval 	0.05; 		// time interval for saving the simulation
+
+timePrecision   6;			// maximum number of digits for time folder 
+
+g 				(0 -9.8 0); // gravity vector (m/s2) 
+
+/*
+	Simulation domain 
+	every particles that goes outside this domain is deleted.
+*/
+domain 
+{
+	min (0.0 -0.06 0.001);
+	max (1.2 1 0.5);
+}
+
+integrationMethod 		AdamsBashforth3; 	// integration method 
+
+timersReport 			Yes;  	// report timers?
+
+timersReportInterval   	0.01;	// time interval for reporting timers